Daily Papers

Predicting which proteins interact together from amino-acid sequences is an important task. We develop a method to pair interacting protein sequences which leverages the power of protein language models trained on multiple sequence alignments, such as MSA Transformer and the EvoFormer module of AlphaFold. We formulate the problem of pairing interacting partners among the paralogs of two protein families in a differentiable way. We introduce a method called DiffPALM that solves it by exploiting the ability of MSA Transformer to fill in masked amino acids in multiple sequence alignments using the surrounding context. MSA Transformer encodes coevolution between functionally or structurally coupled amino acids. We show that it captures inter-chain coevolution, while it was trained on single-chain data, which means that it can be used out-of-distribution. Relying on MSA Transformer without fine-tuning, DiffPALM outperforms existing coevolution-based pairing methods on difficult benchmarks of shallow multiple sequence alignments extracted from ubiquitous prokaryotic protein datasets. It also outperforms an alternative method based on a state-of-the-art protein language model trained on single sequences. Paired alignments of interacting protein sequences are a crucial ingredient of supervised deep learning methods to predict the three-dimensional structure of protein complexes. DiffPALM substantially improves the structure prediction of some eukaryotic protein complexes by AlphaFold-Multimer, without significantly deteriorating any of those we tested. It also achieves competitive performance with using orthology-based pairing.

Small language models (SLMs) are attractive for agentic deployment due to low latency, reduced cost, and on-device privacy, yet they struggle with tool-use tasks where training data is scarce and noisy. Unlike larger models, SLMs cannot compensate for low-quality supervision through sheer capacity, making data quality the critical bottleneck. We present Data Turnstile, an open-source framework that takes user-defined API specifications and generates high-quality synthetic training data for function calling. Turnstile decomposes multi-turn tool-use interactions into constrained, stepwise generation with validation and error-feedback loops, providing fine-grained control over API diversity, conversation complexity, and output correctness. We demonstrate effectiveness of domain adaptation with Turnstile data on two challenging function calling benchmarks. On the BFCL single-turn benchmark, a Qwen3-0.6B fine-tuned on Turnstile data without chain-of-thought achieves 75.9% overall accuracy (versus 67.4% for the base model with thinking enabled), closing the gap with thinking-enabled Qwen3-1.7B (78.4%) and Qwen3-4B (79.9%) despite being 3times and 7times smaller respectively. On τ^2-bench, a multi-turn agentic benchmark, Turnstile-trained Qwen3-1.7B achieves 31.1% pass^1 on the Telecom domain, improving 4.7times over its 6.6% base and surpassing Qwen2.5-32B-Instruct (27.4%), a model 19times larger. Turnstile-trained Qwen3-0.6B achieves 24.6%, improving 7times over its 3.5% base and approaching the 32B model (53times larger). We release Data Turnstile along with a dataset spanning 1,000+ APIs and 100K+ multi-turn interactions.

Logical reasoning is a critical benchmark for evaluating the capabilities of large language models (LLMs), as it reflects their ability to derive valid conclusions from given premises. While the combination of test-time scaling with dedicated outcome or process reward models has opened up new avenues to enhance LLMs performance in complex reasoning tasks, this space is under-explored in deductive logical reasoning. We present a set of Outcome Reward Models (ORMs) for deductive reasoning. To train the ORMs we mainly generate data using Chain-of-Thought (CoT) with single and multiple samples. Additionally, we propose a novel tactic to further expand the type of errors covered in the training dataset of the ORM. In particular, we propose an echo generation technique that leverages LLMs' tendency to reflect incorrect assumptions made in prompts to extract additional training data, covering previously unexplored error types. While a standard CoT chain may contain errors likely to be made by the reasoner, the echo strategy deliberately steers the model toward incorrect reasoning. We show that ORMs trained on CoT and echo-augmented data demonstrate improved performance on the FOLIO, JustLogic, and ProverQA datasets across four different LLMs.

LLM-based agentic systems are increasingly combined with CoT reasoning to solve tasks that require accurate reasoning, external knowledge, and multi-step deliberation. Yet, explicit CoT incurs substantial generation overhead, while implicit CoT, which replaces textual rationales with compact continuous tokens, does not naturally support the explicit communication interface required for agentic tool-use. We propose TAC-CoT, a tool-empowered adaptive implicit CoT framework that replaces explicit reasoning traces with compact latent reasoning segments while retaining textual tokens only for tool calls, observations, and final answers. This interleaved design enables agentic tool-use without verbalizing every intermediate reasoning step. Experiments on agentic math and QA benchmarks show that TAC-CoT improves accuracy by up to 8.8 points while reducing model forward passes by up to 6.8x. Furthermore, analyses show that TAC-CoT improves tool-use quality in both single- and multi-tool settings.

Over the past decade, the revolution in single-cell sequencing has enabled the simultaneous molecular profiling of various modalities across thousands of individual cells, allowing scientists to investigate the diverse functions of complex tissues and uncover underlying disease mechanisms. Among all the analytical steps, assigning individual cells to specific types is fundamental for understanding cellular heterogeneity. However, this process is usually labor-intensive and requires extensive expert knowledge. Recent advances in large language models (LLMs) have demonstrated their ability to efficiently process and synthesize vast corpora of text to automatically extract essential biological knowledge, such as marker genes, potentially promoting more efficient and automated cell type annotations. To thoroughly evaluate the capability of modern instruction-tuned LLMs in automating the cell type identification process, we introduce SOAR, a comprehensive benchmarking study of LLMs for cell type annotation tasks in single-cell genomics. Specifically, we assess the performance of 8 instruction-tuned LLMs across 11 datasets, spanning multiple cell types and species. Our study explores the potential of LLMs to accurately classify and annotate cell types in single-cell RNA sequencing (scRNA-seq) data, while extending their application to multiomics data through cross-modality translation. Additionally, we evaluate the effectiveness of chain-of-thought (CoT) prompting techniques in generating detailed biological insights during the annotation process. The results demonstrate that LLMs can provide robust interpretations of single-cell data without requiring additional fine-tuning, advancing the automation of cell type annotation in genomics research.

Large language models (LLMs) are increasingly used as personal agents, accessing sensitive user data such as calendars, emails, and medical records. Users currently face a trade-off: They can send private records, many of which are stored in remote databases, to powerful but untrusted LLM providers, increasing their exposure risk. Alternatively, they can run less powerful models locally on trusted devices. We bridge this gap. Our Socratic Chain-of-Thought Reasoning first sends a generic, non-private user query to a powerful, untrusted LLM, which generates a Chain-of-Thought (CoT) prompt and detailed sub-queries without accessing user data. Next, we embed these sub-queries and perform encrypted sub-second semantic search using our Homomorphically Encrypted Vector Database across one million entries of a single user's private data. This represents a realistic scale of personal documents, emails, and records accumulated over years of digital activity. Finally, we feed the CoT prompt and the decrypted records to a local language model and generate the final response. On the LoCoMo long-context QA benchmark, our hybrid framework, combining GPT-4o with a local Llama-3.2-1B model, outperforms using GPT-4o alone by up to 7.1 percentage points. This demonstrates a first step toward systems where tasks are decomposed and split between untrusted strong LLMs and weak local ones, preserving user privacy.

Fine-tuning large language models (LLMs) with a collection of large and diverse instructions has improved the model's generalization to different tasks, even for unseen tasks. However, most existing instruction datasets include only single instructions, and they struggle to follow complex instructions composed of multiple subtasks (Wang et al., 2023a). In this work, we propose a novel concept of compositional instructions called chain-of-instructions (CoI), where the output of one instruction becomes an input for the next like a chain. Unlike the conventional practice of solving single instruction tasks, our proposed method encourages a model to solve each subtask step by step until the final answer is reached. CoI-tuning (i.e., fine-tuning with CoI instructions) improves the model's ability to handle instructions composed of multiple subtasks. CoI-tuned models also outperformed baseline models on multilingual summarization, demonstrating the generalizability of CoI models on unseen composite downstream tasks.

Conditional generative adversarial networks (cGANs) have shown superior results in class-conditional generation tasks. To simultaneously control multiple conditions, cGANs require multi-label training datasets, where multiple labels can be assigned to each data instance. Nevertheless, the tremendous annotation cost limits the accessibility of multi-label datasets in real-world scenarios. Therefore, in this study we explore the practical setting called the single positive setting, where each data instance is annotated by only one positive label with no explicit negative labels. To generate multi-label data in the single positive setting, we propose a novel sampling approach called single-to-multi-label (S2M) sampling, based on the Markov chain Monte Carlo method. As a widely applicable "add-on" method, our proposed S2M sampling method enables existing unconditional and conditional GANs to draw high-quality multi-label data with a minimal annotation cost. Extensive experiments on real image datasets verify the effectiveness and correctness of our method, even when compared to a model trained with fully annotated datasets.

Instruction generation is a vital and multidisciplinary research area with broad applications. Existing instruction generation models are limited to generating instructions in a single style from a particular dataset, and the style and content of generated instructions cannot be controlled. Moreover, most existing instruction generation methods also disregard the spatial modeling of the navigation environment. Leveraging the capabilities of Large Language Models (LLMs), we propose C-Instructor, which utilizes the chain-of-thought-style prompt for style-controllable and content-controllable instruction generation. Firstly, we propose a Chain of Thought with Landmarks (CoTL) mechanism, which guides the LLM to identify key landmarks and then generate complete instructions. CoTL renders generated instructions more accessible to follow and offers greater controllability over the manipulation of landmark objects. Furthermore, we present a Spatial Topology Modeling Task to facilitate the understanding of the spatial structure of the environment. Finally, we introduce a Style-Mixed Training policy, harnessing the prior knowledge of LLMs to enable style control for instruction generation based on different prompts within a single model instance. Extensive experiments demonstrate that instructions generated by C-Instructor outperform those generated by previous methods in text metrics, navigation guidance evaluation, and user studies.

Spatial reasoning and visual grounding are core capabilities for vision-language models (VLMs), yet most medical VLMs produce predictions without transparent reasoning or spatial evidence. Existing benchmarks also evaluate VLMs on isolated 2D images, overlooking the volumetric nature of clinical imaging, where findings can span multiple frames or appear on only a few slices. We introduce Spatially Grounded MRI Visual Question Answering (SGMRI-VQA), a 41,307-pair benchmark for multi-frame, spatially grounded reasoning on volumetric MRI. Built from expert radiologist annotations in the fastMRI+ dataset across brain and knee studies, each QA pair includes a clinician-aligned chain-of-thought trace with frame-indexed bounding box coordinates. Tasks are organized hierarchically across detection, localization, counting/classification, and captioning, requiring models to jointly reason about what is present, where it is, and across which frames it extends. We benchmark 10 VLMs and show that supervised fine-tuning of Qwen3-VL-8B with bounding box supervision consistently improves grounding performance over strong zero-shot baselines, indicating that targeted spatial supervision is an effective path toward grounded clinical reasoning.

Emotion recognition in low-resource languages like Marathi remains challenging due to limited annotated data. We present L3Cube-MahaEmotions, a high-quality Marathi emotion recognition dataset with 11 fine-grained emotion labels. The training data is synthetically annotated using large language models (LLMs), while the validation and test sets are manually labeled to serve as a reliable gold-standard benchmark. Building on the MahaSent dataset, we apply the Chain-of-Translation (CoTR) prompting technique, where Marathi sentences are translated into English and emotion labeled via a single prompt. GPT-4 and Llama3-405B were evaluated, with GPT-4 selected for training data annotation due to superior label quality. We evaluate model performance using standard metrics and explore label aggregation strategies (e.g., Union, Intersection). While GPT-4 predictions outperform fine-tuned BERT models, BERT-based models trained on synthetic labels fail to surpass GPT-4. This highlights both the importance of high-quality human-labeled data and the inherent complexity of emotion recognition. An important finding of this work is that generic LLMs like GPT-4 and Llama3-405B generalize better than fine-tuned BERT for complex low-resource emotion recognition tasks. The dataset and model are shared publicly at https://github.com/l3cube-pune/MarathiNLP

Language-Image Pre-training has demonstrated promising results on zero-shot and few-shot downstream tasks by prompting visual models with natural language prompts. However, most recent studies only use a single prompt for tuning, neglecting the inherent step-to-step cognitive reasoning process that humans conduct in complex task settings, for example, when processing images from unfamiliar domains. Chain of Thought is a simple and effective approximation to human reasoning process and has been proven useful for natural language processing (NLP) tasks. Based on this cognitive intuition, we believe that conducting effective reasoning is also an important problem in visual tasks, and a chain of thought could be a solution to this problem. In this work, we propose a novel chain of thought prompt tuning for vision-language modeling. Extensive experiments show that our method not only generalizes better in image classification tasks, has greater transferability beyond a single dataset, and has stronger domain generalization performance, but also performs much better in imagetext retrieval and visual question answering, which require more reasoning capabilities. We are the first to successfully adapt chain-of-thought prompting that combines visual and textual embeddings. We will release our codes

Video-to-Audio (V2A) generation requires balancing four critical perceptual dimensions: semantic consistency, audio-visual temporal synchrony, aesthetic quality, and spatial accuracy; yet existing methods suffer from objective entanglement that conflates competing goals in single loss functions and lack human preference alignment. We introduce PrismAudio, the first framework to integrate Reinforcement Learning into V2A generation with specialized Chain-of-Thought (CoT) planning. Our approach decomposes monolithic reasoning into four specialized CoT modules (Semantic, Temporal, Aesthetic, and Spatial CoT), each paired with targeted reward functions. This CoT-reward correspondence enables multidimensional RL optimization that guides the model to jointly generate better reasoning across all perspectives, solving the objective entanglement problem while preserving interpretability. To make this optimization computationally practical, we propose Fast-GRPO, which employs hybrid ODE-SDE sampling that dramatically reduces the training overhead compared to existing GRPO implementations. We also introduce AudioCanvas, a rigorous benchmark that is more distributionally balanced and covers more realistically diverse and challenging scenarios than existing datasets, with 300 single-event classes and 501 multi-event samples. Experimental results demonstrate that PrismAudio achieves state-of-the-art performance across all four perceptual dimensions on both the in-domain VGGSound test set and out-of-domain AudioCanvas benchmark. The project page is available at https://PrismAudio-Project.github.io.

Composed Image Retrieval (CIR) retrieves target images using a reference image paired with modification text. Despite rapid advances, all existing methods and datasets operate at the image level -- a single reference image plus modification text in, a single target image out -- while real e-commerce users reason about products shown from multiple viewpoints. We term this mismatch View Incompleteness and formally define a new Multi-View CIR task that generalizes standard CIR from image-level to product-level retrieval. To support this task, we construct FashionMV, the first large-scale multi-view fashion dataset for product-level CIR, comprising 127K products, 472K multi-view images, and over 220K CIR triplets, built through a fully automated pipeline leveraging large multimodal models. We further propose ProCIR (Product-level Composed Image Retrieval), a modeling framework built upon a multimodal large language model that employs three complementary mechanisms -- two-stage dialogue, caption-based alignment, and chain-of-thought guidance -- together with an optional supervised fine-tuning (SFT) stage that injects structured product knowledge prior to contrastive training. Systematic ablation across 16 configurations on three fashion benchmarks reveals that: (1) alignment is the single most critical mechanism; (2) the two-stage dialogue architecture is a prerequisite for effective alignment; and (3) SFT and chain-of-thought serve as partially redundant knowledge injection paths. Our best 0.8B-parameter model outperforms all baselines, including general-purpose embedding models 10x its size. The dataset, model, and code are publicly available at https://github.com/yuandaxia2001/FashionMV.

Solving mathematical problems using computer-verifiable languages like Lean has significantly impacted mathematical and computer science communities. State-of-the-art methods utilize single Large Language Models (LLMs) as agents or provers to either generate complete proof or perform tree searches. However, single-agent methods inherently lack a structured way to combine high-level reasoning in Natural Language (NL) with Formal Language (FL) verification feedback. To solve these issues, we propose MA-LoT: Multi-Agent Lean-based Long Chain-of-Thought framework, (to the best of our knowledge), the first multi-agent framework for Lean4 theorem proving that balance high-level NL reasoning and FL verification in Long CoT. Using this structured interaction, our approach enables deeper insights and long-term coherence in proof generation, with which past methods struggle. We do this by leveraging emergent formal reasoning ability in Long CoT using our novel LoT-Transfer Learning training-inference pipeline. Extensive experiments show that our framework achieves 54.51% accuracy rate on the Lean4 version of MiniF2F-Test dataset, largely outperforming GPT-4 (22.95%), single-agent tree search (InternLM-Step-Prover, 50.70%), and whole-proof generation (DeepSeek-Prover-v1.5, 48.36%) baselines. Furthermore, our findings highlight the potential of combining Long CoT with formal verification for a more insightful generation in a broader perspective.

