Daily Papers

We study professional image generation, where a model must synthesize information-dense, scientifically precise illustrations from technical descriptions rather than merely produce visually plausible pictures. To quantify the progress, we introduce ProImage-Bench, a rubric-based benchmark that targets biology schematics, engineering/patent drawings, and general scientific diagrams. For 654 figures collected from real textbooks and technical reports, we construct detailed image instructions and a hierarchy of rubrics that decompose correctness into 6,076 criteria and 44,131 binary checks. Rubrics are derived from surrounding text and reference figures using large multimodal models, and are evaluated by an automated LMM-based judge with a principled penalty scheme that aggregates sub-question outcomes into interpretable criterion scores. We benchmark several representative text-to-image models on ProImage-Bench and find that, despite strong open-domain performance, the best base model reaches only 0.791 rubric accuracy and 0.553 criterion score overall, revealing substantial gaps in fine-grained scientific fidelity. Finally, we show that the same rubrics provide actionable supervision: feeding failed checks back into an editing model for iterative refinement boosts a strong generator from 0.653 to 0.865 in rubric accuracy and from 0.388 to 0.697 in criterion score. ProImage-Bench thus offers both a rigorous diagnostic for professional image generation and a scalable signal for improving specification-faithful scientific illustrations.

The Chandra Source Catalog (CSC) is a general purpose virtual X-ray astrophysics facility that provides access to a carefully selected set of generally useful quantities for individual X-ray sources, and is designed to satisfy the needs of a broad-based group of scientists, including those who may be less familiar with astronomical data analysis in the X-ray regime. The first release of the CSC includes information about 94,676 distinct X-ray sources detected in a subset of public ACIS imaging observations from roughly the first eight years of the Chandra mission. This release of the catalog includes point and compact sources with observed spatial extents <~ 30''. The catalog (1) provides access to the best estimates of the X-ray source properties for detected sources, with good scientific fidelity, and directly supports scientific analysis using the individual source data; (2) facilitates analysis of a wide range of statistical properties for classes of X-ray sources; and (3) provides efficient access to calibrated observational data and ancillary data products for individual X-ray sources, so that users can perform detailed further analysis using existing tools. The catalog includes real X-ray sources detected with flux estimates that are at least 3 times their estimated 1 sigma uncertainties in at least one energy band, while maintaining the number of spurious sources at a level of <~ 1 false source per field for a 100 ks observation. For each detected source, the CSC provides commonly tabulated quantities, including source position, extent, multi-band fluxes, hardness ratios, and variability statistics, derived from the observations in which the source is detected. In addition to these traditional catalog elements, for each X-ray source the CSC includes an extensive set of file-based data products that can be manipulated interactively.

Recent advances in video generation have opened new avenues for macroscopic simulation of complex dynamic systems, but their application to microscopic phenomena remains largely unexplored. Microscale simulation holds great promise for biomedical applications such as drug discovery, organ-on-chip systems, and disease mechanism studies, while also showing potential in education and interactive visualization. In this work, we introduce MicroWorldBench, a multi-level rubric-based benchmark for microscale simulation tasks. MicroWorldBench enables systematic, rubric-based evaluation through 459 unique expert-annotated criteria spanning multiple microscale simulation task (e.g., organ-level processes, cellular dynamics, and subcellular molecular interactions) and evaluation dimensions (e.g., scientific fidelity, visual quality, instruction following). MicroWorldBench reveals that current SOTA video generation models fail in microscale simulation, showing violations of physical laws, temporal inconsistency, and misalignment with expert criteria. To address these limitations, we construct MicroSim-10K, a high-quality, expert-verified simulation dataset. Leveraging this dataset, we train MicroVerse, a video generation model tailored for microscale simulation. MicroVerse can accurately reproduce complex microscale mechanism. Our work first introduce the concept of Micro-World Simulation and present a proof of concept, paving the way for applications in biology, education, and scientific visualization. Our work demonstrates the potential of educational microscale simulations of biological mechanisms. Our data and code are publicly available at https://github.com/FreedomIntelligence/MicroVerse

While synthetic data has proven effective for improving scientific reasoning in the text domain, multimodal reasoning remains constrained by the difficulty of synthesizing scientifically rigorous images. Existing Text-to-Image (T2I) models often produce outputs that are visually plausible yet scientifically incorrect, resulting in a persistent visual-logic divergence that limits their value for downstream reasoning. Motivated by recent advances in next-generation T2I models, we conduct a systematic study of scientific image synthesis across generation paradigms, evaluation, and downstream use. We analyze both direct pixel-based generation and programmatic synthesis, and propose ImgCoder, a logic-driven framework that follows an explicit "understand - plan - code" workflow to improve structural precision. To rigorously assess scientific correctness, we introduce SciGenBench, which evaluates generated images based on information utility and logical validity. Our evaluation reveals systematic failure modes in pixel-based models and highlights a fundamental expressiveness-precision trade-off. Finally, we show that fine-tuning Large Multimodal Models (LMMs) on rigorously verified synthetic scientific images yields consistent reasoning gains, with potential scaling trends analogous to the text domain, validating high-fidelity scientific synthesis as a viable path to unlocking massive multimodal reasoning capabilities.

