Daily Papers

The development of vision-language models (VLMs) is driven by large-scale and diverse multimodal datasets. However, progress toward generalist biomedical VLMs is limited by the lack of annotated, publicly accessible datasets across biology and medicine. Existing efforts are restricted to narrow domains, missing the full diversity of biomedical knowledge encoded in scientific literature. To address this gap, we introduce BIOMEDICA, a scalable, open-source framework to extract, annotate, and serialize the entirety of the PubMed Central Open Access subset into an easy-to-use, publicly accessible dataset.Our framework produces a comprehensive archive with over 24 million unique image-text pairs from over 6 million articles. Metadata and expert-guided annotations are also provided. We demonstrate the utility and accessibility of our resource by releasing BMCA-CLIP, a suite of CLIP-style models continuously pre-trained on the BIOMEDICA dataset via streaming, eliminating the need to download 27 TB of data locally.On average, our models achieve state-of-the-art performance across 40 tasks - spanning pathology, radiology, ophthalmology, dermatology, surgery, molecular biology, parasitology, and cell biology - excelling in zero-shot classification with a 6.56% average improvement (as high as 29.8% and 17.5% in dermatology and ophthalmology, respectively), and stronger image-text retrieval, all while using 10x less compute. To foster reproducibility and collaboration, we release our codebase and dataset for the broader research community.

Recent advances in microscopy have enabled the rapid generation of terabytes of image data in cell biology and biomedical research. Vision-language models (VLMs) offer a promising solution for large-scale biological image analysis, enhancing researchers' efficiency, identifying new image biomarkers, and accelerating hypothesis generation and scientific discovery. However, there is a lack of standardized, diverse, and large-scale vision-language benchmarks to evaluate VLMs' perception and cognition capabilities in biological image understanding. To address this gap, we introduce {\mu}-Bench, an expert-curated benchmark encompassing 22 biomedical tasks across various scientific disciplines (biology, pathology), microscopy modalities (electron, fluorescence, light), scales (subcellular, cellular, tissue), and organisms in both normal and abnormal states. We evaluate state-of-the-art biomedical, pathology, and general VLMs on {\mu}-Bench and find that: i) current models struggle on all categories, even for basic tasks such as distinguishing microscopy modalities; ii) current specialist models fine-tuned on biomedical data often perform worse than generalist models; iii) fine-tuning in specific microscopy domains can cause catastrophic forgetting, eroding prior biomedical knowledge encoded in their base model. iv) weight interpolation between fine-tuned and pre-trained models offers one solution to forgetting and improves general performance across biomedical tasks. We release {\mu}-Bench under a permissive license to accelerate the research and development of microscopy foundation models.

The teaching career shares common global characteristics, such as internal promotion, performance evaluation, recruitment of top candidates, continuous training, specialization, and peer learning. This study aims to describe the factors associated with the value placed on the teaching career in Peru. A total of 28217 public school teachers were analyzed using data from the 2020 National Teacher Survey. A variable measuring the "value of the teaching career" was constructed using eight indicators and categorized as low, medium, or high. Another variable, vision of the future, was classified as pessimistic, conformist, or optimistic. This observational, cross-sectional, and analytical study included variables related to in-service training, working conditions, professional recognition, and sociodemographic characteristics. Among the teachers surveyed, 45.8 % expressed an optimistic outlook on the future of the profession, 48 % held a conformist view, and only 6.2 % reported a pessimistic perspective. A generalized linear model revealed that the value placed on the teaching career was significantly associated with male gender (p = 0.002), a professional career (p < 0.001), an optimistic outlook (p = 0.033), and working at the primary level (p < 0.001). It was concluded that Peruvian teachers predominantly hold conformist or optimistic views of their profession. This highlights the need to reinforce merit-based advancement, competency-based training, intrinsic motivation, and ongoing professional development

Blind all-in-one image restoration models aim to recover a high-quality image from an input degraded with unknown distortions. However, these models require all the possible degradation types to be defined during the training stage while showing limited generalization to unseen degradations, which limits their practical application in complex cases. In this paper, we propose a simple but effective adaptive blind all-in-one restoration (ABAIR) model, which can address multiple degradations, generalizes well to unseen degradations, and efficiently incorporate new degradations by training a small fraction of parameters. First, we train our baseline model on a large dataset of natural images with multiple synthetic degradations, augmented with a segmentation head to estimate per-pixel degradation types, resulting in a powerful backbone able to generalize to a wide range of degradations. Second, we adapt our baseline model to varying image restoration tasks using independent low-rank adapters. Third, we learn to adaptively combine adapters to versatile images via a flexible and lightweight degradation estimator. Our model is both powerful in handling specific distortions and flexible in adapting to complex tasks, it not only outperforms the state-of-the-art by a large margin on five- and three-task IR setups, but also shows improved generalization to unseen degradations and also composite distortions.

White balance (WB) correction in scenes with multiple illuminants remains a persistent challenge in computer vision. Recent methods explored fusion-based approaches, where a neural network linearly blends multiple sRGB versions of an input image, each processed with predefined WB presets. However, we demonstrate that these methods are suboptimal for common multi-illuminant scenarios. Additionally, existing fusion-based methods rely on sRGB WB datasets lacking dedicated multi-illuminant images, limiting both training and evaluation. To address these challenges, we introduce two key contributions. First, we propose an efficient transformer-based model that effectively captures spatial dependencies across sRGB WB presets, substantially improving upon linear fusion techniques. Second, we introduce a large-scale multi-illuminant dataset comprising over 16,000 sRGB images rendered with five different WB settings, along with WB-corrected images. Our method achieves up to 100\% improvement over existing techniques on our new multi-illuminant image fusion dataset.

Semantic Textual Similarity (STS) is a crucial component of many Natural Language Processing (NLP) applications. However, existing approaches typically reduce semantic nuances to a single score, limiting interpretability. To address this, we introduce the task of Dissimilar Span Detection (DSD), which aims to identify semantically differing spans between pairs of texts. This can help users understand which particular words or tokens negatively affect the similarity score, or be used to improve performance in STS-dependent downstream tasks. Furthermore, we release a new dataset suitable for the task, the Span Similarity Dataset (SSD), developed through a semi-automated pipeline combining large language models (LLMs) with human verification. We propose and evaluate different baseline methods for DSD, both unsupervised, based on LIME, SHAP, LLMs, and our own method, as well as an additional supervised approach. While LLMs and supervised models achieve the highest performance, overall results remain low, highlighting the complexity of the task. Finally, we set up an additional experiment that shows how DSD can lead to increased performance in the specific task of paraphrase detection.