Transformers trained via Reinforcement Learning (RL) with outcome-based supervision can spontaneously develop the ability to generate intermediate reasoning steps (Chain-of-Thought). Yet the mechanism by which sparse rewards drive policy gradient to discover such systematic reasoning remains poorly understood. We address this by analyzing the policy gradient dynamics of single-layer Transformers on a synthetic graph traversal task that cannot be solved without Chain-of-Thought but admits a simple iterative solution. We prove that despite training solely on final-answer correctness, policy gradient drives the Transformer to converge to a structured, interpretable algorithm that iteratively traverses the graph vertex-by-vertex. We characterize the distributional properties required for this emergence, identifying the critical role of "simple examples": instances requiring fewer reasoning steps. When the training distribution places sufficient mass on these simpler examples, the Transformer learns a generalizable traversal strategy that extrapolates to longer chains; when this mass vanishes, policy gradient learning becomes infeasible. We corroborate our theoretical results through experiments on synthetic data and with real-world language models on mathematical reasoning tasks, validating that our theoretical findings carry over to practical settings.

Phishing email detection faces critical challenges from evolving adversarial tactics and heterogeneous attack patterns. Traditional detection methods, such as rule-based filters and denylists, often struggle to keep pace with these evolving tactics, leading to false negatives and compromised security. While machine learning approaches have improved detection accuracy, they still face challenges adapting to novel phishing strategies. We present MultiPhishGuard, a dynamic LLM-based multi-agent detection system that synergizes specialized expertise with adversarial-aware reinforcement learning. Our framework employs five cooperative agents (text, URL, metadata, explanation simplifier, and adversarial agents) with automatically adjusted decision weights powered by a Proximal Policy Optimization reinforcement learning algorithm. To address emerging threats, we introduce an adversarial training loop featuring an adversarial agent that generates subtle context-aware email variants, creating a self-improving defense ecosystem and enhancing system robustness. Experimental evaluations on public datasets demonstrate that MultiPhishGuard significantly outperforms Chain-of-Thoughts, single-agent baselines and state-of-the-art detectors, as validated by ablation studies and comparative analyses. Experiments demonstrate that MultiPhishGuard achieves high accuracy (97.89\%) with low false positive (2.73\%) and false negative rates (0.20\%). Additionally, we incorporate an explanation simplifier agent, which provides users with clear and easily understandable explanations for why an email is classified as phishing or legitimate. This work advances phishing defense through dynamic multi-agent collaboration and generative adversarial resilience.

We present Phi-4-reasoning-vision-15B, a compact open-weight multimodal reasoning model, and share the motivations, design choices, experiments, and learnings that informed its development. Our goal is to contribute practical insight to the research community on building smaller, efficient multimodal reasoning models and to share the result of these learnings as an open-weight model that is good at common vision and language tasks and excels at scientific and mathematical reasoning and understanding user interfaces. Our contributions include demonstrating that careful architecture choices and rigorous data curation enable smaller, open-weight multimodal models to achieve competitive performance with significantly less training and inference-time compute and tokens. The most substantial improvements come from systematic filtering, error correction, and synthetic augmentation -- reinforcing that data quality remains the primary lever for model performance. Systematic ablations show that high-resolution, dynamic-resolution encoders yield consistent improvements, as accurate perception is a prerequisite for high-quality reasoning. Finally, a hybrid mix of reasoning and non-reasoning data with explicit mode tokens allows a single model to deliver fast direct answers for simpler tasks and chain-of-thought reasoning for complex problems.

Embodied agents face a critical dilemma that end-to-end models lack interpretability and explicit 3D reasoning, while modular systems ignore cross-component interdependencies and synergies. To bridge this gap, we propose the Dynamic 3D Vision-Language-Planning Model (D3D-VLP). Our model introduces two key innovations: 1) A Dynamic 3D Chain-of-Thought (3D CoT) that unifies planning, grounding, navigation, and question answering within a single 3D-VLM and CoT pipeline; 2) A Synergistic Learning from Fragmented Supervision (SLFS) strategy, which uses a masked autoregressive loss to learn from massive and partially-annotated hybrid data. This allows different CoT components to mutually reinforce and implicitly supervise each other. To this end, we construct a large-scale dataset with 10M hybrid samples from 5K real scans and 20K synthetic scenes that are compatible with online learning methods such as RL and DAgger. Our D3D-VLP achieves state-of-the-art results on multiple benchmarks, including Vision-and-Language Navigation (R2R-CE, REVERIE-CE, NavRAG-CE), Object-goal Navigation (HM3D-OVON), and Task-oriented Sequential Grounding and Navigation (SG3D). Real-world mobile manipulation experiments further validate the effectiveness.

The remarkable progress of Multimodal Large Language Models (MLLMs) has attracted increasing attention to extend them to physical entities like legged robot. This typically requires MLLMs to not only grasp multimodal understanding abilities, but also integrate visual-spatial reasoning and physical interaction capabilities. Nevertheless,existing methods struggle to unify these capabilities due to their fundamental differences.In this paper, we present the Visual Embodied Brain (VeBrain), a unified framework for perception, reasoning, and control in real world. VeBrain reformulates robotic control into common text-based MLLM tasks in the 2D visual space, thus unifying the objectives and mapping spaces of different tasks. Then, a novel robotic adapter is proposed to convert textual control signals from MLLMs to motion policies of real robots. From the data perspective, we further introduce VeBrain-600k, a high-quality instruction dataset encompassing various capabilities of VeBrain. In VeBrain-600k, we take hundreds of hours to collect, curate and annotate the data, and adopt multimodal chain-of-thought(CoT) to mix the different capabilities into a single conversation. Extensive experiments on 13 multimodal benchmarks and 5 spatial intelligence benchmarks demonstrate the superior performance of VeBrain to existing MLLMs like Qwen2.5-VL. When deployed to legged robots and robotic arms, VeBrain shows strong adaptability, flexibility, and compositional capabilities compared to existing methods. For example, compared to Qwen2.5-VL, VeBrain not only achieves substantial gains on MMVet by +5.6%, but also excels in legged robot tasks with +50% average gains.

In tackling the challenges of large language model (LLM) performance for Text-to-SQL tasks, we introduce CHASE-SQL, a new framework that employs innovative strategies, using test-time compute in multi-agent modeling to improve candidate generation and selection. CHASE-SQL leverages LLMs' intrinsic knowledge to generate diverse and high-quality SQL candidates using different LLM generators with: (1) a divide-and-conquer method that decomposes complex queries into manageable sub-queries in a single LLM call; (2) chain-of-thought reasoning based on query execution plans, reflecting the steps a database engine takes during execution; and (3) a unique instance-aware synthetic example generation technique, which offers specific few-shot demonstrations tailored to test questions.To identify the best candidate, a selection agent is employed to rank the candidates through pairwise comparisons with a fine-tuned binary-candidates selection LLM. This selection approach has been demonstrated to be more robust over alternatives. The proposed generators-selector framework not only enhances the quality and diversity of SQL queries but also outperforms previous methods. Overall, our proposed CHASE-SQL achieves the state-of-the-art execution accuracy of 73.0% and 73.01% on the test set and development set of the notable BIRD Text-to-SQL dataset benchmark, rendering CHASE-SQL the top submission of the leaderboard (at the time of paper submission).

Powerful generative AI models of protein-ligand structure have recently been proposed, but few of these methods support both flexible protein-ligand docking and affinity estimation. Of those that do, none can directly model multiple binding ligands concurrently or have been rigorously benchmarked on pharmacologically relevant drug targets, hindering their widespread adoption in drug discovery efforts. In this work, we propose FlowDock, the first deep geometric generative model based on conditional flow matching that learns to directly map unbound (apo) structures to their bound (holo) counterparts for an arbitrary number of binding ligands. Furthermore, FlowDock provides predicted structural confidence scores and binding affinity values with each of its generated protein-ligand complex structures, enabling fast virtual screening of new (multi-ligand) drug targets. For the well-known PoseBusters Benchmark dataset, FlowDock outperforms single-sequence AlphaFold 3 with a 51% blind docking success rate using unbound (apo) protein input structures and without any information derived from multiple sequence alignments, and for the challenging new DockGen-E dataset, FlowDock outperforms single-sequence AlphaFold 3 and matches single-sequence Chai-1 for binding pocket generalization. Additionally, in the ligand category of the 16th community-wide Critical Assessment of Techniques for Structure Prediction (CASP16), FlowDock ranked among the top-5 methods for pharmacological binding affinity estimation across 140 protein-ligand complexes, demonstrating the efficacy of its learned representations in virtual screening. Source code, data, and pre-trained models are available at https://github.com/BioinfoMachineLearning/FlowDock.

High-dimensional point cloud data arise across many scientific domains, especially single-cell biology. The shapes or topologies of these datasets determine the types of information that can be extracted. For example, clustered data supports cell-type identification, trajectory structures support transition analysis, and archetypal structures capture continua of cellular behaviors. Existing analysis pipelines often assume a specific shape. The standard Seurat pipeline combines UMAP visualization with Louvain clustering and therefore assumes clustered data, while tools such as Monocle and SPADE assume tree-like structures, and flow-based models such as MIOFlow and Conditional Flow Matching target trajectories. Choosing which pipeline to apply is therefore often left to bioinformaticians who visually inspect datasets before selecting an analysis strategy. With the rise of agentic AI scientists, automating shape detection is increasingly important for selecting downstream analysis pipelines. To address this problem, we introduce scShapeBench, a benchmark dataset for shape detection containing both synthetic and expert-annotated single-cell datasets. Synthetic datasets are sampled from ground-truth skeleton graphs with controlled variance. Real single-cell datasets are curated from diverse sources and annotated by experts into four categories: clusters, single trajectory, multi-branching, and archetypal. We additionally introduce scReebTower, a baseline method that uses diffusion geometry to extract Reeb graphs and connect visualization with pipeline selection. We provide topology-aware evaluation metrics and compare scReebTower against PAGA and Mapper on synthetic and real data. Our results indicate that scReebTower outperforms existing baselines. Overall, our contributions span benchmarks, evaluation metrics, and a baseline for automated shape detection in single-cell data.

We introduce WebChain, the largest open-source dataset of human-annotated trajectories on real-world websites, designed to accelerate reproducible research in web agents. It contains 31,725 trajectories and 318k steps, featuring a core Triple Alignment of visual, structural, and action data to provide rich, multi-modal supervision. The data is collected via a scalable pipeline that ensures coverage of complex, high-value tasks often missed by synthetic methods. Leveraging this dataset, we propose a Dual Mid-Training recipe that decouples spatial grounding from planning, achieving state-of-the-art performance on our proposed WebChainBench and other public GUI benchmarks. Our work provides the data and insights necessary to build and rigorously evaluate the next generation of scalable web agents.

Materials science is undergoing profound changes due to advances in characterization instrumentation that have resulted in an explosion of data in terms of volume, velocity, variety and complexity. Harnessing these data for scientific research requires an evolution of the associated computing and data infrastructure, bridging scientific instrumentation with super- and cloud- computing. Here, we describe Universal Spectroscopy and Imaging Data (USID), a data model capable of representing data from most common instruments, modalities, dimensionalities, and sizes. We pair this schema with the hierarchical data file format (HDF5) to maximize compatibility, exchangeability, traceability, and reproducibility. We discuss a family of community-driven, open-source, and free python software packages for storing, processing and visualizing data. The first is pyUSID which provides the tools to read and write USID HDF5 files in addition to a scalable framework for parallelizing data analysis. The second is Pycroscopy, which provides algorithms for scientific analysis of nanoscale imaging and spectroscopy modalities and is built on top of pyUSID and USID. The instrument-agnostic nature of USID facilitates the development of analysis code independent of instrumentation and task in Pycroscopy which in turn can bring scientific communities together and break down barriers in the age of open-science. The interested reader is encouraged to be a part of this ongoing community-driven effort to collectively accelerate materials research and discovery through the realms of big data.

Current automated pipelines for audio-visual Question Answering (QA) generally adopt a ``video-caption-QA'' paradigm. However, these methods typically segment videos into short clips and generate separate descriptions for audio and visual modalities. This decoupled processing severs inherent associations between sounds and their visual sources, while independent clip processing often causes inconsistent descriptions of the same entity across segments. Furthermore, coupling long-text comprehension and QA synthesis into a single step often restricts models to localized events, yielding questions lacking long-term temporal connections and deep cross-modal reasoning. To address these issues, we propose an automated data engine featuring two mechanisms: (1) Entity-Anchored Video Scripting transforms videos into structured scripts, comprising summaries, main entity lists, and segment-wise audio-visual descriptions. The entity list serves as a global prior to ensure cross-segment referential consistency and reconstruct audio-visual associations. (2) Clue-Guided QA Generation prompts models to first mine cross-segment, multimodal clues from the script, and subsequently generate QA pairs based on these high-value clues. Leveraging this pipeline, we construct the instruction-tuning dataset OmniVideo-100K and a human-verified test set, OmniVideo-Test. Fine-tuning VITA-1.5, Qwen2.5-Omni-7B and Qwen3-Omni-30B on OmniVideo-100K yields performance gains of up to 20.59% on OmniVideo-Test, demonstrating strong generalization (up to 12.64% improvements) across established benchmarks like Daily-Omni and JointAVBench.

Recently, pre-trained foundation models have enabled significant advancements in multiple fields. In molecular machine learning, however, where datasets are often hand-curated, and hence typically small, the lack of datasets with labeled features, and codebases to manage those datasets, has hindered the development of foundation models. In this work, we present seven novel datasets categorized by size into three distinct categories: ToyMix, LargeMix and UltraLarge. These datasets push the boundaries in both the scale and the diversity of supervised labels for molecular learning. They cover nearly 100 million molecules and over 3000 sparsely defined tasks, totaling more than 13 billion individual labels of both quantum and biological nature. In comparison, our datasets contain 300 times more data points than the widely used OGB-LSC PCQM4Mv2 dataset, and 13 times more than the quantum-only QM1B dataset. In addition, to support the development of foundational models based on our proposed datasets, we present the Graphium graph machine learning library which simplifies the process of building and training molecular machine learning models for multi-task and multi-level molecular datasets. Finally, we present a range of baseline results as a starting point of multi-task and multi-level training on these datasets. Empirically, we observe that performance on low-resource biological datasets show improvement by also training on large amounts of quantum data. This indicates that there may be potential in multi-task and multi-level training of a foundation model and fine-tuning it to resource-constrained downstream tasks.

We resolve difficulties in training and sampling from a discrete generative model by learning a smoothed energy function, sampling from the smoothed data manifold with Langevin Markov chain Monte Carlo (MCMC), and projecting back to the true data manifold with one-step denoising. Our Discrete Walk-Jump Sampling formalism combines the contrastive divergence training of an energy-based model and improved sample quality of a score-based model, while simplifying training and sampling by requiring only a single noise level. We evaluate the robustness of our approach on generative modeling of antibody proteins and introduce the distributional conformity score to benchmark protein generative models. By optimizing and sampling from our models for the proposed distributional conformity score, 97-100% of generated samples are successfully expressed and purified and 70% of functional designs show equal or improved binding affinity compared to known functional antibodies on the first attempt in a single round of laboratory experiments. We also report the first demonstration of long-run fast-mixing MCMC chains where diverse antibody protein classes are visited in a single MCMC chain.

Developing therapeutics is a lengthy and expensive process that requires the satisfaction of many different criteria, and AI models capable of expediting the process would be invaluable. However, the majority of current AI approaches address only a narrowly defined set of tasks, often circumscribed within a particular domain. To bridge this gap, we introduce Tx-LLM, a generalist large language model (LLM) fine-tuned from PaLM-2 which encodes knowledge about diverse therapeutic modalities. Tx-LLM is trained using a collection of 709 datasets that target 66 tasks spanning various stages of the drug discovery pipeline. Using a single set of weights, Tx-LLM simultaneously processes a wide variety of chemical or biological entities(small molecules, proteins, nucleic acids, cell lines, diseases) interleaved with free-text, allowing it to predict a broad range of associated properties, achieving competitive with state-of-the-art (SOTA) performance on 43 out of 66 tasks and exceeding SOTA on 22. Among these, Tx-LLM is particularly powerful and exceeds best-in-class performance on average for tasks combining molecular SMILES representations with text such as cell line names or disease names, likely due to context learned during pretraining. We observe evidence of positive transfer between tasks with diverse drug types (e.g.,tasks involving small molecules and tasks involving proteins), and we study the impact of model size, domain finetuning, and prompting strategies on performance. We believe Tx-LLM represents an important step towards LLMs encoding biochemical knowledge and could have a future role as an end-to-end tool across the drug discovery development pipeline.