The rapid advancement of Large Language Models (LLMs) has led to performance saturation on many established benchmarks, questioning their ability to distinguish frontier models. Concurrently, existing high-difficulty benchmarks often suffer from narrow disciplinary focus, oversimplified answer formats, and vulnerability to data contamination, creating a fidelity gap with real-world scientific inquiry. To address these challenges, we introduce ATLAS (AGI-Oriented Testbed for Logical Application in Science), a large-scale, high-difficulty, and cross-disciplinary evaluation suite composed of approximately 800 original problems. Developed by domain experts (PhD-level and above), ATLAS spans seven core scientific fields: mathematics, physics, chemistry, biology, computer science, earth science, and materials science. Its key features include: (1) High Originality and Contamination Resistance, with all questions newly created or substantially adapted to prevent test data leakage; (2) Cross-Disciplinary Focus, designed to assess models' ability to integrate knowledge and reason across scientific domains; (3) High-Fidelity Answers, prioritizing complex, open-ended answers involving multi-step reasoning and LaTeX-formatted expressions over simple multiple-choice questions; and (4) Rigorous Quality Control, employing a multi-stage process of expert peer review and adversarial testing to ensure question difficulty, scientific value, and correctness. We also propose a robust evaluation paradigm using a panel of LLM judges for automated, nuanced assessment of complex answers. Preliminary results on leading models demonstrate ATLAS's effectiveness in differentiating their advanced scientific reasoning capabilities. We plan to develop ATLAS into a long-term, open, community-driven platform to provide a reliable "ruler" for progress toward Artificial General Intelligence.

Most scientific materials compress reasoning, presenting conclusions while omitting the derivational chains that justify them. This compression hinders verification by lacking explicit, step-wise justifications and inhibits cross-domain links by collapsing the very pathways that establish the logical and causal connections between concepts. We introduce a scalable framework that decompresses scientific reasoning, constructing a verifiable Long Chain-of-Thought (LCoT) knowledge base and projecting it into an emergent encyclopedia, SciencePedia. Our pipeline operationalizes an endpoint-driven, reductionist strategy: a Socratic agent, guided by a curriculum of around 200 courses, generates approximately 3 million first-principles questions. To ensure high fidelity, multiple independent solver models generate LCoTs, which are then rigorously filtered by prompt sanitization and cross-model answer consensus, retaining only those with verifiable endpoints. This verified corpus powers the Brainstorm Search Engine, which performs inverse knowledge search -- retrieving diverse, first-principles derivations that culminate in a target concept. This engine, in turn, feeds the Plato synthesizer, which narrates these verified chains into coherent articles. The initial SciencePedia comprises approximately 200,000 fine-grained entries spanning mathematics, physics, chemistry, biology, engineering, and computation. In evaluations across six disciplines, Plato-synthesized articles (conditioned on retrieved LCoTs) exhibit substantially higher knowledge-point density and significantly lower factual error rates than an equally-prompted baseline without retrieval (as judged by an external LLM). Built on this verifiable LCoT knowledge base, this reasoning-centric approach enables trustworthy, cross-domain scientific synthesis at scale and establishes the foundation for an ever-expanding encyclopedia.

We present a scientific reasoning foundation model that aligns natural language with heterogeneous scientific representations. The model is pretrained on a 206B-token corpus spanning scientific text, pure sequences, and sequence-text pairs, then aligned via SFT on 40M instructions, annealed cold-start bootstrapping to elicit long-form chain-of-thought, and reinforcement learning with task-specific reward shaping, which instills deliberate scientific reasoning. It supports four capability families, covering up to 103 tasks across workflows: (i) faithful translation between text and scientific formats, (ii) text/knowledge extraction, (iii) property prediction, (iv) property classification, (v) unconditional and conditional sequence generation and design. Compared with specialist systems, our approach broadens instruction coverage, improves cross-domain generalization, and enhances fidelity. We detail data curation and training and show that cross-discipline learning strengthens transfer and downstream reliability. The model, instruct tuning datasets and the evaluation code are open-sourced at https://huggingface.co/SciReason and https://github.com/open-sciencelab/SciReason.

We present a novel training-free framework, PosterForest, for automated scientific poster generation. Unlike prior approaches, which largely neglect the hierarchical structure of scientific documents and the semantic integration of textual and visual elements, our method addresses both challenges directly. We introduce the Poster Tree, a hierarchical intermediate representation that jointly encodes document structure and visual-textual relationships at multiple levels. Our framework employs a multi-agent collaboration strategy, where agents specializing in content summarization and layout planning iteratively coordinate and provide mutual feedback. This approach enables the joint optimization of logical consistency, content fidelity, and visual coherence. Extensive experiments on multiple academic domains show that our method outperforms existing baselines in both qualitative and quantitative evaluations. The resulting posters achieve quality closest to expert-designed ground truth and deliver superior information preservation, structural clarity, and user preference.

Scientific diagrams are vital tools for communicating structured knowledge across disciplines. However, they are often published as static raster images, losing symbolic semantics and limiting reuse. While Multimodal Large Language Models (MLLMs) offer a pathway to bridging vision and structure, existing methods lack semantic control and structural interpretability, especially on complex diagrams. We propose Draw with Thought (DwT), a training-free framework that guides MLLMs to reconstruct diagrams into editable mxGraph XML code through cognitively-grounded Chain-of-Thought reasoning. DwT enables interpretable and controllable outputs without model fine-tuning by dividing the task into two stages: Coarse-to-Fine Planning, which handles perceptual structuring and semantic specification, and Structure-Aware Code Generation, enhanced by format-guided refinement. To support evaluation, we release Plot2XML, a benchmark of 247 real-world scientific diagrams with gold-standard XML annotations. Extensive experiments across eight MLLMs show that our approach yields high-fidelity, semantically aligned, and structurally valid reconstructions, with human evaluations confirming strong alignment in both accuracy and visual aesthetics, offering a scalable solution for converting static visuals into executable representations and advancing machine understanding of scientific graphics.

