Scientific Discovery

A musical score provides the essential instructions for its performance while containing indications - at times implicit - regarding the composer's intentions. The presence of authorial variants, and even more so complex series of revisions associated with a single text, presents a challenging path for analytical study. This research, situated within the application of Scientific Methodologies to Music Philology, proposes a methodological approach oriented toward the structural analysis of one of the many settings composed by Gioachino Rossini on the same Metastasio arietta ``Mi lagnerò tacendo''. Through Computational Analysis - incorporating parsing, data mining, and graph theory - the melodic, harmonic, and textual compositional choices have been rigorously explored. The results constitute a significant unicum in the field, laying the foundation for a systematic study that supports philological research and paves the way for the use of generative models to investigate the creative process.

Effectively configuring scalable large language model (LLM) experiments, spanning architecture design, hyperparameter tuning, and beyond, is crucial for advancing LLM research, as poor configuration choices can waste substantial computational resources and prevent models from realizing their full potential. Prior automated methods are designed for low-cost settings where repeated trial and error is feasible, but scalable LLM experiments are too expensive for such extensive iteration. To our knowledge, no work has addressed the automation of high-cost LLM experiment configurations, leaving this problem labor-intensive and dependent on expert intuition. Motivated by this gap, we propose AutoLLMResearch, an agentic framework that mimics how human researchers learn generalizable principles from low-fidelity experiments and extrapolate to efficiently identify promising configurations in expensive LLM settings. The core challenge is how to enable an agent to learn, through interaction with a multi-fidelity experimental environment that captures the structure of the LLM configuration landscape. To achieve this, we propose a systematic framework with two key components: 1) LLMConfig-Gym, a multi-fidelity environment encompassing four critical LLM experiment tasks, supported by over one million GPU hours of verifiable experiment outcomes; 2) A structured training pipeline that formulates configuration research as a long-horizon Markov Decision Process and accordingly incentivizes cross-fidelity extrapolation reasoning. Extensive evaluation against diverse strong baselines on held-out experiments demonstrates the effectiveness, generalization, and interpretability of our framework, supporting its potential as a practical and general solution for scalable real-world LLM experiment automation.

Scientific data processing often requires task-specific algorithms or AI models, creating a barrier for domain scientists who need to analyze their data but may not have extensive computing or image-processing expertise. This barrier is especially pronounced when data are noisy, have a high dynamic range, are sparsely labeled, or are only loosely specified. We introduce CVEvolve, an autonomous agentic harness with a zero-code interface for scientific data-processing algorithm discovery. CVEvolve combines a multi-round search strategy with tools for code execution, evaluation implementation, history management, holdout testing, and optional inspection of scientific data and visual outputs. The search alternates between discovery and improvement actions, and uses lineage-aware stochastic candidate sampling to balance exploration and exploitation. We demonstrate CVEvolve on X-ray fluorescence microscopy image registration, Bragg peak detection, high-energy diffraction microscopy image segmentation, and hybrid analytical-learning-based affine registration. Across these tasks, CVEvolve discovers algorithms that improve over baseline methods, while holdout test tracking helps identify candidates that generalize better than later over-optimized alternatives. These results show that zero-code, autonomous LLM-powered algorithm development can help domain scientists turn unstructured scientific image data into practical algorithms and downstream scientific discoveries.

Automated scientific discovery using large language models relies on identifying genuinely novel solutions. Standard reinforcement learning penalizes high-variance mutations, which leads the policy to prioritize familiar patterns. As a result, the maximum reward plateaus even as the average reward increases. Overcoming this limitation requires a signal that distinguishes unexplored regions from intrinsically difficult problems. This necessitates measuring disagreement across independently adapted weight hypotheses rather than relying on a single network's confidence. UG-TTT addresses this challenge by maintaining a small ensemble of low-rank adapters over a frozen base model. The per-token disagreement, quantified as the mutual information between ensemble predictions and weight hypotheses, isolates epistemic uncertainty and identifies positions where insufficient coverage leads to adapter divergence rather than intrinsic problem difficulty. This measure is incorporated as an exploration bonus into the policy gradient, directing the policy toward positions where persistent adapter disagreement signals low training coverage, the same frontier where genuine discovery is possible. A nuclear norm regularizer ensures the adapters remain distinct from one another, thereby preserving the exploration signal throughout training. Across four scientific discovery benchmarks, UG-TTT increases the maximum reward on three tasks, maintains substantially higher solution diversity, and an ablation study confirms that the regularizer is essential for sustaining this behavior.