With the emergence of data marketplaces, the demand for methods to assess the value of data has increased significantly. While numerous techniques have been proposed for this purpose, none have specifically addressed graphs as the main data modality. Graphs are widely used across various fields, ranging from chemical molecules to social networks. In this study, we break down graphs into two main components: structural and featural, and we focus on evaluating data without relying on specific task-related metrics, making it applicable in practical scenarios where validation requirements may be lacking. We introduce a novel framework called blind message passing, which aligns the seller's and buyer's graphs using a shared node permutation based on graph matching. This allows us to utilize the graph Wasserstein distance to quantify the differences in the structural distribution of graph datasets, called the structural disparities. We then consider featural aspects of buyers' and sellers' graphs for data valuation and capture their statistical similarities and differences, referred to as relevance and diversity, respectively. Our approach ensures that buyers and sellers remain unaware of each other's datasets. Our experiments on real datasets demonstrate the effectiveness of our approach in capturing the relevance, diversity, and structural disparities of seller data for buyers, particularly in graph-based data valuation scenarios.

Time series foundation models (TSFMs) are pretrained on series from diverse domains, where demand series make up only a small fraction. Demand data has properties that such corpora rarely contain: Short histories, frequent zeros, censoring by stock-outs, and exogenous events that the series does not record. To this end, we propose EXAONE Demand, built on 1) a demand-specific corpus and 2) a demand-aware adapter. For the corpus, we assemble 11.3M series and 48.4B observations from 73 sources, and a synthetic generator supplies the behaviour that open demand data under-represents. For the adapter, we attach low-rank branches to a frozen general-domain backbone, one for each of the four demand classes (smooth, intermittent, erratic, and lumpy), and a router that reads eight scale-free statistics of the input series decides how much each branch contributes. We build EXAONE Demand in two versions, one trained on real-world and synthetic demand together and one trained on the synthetic corpus alone. On 22 held-out datasets, both versions outperform 36 TSFMs, and real-world demand adds a gain over synthetic data alone.

In this work we present two video test data sets for the novel computer vision (CV) task of out of distribution tracking (OOD tracking). Here, OOD objects are understood as objects with a semantic class outside the semantic space of an underlying image segmentation algorithm, or an instance within the semantic space which however looks decisively different from the instances contained in the training data. OOD objects occurring on video sequences should be detected on single frames as early as possible and tracked over their time of appearance as long as possible. During the time of appearance, they should be segmented as precisely as possible. We present the SOS data set containing 20 video sequences of street scenes and more than 1000 labeled frames with up to two OOD objects. We furthermore publish the synthetic CARLA-WildLife data set that consists of 26 video sequences containing up to four OOD objects on a single frame. We propose metrics to measure the success of OOD tracking and develop a baseline algorithm that efficiently tracks the OOD objects. As an application that benefits from OOD tracking, we retrieve OOD sequences from unlabeled videos of street scenes containing OOD objects.

Existing text-video retrieval datasets primarily consist of short-form clips containing a single dominant event. While suitable for measuring basic vision-language alignment, they are limited in capturing real-world retrieval scenarios, where long-form videos naturally contain multiple semantically distinct events and a single text query may correspond to several non-contiguous temporal segments. To bridge this gap, we introduce MELON, the first large-scale dataset designed to extend text-video retrieval to long-form videos featuring complex, multi-event structures. MELON explicitly annotates multiple event intervals per video along with their corresponding textual descriptions, enabling both training and evaluation of multi-event understanding in long, untrimmed videos. In addition, we propose a multi-event aware loss that encourages models to differentiate between full-event and partial-event matches, yielding substantial improvements in retrieval accuracy. Together, the MELON dataset and our proposed loss establish a robust foundation for expanding text-to-video retrieval to complex long-form scenarios and provide a more realistic evaluation setting for future research in the field.

Scene extrapolation -- the idea of generating novel views by flying into a given image -- is a promising, yet challenging task. For each predicted frame, a joint inpainting and 3D refinement problem has to be solved, which is ill posed and includes a high level of ambiguity. Moreover, training data for long-range scenes is difficult to obtain and usually lacks sufficient views to infer accurate camera poses. We introduce DiffDreamer, an unsupervised framework capable of synthesizing novel views depicting a long camera trajectory while training solely on internet-collected images of nature scenes. Utilizing the stochastic nature of the guided denoising steps, we train the diffusion models to refine projected RGBD images but condition the denoising steps on multiple past and future frames for inference. We demonstrate that image-conditioned diffusion models can effectively perform long-range scene extrapolation while preserving consistency significantly better than prior GAN-based methods. DiffDreamer is a powerful and efficient solution for scene extrapolation, producing impressive results despite limited supervision. Project page: https://primecai.github.io/diffdreamer.

Warning: this paper contains content that may be offensive or upsetting. Most hate speech datasets neglect the cultural diversity within a single language, resulting in a critical shortcoming in hate speech detection. To address this, we introduce CREHate, a CRoss-cultural English Hate speech dataset. To construct CREHate, we follow a two-step procedure: 1) cultural post collection and 2) cross-cultural annotation. We sample posts from the SBIC dataset, which predominantly represents North America, and collect posts from four geographically diverse English-speaking countries (Australia, United Kingdom, Singapore, and South Africa) using culturally hateful keywords we retrieve from our survey. Annotations are collected from the four countries plus the United States to establish representative labels for each country. Our analysis highlights statistically significant disparities across countries in hate speech annotations. Only 56.2% of the posts in CREHate achieve consensus among all countries, with the highest pairwise label difference rate of 26%. Qualitative analysis shows that label disagreement occurs mostly due to different interpretations of sarcasm and the personal bias of annotators on divisive topics. Lastly, we evaluate large language models (LLMs) under a zero-shot setting and show that current LLMs tend to show higher accuracies on Anglosphere country labels in CREHate. Our dataset and codes are available at: https://github.com/nlee0212/CREHate

This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library (MaStar) accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) survey which publicly releases infra-red spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the sub-survey Time Domain Spectroscopic Survey (TDSS) data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey (SPIDERS) sub-survey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated Value Added Catalogs (VACs). This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper (MWM), Local Volume Mapper (LVM) and Black Hole Mapper (BHM) surveys.

We introduce a framework that automates the transformation of static anime illustrations into manipulatable 2.5D models. Current professional workflows require tedious manual segmentation and the artistic ``hallucination'' of occluded regions to enable motion. Our approach overcomes this by decomposing a single image into fully inpainted, semantically distinct layers with inferred drawing orders. To address the scarcity of training data, we introduce a scalable engine that bootstraps high-quality supervision from commercial Live2D models, capturing pixel-perfect semantics and hidden geometry. Our methodology couples a diffusion-based Body Part Consistency Module, which enforces global geometric coherence, with a pixel-level pseudo-depth inference mechanism. This combination resolves the intricate stratification of anime characters, e.g., interleaving hair strands, allowing for dynamic layer reconstruction. We demonstrate that our approach yields high-fidelity, manipulatable models suitable for professional, real-time animation applications.

We introduce a 3D-aware diffusion model, ZeroNVS, for single-image novel view synthesis for in-the-wild scenes. While existing methods are designed for single objects with masked backgrounds, we propose new techniques to address challenges introduced by in-the-wild multi-object scenes with complex backgrounds. Specifically, we train a generative prior on a mixture of data sources that capture object-centric, indoor, and outdoor scenes. To address issues from data mixture such as depth-scale ambiguity, we propose a novel camera conditioning parameterization and normalization scheme. Further, we observe that Score Distillation Sampling (SDS) tends to truncate the distribution of complex backgrounds during distillation of 360-degree scenes, and propose "SDS anchoring" to improve the diversity of synthesized novel views. Our model sets a new state-of-the-art result in LPIPS on the DTU dataset in the zero-shot setting, even outperforming methods specifically trained on DTU. We further adapt the challenging Mip-NeRF 360 dataset as a new benchmark for single-image novel view synthesis, and demonstrate strong performance in this setting. Our code and data are at http://kylesargent.github.io/zeronvs/

One essential task in information extraction from the medical corpus is drug name recognition. Compared with text sources come from other domains, the medical text is special and has unique characteristics. In addition, the medical text mining poses more challenges, e.g., more unstructured text, the fast growing of new terms addition, a wide range of name variation for the same drug. The mining is even more challenging due to the lack of labeled dataset sources and external knowledge, as well as multiple token representations for a single drug name that is more common in the real application setting. Although many approaches have been proposed to overwhelm the task, some problems remained with poor F-score performance (less than 0.75). This paper presents a new treatment in data representation techniques to overcome some of those challenges. We propose three data representation techniques based on the characteristics of word distribution and word similarities as a result of word embedding training. The first technique is evaluated with the standard NN model, i.e., MLP (Multi-Layer Perceptrons). The second technique involves two deep network classifiers, i.e., DBN (Deep Belief Networks), and SAE (Stacked Denoising Encoders). The third technique represents the sentence as a sequence that is evaluated with a recurrent NN model, i.e., LSTM (Long Short Term Memory). In extracting the drug name entities, the third technique gives the best F-score performance compared to the state of the art, with its average F-score being 0.8645.

Large transformer-based models are able to perform in-context few-shot learning, without being explicitly trained for it. This observation raises the question: what aspects of the training regime lead to this emergent behavior? Here, we show that this behavior is driven by the distributions of the training data itself. In-context learning emerges when the training data exhibits particular distributional properties such as burstiness (items appear in clusters rather than being uniformly distributed over time) and having large numbers of rarely occurring classes. In-context learning also emerges more strongly when item meanings or interpretations are dynamic rather than fixed. These properties are exemplified by natural language, but are also inherent to naturalistic data in a wide range of other domains. They also depart significantly from the uniform, i.i.d. training distributions typically used for standard supervised learning. In our initial experiments, we found that in-context learning traded off against more conventional weight-based learning, and models were unable to achieve both simultaneously. However, our later experiments uncovered that the two modes of learning could co-exist in a single model when it was trained on data following a skewed Zipfian distribution -- another common property of naturalistic data, including language. In further experiments, we found that naturalistic data distributions were only able to elicit in-context learning in transformers, and not in recurrent models. In sum, our findings indicate how the transformer architecture works together with particular properties of the training data to drive the intriguing emergent in-context learning behaviour of large language models, and how future work might encourage both in-context and in-weights learning in domains beyond language.

There is a growing demand for the accessible creation of high-quality 3D avatars that are animatable and customizable. Although 3D morphable models provide intuitive control for editing and animation, and robustness for single-view face reconstruction, they cannot easily capture geometric and appearance details. Methods based on neural implicit representations, such as signed distance functions (SDF) or neural radiance fields, approach photo-realism, but are difficult to animate and do not generalize well to unseen data. To tackle this problem, we propose a novel method for constructing implicit 3D morphable face models that are both generalizable and intuitive for editing. Trained from a collection of high-quality 3D scans, our face model is parameterized by geometry, expression, and texture latent codes with a learned SDF and explicit UV texture parameterization. Once trained, we can reconstruct an avatar from a single in-the-wild image by leveraging the learned prior to project the image into the latent space of our model. Our implicit morphable face models can be used to render an avatar from novel views, animate facial expressions by modifying expression codes, and edit textures by directly painting on the learned UV-texture maps. We demonstrate quantitatively and qualitatively that our method improves upon photo-realism, geometry, and expression accuracy compared to state-of-the-art methods.

Real-world data visualization (DV) requires native environmental grounding, cross-platform evolution, and proactive intent alignment. Yet, existing benchmarks often suffer from code-sandbox confinement, single-language creation-only tasks, and assumption of perfect intent. To bridge these gaps, we introduce DV-World, a benchmark of 260 tasks designed to evaluate DV agents across real-world professional lifecycles. DV-World spans three domains: DV-Sheet for native spreadsheet manipulation including chart and dashboard creation as well as diagnostic repair; DV-Evolution for adapting and restructuring reference visual artifacts to fit new data across diverse programming paradigms and DV-Interact for proactive intent alignment with a user simulator that mimics real-world ambiguous requirements. Our hybrid evaluation framework integrates Table-value Alignment for numerical precision and MLLM-as-a-Judge with rubrics for semantic-visual assessment. Experiments reveal that state-of-the-art models achieve less than 50% overall performance, exposing critical deficits in handling the complex challenges of real-world data visualization. DV-World provides a realistic testbed to steer development toward the versatile expertise required in enterprise workflows. Our data and code are available at https://github.com/DA-Open/DV-World{this project page}.

Extracting key information from scientific papers has the potential to help researchers work more efficiently and accelerate the pace of scientific progress. Over the last few years, research on Scientific Information Extraction (SciIE) witnessed the release of several new systems and benchmarks. However, existing paper-focused datasets mostly focus only on specific parts of a manuscript (e.g., abstracts) and are single-modality (i.e., text- or table-only), due to complex processing and expensive annotations. Moreover, core information can be present in either text or tables or across both. To close this gap in data availability and enable cross-modality IE, while alleviating labeling costs, we propose a semi-supervised pipeline for annotating entities in text, as well as entities and relations in tables, in an iterative procedure. Based on this pipeline, we release novel resources for the scientific community, including a high-quality benchmark, a large-scale corpus, and a semi-supervised annotation pipeline. We further report the performance of state-of-the-art IE models on the proposed benchmark dataset, as a baseline. Lastly, we explore the potential capability of large language models such as ChatGPT for the current task. Our new dataset, results, and analysis validate the effectiveness and efficiency of our semi-supervised pipeline, and we discuss its remaining limitations.

Low-light is an inescapable element of our daily surroundings that greatly affects the efficiency of our vision. Research works on low-light has seen a steady growth, particularly in the field of image enhancement, but there is still a lack of a go-to database as benchmark. Besides, research fields that may assist us in low-light environments, such as object detection, has glossed over this aspect even though breakthroughs-after-breakthroughs had been achieved in recent years, most noticeably from the lack of low-light data (less than 2% of the total images) in successful public benchmark dataset such as PASCAL VOC, ImageNet, and Microsoft COCO. Thus, we propose the Exclusively Dark dataset to elevate this data drought, consisting exclusively of ten different types of low-light images (i.e. low, ambient, object, single, weak, strong, screen, window, shadow and twilight) captured in visible light only with image and object level annotations. Moreover, we share insightful findings in regards to the effects of low-light on the object detection task by analyzing visualizations of both hand-crafted and learned features. Most importantly, we found that the effects of low-light reaches far deeper into the features than can be solved by simple "illumination invariance'". It is our hope that this analysis and the Exclusively Dark dataset can encourage the growth in low-light domain researches on different fields. The Exclusively Dark dataset with its annotation is available at https://github.com/cs-chan/Exclusively-Dark-Image-Dataset

Automatic speaker verification (ASV) is one of the most natural and convenient means of biometric person recognition. Unfortunately, just like all other biometric systems, ASV is vulnerable to spoofing, also referred to as "presentation attacks." These vulnerabilities are generally unacceptable and call for spoofing countermeasures or "presentation attack detection" systems. In addition to impersonation, ASV systems are vulnerable to replay, speech synthesis, and voice conversion attacks. The ASVspoof 2019 edition is the first to consider all three spoofing attack types within a single challenge. While they originate from the same source database and same underlying protocol, they are explored in two specific use case scenarios. Spoofing attacks within a logical access (LA) scenario are generated with the latest speech synthesis and voice conversion technologies, including state-of-the-art neural acoustic and waveform model techniques. Replay spoofing attacks within a physical access (PA) scenario are generated through carefully controlled simulations that support much more revealing analysis than possible previously. Also new to the 2019 edition is the use of the tandem detection cost function metric, which reflects the impact of spoofing and countermeasures on the reliability of a fixed ASV system. This paper describes the database design, protocol, spoofing attack implementations, and baseline ASV and countermeasure results. It also describes a human assessment on spoofed data in logical access. It was demonstrated that the spoofing data in the ASVspoof 2019 database have varied degrees of perceived quality and similarity to the target speakers, including spoofed data that cannot be differentiated from bona-fide utterances even by human subjects.

Code-switching (CS) is the alternating use of two or more languages within a conversation or utterance, often influenced by social context and speaker identity. This linguistic phenomenon poses challenges for Automatic Speech Recognition (ASR) systems, which are typically designed for a single language and struggle to handle multilingual inputs. The growing global demand for multilingual applications, including Code-Switching ASR (CSASR), Text-to-Speech (CSTTS), and Cross-Lingual Information Retrieval (CLIR), highlights the inadequacy of existing monolingual datasets. Although some code-switching datasets exist, most are limited to bilingual mixing within homogeneous ethnic groups, leaving a critical need for a large-scale, diverse benchmark akin to ImageNet in computer vision. To bridge this gap, we introduce LinguaMaster, a multi-agent collaboration framework specifically designed for efficient and scalable multilingual data synthesis. Leveraging this framework, we curate SwitchLingua, the first large-scale multilingual and multi-ethnic code-switching dataset, including: (1) 420K CS textual samples across 12 languages, and (2) over 80 hours of audio recordings from 174 speakers representing 18 countries/regions and 63 racial/ethnic backgrounds, based on the textual data. This dataset captures rich linguistic and cultural diversity, offering a foundational resource for advancing multilingual and multicultural research. Furthermore, to address the issue that existing ASR evaluation metrics lack sensitivity to code-switching scenarios, we propose the Semantic-Aware Error Rate (SAER), a novel evaluation metric that incorporates semantic information, providing a more accurate and context-aware assessment of system performance.