We present SyncLight, the first method to enable consistent, parametric relighting across multiple uncalibrated views of a static scene. While single-view relighting has advanced significantly, existing generative approaches struggle to maintain the rigorous lighting consistency essential for multi-camera broadcasts, stereoscopic cinema, and virtual production. SyncLight addresses this by enabling precise control over light intensity and color across a multi-view capture of a scene, conditioned on a single reference edit. Our method leverages a multi-view diffusion transformer trained using a latent bridge matching formulation, achieving high-fidelity relighting of the entire image set in a single inference step. To facilitate training, we introduce a large-scale hybrid dataset comprising diverse synthetic environments -- curated from existing sources and newly designed scenes -- alongside high-fidelity, real-world multi-view captures under calibrated illumination. Surprisingly, though trained only on image pairs, SyncLight generalizes zero-shot to an arbitrary number of viewpoints, effectively propagating lighting changes across all views, without requiring camera pose information. SyncLight enables practical relighting workflows for multi-view capture systems.

A popular method for enhancing images involves learning the style of a professional photo editor using pairs of training images comprised of the original input with the editor-enhanced version. When manipulating images, many editing tools offer a feature that allows the user to manipulate a limited selection of familiar colors. Editing by color name allows easy adjustment of elements like the "blue" of the sky or the "green" of trees. Inspired by this approach to color manipulation, we propose NamedCurves, a learning-based image enhancement technique that separates the image into a small set of named colors. Our method learns to globally adjust the image for each specific named color via tone curves and then combines the images using an attention-based fusion mechanism to mimic spatial editing. We demonstrate the effectiveness of our method against several competing methods on the well-known Adobe 5K dataset and the PPR10K dataset, showing notable improvements.

Embedding vision-language models (VLMs) are typically pretrained with short text windows (<77 tokens), which forces the truncation of long-format captions. Yet, the distribution of biomedical captions from large-scale open source literature reveals that a huge portion of captions far exceed 77 tokens. To this end, we investigate the impact of pretraining on long-format biomedical captions by extending the context length of text encoders in VLMs. We find that longer context (thus, enabling additional supervision provided in long-format captions) correlates with better retrieval and classification performance. Given this finding, we introduce BIOMEDICA-LongCAP, a dataset of 1M image-caption pairs enriched with context-aware descriptions from full-text articles, providing longer and additional textual supervision. Using BIOMEDICA-LongCAP, we train BMC-LongCLIP, a long-context biomedical VLM with a text encoder supporting windows of up to 512 tokens. Our model extends context capacity by 6.6x, reducing token waste from 55% to just 2.2%. On long-caption retrieval benchmarks, BMC-LongCLIP achieves up to +30% absolute gains in Recall@1 and +2% average improvements in classification, while also converging faster than short-context. Our results demonstrate that long-context modeling is a promising direction for advancing biomedical VLMs.

Object detection is integral to a bevy of real-world applications, from robotics to medical image analysis. To be used reliably in such applications, models must be capable of handling unexpected - or novel - objects. The open world object detection (OWD) paradigm addresses this challenge by enabling models to detect unknown objects and learn discovered ones incrementally. However, OWD method development is hindered due to the stringent benchmark and task definitions. These definitions effectively prohibit foundation models. Here, we aim to relax these definitions and investigate the utilization of pre-trained foundation models in OWD. First, we show that existing benchmarks are insufficient in evaluating methods that utilize foundation models, as even naive integration methods nearly saturate these benchmarks. This result motivated us to curate a new and challenging benchmark for these models. Therefore, we introduce a new benchmark that includes five real-world application-driven datasets, including challenging domains such as aerial and surgical images, and establish baselines. We exploit the inherent connection between classes in application-driven datasets and introduce a novel method, Foundation Object detection Model for the Open world, or FOMO, which identifies unknown objects based on their shared attributes with the base known objects. FOMO has ~3x unknown object mAP compared to baselines on our benchmark. However, our results indicate a significant place for improvement - suggesting a great research opportunity in further scaling object detection methods to real-world domains. Our code and benchmark are available at https://orrzohar.github.io/projects/fomo/.

C_{11}H_9^+ ion is the dominant fragment cation formed from methyl-naphthalene (MeNp) and dimethyl-naphthalene (diMeNp). Using the multiplex capabilities of PIRENEA, a setup dedicated to laboratory astrophysics, we studied the reactivity of the benzylium-like isomers of C_{11}H_9^+ with diMeNp under isolated conditions relevant to radiative association. Two reaction products are observed, C_{12}H_{11}^+ -- also formed in the reaction with MeNp -- and C_{13}H_{13}^+, with branching ratios that depend on the specific diMeNp isomer. The reaction products were subsequently exposed to UV-visible irradiation to gain insight into their structures. The acenaphthylene radical cation, C_{12}H_{8}^{bullet +}, was identified as the most stable photofragment. We show that this experimental approach, supported by density functional theory calculations and molecular dynamics simulations, provides new constraints on the chemistry of benzylium-type species. We highlight the role that long-lived ion-molecule complexes can have in promoting C-C coupling and the formation of a pentagonal cycle. Moreover, the chemistry uncovered here highlights new pathways for the formation of pentagonal rings during PAH growth under low-pressure and cold conditions. In particular, it can lead to efficient formation of acenaphthylene-like species, recently detected in the TMC-1 cold cloud.