Reducing hallucination of Large Language Models (LLMs) is imperative for use in the sciences where reproducibility is crucial. However, LLMs inherently lack long-term memory, making it a nontrivial, ad hoc, and inevitably biased task to fine-tune them on domain-specific literature and data. Here we introduce LLaMP, a multimodal retrieval-augmented generation (RAG) framework of multiple data-aware reasoning-and-acting (ReAct) agents that dynamically interact with computational and experimental data on Materials Project (MP). Without fine-tuning, LLaMP demonstrates an ability to comprehend and integrate various modalities of materials science concepts, fetch relevant data stores on the fly, process higher-order data (such as crystal structures and elastic tensors), and summarize multi-step procedures for solid-state synthesis. We show that LLaMP effectively corrects errors in GPT-3.5's intrinsic knowledge, reducing a 5.21% MAPE on frequently-documented bandgaps and a significant 1103.54% MAPE on formation energies -- errors that GPT-3.5 seems to derive from mixed data sources. Additionally, LLaMP substantially reduces the hallucinated volumetric strain in a diamond cubic silicon structure from 66.3% to 0. The proposed framework offers an intuitive and nearly hallucination-free approach to exploring materials informatics and establishes a pathway for knowledge distillation and fine-tuning other language models. We envision the framework as a valuable component for scientific hypotheses and a foundation for future autonomous laboratories where multiple LLM agents communicate and cooperate with robotics to drive material synthesis and chemical reactions without hard-coded human logic and intervention.

Graphics Program Synthesis is pivotal for interpreting and editing visual data, effectively facilitating the reverse-engineering of static visuals into editable TikZ code. While TikZ is the de facto standard for scientific schematics due to its programmatic flexibility, its requirement for rigorous spatial precision presents a significant challenge for Multimodal Large Language Models. Progress is currently stifled by two primary gaps: (1) Data Quality Gap: existing image-TikZ corpora often lack strict executability and reliable visual alignment; (2) Evaluation Gap: a lack of benchmarks for both structural and visual fidelity. To address these, we present a closed-loop framework featuring: SciTikZ-230K, a large-scale, high-quality dataset from our Execution-Centric Data Engine covering 11 diverse scientific disciplines; SciTikZ-Bench, a multifaceted benchmark spanning from basic geometric constructs to intricate hierarchical schematics to evaluate both visual fidelity and structural logic. To further broaden the scope of visual-code optimization methodology, we introduce a novel Dual Self-Consistency Reinforcement Learning optimization paradigm, which utilizes Round-Trip Verification to penalize degenerate code and boost overall self-consistency. Empowered by these, our trained model SciTikZer-8B achieves state-of-the-art performance, consistently outperforming proprietary giants like Gemini-2.5-Pro and massive models like Qwen3-VL-235B-A22B-Instruct.

Despite advances in scientific AI, a coherent framework for Scientific General Intelligence (SGI)-the ability to autonomously conceive, investigate, and reason across scientific domains-remains lacking. We present an operational SGI definition grounded in the Practical Inquiry Model (PIM: Deliberation, Conception, Action, Perception) and operationalize it via four scientist-aligned tasks: deep research, idea generation, dry/wet experiments, and experimental reasoning. SGI-Bench comprises over 1,000 expert-curated, cross-disciplinary samples inspired by Science's 125 Big Questions, enabling systematic evaluation of state-of-the-art LLMs. Results reveal gaps: low exact match (10--20%) in deep research despite step-level alignment; ideas lacking feasibility and detail; high code executability but low execution result accuracy in dry experiments; low sequence fidelity in wet protocols; and persistent multimodal comparative-reasoning challenges. We further introduce Test-Time Reinforcement Learning (TTRL), which optimizes retrieval-augmented novelty rewards at inference, enhancing hypothesis novelty without reference answer. Together, our PIM-grounded definition, workflow-centric benchmark, and empirical insights establish a foundation for AI systems that genuinely participate in scientific discovery.

The foundation of reproducible science lies in protocols that are precise, logically ordered, and executable. The autonomous generation of these protocols through natural language queries could greatly improve the efficiency of the reproduction process. However, current leading large language models (LLMs) often generate incomplete or inconsistent protocols, limiting their utility. To address this limitation, we first introduce SciRecipe, a large-scale dataset of over 12K structured protocols spanning 27 biological subfields and encompassing both comprehension and problem-solving tasks. To further improve protocol generation, we propose the "Sketch-and-Fill" paradigm, which separates analysis, structuring, and expression to ensure each step is explicit and verifiable. Complementing this, the structured component-based reward mechanism evaluates step granularity, action order, and semantic fidelity, aligning model optimization with experimental reliability. Building on these components, we develop Thoth, trained through a staged Knowledge-to-Action process that progresses from knowledge acquisition to operational reasoning and ultimately to robust, executable protocol generation. Across multiple benchmarks, Thoth consistently surpasses both proprietary and open-source LLMs, achieving significant improvements in step alignment, logical sequencing, and semantic accuracy. Our approach paves the way for reliable scientific assistants that bridge knowledge with experimental execution. All data, code, and models will be released publicly.