As autonomous driving systems mature, motion forecasting has received increasing attention as a critical requirement for planning. Of particular importance are interactive situations such as merges, unprotected turns, etc., where predicting individual object motion is not sufficient. Joint predictions of multiple objects are required for effective route planning. There has been a critical need for high-quality motion data that is rich in both interactions and annotation to develop motion planning models. In this work, we introduce the most diverse interactive motion dataset to our knowledge, and provide specific labels for interacting objects suitable for developing joint prediction models. With over 100,000 scenes, each 20 seconds long at 10 Hz, our new dataset contains more than 570 hours of unique data over 1750 km of roadways. It was collected by mining for interesting interactions between vehicles, pedestrians, and cyclists across six cities within the United States. We use a high-accuracy 3D auto-labeling system to generate high quality 3D bounding boxes for each road agent, and provide corresponding high definition 3D maps for each scene. Furthermore, we introduce a new set of metrics that provides a comprehensive evaluation of both single agent and joint agent interaction motion forecasting models. Finally, we provide strong baseline models for individual-agent prediction and joint-prediction. We hope that this new large-scale interactive motion dataset will provide new opportunities for advancing motion forecasting models.

With the power of large language models (LLMs), open-ended embodied agents can flexibly understand human instructions, generate interpretable guidance strategies, and output executable actions. Nowadays, Multi-modal Language Models~(MLMs) integrate multi-modal signals into LLMs, further bringing richer perception to entity agents and allowing embodied agents to perceive world-understanding tasks more delicately. However, existing works: 1) operate independently by agents, each containing multiple LLMs, from perception to action, resulting in gaps between complex tasks and execution; 2) train MLMs on static data, struggling with dynamics in open-ended scenarios; 3) input prior knowledge directly as prompts, suppressing application flexibility. We propose STEVE-2, a hierarchical knowledge distillation framework for open-ended embodied tasks, characterized by 1) a hierarchical system for multi-granular task division, 2) a mirrored distillation method for parallel simulation data, and 3) an extra expert model for bringing additional knowledge into parallel simulation. After distillation, embodied agents can complete complex, open-ended tasks without additional expert guidance, utilizing the performance and knowledge of a versatile MLM. Extensive evaluations on navigation and creation tasks highlight the superior performance of STEVE-2 in open-ended tasks, with 1.4 times - 7.3 times in performance.

Service robots should be able to operate autonomously in dynamic and daily changing environments over an extended period of time. While Simultaneous Localization And Mapping (SLAM) is one of the most fundamental problems for robotic autonomy, most existing SLAM works are evaluated with data sequences that are recorded in a short period of time. In real-world deployment, there can be out-of-sight scene changes caused by both natural factors and human activities. For example, in home scenarios, most objects may be movable, replaceable or deformable, and the visual features of the same place may be significantly different in some successive days. Such out-of-sight dynamics pose great challenges to the robustness of pose estimation, and hence a robot's long-term deployment and operation. To differentiate the forementioned problem from the conventional works which are usually evaluated in a static setting in a single run, the term lifelong SLAM is used here to address SLAM problems in an ever-changing environment over a long period of time. To accelerate lifelong SLAM research, we release the OpenLORIS-Scene datasets. The data are collected in real-world indoor scenes, for multiple times in each place to include scene changes in real life. We also design benchmarking metrics for lifelong SLAM, with which the robustness and accuracy of pose estimation are evaluated separately. The datasets and benchmark are available online at https://lifelong-robotic-vision.github.io/dataset/scene.

Large multimodal reasoning models (LMRMs) are getting increasingly capable, primarily through generating explicit chain-of-thought reasoning before answering. In language models it has been observed that this performance often comes with sycophancy, the tendency of a model to agree with the user over the evidence. However, for LMRMs no reliable method to measure sycophancy yet exists. We bridge this gap by introducing a benchmark and dataset for evaluating LMRM sycophancy when confronted with a wrong answer from a user. Our benchmark pairs four visually grounded datasets spanning mathematical, clinical, temporal, and demographic reasoning with five pressure conditions in single-turn and multi-turn settings. We evaluate sycophancy in the final answer as well as its emergence within the reasoning chain. We find that sycophancy is prevalent under pressure, with Statement pressure eliciting the highest rates and Conviction the lowest for all models except Mistral-Small-4, and under multi-turn pressure reasoning-level sycophancy intensifies sharply in clinical visual judgement, reaching 95.7% for the most affected model. We further introduce a failure taxonomy separating reasoning-chain from answer-level sycophancy, and a complementary sentence-level taxonomy locating where in the chain drift first emerges. Our results show that sycophancy can corrupt the reasoning chain independently of the final answer, so answer-level evaluation alone is insufficient.

Recent progress in multimodal reasoning has been driven largely by undisclosed datasets and proprietary data synthesis recipes, leaving open questions about how to systematically build large-scale, vision-centric reasoning datasets, particularly for tasks that go beyond visual math. In this work, we introduce a new reasoning data generation framework spanning diverse skills and levels of complexity with over 1M high-quality synthetic vision-centric questions. The dataset also includes preference data and instruction prompts supporting both offline and online RL. Our synthesis framework proceeds in two stages: (1) scale; and (2) complexity. Reasoning traces are then synthesized through a two-stage process that leverages VLMs and reasoning LLMs, producing CoT traces for VLMs that capture the richness and diverse cognitive behaviors found in frontier reasoning models. Remarkably, we show that finetuning Qwen2.5-VL-7B on our data outperforms all open-data baselines across all evaluated vision-centric benchmarks, and even surpasses strong closed-data models such as MiMo-VL-7B-RL on V* Bench, CV-Bench and MMStar-V. Perhaps most surprising, despite being entirely vision-centric, our data transfers positively to text-only reasoning (MMLU-Pro) and audio reasoning (MMAU), demonstrating its effectiveness. Similarly, despite not containing videos or embodied visual data, we observe notable gains when evaluating on a single-evidence embodied QA benchmark (NiEH). Finally, we use our data to analyze the entire VLM post-training pipeline. Our empirical analysis highlights that (i) SFT on high-quality data with non-linear reasoning traces is essential for effective online RL, (ii) staged offline RL matches online RL's performance while reducing compute demands, and (iii) careful SFT on high quality data can substantially improve out-of-domain, cross-modality transfer.

This study presents a structured dataset of blockchain-registered artificial intelligence agents under the ERC-8004 standard on Ethereum. The dataset integrates on-chain identity records, minting transactions, transfer events, reputation summaries, and individual feedback records, together with resolved off-chain metadata where available. Data were collected from Ethereum mainnet using Web3 RPC queries and processed into tabular form to enable reproducible analysis. The dataset covers 10,000 agents within a defined block range and includes both event-level records and aggregated summaries. It enables empirical research on agent identity formation, reputation systems, service exposure, and early-stage decentralized AI ecosystems. This resource supports studies in blockchain analytics, decentralized trust infrastructure, and the emerging agentic economy.

Due to the steadily rising amount of valuable goods in supply chains, tampering detection for parcels is becoming increasingly important. In this work, we focus on the use-case last-mile delivery, where only a single RGB image is taken and compared against a reference from an existing database to detect potential appearance changes that indicate tampering. We propose a tampering detection pipeline that utilizes keypoint detection to identify the eight corner points of a parcel. This permits applying a perspective transformation to create normalized fronto-parallel views for each visible parcel side surface. These viewpoint-invariant parcel side surface representations facilitate the identification of signs of tampering on parcels within the supply chain, since they reduce the problem to parcel side surface matching with pair-wise appearance change detection. Experiments with multiple classical and deep learning-based change detection approaches are performed on our newly collected TAMpering detection dataset for PARcels, called TAMPAR. We evaluate keypoint and change detection separately, as well as in a unified system for tampering detection. Our evaluation shows promising results for keypoint (Keypoint AP 75.76) and tampering detection (81% accuracy, F1-Score 0.83) on real images. Furthermore, a sensitivity analysis for tampering types, lens distortion and viewing angles is presented. Code and dataset are available at https://a-nau.github.io/tampar.

Protein-protein interaction (PPI) databases do not faithfully reflect biological realities. Instead, they are influenced by study and technical biases that distort certain protein and interaction attributes. Machine learning models can exploit these as learning shortcuts if the negative dataset is not constructed with care. So far, the shortcuts introduced during PPI dataset construction have only been examined in isolation. Here, we systematically characterize both reported and, to our knowledge, previously unreported biases in PPI datasets that lead machine learning models to learn shortcuts instead of biological signal. We analyze HIPPIE, IntAct, and STRING, dedicated PPI databases, as well as two datasets derived from 3D-structural information in the Protein Data Bank (PDB). We show that random data splitting introduces strong topological shortcuts. When train-test protein overlap is removed, the resulting datasets still retain usable shortcuts stemming from self-interactions, taxonomic identity, and functional relatedness, whose prevalence interestingly depends on the data source. We further show that sampling negatives from a set of high-confidence non-interactors, an intuitively appealing choice, can amplify the shortcut stemming from functional relatedness. To detect and mitigate these biases, we provide an open Nextflow pipeline that combines similarity-aware, data-loss-minimizing dataset splitting with bias-minimizing negative sampling, both formulated as integer linear programs. Its key concept of quantifying biases to minimize them through optimization-based negative sampling can, in principle, be extended to any machine learning problem where the pool of negative candidates is much larger than the positives and is thus of interest also beyond PPI prediction.

Unified generation of sequence and structure for scientific data (e.g., materials, molecules, proteins) is a critical task. Existing approaches primarily rely on either autoregressive sequence models or diffusion models, each offering distinct advantages and facing notable limitations. Autoregressive models, such as GPT, Llama, and Phi-4, have demonstrated remarkable success in natural language generation and have been extended to multimodal tasks (e.g., image, video, and audio) using advanced encoders like VQ-VAE to represent complex modalities as discrete sequences. However, their direct application to scientific domains is challenging due to the high precision requirements and the diverse nature of scientific data. On the other hand, diffusion models excel at generating high-dimensional scientific data, such as protein, molecule, and material structures, with remarkable accuracy. Yet, their inability to effectively model sequences limits their potential as general-purpose multimodal foundation models. To address these challenges, we propose UniGenX, a unified framework that combines autoregressive next-token prediction with conditional diffusion models. This integration leverages the strengths of autoregressive models to ease the training of conditional diffusion models, while diffusion-based generative heads enhance the precision of autoregressive predictions. We validate the effectiveness of UniGenX on material and small molecule generation tasks, achieving a significant leap in state-of-the-art performance for material crystal structure prediction and establishing new state-of-the-art results for small molecule structure prediction, de novo design, and conditional generation. Notably, UniGenX demonstrates significant improvements, especially in handling long sequences for complex structures, showcasing its efficacy as a versatile tool for scientific data generation.

Single-cell transcriptomes are sparse observations of coordinated biological programmes, yet most self-supervised models learn by reconstructing individual genes. Here we present BioM-JEPA, a joint-embedding predictive architecture that instead predicts aggregate representations of graph-connected gene blocks defined by protein-association and corpus-derived coexpression evidence. A student network infers each target-block representation from the remaining genes in a cell, while a slowly updated teacher supplies the corresponding target from the full observed gene set. Under the reported extraction procedure, block-level prediction produced embeddings with higher effective rank and weaker association with detected-gene depth in the tested diagnostics than token-prediction, random-block and reconstruction controls. Across CellBench tasks, frozen BioM-JEPA embeddings retained expression, pathway and neighbourhood information and achieved the lowest aggregate perturbation-response error among the evaluated models. Representation diagnostics were also consistent with canonical pancreatic programmes and compositional relationships between genetic perturbations. Linear attention avoids constructing a quadratic gene-by-gene attention matrix; in a matched one-epoch hPancreas experiment at batch size 8, BioM-JEPA provided 5.75-fold higher fine-tuning throughput and 3.76-fold higher held-out embedding throughput than scFoundation. Together, these results support graph-connected gene blocks as useful prediction units for JEPA-style representation learning in single-cell biology.

Clinical MRI encompasses diverse imaging protocols--spanning anatomical targets (cardiac, brain, knee), contrasts (T1, T2, mapping), sampling patterns (Cartesian, radial, spiral, kt-space), and acceleration factors--yet current deep learning reconstructions are typically protocol-specific, hindering generalization and deployment. We introduce Scalable Deep Unrolled Model (SDUM), a universal framework combining a Restormer-based reconstructor, a learned coil sensitivity map estimator (CSME), sampling-aware weighted data consistency (SWDC), universal conditioning (UC) on cascade index and protocol metadata, and progressive cascade expansion training. SDUM exhibits foundation-model-like scaling behavior: reconstruction quality follows PSNR {sim} log(parameters) with correlation r{=}0.986 (R^2{=}0.973) up to 18 cascades, demonstrating predictable performance gains with model depth. A single SDUM trained on heterogeneous data achieves state-of-the-art results across all four CMRxRecon2025 challenge tracks--multi-center, multi-disease, 5T, and pediatric--without task-specific fine-tuning, surpassing specialized baselines by up to {+}1.0~dB. On CMRxRecon2024, SDUM outperforms the winning method PromptMR+ by {+}0.55~dB; on fastMRI brain, it exceeds PC-RNN by {+}1.8~dB. Ablations validate each component: SWDC {+}0.43~dB over standard DC, per-cascade CSME {+}0.51~dB, UC {+}0.38~dB. These results establish SDUM as a practical path toward universal, scalable MRI reconstruction.

Markerless methods for animal posture tracking have been rapidly developing recently, but frameworks and benchmarks for tracking large animal groups in 3D are still lacking. To overcome this gap in the literature, we present 3D-MuPPET, a framework to estimate and track 3D poses of up to 10 pigeons at interactive speed using multiple camera views. We train a pose estimator to infer 2D keypoints and bounding boxes of multiple pigeons, then triangulate the keypoints to 3D. For identity matching of individuals in all views, we first dynamically match 2D detections to global identities in the first frame, then use a 2D tracker to maintain IDs across views in subsequent frames. We achieve comparable accuracy to a state of the art 3D pose estimator in terms of median error and Percentage of Correct Keypoints. Additionally, we benchmark the inference speed of 3D-MuPPET, with up to 9.45 fps in 2D and 1.89 fps in 3D, and perform quantitative tracking evaluation, which yields encouraging results. Finally, we showcase two novel applications for 3D-MuPPET. First, we train a model with data of single pigeons and achieve comparable results in 2D and 3D posture estimation for up to 5 pigeons. Second, we show that 3D-MuPPET also works in outdoors without additional annotations from natural environments. Both use cases simplify the domain shift to new species and environments, largely reducing annotation effort needed for 3D posture tracking. To the best of our knowledge we are the first to present a framework for 2D/3D animal posture and trajectory tracking that works in both indoor and outdoor environments for up to 10 individuals. We hope that the framework can open up new opportunities in studying animal collective behaviour and encourages further developments in 3D multi-animal posture tracking.

We present a scalable, bottom-up and intrinsically diverse data collection scheme that can be used for high-level reasoning with long and medium horizons and that has 2.2x higher throughput compared to traditional narrow top-down step-by-step collection. We collect realistic data by performing any user requests within the entirety of 3 office buildings and using multiple robot and human embodiments. With this data, we show that models trained on all embodiments perform better than ones trained on the robot data only, even when evaluated solely on robot episodes. We find that for a fixed collection budget it is beneficial to take advantage of cheaper human collection along with robot collection. We release a large and highly diverse (29,520 unique instructions) dataset dubbed RoboVQA containing 829,502 (video, text) pairs for robotics-focused visual question answering. We also demonstrate how evaluating real robot experiments with an intervention mechanism enables performing tasks to completion, making it deployable with human oversight even if imperfect while also providing a single performance metric. We demonstrate a single video-conditioned model named RoboVQA-VideoCoCa trained on our dataset that is capable of performing a variety of grounded high-level reasoning tasks in broad realistic settings with a cognitive intervention rate 46% lower than the zero-shot state of the art visual language model (VLM) baseline and is able to guide real robots through long-horizon tasks. The performance gap with zero-shot state-of-the-art models indicates that a lot of grounded data remains to be collected for real-world deployment, emphasizing the critical need for scalable data collection approaches. Finally, we show that video VLMs significantly outperform single-image VLMs with an average error rate reduction of 19% across all VQA tasks. Data and videos available at https://robovqa.github.io

Large Language Models (LLMs) are attracting significant research attention due to their instruction-following abilities, allowing users and developers to leverage LLMs for a variety of tasks. However, LLMs are vulnerable to prompt-injection attacks: a class of attacks that hijack the model's instruction-following abilities, changing responses to prompts to undesired, possibly malicious ones. In this work, we introduce Jatmo, a method for generating task-specific models resilient to prompt-injection attacks. Jatmo leverages the fact that LLMs can only follow instructions once they have undergone instruction tuning. It harnesses a teacher instruction-tuned model to generate a task-specific dataset, which is then used to fine-tune a base model (i.e., a non-instruction-tuned model). Jatmo only needs a task prompt and a dataset of inputs for the task: it uses the teacher model to generate outputs. For situations with no pre-existing datasets, Jatmo can use a single example, or in some cases none at all, to produce a fully synthetic dataset. Our experiments on six tasks show that Jatmo models provide the same quality of outputs on their specific task as standard LLMs, while being resilient to prompt injections. The best attacks succeeded in less than 0.5% of cases against our models, versus over 90% success rate against GPT-3.5-Turbo. We release Jatmo at https://github.com/wagner-group/prompt-injection-defense.