Imaging in low-light environments is challenging due to reduced scene radiance, which leads to elevated sensor noise and reduced color saturation. Most learning-based low-light enhancement methods rely on paired training data captured under a single low-light condition and a well-lit reference. The lack of radiance diversity limits our understanding of how enhancement techniques perform across varying illumination intensities. We introduce the Multi-Illumination Low-Light (MILL) dataset, containing images captured at diverse light intensities under controlled conditions with fixed camera settings and precise illuminance measurements. MILL enables comprehensive evaluation of enhancement algorithms across variable lighting conditions. We benchmark several state-of-the-art methods and reveal significant performance variations across intensity levels. Leveraging the unique multi-illumination structure of our dataset, we propose improvements that enhance robustness across diverse illumination scenarios. Our modifications achieve up to 10 dB PSNR improvement for DSLR and 2 dB for the smartphone on Full HD images.

Large language models underestimate the impact of negations on how much they change the meaning of a sentence. Therefore, learned evaluation metrics based on these models are insensitive to negations. In this paper, we propose NegBLEURT, a negation-aware version of the BLEURT evaluation metric. For that, we designed a rule-based sentence negation tool and used it to create the CANNOT negation evaluation dataset. Based on this dataset, we fine-tuned a sentence transformer and an evaluation metric to improve their negation sensitivity. Evaluating these models on existing benchmarks shows that our fine-tuned models outperform existing metrics on the negated sentences by far while preserving their base models' performances on other perturbations.

End-to-end neural diarization (EEND) is nowadays one of the most prominent research topics in speaker diarization. EEND presents an attractive alternative to standard cascaded diarization systems since a single system is trained at once to deal with the whole diarization problem. Several EEND variants and approaches are being proposed, however, all these models require large amounts of annotated data for training but available annotated data are scarce. Thus, EEND works have used mostly simulated mixtures for training. However, simulated mixtures do not resemble real conversations in many aspects. In this work we present an alternative method for creating synthetic conversations that resemble real ones by using statistics about distributions of pauses and overlaps estimated on genuine conversations. Furthermore, we analyze the effect of the source of the statistics, different augmentations and amounts of data. We demonstrate that our approach performs substantially better than the original one, while reducing the dependence on the fine-tuning stage. Experiments are carried out on 2-speaker telephone conversations of Callhome and DIHARD 3. Together with this publication, we release our implementations of EEND and the method for creating simulated conversations.

Are Capture-the-Flag competitions obsolete? In 2025, Cybersecurity AI (CAI) systematically conquered some of the world's most prestigious hacking competitions, achieving Rank #1 at multiple events and consistently outperforming thousands of human teams. Across five major circuits-HTB's AI vs Humans, Cyber Apocalypse (8,129 teams), Dragos OT CTF, UWSP Pointer Overflow, and the Neurogrid CTF showdown-CAI demonstrated that Jeopardy-style CTFs have become a solved game for well-engineered AI agents. At Neurogrid, CAI captured 41/45 flags to claim the 50,000 top prize; at Dragos OT, it sprinted 37% faster to 10K points than elite human teams; even when deliberately paused mid-competition, it maintained top-tier rankings. Critically, CAI achieved this dominance through our specialized alias1 model architecture, which delivers enterprise-scale AI security operations at unprecedented cost efficiency and with augmented autonomy-reducing 1B token inference costs from 5,940 to just $119, making continuous security agent operation financially viable for the first time. These results force an uncomfortable reckoning: if autonomous agents now dominate competitions designed to identify top security talent at negligible cost, what are CTFs actually measuring? This paper presents comprehensive evidence of AI capability across the 2025 CTF circuit and argues that the security community must urgently transition from Jeopardy-style contests to Attack & Defense formats that genuinely test adaptive reasoning and resilience-capabilities that remain uniquely human, for now.

By 2028 most cybersecurity actions will be autonomous, with humans teleoperating. We present the first classification of autonomy levels in cybersecurity and introduce Cybersecurity AI (CAI), an open-source framework that democratizes advanced security testing through specialized AI agents. Through rigorous empirical evaluation, we demonstrate that CAI consistently outperforms state-of-the-art results in CTF benchmarks, solving challenges across diverse categories with significantly greater efficiency -up to 3,600x faster than humans in specific tasks and averaging 11x faster overall. CAI achieved first place among AI teams and secured a top-20 position worldwide in the "AI vs Human" CTF live Challenge, earning a monetary reward of $750. Based on our results, we argue against LLM-vendor claims about limited security capabilities. Beyond cybersecurity competitions, CAI demonstrates real-world effectiveness, reaching top-30 in Spain and top-500 worldwide on Hack The Box within a week, while dramatically reducing security testing costs by an average of 156x. Our framework transcends theoretical benchmarks by enabling non-professionals to discover significant security bugs (CVSS 4.3-7.5) at rates comparable to experts during bug bounty exercises. By combining modular agent design with seamless tool integration and human oversight (HITL), CAI addresses critical market gaps, offering organizations of all sizes access to AI-powered bug bounty security testing previously available only to well-resourced firms -thereby challenging the oligopolistic ecosystem currently dominated by major bug bounty platforms.

Suspense is an affective response to narrative text that is believed to involve complex cognitive processes in humans. Several psychological models have been developed to describe this phenomenon and the circumstances under which text might trigger it. We replicate four seminal psychological studies of human perceptions of suspense, substituting human responses with those of different open-weight and closed-source LMs. We conclude that while LMs can distinguish whether a text is intended to induce suspense in people, LMs cannot accurately estimate the relative amount of suspense within a text sequence as compared to human judgments, nor can LMs properly capture the human perception for the rise and fall of suspense across multiple text segments. We probe the abilities of LM suspense understanding by adversarially permuting the story text to identify what cause human and LM perceptions of suspense to diverge. We conclude that, while LMs can superficially identify and track certain facets of suspense, they do not process suspense in the same way as human readers.

The ability of large language models (LLMs) to follow natural language instructions with human-level fluency suggests many opportunities in healthcare to reduce administrative burden and improve quality of care. However, evaluating LLMs on realistic text generation tasks for healthcare remains challenging. Existing question answering datasets for electronic health record (EHR) data fail to capture the complexity of information needs and documentation burdens experienced by clinicians. To address these challenges, we introduce MedAlign, a benchmark dataset of 983 natural language instructions for EHR data. MedAlign is curated by 15 clinicians (7 specialities), includes clinician-written reference responses for 303 instructions, and provides 276 longitudinal EHRs for grounding instruction-response pairs. We used MedAlign to evaluate 6 general domain LLMs, having clinicians rank the accuracy and quality of each LLM response. We found high error rates, ranging from 35% (GPT-4) to 68% (MPT-7B-Instruct), and an 8.3% drop in accuracy moving from 32k to 2k context lengths for GPT-4. Finally, we report correlations between clinician rankings and automated natural language generation metrics as a way to rank LLMs without human review. We make MedAlign available under a research data use agreement to enable LLM evaluations on tasks aligned with clinician needs and preferences.