Recent years have seen rapid advances in AI-driven image generation. Early diffusion models emphasized perceptual quality, while newer multimodal models like GPT-4o-image integrate high-level reasoning, improving semantic understanding and structural composition. Scientific illustration generation exemplifies this evolution: unlike general image synthesis, it demands accurate interpretation of technical content and transformation of abstract ideas into clear, standardized visuals. This task is significantly more knowledge-intensive and laborious, often requiring hours of manual work and specialized tools. Automating it in a controllable, intelligent manner would provide substantial practical value. Yet, no benchmark currently exists to evaluate AI on this front. To fill this gap, we introduce SridBench, the first benchmark for scientific figure generation. It comprises 1,120 instances curated from leading scientific papers across 13 natural and computer science disciplines, collected via human experts and MLLMs. Each sample is evaluated along six dimensions, including semantic fidelity and structural accuracy. Experimental results reveal that even top-tier models like GPT-4o-image lag behind human performance, with common issues in text/visual clarity and scientific correctness. These findings highlight the need for more advanced reasoning-driven visual generation capabilities.

While previous AI Scientist systems can generate novel findings, they often lack the focus to produce scientifically valuable contributions that address pressing human-defined challenges. We introduce DeepScientist, a system designed to overcome this by conducting goal-oriented, fully autonomous scientific discovery over month-long timelines. It formalizes discovery as a Bayesian Optimization problem, operationalized through a hierarchical evaluation process consisting of "hypothesize, verify, and analyze". Leveraging a cumulative Findings Memory, this loop intelligently balances the exploration of novel hypotheses with exploitation, selectively promoting the most promising findings to higher-fidelity levels of validation. Consuming over 20,000 GPU hours, the system generated about 5,000 unique scientific ideas and experimentally validated approximately 1100 of them, ultimately surpassing human-designed state-of-the-art (SOTA) methods on three frontier AI tasks by 183.7\%, 1.9\%, and 7.9\%. This work provides the first large-scale evidence of an AI achieving discoveries that progressively surpass human SOTA on scientific tasks, producing valuable findings that genuinely push the frontier of scientific discovery. To facilitate further research into this process, we will open-source all experimental logs and system code at https://github.com/ResearAI/DeepScientist/.

We present Omni-I2C, a comprehensive benchmark designed to evaluate the capability of Large Multimodal Models (LMMs) in converting complex, structured digital graphics into executable code. We argue that this task represents a non-trivial challenge for the current generation of LMMs: it demands an unprecedented synergy between high-fidelity visual perception -- to parse intricate spatial hierarchies and symbolic details -- and precise generative expression -- to synthesize syntactically sound and logically consistent code. Unlike traditional descriptive tasks, Omni-I2C requires a holistic understanding where any minor perceptual hallucination or coding error leads to a complete failure in visual reconstruction. Omni-I2C features 1080 meticulously curated samples, defined by its breadth across subjects, image modalities, and programming languages. By incorporating authentic user-sourced cases, the benchmark spans a vast spectrum of digital content -- from scientific visualizations to complex symbolic notations -- each paired with executable reference code. To complement this diversity, our evaluation framework provides necessary depth; by decoupling performance into perceptual fidelity and symbolic precision, it transcends surface-level accuracy to expose the granular structural failures and reasoning bottlenecks of current LMMs. Our evaluation reveals a substantial performance gap among leading LMMs; even state-of-the-art models struggle to preserve structural integrity in complex scenarios, underscoring that multimodal code generation remains a formidable challenge. Data and code are available at https://github.com/MiliLab/Omni-I2C.

Multimodal Large Language Models demonstrate strong performance on natural image understanding, yet exhibit limited capability in interpreting scientific images, including but not limited to schematic diagrams, experimental characterizations, and analytical charts. This limitation is particularly pronounced in open-source MLLMs. The gap largely stems from existing datasets with limited domain coverage, coarse structural annotations, and weak semantic grounding. We introduce OmniScience, a large-scale, high-fidelity multi-modal dataset comprising 1.5 million figure-caption-context triplets, spanning more than 10 major scientific disciplines. To obtain image caption data with higher information density and accuracy for multi-modal large-model training, we develop a dynamic model-routing re-captioning pipeline that leverages state-of-the-art multi-modal large language models to generate dense, self-contained descriptions by jointly synthesizing visual features, original figure captions, and corresponding in-text references authored by human scientists. The pipeline is further reinforced with rigorous quality filtering and alignment with human expert judgments, ensuring both factual accuracy and semantic completeness, and boosts the image-text multi-modal similarity score from 0.769 to 0.956. We further propose a caption QA protocol as a proxy task for evaluating visual understanding. Under this setting, Qwen2.5-VL-3B model finetuned on OmniScience show substantial gains over baselines, achieving a gain of 0.378 on MM-MT-Bench and a gain of 0.140 on MMMU.

Equation discovery from data is a core challenge in machine learning for science, requiring the recovery of concise symbolic expressions that govern complex physical and geometric phenomena. Recent approaches with large language models (LLMs) show promise in symbolic regression, but their success often hinges on memorized formulas or overly simplified functional forms. Existing benchmarks exacerbate this limitation: they focus on scalar functions, ignore domain grounding, and rely on brittle string-matching based metrics that fail to capture scientific equivalence. We introduce SurfaceBench, first comprehensive benchmark for symbolic surface discovery. SurfaceBench comprises 183 tasks across 15 categories of symbolic complexity, spanning explicit, implicit, and parametric equation representation forms. Each task includes ground-truth equations, variable semantics, and synthetically sampled three dimensional data. Unlike prior SR datasets, our tasks reflect surface-level structure, resist LLM memorization through novel symbolic compositions, and are grounded in scientific domains such as fluid dynamics, robotics, electromagnetics, and geometry. To evaluate equation discovery quality, we pair symbolic checks with geometry-aware metrics such as Chamfer and Hausdorff distances, capturing both algebraic fidelity and spatial reconstruction accuracy. Our experiments reveal that state-of-the-art frameworks, while occasionally successful on specific families, struggle to generalize across representation types and surface complexities. SurfaceBench thus establishes a challenging and diagnostic testbed that bridges symbolic reasoning with geometric reconstruction, enabling principled benchmarking of progress in compositional generalization, data-driven scientific induction, and geometry-aware reasoning with LLMs. We release the code here: https://github.com/Sanchit-404/surfacebench