The development of reliable and extensible molecular mechanics (MM) force fields -- fast, empirical models characterizing the potential energy surface of molecular systems -- is indispensable for biomolecular simulation and computer-aided drug design. Here, we introduce a generalized and extensible machine-learned MM force field, espaloma-0.3, and an end-to-end differentiable framework using graph neural networks to overcome the limitations of traditional rule-based methods. Trained in a single GPU-day to fit a large and diverse quantum chemical dataset of over 1.1M energy and force calculations, espaloma-0.3 reproduces quantum chemical energetic properties of chemical domains highly relevant to drug discovery, including small molecules, peptides, and nucleic acids. Moreover, this force field maintains the quantum chemical energy-minimized geometries of small molecules and preserves the condensed phase properties of peptides, self-consistently parametrizing proteins and ligands to produce stable simulations leading to highly accurate predictions of binding free energies. This methodology demonstrates significant promise as a path forward for systematically building more accurate force fields that are easily extensible to new chemical domains of interest.

Web platforms, mobile applications, and connected sensing systems generate multivariate time series with states at multiple levels of granularity, from coarse regimes to fine-grained events. Effective segmentation in these settings requires integrating across granularities while supporting iterative refinement through sparse prompt signals, which provide a compact mechanism for injecting domain knowledge. Yet existing prompting approaches for time series segmentation operate only within local contexts, so the effect of a prompt quickly fades and cannot guide predictions across the entire sequence. To overcome this limitation, we propose MemPromptTSS, a framework for iterative multi-granularity segmentation that introduces persistent prompt memory. A memory encoder transforms prompts and their surrounding subsequences into memory tokens stored in a bank. This persistent memory enables each new prediction to condition not only on local cues but also on all prompts accumulated across iterations, ensuring their influence persists across the entire sequence. Experiments on six datasets covering wearable sensing and industrial monitoring show that MemPromptTSS achieves 23% and 85% accuracy improvements over the best baseline in single- and multi-granularity segmentation under single iteration inference, and provides stronger refinement in iterative inference with average per-iteration gains of 2.66 percentage points compared to 1.19 for PromptTSS. These results highlight the importance of persistent memory for prompt-guided segmentation, establishing MemPromptTSS as a practical and effective framework for real-world applications.

Large Language Models (LLMs) exhibit remarkable capabilities but are prone to generating inaccurate or hallucinatory responses. This limitation stems from their reliance on vast pretraining datasets, making them susceptible to errors in unseen scenarios. To tackle these challenges, Retrieval-Augmented Generation (RAG) addresses this by incorporating external, relevant documents into the response generation process, thus leveraging non-parametric knowledge alongside LLMs' in-context learning abilities. However, existing RAG implementations primarily focus on initial input for context retrieval, overlooking the nuances of ambiguous or complex queries that necessitate further clarification or decomposition for accurate responses. To this end, we propose learning to Refine Query for Retrieval Augmented Generation (RQ-RAG) in this paper, endeavoring to enhance the model by equipping it with capabilities for explicit rewriting, decomposition, and disambiguation. Our experimental results indicate that our method, when applied to a 7B Llama2 model, surpasses the previous state-of-the-art (SOTA) by an average of 1.9\% across three single-hop QA datasets, and also demonstrates enhanced performance in handling complex, multi-hop QA datasets. Our code is available at https://github.com/chanchimin/RQ-RAG.

A significant use case of instruction-finetuned Large Language Models (LLMs) is to solve question-answering tasks interactively. In this setting, an LLM agent is tasked with making a prediction by sequentially querying relevant information from the user, as opposed to a single-turn conversation. This paper explores sequential querying strategies that aim to minimize the expected number of queries. One such strategy is Information Pursuit (IP), a greedy algorithm that at each iteration selects the query that maximizes information gain or equivalently minimizes uncertainty. However, obtaining accurate estimates of mutual information or conditional entropy for LLMs is very difficult in practice due to over- or under-confident LLM probabilities, which leads to suboptimal query selection and predictive performance. To better estimate the uncertainty at each iteration, we propose Conformal Information Pursuit (C-IP), an alternative approach to sequential information gain based on conformal prediction sets. More specifically, C-IP leverages a relationship between prediction sets and conditional entropy at each iteration to estimate uncertainty based on the average size of conformal prediction sets. In contrast to conditional entropy, we find that conformal prediction sets are a distribution-free and robust method of measuring uncertainty. Experiments with 20 Questions show that C-IP obtains better predictive performance and shorter query-answer chains compared to previous approaches to IP and uncertainty-based chain-of-thought methods. Furthermore, extending to an interactive medical setting between a doctor and a patient on the MediQ dataset, C-IP achieves competitive performance with direct single-turn prediction while offering greater interpretability.

Current state-of-the-art automatic speech recognition systems are trained to work in specific `domains', defined based on factors like application, sampling rate and codec. When such recognizers are used in conditions that do not match the training domain, performance significantly drops. This work explores the idea of building a single domain-invariant model for varied use-cases by combining large scale training data from multiple application domains. Our final system is trained using 162,000 hours of speech. Additionally, each utterance is artificially distorted during training to simulate effects like background noise, codec distortion, and sampling rates. Our results show that, even at such a scale, a model thus trained works almost as well as those fine-tuned to specific subsets: A single model can be robust to multiple application domains, and variations like codecs and noise. More importantly, such models generalize better to unseen conditions and allow for rapid adaptation -- we show that by using as little as 10 hours of data from a new domain, an adapted domain-invariant model can match performance of a domain-specific model trained from scratch using 70 times as much data. We also highlight some of the limitations of such models and areas that need addressing in future work.

Access to high-quality and diverse 3D articulated digital human assets is crucial in various applications, ranging from virtual reality to social platforms. Generative approaches, such as 3D generative adversarial networks (GANs), are rapidly replacing laborious manual content creation tools. However, existing 3D GAN frameworks typically rely on scene representations that leverage either template meshes, which are fast but offer limited quality, or volumes, which offer high capacity but are slow to render, thereby limiting the 3D fidelity in GAN settings. In this work, we introduce layered surface volumes (LSVs) as a new 3D object representation for articulated digital humans. LSVs represent a human body using multiple textured mesh layers around a conventional template. These layers are rendered using alpha compositing with fast differentiable rasterization, and they can be interpreted as a volumetric representation that allocates its capacity to a manifold of finite thickness around the template. Unlike conventional single-layer templates that struggle with representing fine off-surface details like hair or accessories, our surface volumes naturally capture such details. LSVs can be articulated, and they exhibit exceptional efficiency in GAN settings, where a 2D generator learns to synthesize the RGBA textures for the individual layers. Trained on unstructured, single-view 2D image datasets, our LSV-GAN generates high-quality and view-consistent 3D articulated digital humans without the need for view-inconsistent 2D upsampling networks.

Language models (LMs) often struggle to generate diverse, human-like creative content, raising concerns about the long-term homogenization of human thought through repeated exposure to similar outputs. Yet scalable methods for evaluating LM output diversity remain limited, especially beyond narrow tasks such as random number or name generation, or beyond repeated sampling from a single model. We introduce Infinity-Chat, a large-scale dataset of 26K diverse, real-world, open-ended user queries that admit a wide range of plausible answers with no single ground truth. We introduce the first comprehensive taxonomy for characterizing the full spectrum of open-ended prompts posed to LMs, comprising 6 top-level categories (e.g., brainstorm & ideation) that further breaks down to 17 subcategories. Using Infinity-Chat, we present a large-scale study of mode collapse in LMs, revealing a pronounced Artificial Hivemind effect in open-ended generation of LMs, characterized by (1) intra-model repetition, where a single model consistently generates similar responses, and more so (2) inter-model homogeneity, where different models produce strikingly similar outputs. Infinity-Chat also includes 31,250 human annotations, across absolute ratings and pairwise preferences, with 25 independent human annotations per example. This enables studying collective and individual-specific human preferences in response to open-ended queries. Our findings show that LMs, reward models, and LM judges are less well calibrated to human ratings on model generations that elicit differing idiosyncratic annotator preferences, despite maintaining comparable overall quality. Overall, INFINITY-CHAT presents the first large-scale resource for systematically studying real-world open-ended queries to LMs, revealing critical insights to guide future research for mitigating long-term AI safety risks posed by the Artificial Hivemind.

Medical imaging is critical for diagnostics, but clinical adoption of advanced AI-driven imaging faces challenges due to patient variability, image artifacts, and limited model generalization. While deep learning has transformed image analysis, 3D medical imaging still suffers from data scarcity and inconsistencies due to acquisition protocols, scanner differences, and patient motion. Traditional augmentation uses a single pipeline for all transformations, disregarding the unique traits of each augmentation and struggling with large data volumes. To address these challenges, we propose a Multi-encoder Augmentation-Aware Learning (MEAL) framework that leverages four distinct augmentation variants processed through dedicated encoders. Three fusion strategies such as concatenation (CC), fusion layer (FL), and adaptive controller block (BD) are integrated to build multi-encoder models that combine augmentation-specific features before decoding. MEAL-BD uniquely preserves augmentation-aware representations, enabling robust, protocol-invariant feature learning. As demonstrated in a Computed Tomography (CT)-to-T1-weighted Magnetic Resonance Imaging (MRI) translation study, MEAL-BD consistently achieved the best performance on both unseen- and predefined-test data. On both geometric transformations (like rotations and flips) and non-augmented inputs, MEAL-BD outperformed other competing methods, achieving higher mean peak signal-to-noise ratio (PSNR) and structural similarity index measure (SSIM) scores. These results establish MEAL as a reliable framework for preserving structural fidelity and generalizing across clinically relevant variability. By reframing augmentation as a source of diverse, generalizable features, MEAL supports robust, protocol-invariant learning, advancing clinically reliable medical imaging solutions.

Learning-based methods have dominated the 3D human pose estimation (HPE) tasks with significantly better performance in most benchmarks than traditional optimization-based methods. Nonetheless, 3D HPE in the wild is still the biggest challenge of learning-based models, whether with 2D-3D lifting, image-to-3D, or diffusion-based methods, since the trained networks implicitly learn camera intrinsic parameters and domain-based 3D human pose distributions and estimate poses by statistical average. On the other hand, the optimization-based methods estimate results case-by-case, which can predict more diverse and sophisticated human poses in the wild. By combining the advantages of optimization-based and learning-based methods, we propose the Zero-shot Diffusion-based Optimization (ZeDO) pipeline for 3D HPE to solve the problem of cross-domain and in-the-wild 3D HPE. Our multi-hypothesis ZeDO achieves state-of-the-art (SOTA) performance on Human3.6M as minMPJPE 51.4mm without training with any 2D-3D or image-3D pairs. Moreover, our single-hypothesis ZeDO achieves SOTA performance on 3DPW dataset with PA-MPJPE 42.6mm on cross-dataset evaluation, which even outperforms learning-based methods trained on 3DPW.

This paper presents a comprehensive review of the NTIRE 2025 Challenge on Single-Image Efficient Super-Resolution (ESR). The challenge aimed to advance the development of deep models that optimize key computational metrics, i.e., runtime, parameters, and FLOPs, while achieving a PSNR of at least 26.90 dB on the DIV2K_LSDIR_valid dataset and 26.99 dB on the DIV2K_LSDIR_test dataset. A robust participation saw 244 registered entrants, with 43 teams submitting valid entries. This report meticulously analyzes these methods and results, emphasizing groundbreaking advancements in state-of-the-art single-image ESR techniques. The analysis highlights innovative approaches and establishes benchmarks for future research in the field.

Multi-attribution learning (MAL), which enhances model performance by learning from conversion labels yielded by multiple attribution mechanisms, has emerged as a promising learning paradigm for conversion rate (CVR) prediction. However, the conversion labels in public CVR datasets are generated by a single attribution mechanism, hindering the development of MAL approaches. To address this data gap, we establish the Multi-Attribution Benchmark (MAC), the first public CVR dataset featuring labels from multiple attribution mechanisms. Besides, to promote reproducible research on MAL, we develop PyMAL, an open-source library covering a wide array of baseline methods. We conduct comprehensive experimental analyses on MAC and reveal three key insights: (1) MAL brings consistent performance gains across different attribution settings, especially for users featuring long conversion paths. (2) The performance growth scales up with objective complexity in most settings; however, when predicting first-click conversion targets, simply adding auxiliary objectives is counterproductive, underscoring the necessity of careful selection of auxiliary objectives. (3) Two architectural design principles are paramount: first, to fully learn the multi-attribution knowledge, and second, to fully leverage this knowledge to serve the main task. Motivated by these findings, we propose Mixture of Asymmetric Experts (MoAE), an effective MAL approach incorporating multi-attribution knowledge learning and main task-centric knowledge utilization. Experiments on MAC show that MoAE substantially surpasses the existing state-of-the-art MAL method. We believe that our benchmark and insights will foster future research in the MAL field. Our MAC benchmark and the PyMAL algorithm library are publicly available at https://github.com/alimama-tech/PyMAL.

Offline reinforcement learning requires improving a policy from fixed data while avoiding out-of-distribution actions with unreliable value estimates. Diffusion and flow policies handle this trade-off by modeling the behavior distribution to regularize the RL objective, but they require iterative denoising, solver integrations, and in more efficient variants, distillation or other approximations at inference. We propose DriftQL, which combines a drift-based behavioral regularizer with critic-driven policy improvement. The value signal biases the policy toward high-value regions of the data support, while attraction and repulsion together keep generated actions near the data and prevent collapse onto a single mode. DriftQL is implemented as a single network with a unified training objective and generates actions in a single forward pass. On D4RL and OGBench, DriftQL consistently outperforms diffusion and flow methods, advancing the state of the art. Under degraded data quality, where the baselines visibly struggle, DriftQL remains close to its clean-data performance, positioning it as a promising alternative to diffusion and flow-based methods while maintaining the simplicity and efficiency of deterministic approaches. Project page: https://driftql.github.io/

Radiological artificial intelligence has advanced rapidly, yet most systems remain narrowly task-specific, data-intensive, and fragile under domain shift. Foundation models promise more transferable and data-efficient solutions, but existing approaches are limited in scale, evaluated narrowly, and often assume that a single pretrained model can support diverse downstream tasks. Here we present nnFoundation, complementary convolutional and transformer-based 3D radiological foundation models. Developed within the Human Radiome Project (THRP), nnFoundation is trained on 2.1 million CT, MRI, and PET image volumes from 125 institutional and public datasets. We evaluate them across 108 tasks spanning segmentation, detection, classification, report generation, and image retrieval, including evaluations under domain shift, by external partners and in low-data and low-compute regimes. Across all task types, our convolution- and transformer-based nnFoundation models consistently outperform both prior 3D foundation models and training from scratch, establishing state-of-the-art performance for radiological imaging. However, performance follows a consistent task-dependent structure: the convolutional nnFoundation model dominates spatially localized tasks, whereas the transformer-based nnFoundation model excels in tasks requiring global semantic reasoning and in frozen-feature settings. Dynamically aligning the foundation model topology with the dataset characteristics post-hoc further improves transfer across heterogeneous 3D settings. These results show that transferable 3D radiological performance is governed not by a single universal model, but by the interplay of scalable pretraining, complementary architectures, and dataset-aware adaptation. We release nnFoundation models integrated into nnU-Net and nnDetection, enabling immediate application across established radiology workflows.