How do two individuals differ when performing the same action? In this work, we introduce Video Action Differencing (VidDiff), the novel task of identifying subtle differences between videos of the same action, which has many applications, such as coaching and skill learning. To enable development on this new task, we first create VidDiffBench, a benchmark dataset containing 549 video pairs, with human annotations of 4,469 fine-grained action differences and 2,075 localization timestamps indicating where these differences occur. Our experiments demonstrate that VidDiffBench poses a significant challenge for state-of-the-art large multimodal models (LMMs), such as GPT-4o and Qwen2-VL. By analyzing failure cases of LMMs on VidDiffBench, we highlight two key challenges for this task: localizing relevant sub-actions over two videos and fine-grained frame comparison. To overcome these, we propose the VidDiff method, an agentic workflow that breaks the task into three stages: action difference proposal, keyframe localization, and frame differencing, each stage utilizing specialized foundation models. To encourage future research in this new task, we release the benchmark at https://huggingface.co/datasets/jmhb/VidDiffBench and code at http://jmhb0.github.io/viddiff.

Efficient and accurate updating of knowledge stored in Large Language Models (LLMs) is one of the most pressing research challenges today. This paper presents Larimar - a novel, brain-inspired architecture for enhancing LLMs with a distributed episodic memory. Larimar's memory allows for dynamic, one-shot updates of knowledge without the need for computationally expensive re-training or fine-tuning. Experimental results on multiple fact editing benchmarks demonstrate that Larimar attains accuracy comparable to most competitive baselines, even in the challenging sequential editing setup, but also excels in speed - yielding speed-ups of 4-10x depending on the base LLM - as well as flexibility due to the proposed architecture being simple, LLM-agnostic, and hence general. We further provide mechanisms for selective fact forgetting and input context length generalization with Larimar and show their effectiveness.

Scientific research demands sophisticated reasoning over multimodal data, a challenge especially prevalent in biology. Despite recent advances in multimodal large language models (MLLMs) for AI-assisted research, existing multimodal reasoning benchmarks only target up to college-level difficulty, while research-level benchmarks emphasize lower-level perception, falling short of the complex multimodal reasoning needed for scientific discovery. To bridge this gap, we introduce MicroVQA, a visual-question answering (VQA) benchmark designed to assess three reasoning capabilities vital in research workflows: expert image understanding, hypothesis generation, and experiment proposal. MicroVQA consists of 1,042 multiple-choice questions (MCQs) curated by biology experts across diverse microscopy modalities, ensuring VQA samples represent real scientific practice. In constructing the benchmark, we find that standard MCQ generation methods induce language shortcuts, motivating a new two-stage pipeline: an optimized LLM prompt structures question-answer pairs into MCQs; then, an agent-based `RefineBot' updates them to remove shortcuts. Benchmarking on state-of-the-art MLLMs reveal a peak performance of 53\%; models with smaller LLMs only slightly underperform top models, suggesting that language-based reasoning is less challenging than multimodal reasoning; and tuning with scientific articles enhances performance. Expert analysis of chain-of-thought responses shows that perception errors are the most frequent, followed by knowledge errors and then overgeneralization errors. These insights highlight the challenges in multimodal scientific reasoning, showing MicroVQA is a valuable resource advancing AI-driven biomedical research. MicroVQA is available at https://huggingface.co/datasets/jmhb/microvqa, and project page at https://jmhb0.github.io/microvqa.

Search agents are language models (LMs) that reason and search knowledge bases (or the web) to answer questions; recent methods supervise only the final answer accuracy using reinforcement learning with verifiable rewards (RLVR). Most RLVR search agents tackle general-domain QA, which limits their relevance to technical AI systems in science, engineering, and medicine. In this work we propose training agents to search and reason over scientific papers -- this tests technical question-answering, it is directly relevant to real scientists, and the capabilities will be crucial to future AI Scientist systems. Concretely, we release a search corpus of 16 million biomedical paper abstracts and construct a challenging factoid QA dataset called PaperSearchQA with 60k samples answerable from the corpus, along with benchmarks. We train search agents in this environment to outperform non-RL retrieval baselines; we also perform further quantitative analysis and observe interesting agent behaviors like planning, reasoning, and self-verification. Our corpus, datasets, and benchmarks are usable with the popular Search-R1 codebase for RLVR training and released on https://huggingface.co/collections/jmhb/papersearchqa. Finally, our data creation methods are scalable and easily extendable to other scientific domains.

This paper introduces an approach for learning to solve continuous constraint satisfaction problems (CCSP) in robotic reasoning and planning. Previous methods primarily rely on hand-engineering or learning generators for specific constraint types and then rejecting the value assignments when other constraints are violated. By contrast, our model, the compositional diffusion continuous constraint solver (Diffusion-CCSP) derives global solutions to CCSPs by representing them as factor graphs and combining the energies of diffusion models trained to sample for individual constraint types. Diffusion-CCSP exhibits strong generalization to novel combinations of known constraints, and it can be integrated into a task and motion planner to devise long-horizon plans that include actions with both discrete and continuous parameters. Project site: https://diffusion-ccsp.github.io/

While recent advancing image super-resolution (SR) techniques are continually improving the perceptual quality of their outputs, they can usually fail in quantitative evaluations. This inconsistency leads to a growing distrust in existing image metrics for SR evaluations. Though image evaluation depends on both the metric and the reference ground truth (GT), researchers typically do not inspect the role of GTs, as they are generally accepted as `perfect' references. However, due to the data being collected in the early years and the ignorance of controlling other types of distortions, we point out that GTs in existing SR datasets can exhibit relatively poor quality, which leads to biased evaluations. Following this observation, in this paper, we are interested in the following questions: Are GT images in existing SR datasets 100% trustworthy for model evaluations? How does GT quality affect this evaluation? And how to make fair evaluations if there exist imperfect GTs? To answer these questions, this paper presents two main contributions. First, by systematically analyzing seven state-of-the-art SR models across three real-world SR datasets, we show that SR performances can be consistently affected across models by low-quality GTs, and models can perform quite differently when GT quality is controlled. Second, we propose a novel perceptual quality metric, Relative Quality Index (RQI), that measures the relative quality discrepancy of image pairs, thus issuing the biased evaluations caused by unreliable GTs. Our proposed model achieves significantly better consistency with human opinions. We expect our work to provide insights for the SR community on how future datasets, models, and metrics should be developed.

Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language models lack explicit structural supervision, despite its relevance to protein function. To address this issue, we introduce the integration of remote homology detection to distill structural information into protein language models without requiring explicit protein structures as input. We evaluate the impact of this structure-informed training on downstream protein function prediction tasks. Experimental results reveal consistent improvements in function annotation accuracy for EC number and GO term prediction. Performance on mutant datasets, however, varies based on the relationship between targeted properties and protein structures. This underscores the importance of considering this relationship when applying structure-aware training to protein function prediction tasks. Code and model weights are available at https://github.com/DeepGraphLearning/esm-s.

Reliable assessment of the abilities of large audio language models (LALMs) is essential to advancing the state of the art. As benchmarks rapidly evolve to incorporate complex reasoning and subjective tasks, they increasingly necessitate open-ended responses from LALMs. We present Open-ended Response Correctness Assessment (ORCA) -- a reliable and lightweight model-based approach for answer correctness and disagreement modeling. We employ a three-stage annotation pipeline combining human judgment, structured feedback, and human-AI correction, yielding 9,663 annotations across 3,699 question-answer pairs from 15 LALMs on three audio understanding and reasoning benchmarks (achieving a Krippendorff's alpha of 0.82). Our experiments employing curriculum learning show that ORCA models achieve a Spearman correlation of 0.91 with average human correctness ratings on seen benchmarks and generalize to unseen benchmarks with a score of 0.85, outperforming several LLM judge baselines including Gemini 2.5 Flash. Furthermore, we demonstrate that ORCA's predicted variance correlates strongly with human disagreement, allowing it to effectively identify problematic benchmark items.

This paper explores the use of generative models to synthesize high-quality, site-specific multiple-input multiple-output (MIMO) channel data, addressing the high cost of the extensive measurement campaigns required to acquire real-world data for AI-native wireless networks. Two location-conditioned generative paradigms are compared: a conditional denoising diffusion implicit model (cDDIM), and a conditional flow matching model (cFMM). Both these models generate MIMO channel matrices conditioned on user coordinates, to preserve the spatial structure of the deployment site. The approaches are evaluated across three dimensions: statistical fidelity (including beam consistency and effective rank), generation efficiency, and utility in downstream tasks such as channel-state information compression and beam alignment. Results across diverse propagation scenarios (28 GHz and 3.5 GHz, both line-of-sight and non-line-of-sight) demonstrate that both models accurately capture site-specific characteristics, even when trained on scarce ground-truth data. Notably, cFMM achieves a quality comparable to cDDIM with roughly an order of magnitude less inference time. Augmenting scarce site-specific datasets with these synthetic channels yields hefty performance gains in downstream physical layer tasks compared to using scarce data alone or stochastic channels.

This paper presents a fully automated, data-driven framework for the large-scale deployment of reconfigurable intelligent surfaces (RISs) in cellular networks. Leveraging physically consistent ray tracing and empirical data from a commercial deployment in the UK, the proposed method jointly optimizes RIS placement, orientation, configuration, and base station beamforming in dense urban environments across frequency bands (corresponding to 4G, 5G, and a hypothetical 6G system). Candidate RIS locations are identified via reflection- and scattering-based heuristics using calibrated electromagnetic models within the Sionna Ray Tracing (RT) engine. Outage users are clustered to reduce deployment complexity, and the tradeoff between coverage gains and infrastructure cost is systematically evaluated. It is shown that achieving meaningful coverage improvement in urban areas requires a dense deployment of large-aperture RIS units, raising questions about cost-effectiveness. To facilitate reproducibility and future research, the complete simulation framework and RIS deployment algorithms are provided as open-source software.

This work introduces a fully-automated RIS deployment strategy validated through a digital twin, powered by Sionna ray tracing, of a UK city. On a scene calibrated with measured data, the method jointly optimizes RIS placement, orientation, configuration, and BS beamforming across 4G, 5G, and hypothetical 6G frequencies. Candidate RIS sites are identified via scattering-based rays, while user clustering reduces deployment overhead. Results show that meaningful coverage enhancement requires dense, large-aperture RIS deployments, raising questions about the practicality and cost of large-scale RIS adoption.

Recent advances in diffusion/flow-matching policies have enabled imitation learning of complex, multi-modal action trajectories. However, they are computationally expensive because they sample a trajectory of trajectories: a diffusion/flow trajectory of action trajectories. They discard intermediate action trajectories, and must wait for the sampling process to complete before any actions can be executed on the robot. We simplify diffusion/flow policies by treating action trajectories as flow trajectories. Instead of starting from pure noise, our algorithm samples from a narrow Gaussian around the last action. Then, it incrementally integrates a velocity field learned via flow matching to produce a sequence of actions that constitute a single trajectory. This enables actions to be streamed to the robot on-the-fly during the flow sampling process, and is well-suited for receding horizon policy execution. Despite streaming, our method retains the ability to model multi-modal behavior. We train flows that stabilize around demonstration trajectories to reduce distribution shift and improve imitation learning performance. Streaming flow policy outperforms prior methods while enabling faster policy execution and tighter sensorimotor loops for learning-based robot control. Project website: https://streaming-flow-policy.github.io/