The rapid expansion of enzyme kinetics literature has outpaced the curation capabilities of major biochemical databases, creating a substantial barrier to AI-driven modeling and knowledge discovery. We present zERExtractor, an automated and extensible platform for comprehensive extraction of enzyme-catalyzed reaction and activity data from scientific literature. zERExtractor features a unified, modular architecture that supports plug-and-play integration of state-of-the-art models, including large language models (LLMs), as interchangeable components, enabling continuous system evolution alongside advances in AI. Our pipeline combines domain-adapted deep learning, advanced OCR, semantic entity recognition, and prompt-driven LLM modules, together with human expert corrections, to extract kinetic parameters (e.g., kcat, Km), enzyme sequences, substrate SMILES, experimental conditions, and molecular diagrams from heterogeneous document formats. Through active learning strategies integrating AI-assisted annotation, expert validation, and iterative refinement, the system adapts rapidly to new data sources. We also release a large benchmark dataset comprising over 1,000 annotated tables and 5,000 biological fields from 270 P450-related enzymology publications. Benchmarking demonstrates that zERExtractor consistently outperforms existing baselines in table recognition (Acc 89.9%), molecular image interpretation (up to 99.1%), and relation extraction (accuracy 94.2%). zERExtractor bridges the longstanding data gap in enzyme kinetics with a flexible, plugin-ready framework and high-fidelity extraction, laying the groundwork for future AI-powered enzyme modeling and biochemical knowledge discovery.

Large language models (LLMs) are increasingly used as simulated participants in social science experiments, but their behavior is often unstable and highly sensitive to design choices. Prior evaluations frequently conflate base-model capabilities with experimental instantiation, obscuring whether outcomes reflect the model itself or the agent setup. We instead frame participant simulation as an agent-design problem over full experimental protocols, where an agent is defined by a base model and a specification (e.g., participant attributes) that encodes behavioral assumptions. We introduce HUMANSTUDY-BENCH, a benchmark and execution engine that orchestrates LLM-based agents to reconstruct published human-subject experiments via a Filter--Extract--Execute--Evaluate pipeline, replaying trial sequences and running the original analysis pipeline in a shared runtime that preserves the original statistical procedures end to end. To evaluate fidelity at the level of scientific inference, we propose new metrics to quantify how much human and agent behaviors agree. We instantiate 12 foundational studies as an initial suite in this dynamic benchmark, spanning individual cognition, strategic interaction, and social psychology, and covering more than 6,000 trials with human samples ranging from tens to over 2,100 participants.

We present LingBot-World, an open-sourced world simulator stemming from video generation. Positioned as a top-tier world model, LingBot-World offers the following features. (1) It maintains high fidelity and robust dynamics in a broad spectrum of environments, including realism, scientific contexts, cartoon styles, and beyond. (2) It enables a minute-level horizon while preserving contextual consistency over time, which is also known as "long-term memory". (3) It supports real-time interactivity, achieving a latency of under 1 second when producing 16 frames per second. We provide public access to the code and model in an effort to narrow the divide between open-source and closed-source technologies. We believe our release will empower the community with practical applications across areas like content creation, gaming, and robot learning.

Sparse autoencoders (SAEs) have shown promise in extracting interpretable features from complex neural networks. We present one of the first applications of SAEs to dense text embeddings from large language models, demonstrating their effectiveness in disentangling semantic concepts. By training SAEs on embeddings of over 420,000 scientific paper abstracts from computer science and astronomy, we show that the resulting sparse representations maintain semantic fidelity while offering interpretability. We analyse these learned features, exploring their behaviour across different model capacities and introducing a novel method for identifying ``feature families'' that represent related concepts at varying levels of abstraction. To demonstrate the practical utility of our approach, we show how these interpretable features can be used to precisely steer semantic search, allowing for fine-grained control over query semantics. This work bridges the gap between the semantic richness of dense embeddings and the interpretability of sparse representations. We open source our embeddings, trained sparse autoencoders, and interpreted features, as well as a web app for exploring them.

Foundation models have revolutionized natural language processing through a ``train once, deploy anywhere'' paradigm, where a single pre-trained model adapts to countless downstream tasks without retraining. Access to a Physics Foundation Model (PFM) would be transformative -- democratizing access to high-fidelity simulations, accelerating scientific discovery, and eliminating the need for specialized solver development. Yet current physics-aware machine learning approaches remain fundamentally limited to single, narrow domains and require retraining for each new system. We present the General Physics Transformer (GPhyT), trained on 1.8 TB of diverse simulation data, that demonstrates foundation model capabilities are achievable for physics. Our key insight is that transformers can learn to infer governing dynamics from context, enabling a single model to simulate fluid-solid interactions, shock waves, thermal convection, and multi-phase dynamics without being told the underlying equations. GPhyT achieves three critical breakthroughs: (1) superior performance across multiple physics domains, outperforming specialized architectures by up to 29x, (2) zero-shot generalization to entirely unseen physical systems through in-context learning, and (3) stable long-term predictions through 50-timestep rollouts. By establishing that a single model can learn generalizable physical principles from data alone, this work opens the path toward a universal PFM that could transform computational science and engineering.