Artificial Intelligence Virtual Cells (AIVCs) aim to learn executable, decision-relevant models of cell state from multimodal, multiscale measurements. Recent studies have introduced single-cell and spatial foundation models, improved cross-modality alignment, scaled perturbation atlases, and explored pathway-level readouts. Nevertheless, although held-out validation is standard practice, evaluations remain predominantly within single datasets and settings; evidence indicates that transport across laboratories and platforms is often limited, that some data splits are vulnerable to leakage and coverage bias, and that dose, time and combination effects are not yet systematically handled. Cross-scale coupling also remains constrained, as anchors linking molecular, cellular and tissue levels are sparse, and alignment to scientific or clinical readouts varies across studies. We propose a model-agnostic Cell-State Latent (CSL) perspective that organizes learning via an operator grammar: measurement, lift/project for cross-scale coupling, and intervention for dosing and scheduling. This view motivates a decision-aligned evaluation blueprint across modality, scale, context and intervention, and emphasizes function-space readouts such as pathway activity, spatial neighborhoods and clinically relevant endpoints. We recommend operator-aware data design, leakage-resistant partitions, and transparent calibration and reporting to enable reproducible, like-for-like comparisons.

With the rapid rise of large language models (LLMs), phone automation has undergone transformative changes. This paper systematically reviews LLM-driven phone GUI agents, highlighting their evolution from script-based automation to intelligent, adaptive systems. We first contextualize key challenges, (i) limited generality, (ii) high maintenance overhead, and (iii) weak intent comprehension, and show how LLMs address these issues through advanced language understanding, multimodal perception, and robust decision-making. We then propose a taxonomy covering fundamental agent frameworks (single-agent, multi-agent, plan-then-act), modeling approaches (prompt engineering, training-based), and essential datasets and benchmarks. Furthermore, we detail task-specific architectures, supervised fine-tuning, and reinforcement learning strategies that bridge user intent and GUI operations. Finally, we discuss open challenges such as dataset diversity, on-device deployment efficiency, user-centric adaptation, and security concerns, offering forward-looking insights into this rapidly evolving field. By providing a structured overview and identifying pressing research gaps, this paper serves as a definitive reference for researchers and practitioners seeking to harness LLMs in designing scalable, user-friendly phone GUI agents.

Restoring facial details from low-quality (LQ) images has remained a challenging problem due to its ill-posedness induced by various degradations in the wild. The existing codebook prior mitigates the ill-posedness by leveraging an autoencoder and learned codebook of high-quality (HQ) features, achieving remarkable quality. However, existing approaches in this paradigm frequently depend on a single encoder pre-trained on HQ data for restoring HQ images, disregarding the domain gap between LQ and HQ images. As a result, the encoding of LQ inputs may be insufficient, resulting in suboptimal performance. To tackle this problem, we propose a novel dual-branch framework named DAEFR. Our method introduces an auxiliary LQ branch that extracts crucial information from the LQ inputs. Additionally, we incorporate association training to promote effective synergy between the two branches, enhancing code prediction and output quality. We evaluate the effectiveness of DAEFR on both synthetic and real-world datasets, demonstrating its superior performance in restoring facial details. Project page: https://liagm.github.io/DAEFR/

This report presents an overview of the AIM 2025 RipSeg Challenge, a competition designed to advance techniques for automatic rip current segmentation in still images. Rip currents are dangerous, fast-moving flows that pose a major risk to beach safety worldwide, making accurate visual detection an important and underexplored research task. The challenge builds on RipVIS, the largest available rip current dataset, and focuses on single-class instance segmentation, where precise delineation is critical to fully capture the extent of rip currents. The dataset spans diverse locations, rip current types, and camera orientations, providing a realistic and challenging benchmark. In total, 75 participants registered for this first edition, resulting in 5 valid test submissions. Teams were evaluated on a composite score combining F_1, F_2, AP_{50}, and AP_{[50:95]}, ensuring robust and application-relevant rankings. The top-performing methods leveraged deep learning architectures, domain adaptation techniques, pretrained models, and domain generalization strategies to improve performance under diverse conditions. This report outlines the dataset details, competition framework, evaluation metrics, and final results, providing insights into the current state of rip current segmentation. We conclude with a discussion of key challenges, lessons learned from the submissions, and future directions for expanding RipSeg.

Foundation models have begun to transform image analysis by acting as pretrained generalist backbones that can be adapted to many tasks even when post-training data are limited, yet their impact on spatial proteomics, imaging that maps proteins at single-cell resolution, remains limited. Here, we introduce KRONOS, a foundation model built for spatial proteomics. KRONOS was trained in a self-supervised manner on over 47 million image patches covering 175 protein markers, 16 tissue types, and 8 fluorescence-based imaging platforms. We introduce key architectural adaptations to address the high-dimensional, multi-channel, and heterogeneous nature of multiplex imaging. We demonstrate that KRONOS learns biologically meaningful representations across multiple scales, ranging from cellular and microenvironment to tissue levels, enabling it to address diverse downstream tasks, including cell phenotyping, region classification, and patient stratification. Evaluated across 11 independent cohorts, KRONOS achieves state-of-the-art performance across cell phenotyping, treatment response prediction, and retrieval tasks, and is highly data-efficient. KRONOS also introduces the paradigm of segmentation-free patch-level processing for efficient and scalable spatial proteomics analysis, allowing cross-institutional comparisons, and as an image reverse search engine for spatial patterns. Together, these results position KRONOS as a flexible and scalable tool for spatial proteomics. The model is publicly accessible at https://github.com/mahmoodlab/KRONOS.

Predicting single-cell responses to genetic and chemical perturbations is important for understanding regulatory mechanisms and prioritizing therapeutic interventions. Existing methods have made progress by modeling perturbation-conditioned expression shifts with neural networks, graph priors, foundation-model representations, or distributional generative models. However, combinatorial perturbation prediction remains challenging because much of the response can be explained by additive single-perturbation effects, while the biologically informative signal often lies in a smaller non-additive residual induced by perturbation interactions. Directly generating the full post-perturbation expression profile may therefore allocate substantial capacity to the dominant additive component and underemphasize synergy-specific structure. To address this issue, we propose SynGeneFlow, a synergy-aware flow matching framework that anchors the source distribution at an additive prior and learns a residual flow toward the true perturbed state. SynGeneFlow further incorporates perturbation-conditioned gene interaction modeling, where a static gene-gene mask provides biological structure and a perturbation-dependent deformation bias dynamically modulates gene-gene coupling. To preserve population-level response structure, we align both endpoint distributions and biological residual distributions with MMD-based regularization. We evaluate SynGeneFlow on genetic and drug perturbation benchmarks under observed-single, held-out, and cross-modality settings. The results demonstrate that residualizing flow matching around additive perturbation effects provides a biologically grounded and robust framework for single-cell perturbation response prediction.

Nanobodies, single-domain antibody fragments derived from camelid heavy-chain-only antibodies, exhibit unique advantages such as compact size, high stability, and strong binding affinity, making them valuable tools in therapeutics and diagnostics. While recent advances in pretrained protein and antibody language models (PPLMs and PALMs) have greatly enhanced biomolecular understanding, nanobody-specific modeling remains underexplored and lacks a unified benchmark. To address this gap, we introduce NbBench, the first comprehensive benchmark suite for nanobody representation learning. Spanning eight biologically meaningful tasks across nine curated datasets, NbBench encompasses structure annotation, binding prediction, and developability assessment. We systematically evaluate eleven representative models--including general-purpose protein LMs, antibody-specific LMs, and nanobody-specific LMs--in a frozen setting. Our analysis reveals that antibody language models excel in antigen-related tasks, while performance on regression tasks such as thermostability and affinity remains challenging across all models. Notably, no single model consistently outperforms others across all tasks. By standardizing datasets, task definitions, and evaluation protocols, NbBench offers a reproducible foundation for assessing and advancing nanobody modeling.

Foundation models applied to bio-molecular space hold promise to accelerate drug discovery. Molecular representation is key to building such models. Previous works have typically focused on a single representation or view of the molecules. Here, we develop a multi-view foundation model approach, that integrates molecular views of graph, image and text. Single-view foundation models are each pre-trained on a dataset of up to 200M molecules and then aggregated into combined representations. Our multi-view model is validated on a diverse set of 18 tasks, encompassing ligand-protein binding, molecular solubility, metabolism and toxicity. We show that the multi-view models perform robustly and are able to balance the strengths and weaknesses of specific views. We then apply this model to screen compounds against a large (>100 targets) set of G Protein-Coupled receptors (GPCRs). From this library of targets, we identify 33 that are related to Alzheimer's disease. On this subset, we employ our model to identify strong binders, which are validated through structure-based modeling and identification of key binding motifs.

We consider the problem of embedding point cloud data sampled from an underlying manifold with an associated flow or velocity. Such data arises in many contexts where static snapshots of dynamic entities are measured, including in high-throughput biology such as single-cell transcriptomics. Existing embedding techniques either do not utilize velocity information or embed the coordinates and velocities independently, i.e., they either impose velocities on top of an existing point embedding or embed points within a prescribed vector field. Here we present FlowArtist, a neural network that embeds points while jointly learning a vector field around the points. The combination allows FlowArtist to better separate and visualize velocity-informed structures. Our results, on toy datasets and single-cell RNA velocity data, illustrate the value of utilizing coordinate and velocity information in tandem for embedding and visualizing high-dimensional data.

Predicting how a dynamical unit evolves over time - how an individual ages, an epidemic spreads, or a physical system degrades - typically requires dense longitudinal tracking. When only extremely sparse or entirely cross-sectional data is available, inferring individualized, continuous-time trajectories is fundamentally ill-posed. Existing methods force a strict compromise: sequence models (e.g. latent ODEs) require dense longitudinal data, while cross-sectional methods (e.g. optimal transport, flow matching-based) map aggregate populations, losing individual dynamics. In this paper, we demonstrate that this dichotomy can be broken. We introduce CADENCE, a principled probabilistic framework that recovers continuous individual trajectories from isolated snapshots by anchoring latent dynamics to static, individual-level contexts. We provide novel identifiability guarantees for single-timepoint trajectory inference. By combining a score-based spatial encoder (bijective Probability Flow ODE) to eliminate diffeomorphic ambiguities with a Soft Mixture-of-Experts (SMoE) router, we show that individual dynamical parameters and routing function are jointly identifiable. Across a suite of benchmarks spanning physical systems to real-world biological data, CADENCE, trained strictly on extremely sparse snapshots with context structure, matches or exceeds the performance of state-of-the-art sequential models trained on dense, full-trajectory data.

The detection of ligand binding sites for proteins is a fundamental step in Structure-Based Drug Design. Despite notable advances in recent years, existing methods, datasets, and evaluation metrics are confronted with several key challenges: (1) current datasets and methods are centered on individual protein-ligand complexes and neglect that diverse binding sites may exist across multiple complexes of the same protein, introducing significant statistical bias; (2) ligand binding site detection is typically modeled as a discontinuous workflow, employing binary segmentation and subsequent clustering algorithms; (3) traditional evaluation metrics do not adequately reflect the actual performance of different binding site prediction methods. To address these issues, we first introduce UniSite-DS, the first UniProt (Unique Protein)-centric ligand binding site dataset, which contains 4.81 times more multi-site data and 2.08 times more overall data compared to the previously most widely used datasets. We then propose UniSite, the first end-to-end ligand binding site detection framework supervised by set prediction loss with bijective matching. In addition, we introduce Average Precision based on Intersection over Union (IoU) as a more accurate evaluation metric for ligand binding site prediction. Extensive experiments on UniSite-DS and several representative benchmark datasets demonstrate that IoU-based Average Precision provides a more accurate reflection of prediction quality, and that UniSite outperforms current state-of-the-art methods in ligand binding site detection. The dataset and codes will be made publicly available at https://github.com/quanlin-wu/unisite.

High-quality structured organic reaction data are essential for developing artificial intelligence for chemistry (AI4Chem), yet much of this knowledge remains dispersed across patent text, images, and reaction schemes. We present DianShi-RxnDB, a large-scale, fine-grained organic reaction data platform built via a fully automated extraction and normalization pipeline integrating patent text, images, and reaction schemes. Its corpus covers organic synthesis patents from the USPTO and EPO published between 1976 and 2025, yielding approximately 24 million reaction instances, of which approximately 14.8 million (61.7%) pass automated qualification checks. Each instance represents a specific single-step experiment recording participants, roles, quantities, temperatures, reaction times, yields, experimental procedures, and provenance links to source patents. In a manual evaluation of 1,300 sampled qualified instances, the micro-averaged field-level accuracy was 92.95%. A matched comparison with Pistachio further indicated advantages in deduplicated record counts, representation granularity, and field-level exact agreement. The platform provides a Web research workbench for searching, filtering, comparing, and source-verifying records, and a Model Context Protocol (MCP) service offering AI agents composable structured retrieval tools. DianShi-RxnDB is available at https://dianshi.opendatalab.org.cn/ .

Designing a single model to address multiple tasks has been a long-standing objective in artificial intelligence. Recently, large language models have demonstrated exceptional capability in solving different tasks within the language domain. However, a unified model for various graph tasks remains underexplored, primarily due to the challenges unique to the graph learning domain. First, graph data from different areas carry distinct attributes and follow different distributions. Such discrepancy makes it hard to represent graphs in a single representation space. Second, tasks on graphs diversify into node, link, and graph tasks, requiring distinct embedding strategies. Finally, an appropriate graph prompting paradigm for in-context learning is unclear. We propose One for All (OFA), the first general framework that can use a single graph model to address the above challenges. Specifically, OFA proposes text-attributed graphs to unify different graph data by describing nodes and edges with natural language and uses language models to encode the diverse and possibly cross-domain text attributes to feature vectors in the same embedding space. Furthermore, OFA introduces the concept of nodes-of-interest to standardize different tasks with a single task representation. For in-context learning on graphs, OFA introduces a novel graph prompting paradigm that appends prompting substructures to the input graph, which enables it to address varied tasks without fine-tuning. We train the OFA model using graph data from multiple domains (including citation networks, molecular graphs, knowledge graphs, etc.) simultaneously and evaluate its ability in supervised, few-shot, and zero-shot learning scenarios. OFA performs well across different tasks, making it the first general-purpose across-domains classification model on graphs.

Single-cell technologies generate high-dimensional point clouds of cells, enabling detailed characterization of complex patient states and treatment responses. Yet each patient is represented by an irregular point cloud rather than a simple vector, making it difficult to directly quantify and compare biological differences between individuals. Nonlinear methods such as kernels and neural networks achieve predictive accuracy but act as black boxes, offering little biological interpretability. To address these limitations, we adapt the Linear Optimal Transport (LOT) framework to this setting, embedding irregular point clouds into a fixed-dimensional Euclidean space while preserving distributional structure. This embedding provides a principled linear representation that preserves optimal transport geometry while enabling downstream analysis. It also forms a registration between any two patients, enabling direct comparison of their cellular distributions. Within this space, LOT enables: (i) accurate and interpretable classification of COVID-19 patient states, where classifier weights map back to specific markers and spatial regions driving predictions; and (ii) synthetic data generation for patient-derived organoids, exploiting the linearity of the LOT embedding. LOT barycenters yield averaged cellular profiles representing combined conditions or samples, supporting drug interaction testing. Together, these results establish LOT as a unified framework that bridges predictive performance, interpretability, and generative modeling. By transforming heterogeneous point clouds into structured embeddings directly traceable to the original data, LOT opens new opportunities for understanding immune variation and treatment effects in high-dimensional biological systems.

We introduce a comprehensive framework for modeling single cell transcriptomic responses to perturbations, aimed at standardizing benchmarking in this rapidly evolving field. Our approach includes a modular and user-friendly model development and evaluation platform, a collection of diverse perturbational datasets, and a set of metrics designed to fairly compare models and dissect their performance. Through extensive evaluation of both published and baseline models across diverse datasets, we highlight the limitations of widely used models, such as mode collapse. We also demonstrate the importance of rank metrics which complement traditional model fit measures, such as RMSE, for validating model effectiveness. Notably, our results show that while no single model architecture clearly outperforms others, simpler architectures are generally competitive and scale well with larger datasets. Overall, this benchmarking exercise sets new standards for model evaluation, supports robust model development, and furthers the use of these models to simulate genetic and chemical screens for therapeutic discovery.

High-quality training datasets are crucial for the development of effective protein design models, but existing synthetic datasets often include unfavorable sequence-structure pairs, impairing generative model performance. We leverage ProteinMPNN, whose sequences are experimentally favorable as well as amenable to folding, together with structure prediction models to align high-quality synthetic structures with recoverable synthetic sequences. In that way, we create a new dataset designed specifically for training expressive, fully atomistic protein generators. By retraining La-Proteina, which models discrete residue type and side chain structure in a continuous latent space, on this dataset, we achieve new state-of-the-art results, with improvements of +54% in structural diversity and +27% in co-designability. To validate the broad utility of our approach, we further introduce Proteina Atomistica, a unified flow-based framework that jointly learns the distribution of protein backbone structure, discrete sequences, and atomistic side chains without latent variables. We again find that training on our new sequence-structure data dramatically boosts benchmark performance, improving \method's structural diversity by +73% and co-designability by +5%. Our work highlights the critical importance of aligned sequence-structure data for training high-performance de novo protein design models. Our new dataset https://catalog.ngc.nvidia.com/orgs/nvidia/teams/clara/resources/proteina-atomistica_data/files?version=release , the Consistency Distilled Synthetic Protein Database, is made available as an open-source resource.