Planning long-horizon robot manipulation requires making discrete decisions about which objects to interact with and continuous decisions about how to interact with them. A robot planner must select grasps, placements, and motions that are feasible and safe. This class of problems falls under Task and Motion Planning (TAMP) and poses significant computational challenges in terms of algorithm runtime and solution quality, particularly when the solution space is highly constrained. To address these challenges, we propose a new bilevel TAMP algorithm that leverages GPU parallelism to efficiently explore thousands of candidate continuous solutions simultaneously. Our approach uses GPU parallelism to sample an initial batch of solution seeds for a plan skeleton and to apply differentiable optimization on this batch to satisfy plan constraints and minimize solution cost with respect to soft objectives. We demonstrate that our algorithm can effectively solve highly constrained problems with non-convex constraints in just seconds, substantially outperforming serial TAMP approaches, and validate our approach on multiple real-world robots. Project website and code: https://cutamp.github.io

The lack of transparency of Deep Neural Networks continues to be a limitation that severely undermines their reliability and usage in high-stakes applications. Promising approaches to overcome such limitations are Prototype-Based Self-Explainable Neural Networks (PSENNs), whose predictions rely on the similarity between the input at hand and a set of prototypical representations of the output classes, offering therefore a deep, yet transparent-by-design, architecture. So far, such models have been designed by considering pointwise estimates for the prototypes, which remain fixed after the learning phase of the model. In this paper, we introduce a probabilistic reformulation of PSENNs, called Prob-PSENN, which replaces point estimates for the prototypes with probability distributions over their values. This provides not only a more flexible framework for an end-to-end learning of prototypes, but can also capture the explanatory uncertainty of the model, which is a missing feature in previous approaches. In addition, since the prototypes determine both the explanation and the prediction, Prob-PSENNs allow us to detect when the model is making uninformed or uncertain predictions, and to obtain valid explanations for them. Our experiments demonstrate that Prob-PSENNs provide more meaningful and robust explanations than their non-probabilistic counterparts, thus enhancing the explainability and reliability of the models.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based tasks, but their direct adaptation to tasks involving protein structures remains a challenge. In contrast, structure-based methods leverage 3D structural information with graph neural networks and geometric pre-training methods show potential in function prediction tasks, but still suffers from the limited number of available structures. To bridge this gap, our study undertakes a comprehensive exploration of joint protein representation learning by integrating a state-of-the-art PLM (ESM-2) with distinct structure encoders (GVP, GearNet, CDConv). We introduce three representation fusion strategies and explore different pre-training techniques. Our method achieves significant improvements over existing sequence- and structure-based methods, setting new state-of-the-art for function annotation. This study underscores several important design choices for fusing protein sequence and structure information. Our implementation is available at https://github.com/DeepGraphLearning/ESM-GearNet.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain protein language models on a large number of unlabeled amino acid sequences and then finetune the models with some labeled data in downstream tasks. Despite the effectiveness of sequence-based approaches, the power of pretraining on known protein structures, which are available in smaller numbers only, has not been explored for protein property prediction, though protein structures are known to be determinants of protein function. In this paper, we propose to pretrain protein representations according to their 3D structures. We first present a simple yet effective encoder to learn the geometric features of a protein. We pretrain the protein graph encoder by leveraging multiview contrastive learning and different self-prediction tasks. Experimental results on both function prediction and fold classification tasks show that our proposed pretraining methods outperform or are on par with the state-of-the-art sequence-based methods, while using much less pretraining data. Our implementation is available at https://github.com/DeepGraphLearning/GearNet.

Reliable deployment of machine learning models such as neural networks continues to be challenging due to several limitations. Some of the main shortcomings are the lack of interpretability and the lack of robustness against adversarial examples or out-of-distribution inputs. In this exploratory review, we explore the possibilities and limits of adversarial attacks for explainable machine learning models. First, we extend the notion of adversarial examples to fit in explainable machine learning scenarios, in which the inputs, the output classifications and the explanations of the model's decisions are assessed by humans. Next, we propose a comprehensive framework to study whether (and how) adversarial examples can be generated for explainable models under human assessment, introducing and illustrating novel attack paradigms. In particular, our framework considers a wide range of relevant yet often ignored factors such as the type of problem, the user expertise or the objective of the explanations, in order to identify the attack strategies that should be adopted in each scenario to successfully deceive the model (and the human). The intention of these contributions is to serve as a basis for a more rigorous and realistic study of adversarial examples in the field of explainable machine learning.

Statistical channel models are instrumental to design and evaluate wireless communication systems. In the millimeter wave bands, such models become acutely challenging; they must capture the delay, directions, and path gains, for each link and with high resolution. This paper presents a general modeling methodology based on training generative neural networks from data. The proposed generative model consists of a two-stage structure that first predicts the state of each link (line-of-sight, non-line-of-sight, or outage), and subsequently feeds this state into a conditional variational autoencoder that generates the path losses, delays, and angles of arrival and departure for all its propagation paths. Importantly, minimal prior assumptions are made, enabling the model to capture complex relationships within the data. The methodology is demonstrated for 28GHz air-to-ground channels in an urban environment, with training datasets produced by means of ray tracing.

Doctors and patients alike increasingly use Large Language Models (LLMs) to diagnose clinical cases. However, unlike domains such as math or coding, where correctness can be objectively defined by the final answer, medical diagnosis requires both the outcome and the reasoning process to be accurate. Currently, widely used medical benchmarks like MedQA and MMLU assess only accuracy in the final answer, overlooking the quality and faithfulness of the clinical reasoning process. To address this limitation, we introduce MedCaseReasoning, the first open-access dataset for evaluating LLMs on their ability to align with clinician-authored diagnostic reasoning. The dataset includes 14,489 diagnostic question-and-answer cases, each paired with detailed reasoning statements derived from open-access medical case reports. We evaluate state-of-the-art reasoning LLMs on MedCaseReasoning and find significant shortcomings in their diagnoses and reasoning: for instance, the top-performing open-source model, DeepSeek-R1, achieves only 48% 10-shot diagnostic accuracy and mentions only 64% of the clinician reasoning statements (recall). However, we demonstrate that fine-tuning LLMs on the reasoning traces derived from MedCaseReasoning significantly improves diagnostic accuracy and clinical reasoning recall by an average relative gain of 29% and 41%, respectively. The open-source dataset, code, and models are available at https://github.com/kevinwu23/Stanford-MedCaseReasoning.