Recent advances in large language models (LLMs) have given rise to powerful coding agents, making it possible for code assistants to evolve into code engineers. However, existing methods still face significant challenges in achieving high-fidelity document-to-codebase synthesis--such as scientific papers to code--primarily due to a fundamental conflict between information overload and the context bottlenecks of LLMs. In this work, we introduce DeepCode, a fully autonomous framework that fundamentally addresses this challenge through principled information-flow management. By treating repository synthesis as a channel optimization problem, DeepCode seamlessly orchestrates four information operations to maximize task-relevant signals under finite context budgets: source compression via blueprint distillation, structured indexing using stateful code memory, conditional knowledge injection via retrieval-augmented generation, and closed-loop error correction. Extensive evaluations on the PaperBench benchmark demonstrate that DeepCode achieves state-of-the-art performance, decisively outperforming leading commercial agents such as Cursor and Claude Code, and crucially, surpassing PhD-level human experts from top institutes on key reproduction metrics. By systematically transforming paper specifications into production-grade implementations comparable to human expert quality, this work establishes new foundations for autonomous scientific reproduction that can accelerate research evaluation and discovery.

Academic citations are widely used for evaluating research and tracing knowledge flows. Such uses typically rely on raw citation counts and neglect variability in citation types. In particular, citations can vary in their fidelity as original knowledge from cited studies may be paraphrased, summarized, or reinterpreted, possibly wrongly, leading to variation in how much information changes from cited to citing paper. In this study, we introduce a computational pipeline to quantify citation fidelity at scale. Using full texts of papers, the pipeline identifies citations in citing papers and the corresponding claims in cited papers, and applies supervised models to measure fidelity at the sentence level. Analyzing a large-scale multi-disciplinary dataset of approximately 13 million citation sentence pairs, we find that citation fidelity is higher when authors cite papers that are 1) more recent and intellectually close, 2) more accessible, and 3) the first author has a lower H-index and the author team is medium-sized. Using a quasi-experiment, we establish the "telephone effect" - when citing papers have low fidelity to the original claim, future papers that cite the citing paper and the original have lower fidelity to the original. Our work reveals systematic differences in citation fidelity, underscoring the limitations of analyses that rely on citation quantity alone and the potential for distortion of evidence.

Accelerating scientific discovery requires the identification of which experiments would yield the best outcomes before committing resources to costly physical validation. While existing benchmarks evaluate LLMs on scientific knowledge and reasoning, their ability to predict experimental outcomes - a task where AI could significantly exceed human capabilities - remains largely underexplored. We introduce SciPredict, a benchmark comprising 405 tasks derived from recent empirical studies in 33 specialized sub-fields of physics, biology, and chemistry. SciPredict addresses two critical questions: (a) can LLMs predict the outcome of scientific experiments with sufficient accuracy? and (b) can such predictions be reliably used in the scientific research process? Evaluations reveal fundamental limitations on both fronts. Model accuracies are 14-26% and human expert performance is approx20%. Although some frontier models exceed human performance model accuracy is still far below what would enable reliable experimental guidance. Even within the limited performance, models fail to distinguish reliable predictions from unreliable ones, achieving only approx20% accuracy regardless of their confidence or whether they judge outcomes as predictable without physical experimentation. Human experts, in contrast, demonstrate strong calibration: their accuracy increases from approx5% to approx80% as they deem outcomes more predictable without conducting the experiment. SciPredict establishes a rigorous framework demonstrating that superhuman performance in experimental science requires not just better predictions, but better awareness of prediction reliability. For reproducibility all our data and code are provided at https://github.com/scaleapi/scipredict

We present a novel approach to integrating scientific knowledge into generative models, enhancing their realism and consistency in image synthesis. First, we introduce Science-T2I, an expert-annotated adversarial dataset comprising adversarial 20k image pairs with 9k prompts, covering wide distinct scientific knowledge categories. Leveraging Science-T2I, we present SciScore, an end-to-end reward model that refines the assessment of generated images based on scientific knowledge, which is achieved by augmenting both the scientific comprehension and visual capabilities of pre-trained CLIP model. Additionally, based on SciScore, we propose a two-stage training framework, comprising a supervised fine-tuning phase and a masked online fine-tuning phase, to incorporate scientific knowledge into existing generative models. Through comprehensive experiments, we demonstrate the effectiveness of our framework in establishing new standards for evaluating the scientific realism of generated content. Specifically, SciScore attains performance comparable to human-level, demonstrating a 5% improvement similar to evaluations conducted by experienced human evaluators. Furthermore, by applying our proposed fine-tuning method to FLUX, we achieve a performance enhancement exceeding 50% on SciScore.

Scientific research relies on accurate citation for attribution and integrity, yet large language models (LLMs) introduce a new risk: fabricated references that appear plausible but correspond to no real publications. Such hallucinated citations have already been observed in submissions and accepted papers at major machine learning venues, exposing vulnerabilities in peer review. Meanwhile, rapidly growing reference lists make manual verification impractical, and existing automated tools remain fragile to noisy and heterogeneous citation formats and lack standardized evaluation. We present the first comprehensive benchmark and detection framework for hallucinated citations in scientific writing. Our multi-agent verification pipeline decomposes citation checking into claim extraction, evidence retrieval, passage matching, reasoning, and calibrated judgment to assess whether a cited source truly supports its claim. We construct a large-scale human-validated dataset across domains and define unified metrics for citation faithfulness and evidence alignment. Experiments with state-of-the-art LLMs reveal substantial citation errors and show that our framework significantly outperforms prior methods in both accuracy and interpretability. This work provides the first scalable infrastructure for auditing citations in the LLM era and practical tools to improve the trustworthiness of scientific references.