Open time-series forecasting (TSF) benchmarks cover retail, energy, weather, and traffic, but supply-chain logistics remains underserved. We introduce ISOMORPH, the first public digital twin of a multi-echelon logistics network with fully interpretable, user-configurable parameters and modular topology, demand process, and control rules. The simulator advances a directed routing graph in discrete time: demand arrives at the destination, is served from stock or recorded as backlog, and triggers replenishment through the network. The state vector tracks per-node on-hand inventory with outstanding orders, in-transit shipments, and a smoothed demand estimate, so the dynamics close as a Markov chain on a tractable state space whose transition kernel acts linearly on the empirical distribution of the state. The released data reproduces the bullwhip effect at empirically consistent magnitudes, and three conservation laws encoded in the Markov chain serve as verification tools when users extend the simulator. We release datasets at two catalogue scales (C=50 and C=200) with six scenario sweeps producing 30 additional rollouts and 20 Latin-hypercube perturbations, exhibiting dynamics absent from fixed TSF benchmarks: variance amplification, cascading bottlenecks, regime shifts, and cross-channel coupling through shared macro shocks. Zero-shot evaluation of four foundation models (Chronos, Moirai, TimesFM, Lag-Llama) shows MASE values exceeding public GIFT-Eval references at low-to-moderate horizons, supporting incorporation into existing benchmarks. The same pairing produces forecast confidence bands via Latin-hypercube perturbation of demand-side knobs, forward UQ from parameter uncertainty unavailable on standard TSF datasets, demonstrating that foundation models can serve as fast surrogates for the digital twin's forward UQ. Code (MIT): https://github.com/tuhinsahai/ISOMORPH.

Recent advances in machine learning have made significant contributions to drug discovery. Deep neural networks in particular have been demonstrated to provide significant boosts in predictive power when inferring the properties and activities of small-molecule compounds. However, the applicability of these techniques has been limited by the requirement for large amounts of training data. In this work, we demonstrate how one-shot learning can be used to significantly lower the amounts of data required to make meaningful predictions in drug discovery applications. We introduce a new architecture, the residual LSTM embedding, that, when combined with graph convolutional neural networks, significantly improves the ability to learn meaningful distance metrics over small-molecules. We open source all models introduced in this work as part of DeepChem, an open-source framework for deep-learning in drug discovery.

Large language models (LLMs) and emerging agentic frameworks are beginning to transform single-cell biology by enabling natural-language reasoning, generative annotation, and multimodal data integration. However, progress remains fragmented across data modalities, architectures, and evaluation standards. LLM4Cell presents the first unified survey of 58 foundation and agentic models developed for single-cell research, spanning RNA, ATAC, multi-omic, and spatial modalities. We categorize these methods into five families-foundation, text-bridge, spatial, multimodal, epigenomic, and agentic-and map them to eight key analytical tasks including annotation, trajectory and perturbation modeling, and drug-response prediction. Drawing on over 40 public datasets, we analyze benchmark suitability, data diversity, and ethical or scalability constraints, and evaluate models across 10 domain dimensions covering biological grounding, multi-omics alignment, fairness, privacy, and explainability. By linking datasets, models, and evaluation domains, LLM4Cell provides the first integrated view of language-driven single-cell intelligence and outlines open challenges in interpretability, standardization, and trustworthy model development.

We present TableSeq, an image-only, end-to-end framework for joint table structure recognition, content recognition, and cell localization. The model formulates these tasks as a single sequence-generation problem: one decoder produces an interleaved stream of HTML tags, cell text, and discretized coordinate tokens, thereby aligning logical structure, textual content, and cell geometry within a unified autoregressive sequence. This design avoids external OCR, auxiliary decoders, and complex multi-stage post-processing. TableSeq combines a lightweight high-resolution FCN-H16 encoder with a minimal structure-prior head and a single-layer transformer encoder, yielding a compact architecture that remains effective on challenging layouts. Across standard benchmarks, TableSeq achieves competitive or state-of-the-art results while preserving architectural simplicity. It reaches 95.23 TEDS / 96.83 S-TEDS on PubTabNet, 97.45 TEDS / 98.69 S-TEDS on FinTabNet, and 99.79 / 99.54 / 99.66 precision / recall / F1 on SciTSR under the CAR protocol, while remaining competitive on PubTables-1M under GriTS. Beyond TSR/TCR, the same sequence interface generalizes to index-based table querying without task-specific heads, achieving the best IRDR score and competitive ICDR/ICR performance. We also study multi-token prediction for faster blockwise decoding and show that it reduces inference latency with only limited accuracy degradation. Overall, TableSeq provides a practical and reproducible single-stream baseline for unified table recognition, and the source code will be made publicly available at https://github.com/hamdilaziz/TableSeq.

Data synthesis is gaining momentum as a privacy-enhancing technology. While single-table tabular data generation has seen considerable progress, current methods for multi-table data often lack the flexibility and expressiveness needed to capture complex relational structures. In particular, they struggle with long-range dependencies and complex foreign-key relationships, such as tables with multiple parent tables or multiple types of links between the same pair of tables. We propose a generative model for relational data that generates the content of a relational dataset given the graph formed by the foreign-key relationships. We do this by learning a deep generative model of the content of the whole relational database by flow matching, where the neural network trained to denoise records leverages a graph neural network to obtain information from connected records. Our method is flexible, as it can support relational datasets with complex structures, and expressive, as the generation of each record can be influenced by any other record within the same connected component. We evaluate our method on several benchmark datasets and show that it achieves state-of-the-art performance in terms of synthetic data fidelity.

We study the implications of the modeling choice to use a graph, instead of a hypergraph, to represent real-world interconnected systems whose constituent relationships are of higher order by nature. Such a modeling choice typically involves an underlying projection process that maps the original hypergraph onto a graph, and is common in graph-based analysis. While hypergraph projection can potentially lead to loss of higher-order relations, there exists very limited studies on the consequences of doing so, as well as its remediation. This work fills this gap by doing two things: (1) we develop analysis based on graph and set theory, showing two ubiquitous patterns of hyperedges that are root to structural information loss in all hypergraph projections; we also quantify the combinatorial impossibility of recovering the lost higher-order structures if no extra help is provided; (2) we still seek to recover the lost higher-order structures in hypergraph projection, and in light of (1)'s findings we propose to relax the problem into a learning-based setting. Under this setting, we develop a learning-based hypergraph reconstruction method based on an important statistic of hyperedge distributions that we find. Our reconstruction method is evaluated on 8 real-world datasets under different settings, and exhibits consistently good performance. We also demonstrate benefits of the reconstructed hypergraphs via use cases of protein rankings and link predictions.

Scientific information extraction (SciIE), which aims to automatically extract information from scientific literature, is becoming more important than ever. However, there are no existing SciIE datasets for polymer materials, which is an important class of materials used ubiquitously in our daily lives. To bridge this gap, we introduce POLYIE, a new SciIE dataset for polymer materials. POLYIE is curated from 146 full-length polymer scholarly articles, which are annotated with different named entities (i.e., materials, properties, values, conditions) as well as their N-ary relations by domain experts. POLYIE presents several unique challenges due to diverse lexical formats of entities, ambiguity between entities, and variable-length relations. We evaluate state-of-the-art named entity extraction and relation extraction models on POLYIE, analyze their strengths and weaknesses, and highlight some difficult cases for these models. To the best of our knowledge, POLYIE is the first SciIE benchmark for polymer materials, and we hope it will lead to more research efforts from the community on this challenging task. Our code and data are available on: https://github.com/jerry3027/PolyIE.

Sequence generative models are transforming protein engineering. However, no principled framework exists for conditioning these models on auxiliary information, such as experimental data, without additional training of a generative model. Herein, we present ProteinGuide, a method for such "on-the-fly" conditioning, amenable to a broad class of protein generative models including Masked Language Models (e.g. ESM3), any-order auto-regressive models (e.g. ProteinMPNN) as well as diffusion and flow matching models (e.g. MultiFlow). ProteinGuide stems from our unifying view of these model classes under a single statistical framework. As proof of principle, we perform several in silico experiments. We first guide pre-trained generative models to design proteins with user-specified properties, such as higher stability or activity. Next, we design for optimizing two desired properties that are in tension with each other. Finally, we apply our method in the wet lab, using ProteinGuide to increase the editing activity of an adenine base editor in vivo with data from only a single pooled library of 2,000 variants. We find that a single round of ProteinGuide achieves a higher editing efficiency than was previously achieved using seven rounds of directed evolution.

Single-cell sequencing technologies reveal cellular heterogeneity at high resolution, advancing our understanding of biological complexity. As datasets start to scale to tens of millions of cells, computational workflows face substantial bottlenecks, with CPU-based analytical pipelines requiring hours or days for routine processing steps like filtering, normalization, and clustering. These scalability limitations fundamentally restrict common interactive data exploration and iterative hypothesis testing. Here we introduce rapids-singlecell, a GPU-accelerated framework that integrates natively with the scverse ecosystem and operates directly on the AnnData data structure, which delivers orders-of-magnitude speedups for single-cell workflows. Built on CuPy arrays and the NVIDIA CUDA-X Data Science (RAPIDS) ecosystem, rapids-singlecell provides near drop-in GPU replacements for core scanpy-based analysis steps. Across standard single-cell workflows such as preprocessing, dimensionality reduction, neighborhood graph construction, clustering, and batch correction, rapids-singlecell achieves speedups of up to several hundred-fold compared to optimized CPU baselines. This reduces analysis time from hours to minutes on standard hardware, while maintaining consistent biological interpretations. These performance improvements make it possible to analyze large data sets in close to real time, without the need for data splitting. Together with real-time parameter tuning and iterative workflows, rapids-singlecell makes interactive large-scale single-cell analysis possible.

Understanding the biological mechanism of disease is critical for medicine, and in particular drug discovery. AI-powered analysis of genome-scale biological data hold great potential in this regard. The increasing availability of single-cell RNA sequencing data has enabled the development of large foundation models for disease biology. However, existing foundation models either do not improve or only modestly improve over task-specific models in downstream applications. Here, we explored two avenues for improving the state-of-the-art. First, we scaled the pre-training dataset to 116 million cells, which is larger than those used by previous models. Second, we leveraged the availability of large-scale biological annotations as a form of supervision during pre-training. We trained the TEDDY family of models comprising six transformer-based state-of-the-art single-cell foundation models with 70 million, 160 million, and 400 million parameters. We vetted our models on two downstream evaluation tasks -- identifying the underlying disease state of held-out donors not seen during training and distinguishing healthy cells from diseased ones for disease conditions and donors not seen during training. Scaling experiments showed that performance improved predictably with both data volume and parameter count. Our models showed substantial improvement over existing work on the first task and more muted improvements on the second.

Time series clustering promises to uncover hidden structural patterns in data with applications across healthcare, finance, industrial systems, and other critical domains. However, without validated ground truth information, researchers cannot objectively assess clustering quality or determine whether poor results stem from absent structures in the data, algorithmic limitations, or inappropriate validation methods, raising the question whether clustering is "more art than science" (Guyon et al., 2009). To address these challenges, we introduce CSTS (Correlation Structures in Time Series), a synthetic benchmark for evaluating the discovery of correlation structures in multivariate time series data. CSTS provides a clean benchmark that enables researchers to isolate and identify specific causes of clustering failures by differentiating between correlation structure deterioration and limitations of clustering algorithms and validation methods. Our contributions are: (1) a comprehensive benchmark for correlation structure discovery with distinct correlation structures, systematically varied data conditions, established performance thresholds, and recommended evaluation protocols; (2) empirical validation of correlation structure preservation showing moderate distortion from downsampling and minimal effects from distribution shifts and sparsification; and (3) an extensible data generation framework enabling structure-first clustering evaluation. A case study demonstrates CSTS's practical utility by identifying an algorithm's previously undocumented sensitivity to non-normal distributions, illustrating how the benchmark enables precise diagnosis of methodological limitations. CSTS advances rigorous evaluation standards for correlation-based time series clustering.

Deep learning models facilitate the discovery of molecules with tailored properties among billions of candidate compounds. However, the computational burden to develop and deploy state-of-the-art models continuously increases, limiting their scalability. Most large-scale models are unimodal in nature and overlook the potential to leverage complementary molecular data modalities. To address these shortcomings, this paper introduces the Graph-Language Alignment for Chemical Inference and Exploration using Representations (GLACIER) model, a student-teacher framework that integrates molecular graphs, SMILES strings, and physicochemical descriptors to learn rich molecular embeddings. Our framework consists of three stages: (1) we pretrain three student encoders on 100,000 drug-like molecules: a message-passing neural network for molecular graphs, a transformer-based encoder for SMILES strings, and a multilayer perceptron for physicochemical descriptors, (2) we fuse these student modalities using a novel Finsler geometry-aware module, and (3) distill complementary knowledge from large teacher models, including MiniMol and MolFormer, into a single lightweight model via contrastive learning. We demonstrate that GLACIER is a robust framework that delivers high predictive performance and computational efficiency in complex molecular property prediction tasks. Our code is publicly available at https://github.com/eemokey/glacier.

Language-molecule models have emerged as an exciting direction for molecular discovery and understanding. However, training these models is challenging due to the scarcity of molecule-language pair datasets. At this point, datasets have been released which are 1) small and scraped from existing databases, 2) large but noisy and constructed by performing entity linking on the scientific literature, and 3) built by converting property prediction datasets to natural language using templates. In this document, we detail the L+M-24 dataset, which has been created for the Language + Molecules Workshop shared task at ACL 2024. In particular, L+M-24 is designed to focus on three key benefits of natural language in molecule design: compositionality, functionality, and abstraction.

Archetypal Analysis (AA) represents observations as convex combinations of extremal data-driven profiles, yielding interpretable low-dimensional descriptions of complex datasets. Classical AA relies on a least-squares objective, which is poorly suited to discrete observations such as binary, count, and categorical data. We introduce an efficient likelihood-based framework for AA supporting Bernoulli, Poisson, and multinomial observation models. Our optimization scheme employs local quadratic approximations of the negative log-likelihood, enabling constrained updates through sequential minimal optimization (SMO) and an active-set method. Scalability is improved by bounding the active set while preserving simplex feasibility. We further introduce a cross-validated predictive likelihood criterion for selecting the number of archetypes, providing a principled alternative to reconstruction-error heuristics and stability-based diagnostics. Synthetic experiments demonstrate computational efficiency and accurate recovery of model complexity. Applications to single-cell RNA sequencing, microbiome composition, and somatic mutation data show that the learned archetypes capture interpretable domain-specific structures while achieving competitive likelihood fits and stable solutions. Overall, the proposed framework enables efficient likelihood-based archetypal analysis of discrete data, complemented by predictive likelihood-based model selection.

Scientific research often seeks to understand the causal structure underlying high-level variables in a system. For example, climate scientists study how phenomena, such as El Niño, affect other climate processes at remote locations across the globe. However, scientists typically collect low-level measurements, such as geographically distributed temperature readings. From these, one needs to learn both a mapping to causally-relevant latent variables, such as a high-level representation of the El Niño phenomenon and other processes, as well as the causal model over them. The challenge is that this task, called causal representation learning, is highly underdetermined from observational data alone, requiring other constraints during learning to resolve the indeterminacies. In this work, we consider a temporal model with a sparsity assumption, namely single-parent decoding: each observed low-level variable is only affected by a single latent variable. Such an assumption is reasonable in many scientific applications that require finding groups of low-level variables, such as extracting regions from geographically gridded measurement data in climate research or capturing brain regions from neural activity data. We demonstrate the identifiability of the resulting model and propose a differentiable method, Causal Discovery with Single-parent Decoding (CDSD), that simultaneously learns the underlying latents and a causal graph over them. We assess the validity of our theoretical results using simulated data and showcase the practical validity of our method in an application to real-world data from the climate science field.

Physics education researchers (PER) often analyze student data with single-level regression models (e.g., linear and logistic regression). However, education datasets can have hierarchical structures, such as students nested within courses, that single-level models fail to account for. The improper use of single-level models to analyze hierarchical datasets can lead to biased findings. Hierarchical models (a.k.a., multi-level models) account for this hierarchical nested structure in the data. In this publication, we outline the theoretical differences between how single-level and multi-level models handle hierarchical datasets. We then present analysis of a dataset from 112 introductory physics courses using both multiple linear regression and hierarchical linear modeling to illustrate the potential impact of using an inappropriate analytical method on PER findings and implications. Research can leverage multi-institutional datasets to improve the field's understanding of how to support student success in physics. There is no post hoc fix, however, if researchers use inappropriate single-level models to analyze multi-level datasets. To continue developing reliable and generalizable knowledge, PER should use hierarchical models when analyzing hierarchical datasets. The supplemental materials include a sample dataset, R code to model the building and analysis presented in the paper, and an HTML output from the R code.