The rapid development of vision language models (VLMs) demands rigorous and reliable evaluation. However, current visual question answering (VQA) benchmarks often depend on open-ended questions, making accurate evaluation difficult due to the variability in natural language responses. To address this, we introduce AutoConverter, an agentic framework that automatically converts these open-ended questions into multiple-choice format, enabling objective evaluation while reducing the costly question creation process. Our experiments demonstrate that AutoConverter can generate correct and challenging multiple-choice questions, with VLMs demonstrating consistently similar or lower accuracy on these questions compared to human-created ones. Using AutoConverter, we construct VMCBench, a benchmark created by transforming 20 existing VQA datasets into a unified multiple-choice format, totaling 9,018 questions. We comprehensively evaluate 33 state-of-the-art VLMs on VMCBench, setting a new standard for scalable, consistent, and reproducible VLM evaluation.

We present TiPToP, an extensible modular system that combines pretrained vision foundation models with an existing Task and Motion Planner (TAMP) to solve multi-step manipulation tasks directly from input RGB images and natural-language instructions. Our system aims to be simple and easy-to-use: it can be installed and run on a standard DROID setup in under one hour and adapted to new embodiments with minimal effort. We evaluate TiPToP -- which requires zero robot data -- over 28 tabletop manipulation tasks in simulation and the real world and find it matches or outperforms π_{0.5}-DROID, a vision-language-action (VLA) model fine-tuned on 350 hours of embodiment-specific demonstrations. TiPToP's modular architecture enables us to analyze the system's failure modes at the component level. We analyze results from an evaluation of 173 trials and identify directions for improvement. We release TiPToP open-source to further research on modular manipulation systems and tighter integration between learning and planning. Project website and code: https://tiptop-robot.github.io

Foundation models have emerged as a driving force in computational pathology, with the potential to transform cancer diagnosis, prognosis, and treatment selection by learning transferable representations from large-scale histopathology data. A growing landscape of pathology foundation models now spans diverse data sources, architectures, and downstream applications. However, most pretrained models operate only at the image-tile level, use restrictive licenses, and remain computationally expensive, limiting large-scale slide-level clinical and research use. Here, we introduce GigaPath-Flash and GigaTIME-Flash, efficient models for whole-slide pathology AI and spatial proteomics prediction. GigaPath-Flash combines a 22M-parameter ViT-S tile encoder with a 21M-parameter LongNet slide encoder, both pretrained on large-scale real-world histopathology data. Its compact tile encoder is distilled from the billion-parameter GigaPath (ViT-g) teacher and shared by both models. GigaPath-Flash retains 97% of GigaPath's average slide-level performance with 50x less compute. GigaTIME-Flash extends this backbone to predict the tumor immune microenvironment directly from routine H&E images. It surpasses the original CNN-based GigaTIME in prediction quality while running 6x faster and using 8x less GPU memory. Together with GigaPath and GigaTIME, these models form an open-weight, Apache-2.0-licensed family pretrained on large-scale real-world clinical data. By releasing all models and weights, we provide accessible building blocks for computational pathology, immuno-oncology, and precision health.

Building a virtual cell capable of accurately simulating cellular behaviors in silico has long been a dream in computational biology. We introduce CellFlux, an image-generative model that simulates cellular morphology changes induced by chemical and genetic perturbations using flow matching. Unlike prior methods, CellFlux models distribution-wise transformations from unperturbed to perturbed cell states, effectively distinguishing actual perturbation effects from experimental artifacts such as batch effects -- a major challenge in biological data. Evaluated on chemical (BBBC021), genetic (RxRx1), and combined perturbation (JUMP) datasets, CellFlux generates biologically meaningful cell images that faithfully capture perturbation-specific morphological changes, achieving a 35% improvement in FID scores and a 12% increase in mode-of-action prediction accuracy over existing methods. Additionally, CellFlux enables continuous interpolation between cellular states, providing a potential tool for studying perturbation dynamics. These capabilities mark a significant step toward realizing virtual cell modeling for biomedical research. Project page: https://yuhui-zh15.github.io/CellFlux/.

The third ML4H symposium was held in person on December 10, 2023, in New Orleans, Louisiana, USA. The symposium included research roundtable sessions to foster discussions between participants and senior researchers on timely and relevant topics for the ML4H community. Encouraged by the successful virtual roundtables in the previous year, we organized eleven in-person roundtables and four virtual roundtables at ML4H 2022. The organization of the research roundtables at the conference involved 17 Senior Chairs and 19 Junior Chairs across 11 tables. Each roundtable session included invited senior chairs (with substantial experience in the field), junior chairs (responsible for facilitating the discussion), and attendees from diverse backgrounds with interest in the session's topic. Herein we detail the organization process and compile takeaways from these roundtable discussions, including recent advances, applications, and open challenges for each topic. We conclude with a summary and lessons learned across all roundtables. This document serves as a comprehensive review paper, summarizing the recent advancements in machine learning for healthcare as contributed by foremost researchers in the field.

A community of developers has formed to modernize the Fortran ecosystem. In this article, we describe the high-level features of Fortran that continue to make it a good choice for scientists and engineers in the 21st century. Ongoing efforts include the development of a Fortran standard library and package manager, the fostering of a friendly and welcoming online community, improved compiler support, and language feature development. The lessons learned are common across contemporary programming languages and help reduce the learning curve and increase adoption of Fortran.