Recent breakthroughs in Large Language Models (LLMs) have revolutionized natural language understanding and generation, igniting a surge of interest in leveraging these technologies in the field of scientific literature analysis. Existing benchmarks, however, inadequately evaluate the proficiency of LLMs in scientific literature analysis, especially in scenarios involving complex comprehension and multimodal data. In response, we introduced SciAssess, a benchmark tailored for the in-depth analysis of scientific literature, crafted to provide a thorough assessment of LLMs' efficacy. SciAssess focuses on evaluating LLMs' abilities in memorization, comprehension, and analysis within the context of scientific literature analysis. It includes representative tasks from diverse scientific fields, such as general chemistry, organic materials, and alloy materials. And rigorous quality control measures ensure its reliability in terms of correctness, anonymization, and copyright compliance. SciAssess evaluates leading LLMs, including GPT-4, GPT-3.5, and Gemini, identifying their strengths and aspects for improvement and supporting the ongoing development of LLM applications in scientific literature analysis. SciAssess and its resources are made available at https://sci-assess.github.io, offering a valuable tool for advancing LLM capabilities in scientific literature analysis.

Frontier AI agents show increasing promise as scientific research assistants, and may eventually be useful for extended, open-ended research workflows. However, in order to use agents for novel research, we must first assess the underlying faithfulness and correctness of their work. To evaluate agents as research assistants, we introduce ReplicationBench, an evaluation framework that tests whether agents can replicate entire research papers drawn from the astrophysics literature. Astrophysics, where research relies heavily on archival data and computational study while requiring little real-world experimentation, is a particularly useful testbed for AI agents in scientific research. We split each paper into tasks which require agents to replicate the paper's core contributions, including the experimental setup, derivations, data analysis, and codebase. Each task is co-developed with the original paper authors and targets a key scientific result, enabling objective evaluation of both faithfulness (adherence to original methods) and correctness (technical accuracy of results). ReplicationBench is extremely challenging for current frontier language models: even the best-performing language models score under 20%. We analyze ReplicationBench trajectories in collaboration with domain experts and find a rich, diverse set of failure modes for agents in scientific research. ReplicationBench establishes the first benchmark of paper-scale, expert-validated astrophysics research tasks, reveals insights about agent performance generalizable to other domains of data-driven science, and provides a scalable framework for measuring AI agents' reliability in scientific research.

Public trust in science depends on honest and factual communication of scientific papers. However, recent studies have demonstrated a tendency of news media to misrepresent scientific papers by exaggerating their findings. Given this, we present a formalization of and study into the problem of exaggeration detection in science communication. While there are an abundance of scientific papers and popular media articles written about them, very rarely do the articles include a direct link to the original paper, making data collection challenging. We address this by curating a set of labeled press release/abstract pairs from existing expert annotated studies on exaggeration in press releases of scientific papers suitable for benchmarking the performance of machine learning models on the task. Using limited data from this and previous studies on exaggeration detection in science, we introduce MT-PET, a multi-task version of Pattern Exploiting Training (PET), which leverages knowledge from complementary cloze-style QA tasks to improve few-shot learning. We demonstrate that MT-PET outperforms PET and supervised learning both when data is limited, as well as when there is an abundance of data for the main task.

Large Reasoning Models (LRMs) exhibit strong performance, yet often produce rationales that sound plausible but fail to reflect their true decision process, undermining reliability and trust. We introduce a formal framework for reasoning faithfulness, defined by two testable conditions: stance consistency (a coherent stance linking reasoning to answer) and causal influence (the stated reasoning causally drives the answer under output-level interventions), explicitly decoupled from accuracy. To operationalize this, we present RFEval, a benchmark of 7,186 instances across seven tasks that probes faithfulness via controlled, output-level counterfactual interventions. Evaluating twelve open-source LRMs, we find unfaithfulness in 49.7% of outputs, predominantly from stance inconsistency. Failures are concentrated in brittle, convergent domains such as math and code, and correlate more with post-training regimes than with scale: within-family ablations indicate that adding current RL-style objectives on top of supervised fine-tuning can reduce reasoning faithfulness, even when accuracy is maintained. Crucially, accuracy is neither a sufficient nor a reliable proxy for faithfulness: once controlling for model and task, the accuracy-faithfulness link is weak and statistically insignificant. Our work establishes a rigorous methodology for auditing LRM reliability and shows that trustworthy AI requires optimizing not only for correct outcomes but also for the structural integrity of the reasoning process. Our code and dataset can be found at project page: https://aidaslab.github.io/RFEval/}{https://aidaslab.github.io/RFEval/