Atomic-scale simulations have been transformed by machine-learning models that predict the properties of atomistic structures with the accuracy of quantum calculations, but at a small fraction of the cost. These models have increased dramatically in generality, thanks to the availability of synthetic datasets of ever-increasing size and scope. The proliferation of datasets, with properties often computed using different levels of electronic-structure approximation, is problematic, as there is often overlap between different datasets, and strong correlations between structures obtained with short molecular dynamics trajectories or geometry optimization. To address these problems, we introduce a protocol to stratify a dataset into a hierarchy of nested subsets, subsampling from the coarsest to the finest resolution based on an "ecumetric" built to reflect the latent space representation of several popular universal machine-learning interatomic potentials. We then use this approach to combine most of the open structural datasets currently available, consolidating them into MAD-COSMO, a well-organized collection of almost 1.7 billion structures, whose 2^{24} most diverse members form the MAD-CORE stratified coreset, which can be easily used for all sorts of tasks, from exploratory experiments to the training of foundation models at scale. We envision that this collection will guide and help coordinate future efforts, focusing them on the most relevant and/or undersampled regions of chemical and structural space, and that it will be further extended to incorporate the outcomes of the collective work of this community.

Developing large-scale foundational datasets is a critical milestone in advancing artificial intelligence (AI)-driven scientific innovation. However, unlike AI-mature fields such as natural language processing, materials science, particularly polymer research, has significantly lagged in developing extensive open datasets. This lag is primarily due to the high costs of polymer synthesis and property measurements, along with the vastness and complexity of the chemical space. This study presents PolyOmics, an omics-scale computational database generated through fully automated molecular dynamics simulation pipelines that provide diverse physical properties for over 10^5 polymeric materials. The PolyOmics database is collaboratively developed by approximately 260 researchers from 48 institutions to bridge the gap between academia and industry. Machine learning models pretrained on PolyOmics can be efficiently fine-tuned for a wide range of real-world downstream tasks, even when only limited experimental data are available. Notably, the generalisation capability of these simulation-to-real transfer models improve significantly as the size of the PolyOmics database increases, exhibiting power-law scaling. The emergence of scaling laws supports the "more is better" principle, highlighting the significance of ultralarge-scale computational materials data for improving real-world prediction performance. This unprecedented omics-scale database reveals vast unexplored regions of polymer materials, providing a foundation for AI-driven polymer science.

The current landscape of AI for Science (AI4S) is predominantly anchored in large-scale textual corpora, where generative AI systems excel at hypothesis generation, literature search, and multi-modal reasoning. However, a critical bottleneck for accelerating closed-loop scientific discovery remains the utilization of raw experimental data. Characterized by extreme heterogeneity, high specificity, and deep domain expertise requirements, raw data possess neither direct semantic alignment with linguistic representations nor structural homogeneity suitable for a unified embedding space. The disconnect prevents the emerging class of Artificial General Intelligence for Science (AGI4S) from effectively interfacing with the physical reality of experimentation. In this work, we extend the text-centric AI-Ready concept to Scientific AI-Ready data paradigm, explicitly formalizing how scientific data is specified, structured, and composed within a computational workflow. To operationalize this idea, we propose SciDataCopilot, an autonomous agentic framework designed to handle data ingestion, scientific intent parsing, and multi-modal integration in a end-to-end manner. By positioning data readiness as a core operational primitive, the framework provides a principled foundation for reusable, transferable systems, enabling the transition toward experiment-driven scientific general intelligence. Extensive evaluations across three heterogeneous scientific domains show that SciDataCopilot improves efficiency, scalability, and consistency over manual pipelines, with up to 30times speedup in data preparation.

Single-cell transcriptomics enabled the study of cellular heterogeneity in response to perturbations at the resolution of individual cells. However, scaling high-throughput screens (HTSs) to measure cellular responses for many drugs remains a challenge due to technical limitations and, more importantly, the cost of such multiplexed experiments. Thus, transferring information from routinely performed bulk RNA HTS is required to enrich single-cell data meaningfully. We introduce chemCPA, a new encoder-decoder architecture to study the perturbational effects of unseen drugs. We combine the model with an architecture surgery for transfer learning and demonstrate how training on existing bulk RNA HTS datasets can improve generalisation performance. Better generalisation reduces the need for extensive and costly screens at single-cell resolution. We envision that our proposed method will facilitate more efficient experiment designs through its ability to generate in-silico hypotheses, ultimately accelerating drug discovery.

This paper presents algorithms for hierarchical, agglomerative clustering which perform most efficiently in the general-purpose setup that is given in modern standard software. Requirements are: (1) the input data is given by pairwise dissimilarities between data points, but extensions to vector data are also discussed (2) the output is a "stepwise dendrogram", a data structure which is shared by all implementations in current standard software. We present algorithms (old and new) which perform clustering in this setting efficiently, both in an asymptotic worst-case analysis and from a practical point of view. The main contributions of this paper are: (1) We present a new algorithm which is suitable for any distance update scheme and performs significantly better than the existing algorithms. (2) We prove the correctness of two algorithms by Rohlf and Murtagh, which is necessary in each case for different reasons. (3) We give well-founded recommendations for the best current algorithms for the various agglomerative clustering schemes.

Machine learning models are susceptible to being misled by biases in training data that emphasize incidental correlations over the intended learning task. In this study, we demonstrate the impact of data bias on the performance of a machine learning model designed to predict the synthesizability likelihood of crystal compounds. The model performs a binary classification on labeled crystal samples. Despite using the same architecture for the machine learning model, we showcase how the model's learning and prediction behavior differs once trained on distinct data. We use two data sets for illustration: a mixed-source data set that integrates experimental and computational crystal samples and a single-source data set consisting of data exclusively from one computational database. We present simple procedures to detect data bias and to evaluate its effect on the model's performance and generalization. This study reveals how inconsistent, unbalanced data can propagate bias, undermining real-world applicability even for advanced machine learning techniques.

Label-free single-cell imaging offers a scalable, non-invasive alternative to fluorescence-based cytometry, yet inferring molecular phenotypes directly from bright-field morphology remains challenging. We present a unified Deep Learning (DL) framework that jointly performs White Blood Cell (WBC) classification and continuous protein-expression regression from label-free Differential Phase Contrast (DPC) images. Our model employs a Hybrid architecture that fuses convolutional fine-grained texture features with transformer-based global representations through a learnable cross-branch gating module, enabling robust morpho-molecular inference from DPC images. To support downstream interpretability, we further incorporate a Large Language Model (LLM) that generates concise, biologically grounded summaries of the predicted cell states. Experiments on the Berkeley Single Cell Computational Microscopy (BSCCM) and Blood Cells Image benchmarks demonstrate strong performance, achieving a 91.3% WBC classification accuracy and a 0.72 Pearson correlation for CD16 expression regression on BSCCM. These results underscore the promise of label-free single-cell imaging for cost-effective hematological profiling, enabling simultaneous phenotype identification and quantitative biomarker estimation without fluorescent staining. The source code is available at https://github.com/saqibnaziir/Single-Cell-Phenotyping.

While learning models are typically studied for inputs in the form of a fixed dimensional feature vector, real world data is rarely found in this form. In order to meet the basic requirement of traditional learning models, structural data generally have to be converted into fix-length vectors in a handcrafted manner, which is tedious and may even incur information loss. A common form of structured data is what we term "semantic tree-structures", corresponding to data where rich semantic information is encoded in a compositional manner, such as those expressed in JavaScript Object Notation (JSON) and eXtensible Markup Language (XML). For tree-structured data, several learning models have been studied to allow for working directly on raw tree-structure data, However such learning models are limited to either a specific tree-topology or a specific tree-structured data format, e.g., synthetic parse trees. In this paper, we propose a novel framework for end-to-end learning on generic semantic tree-structured data of arbitrary topology and heterogeneous data types, such as data expressed in JSON, XML and so on. Motivated by the works in recursive and recurrent neural networks, we develop exemplar neural implementations of our framework for the JSON format. We evaluate our approach on several UCI benchmark datasets, including ablation and data-efficiency studies, and on a toy reinforcement learning task. Experimental results suggest that our framework yields comparable performance to use of standard models with dedicated feature-vectors in general, and even exceeds baseline performance in cases where compositional nature of the data is particularly important. The source code for a JSON-based implementation of our framework along with experiments can be downloaded at https://github.com/EndingCredits/json2vec.

Recent advances in sequencing technologies have enabled researchers to explore cellular heterogeneity at single-cell resolution. Meanwhile, interpretability has gained prominence parallel to the rapid increase in the complexity and performance of deep learning models. In recent years, topic models have been widely used for interpretable single-cell embedding learning and clustering analysis, which we refer to as single-cell embedded topic models. However, previous studies evaluated the interpretability of the models mainly through qualitative analysis, and these single-cell embedded topic models suffer from the potential problem of interpretation collapse. Furthermore, their neglect of external biological knowledge constrains analytical performance. Here, we present scE2TM, an external knowledge-guided single-cell embedded topic model that provides a high-quality cell embedding and strong interpretation, contributing to comprehensive scRNA-seq data analysis. Our comprehensive evaluation across 20 scRNA-seq datasets demonstrates that scE2TM achieves significant clustering performance gains compared to 7 state-of-the-art methods. In addition, we propose a new interpretability evaluation benchmark that introduces 10 metrics to quantitatively assess the interpretability of single-cell embedded topic models. The results show that the interpretation provided by scE2TM performs encouragingly in terms of diversity and consistency with the underlying biological signals, contributing to a better revealing of the underlying biological mechanisms.

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted descriptions of biomolecules contained within textual data sources to enhance our fundamental understanding and enable downstream computational tasks such as biomolecule property prediction. The fusion of the nuanced narratives expressed through natural language with the structural and functional specifics of biomolecules described via various molecular modeling techniques opens new avenues for comprehensively representing and analyzing biomolecules. By incorporating the contextual language data that surrounds biomolecules into their modeling, BL aims to capture a holistic view encompassing both the symbolic qualities conveyed through language as well as quantitative structural characteristics. In this review, we provide an extensive analysis of recent advancements achieved through cross modeling of biomolecules and natural language. (1) We begin by outlining the technical representations of biomolecules employed, including sequences, 2D graphs, and 3D structures. (2) We then examine in depth the rationale and key objectives underlying effective multi-modal integration of language and molecular data sources. (3) We subsequently survey the practical applications enabled to date in this developing research area. (4) We also compile and summarize the available resources and datasets to facilitate future work. (5) Looking ahead, we identify several promising research directions worthy of further exploration and investment to continue advancing the field. The related resources and contents are updating in https://github.com/QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling.

Networks provide a powerful formalism for modeling complex systems by using a model of pairwise interactions. But much of the structure within these systems involves interactions that take place among more than two nodes at once; for example, communication within a group rather than person-to person, collaboration among a team rather than a pair of coauthors, or biological interaction between a set of molecules rather than just two. Such higher-order interactions are ubiquitous, but their empirical study has received limited attention, and little is known about possible organizational principles of such structures. Here we study the temporal evolution of 19 datasets with explicit accounting for higher-order interactions. We show that there is a rich variety of structure in our datasets but datasets from the same system types have consistent patterns of higher-order structure. Furthermore, we find that tie strength and edge density are competing positive indicators of higher-order organization, and these trends are consistent across interactions involving differing numbers of nodes. To systematically further the study of theories for such higher-order structures, we propose higher-order link prediction as a benchmark problem to assess models and algorithms that predict higher-order structure. We find a fundamental differences from traditional pairwise link prediction, with a greater role for local rather than long-range information in predicting the appearance of new interactions.

Persistent homology (PH) provides topological descriptors for geometric data, such as weighted graphs, which are interpretable, stable to perturbations, and invariant under, e.g., relabeling. Most applications of PH focus on the one-parameter case -- where the descriptors summarize the changes in topology of data as it is filtered by a single quantity of interest -- and there is now a wide array of methods enabling the use of one-parameter PH descriptors in data science, which rely on the stable vectorization of these descriptors as elements of a Hilbert space. Although the multiparameter PH (MPH) of data that is filtered by several quantities of interest encodes much richer information than its one-parameter counterpart, the scarceness of stability results for MPH descriptors has so far limited the available options for the stable vectorization of MPH. In this paper, we aim to bring together the best of both worlds by showing how the interpretation of signed barcodes -- a recent family of MPH descriptors -- as signed measures leads to natural extensions of vectorization strategies from one parameter to multiple parameters. The resulting feature vectors are easy to define and to compute, and provably stable. While, as a proof of concept, we focus on simple choices of signed barcodes and vectorizations, we already see notable performance improvements when comparing our feature vectors to state-of-the-art topology-based methods on various types of data.

Recent advancements in large language models and their multi-modal extensions have demonstrated the effectiveness of unifying generation and understanding through autoregressive next-token prediction. However, despite the critical role of 3D structural generation and understanding ({3D GU}) in AI for science, these tasks have largely evolved independently, with autoregressive methods remaining underexplored. To bridge this gap, we introduce Uni-3DAR, a unified framework that seamlessly integrates {3D GU} tasks via autoregressive prediction. At its core, Uni-3DAR employs a novel hierarchical tokenization that compresses 3D space using an octree, leveraging the inherent sparsity of 3D structures. It then applies an additional tokenization for fine-grained structural details, capturing key attributes such as atom types and precise spatial coordinates in microscopic 3D structures. We further propose two optimizations to enhance efficiency and effectiveness. The first is a two-level subtree compression strategy, which reduces the octree token sequence by up to 8x. The second is a masked next-token prediction mechanism tailored for dynamically varying token positions, significantly boosting model performance. By combining these strategies, Uni-3DAR successfully unifies diverse {3D GU} tasks within a single autoregressive framework. Extensive experiments across multiple microscopic {3D GU} tasks, including molecules, proteins, polymers, and crystals, validate its effectiveness and versatility. Notably, Uni-3DAR surpasses previous state-of-the-art diffusion models by a substantial margin, achieving up to 256\% relative improvement while delivering inference speeds up to 21.8x faster. The code is publicly available at https://github.com/dptech-corp/Uni-3DAR.

Background. In the last decades, several life science resources have structured data using the same framework and made these accessible using the same query language to facilitate interoperability. Knowledge graphs have seen increased adoption in bioinformatics due to their advantages for representing data in a generic graph format. For example, yummydata.org catalogs more than 60 knowledge graphs accessible through SPARQL, a technical query language. Although SPARQL allows powerful, expressive queries, even across physically distributed knowledge graphs, formulating such queries is a challenge for most users. Therefore, to guide users in retrieving the relevant data, many of these resources provide representative examples. These examples can also be an important source of information for machine learning, if a sufficiently large number of examples are provided and published in a common, machine-readable and standardized format across different resources. Findings. We introduce a large collection of human-written natural language questions and their corresponding SPARQL queries over federated bioinformatics knowledge graphs (KGs) collected for several years across different research groups at the SIB Swiss Institute of Bioinformatics. The collection comprises more than 1000 example questions and queries, including 65 federated queries. We propose a methodology to uniformly represent the examples with minimal metadata, based on existing standards. Furthermore, we introduce an extensive set of open-source applications, including query graph visualizations and smart query editors, easily reusable by KG maintainers who adopt the proposed methodology. Conclusions. We encourage the community to adopt and extend the proposed methodology, towards richer KG metadata and improved Semantic Web services.

Reaction data underpin machine learning for reaction prediction, condition recommendation, and retrosynthetic planning, yet extracting these data from literature figures still requires substantial manual effort. Many figures encode multiple experiments through shared templates, substituent tables, and product grids. Recovering concrete reaction records therefore requires molecular recognition, association of evidence with individual experimental entries, and reconstruction of indirectly specified participants. We present RxnMiner, a multimodal agent system that combines an expert-informed extraction procedure with a chemistry toolbox to coordinate these operations. The agent reads molecular structures, resolves shared and entry-specific evidence, and instantiates participants from templates to assemble source-linked reaction records. We also introduce ChemRxn-Bench, a benchmark of 603 reaction figures with 8,547 manually annotated and reviewed reaction records, evaluated under a common protocol for exact molecular identity and reactant-product pairing. On this benchmark, with Qwen3.8-Flash-Next as the backbone, RxnMiner raises stereochemistry-aware reaction macro-F1 from 21.0% under direct prediction to 71.0%, compared with 25.0% for the strongest existing extraction system. Across five backbones, it also outperforms the same base agent without the extraction procedure and chemistry toolbox by 9.4 to 25.5 points. Applied without human intervention to 10,107 literature figures, RxnMiner produces a silver corpus of 88,202 source-linked reaction records.