Foundation models have demonstrated remarkable success across diverse domains and tasks, primarily due to the thrive of large-scale, diverse, and high-quality datasets. However, in the field of medical imaging, the curation and assembling of such medical datasets are highly challenging due to the reliance on clinical expertise and strict ethical and privacy constraints, resulting in a scarcity of large-scale unified medical datasets and hindering the development of powerful medical foundation models. In this work, we present the largest survey to date of medical image datasets, covering over 1,000 open-access datasets with a systematic catalog of their modalities, tasks, anatomies, annotations, limitations, and potential for integration. Our analysis exposes a landscape that is modest in scale, fragmented across narrowly scoped tasks, and unevenly distributed across organs and modalities, which in turn limits the utility of existing medical image datasets for developing versatile and robust medical foundation models. To turn fragmentation into scale, we propose a metadata-driven fusion paradigm (MDFP) that integrates public datasets with shared modalities or tasks, thereby transforming multiple small data silos into larger, more coherent resources. Building on MDFP, we release an interactive discovery portal that enables end-to-end, automated medical image dataset integration, and compile all surveyed datasets into a unified, structured table that clearly summarizes their key characteristics and provides reference links, offering the community an accessible and comprehensive repository. By charting the current terrain and offering a principled path to dataset consolidation, our survey provides a practical roadmap for scaling medical imaging corpora, supporting faster data discovery, more principled dataset creation, and more capable medical foundation models.

Audio comprehension-including speech, non-speech sounds, and music-is essential for achieving human-level intelligence. Consequently, AI agents must demonstrate holistic audio understanding to qualify as generally intelligent. However, evaluating auditory intelligence comprehensively remains challenging. To address this gap, we introduce MMAU-Pro, the most comprehensive and rigorously curated benchmark for assessing audio intelligence in AI systems. MMAU-Pro contains 5,305 instances, where each instance has one or more audios paired with human expert-generated question-answer pairs, spanning speech, sound, music, and their combinations. Unlike existing benchmarks, MMAU-Pro evaluates auditory intelligence across 49 unique skills and multiple complex dimensions, including long-form audio comprehension, spatial audio reasoning, multi-audio understanding, among others. All questions are meticulously designed to require deliberate multi-hop reasoning, including both multiple-choice and open-ended response formats. Importantly, audio data is sourced directly ``from the wild" rather than from existing datasets with known distributions. We evaluate 22 leading open-source and proprietary multimodal AI models, revealing significant limitations: even state-of-the-art models such as Gemini 2.5 Flash and Audio Flamingo 3 achieve only 59.2% and 51.7% accuracy, respectively, approaching random performance in multiple categories. Our extensive analysis highlights specific shortcomings and provides novel insights, offering actionable perspectives for the community to enhance future AI systems' progression toward audio general intelligence. The benchmark and code is available at https://sonalkum.github.io/mmau-pro.

AI agents hold the potential to revolutionize scientific productivity by automating literature reviews, replicating experiments, analyzing data, and even proposing new directions of inquiry; indeed, there are now many such agents, ranging from general-purpose "deep research" systems to specialized science-specific agents, such as AI Scientist and AIGS. Rigorous evaluation of these agents is critical for progress. Yet existing benchmarks fall short on several fronts: they (1) fail to provide holistic, product-informed measures of real-world use cases such as science research; (2) lack reproducible agent tools necessary for a controlled comparison of core agentic capabilities; (3) do not account for confounding variables such as model cost and tool access; (4) do not provide standardized interfaces for quick agent prototyping and evaluation; and (5) lack comprehensive baseline agents necessary to identify true advances. In response, we define principles and tooling for more rigorously benchmarking agents. Using these, we present AstaBench, a suite that provides the first holistic measure of agentic ability to perform scientific research, comprising 2400+ problems spanning the entire scientific discovery process and multiple scientific domains, and including many problems inspired by actual user requests to deployed Asta agents. Our suite comes with the first scientific research environment with production-grade search tools that enable controlled, reproducible evaluation, better accounting for confounders. Alongside, we provide a comprehensive suite of nine science-optimized classes of Asta agents and numerous baselines. Our extensive evaluation of 57 agents across 22 agent classes reveals several interesting findings, most importantly that despite meaningful progress on certain individual aspects, AI remains far from solving the challenge of science research assistance.

We conduct an extended analysis of dark energy constraints, in support of the findings of the DESI DR2 cosmology key paper, including DESI data, Planck CMB observations, and three different supernova compilations. Using a broad range of parametric and non-parametric methods, we explore the dark energy phenomenology and find consistent trends across all approaches, in good agreement with the w_0w_aCDM key paper results. Even with the additional flexibility introduced by non-parametric approaches, such as binning and Gaussian Processes, we find that extending LambdaCDM to include a two-parameter w(z) is sufficient to capture the trends present in the data. Finally, we examine three dark energy classes with distinct dynamics, including quintessence scenarios satisfying w geq -1, to explore what underlying physics can explain such deviations. The current data indicate a clear preference for models that feature a phantom crossing; although alternatives lacking this feature are disfavored, they cannot yet be ruled out. Our analysis confirms that the evidence for dynamical dark energy, particularly at low redshift (z lesssim 0.3), is robust and stable under different modeling choices.

We present baryon acoustic oscillation (BAO) measurements from more than 14 million galaxies and quasars drawn from the Dark Energy Spectroscopic Instrument (DESI) Data Release 2 (DR2), based on three years of operation. For cosmology inference, these galaxy measurements are combined with DESI Lyman-α forest BAO results presented in a companion paper. The DR2 BAO results are consistent with DESI DR1 and SDSS, and their distance-redshift relationship matches those from recent compilations of supernovae (SNe) over the same redshift range. The results are well described by a flat ΛCDM model, but the parameters preferred by BAO are in mild, 2.3σ tension with those determined from the cosmic microwave background (CMB), although the DESI results are consistent with the acoustic angular scale θ_* that is well-measured by Planck. This tension is alleviated by dark energy with a time-evolving equation of state parametrized by w_0 and w_a, which provides a better fit to the data, with a favored solution in the quadrant with w_0>-1 and w_a<0. This solution is preferred over ΛCDM at 3.1σ for the combination of DESI BAO and CMB data. When also including SNe, the preference for a dynamical dark energy model over ΛCDM ranges from 2.8-4.2σ depending on which SNe sample is used. We present evidence from other data combinations which also favor the same behavior at high significance. From the combination of DESI and CMB we derive 95% upper limits on the sum of neutrino masses, finding sum m_ν<0.064 eV assuming ΛCDM and sum m_ν<0.16 eV in the w_0w_a model. Unless there is an unknown systematic error associated with one or more datasets, it is clear that ΛCDM is being challenged by the combination of DESI BAO with other measurements and that dynamical dark energy offers a possible solution.