Recent advancements in large language model (LLM) agents have significantly accelerated scientific discovery automation, yet concurrently raised critical ethical and safety concerns. To systematically address these challenges, we introduce SafeScientist, an innovative AI scientist framework explicitly designed to enhance safety and ethical responsibility in AI-driven scientific exploration. SafeScientist proactively refuses ethically inappropriate or high-risk tasks and rigorously emphasizes safety throughout the research process. To achieve comprehensive safety oversight, we integrate multiple defensive mechanisms, including prompt monitoring, agent-collaboration monitoring, tool-use monitoring, and an ethical reviewer component. Complementing SafeScientist, we propose SciSafetyBench, a novel benchmark specifically designed to evaluate AI safety in scientific contexts, comprising 240 high-risk scientific tasks across 6 domains, alongside 30 specially designed scientific tools and 120 tool-related risk tasks. Extensive experiments demonstrate that SafeScientist significantly improves safety performance by 35\% compared to traditional AI scientist frameworks, without compromising scientific output quality. Additionally, we rigorously validate the robustness of our safety pipeline against diverse adversarial attack methods, further confirming the effectiveness of our integrated approach. The code and data will be available at https://github.com/ulab-uiuc/SafeScientist. red{Warning: this paper contains example data that may be offensive or harmful.}

The scholarly publishing ecosystem faces a dual crisis of unmanageable submission volumes and unregulated AI, creating an urgent need for new governance models to safeguard scientific integrity. The traditional human-only peer review regime lacks a scalable, objective benchmark, making editorial processes opaque and difficult to audit. Here we investigate a deterministic simulation framework that provides the first stable, evidence-based standard for evaluating AI-generated peer review reports. Analyzing 352 peer-review simulation reports, we identify consistent system state indicators that demonstrate its reliability. First, the system is able to simulate calibrated editorial judgment, with 'Revise' decisions consistently forming the majority outcome (>50%) across all disciplines, while 'Reject' rates dynamically adapt to field-specific norms, rising to 45% in Health Sciences. Second, it maintains unwavering procedural integrity, enforcing a stable 29% evidence-anchoring compliance rate that remains invariant across diverse review tasks and scientific domains. These findings demonstrate a system that is predictably rule-bound, mitigating the stochasticity of generative AI. For the scientific community, this provides a transparent tool to ensure fairness; for publishing strategists, it offers a scalable instrument for auditing workflows, managing integrity risks, and implementing evidence-based governance. The framework repositions AI as an essential component of institutional accountability, providing the critical infrastructure to maintain trust in scholarly communication.

As foundation models grow rapidly in capability and deployment, evaluating their scientific understanding becomes increasingly critical. Existing science benchmarks have made progress towards broad **Range**, wide **Reach**, and high **Rigor**, yet they often face two major challenges: **data leakage risks** that compromise benchmarking validity, and **evaluation inefficiency** due to large-scale testing. To address these issues, we introduce the **Ever-Evolving Science Exam (EESE)**, a dynamic benchmark designed to reliably assess scientific capabilities in foundation models. Our approach consists of two components: 1) a non-public **EESE-Pool** with over 100K expertly constructed science instances (question-answer pairs) across 5 disciplines and 500+ subfields, built through a multi-stage pipeline ensuring **Range**, **Reach**, and **Rigor**, 2) a periodically updated 500-instance subset **EESE**, sampled and validated to enable leakage-resilient, low-overhead evaluations. Experiments on 32 open- and closed-source models demonstrate that EESE effectively differentiates the strengths and weaknesses of models in scientific fields and cognitive dimensions. Overall, EESE provides a robust, scalable, and forward-compatible solution for science benchmark design, offering a realistic measure of how well foundation models handle science questions. The project page is at: https://github.com/aiben-ch/EESE.

We introduce SciEvalKit, a unified benchmarking toolkit designed to evaluate AI models for science across a broad range of scientific disciplines and task capabilities. Unlike general-purpose evaluation platforms, SciEvalKit focuses on the core competencies of scientific intelligence, including Scientific Multimodal Perception, Scientific Multimodal Reasoning, Scientific Multimodal Understanding, Scientific Symbolic Reasoning, Scientific Code Generation, Science Hypothesis Generation and Scientific Knowledge Understanding. It supports six major scientific domains, spanning from physics and chemistry to astronomy and materials science. SciEvalKit builds a foundation of expert-grade scientific benchmarks, curated from real-world, domain-specific datasets, ensuring that tasks reflect authentic scientific challenges. The toolkit features a flexible, extensible evaluation pipeline that enables batch evaluation across models and datasets, supports custom model and dataset integration, and provides transparent, reproducible, and comparable results. By bridging capability-based evaluation and disciplinary diversity, SciEvalKit offers a standardized yet customizable infrastructure to benchmark the next generation of scientific foundation models and intelligent agents. The toolkit is open-sourced and actively maintained to foster community-driven development and progress in AI4Science.

The adoption of Large Language Models (LLMs) in scientific writing promises efficiency but risks introducing informational entropy. While "hallucinated papers" are a known artifact, the systematic degradation of valid citation chains remains unquantified. We conducted a forensic audit of 50 recent survey papers in Artificial Intelligence (N=5,514 citations) published between September 2024 and January 2026. We utilized a hybrid verification pipeline combining DOI resolution, Crossref metadata analysis, Semantic Scholar queries, and fuzzy text matching to distinguish between formatting errors ("Sloppiness") and verifiable non-existence ("Phantoms). We detect a persistent 17.0% Phantom Rate -- citations that cannot be resolved to any digital object despite aggressive forensic recovery. Diagnostic categorization reveals three distinct failure modes: pure hallucinations (5.1%), hallucinated identifiers with valid titles (16.4%), and parsing-induced matching failures (78.5%). Longitudinal analysis reveals a flat trend (+0.07 pp/month), suggesting that high-entropy citation practices have stabilized as an endemic feature of the field. The scientific citation graph in AI survey literature exhibits "link rot" at scale. This suggests a mechanism where AI tools act as "lazy research assistants," retrieving correct titles but hallucinating metadata, thereby severing the digital chain of custody required for reproducible science.