Modern gravitational wave astronomy relies on modeling tasks that often require months of graduate-level effort, including building fast waveform surrogates from expensive numerical relativity simulations, modeling orbital dynamics of black holes, fitting merger remnant properties and constructing template banks. These problems demand extreme precision to support detection and parameter inference, with state-of-the-art models achieving $\lesssim 10^{-4}$ relative error. We study whether state-of-the-art LLM coding agents can perform such end-to-end scientific modeling, where success requires constructing models with stringent accuracy criteria and reasoning about physical systems. We introduce gwBenchmarks, a suite of eight tasks grounded in gravitational wave analytic calculations and numerical simulations collectively representing over $10^8$ core-hours of compute. The tasks span interpolation, regression, and high-dimensional time-series modeling, requiring a combination of numerical methods, machine learning, and physics-informed approaches. In preliminary experiments, agents frequently relied on proxy metrics, partial evaluation, or fabricated results to spuriously complete tasks. We therefore implement an external pre-defined framework to gauge agent progress. Evaluating twelve coding agents, we find no consistent winner. On the easiest task, multiple agents converge to the same cubic spline solution, with one rediscovering a coordinate transformation widely used in the literature. On harder tasks like analytic waveform modeling, all agents fall 1-2 orders of magnitude short of domain requirements and exhibit systematic failures, including metric misuse, constraint violations, and result fabrication. Our code, data, and website are publicly available.

Autonomous science promises to augment scientific discovery, particularly in complex fields like biomedicine. However, this requires AI systems that can consistently generate novel and diverse solutions to open-ended problems. We evaluate LLMs on the task of open-ended solution generation and quantify their tendency to mode collapse into low-diversity generations. To mitigate this mode collapse, we introduce analogical reasoning (AR) as a new approach to solution generation. AR generates analogies to cross-domain problems based on shared relational structure, then uses those analogies to search for novel solutions. Compared to baselines, AR discovers significantly more diverse generations (improving solution diversity metrics by 90-173%), generates novel solutions over 50% of the time (compared to as little as 1.6% for baselines), and produces high-quality analogies. To validate the real-world feasibility of AR, we implement AR-generated solutions across four biomedical problems, yielding consistent quantitative gains. AR-generated approaches achieve a nearly 13-fold improvement on distributional metrics for perturbation effect prediction, outperform all baselines on AUPRC when predicting cell-cell communication, infer brain region interactions with a high Spearman correlation ($ρ$=0.729) to published methods, and establish state-of-the-art performance on 2 datasets for oligonucleotide property prediction. The novel and diverse solutions produced by AR can be used to augment the search space of existing solution generation methods.

Scientific methods are developed for classes of problems, so knowledge transfers across structurally related cases. Language-model agents can execute scientific workflows, but their problem--method relationships remain implicit, so each new problem restarts the search and little of what worked transfers. We introduce GRAFT--ATHENA, which makes this problem-to-method map explicit as an expandable probabilistic structure of admissible problems, methods, and their dependencies. Graph factorization keeps the substrate tractable, and semantic fingerprints measure similarity, so experience guides related problems. As a result, the framework matched or exceeded expert baselines, attaining near-machine-precision losses in physics-informed learning, reproducing clinically consistent blood-rheology trends, and developing a high-order hypersonic-flow solver for the Apollo Command Module that matched experimental measurements within $1.8\%$. It also proposed a certified regularization for ill-posed in vivo brain-flow reconstruction, developed a spectrally convergent physics-informed architecture, and established machine-checked universal-approximation theorems for two widely used architectures. Scientific structure enables cumulative and verifiable agentic discovery.

As model families, training recipes, and compute budgets become increasingly standardized, further gains in machine learning systems depend increasingly on data. Yet data engineering remains largely manual and ad hoc: practitioners repeatedly search for external datasets, adapt them to existing pipelines, validate candidate data through downstream training, and carry forward lessons from prior attempts. We study task-conditioned autonomous data engineering, where an autonomous agent improves a fixed learning algorithm by optimizing only the data side, including external data discovery, data selection and composition, cleaning and transformation. The goal is to obtain a stronger downstream solution while leaving the learning algorithm unchanged. To address the open-ended search space, branch-dependent refinement, and delayed validation inherent in autonomous data engineering, we propose DataMaster, a data-agent framework that integrates tree-structured search, shared candidate data, and cumulative memory. DataMaster consists of three key components: a DataTree that organizes alternative data-engineering branches, a shared Data Pool that stores discovered external data sources for reuse, and a Global Memory that records node outcomes, artifacts, and reusable findings. Together, these components allow the agent to discover candidate data, construct executable training inputs, evaluate them through downstream feedback, and carry useful evidence across branches. We evaluate DataMaster on two types of benchmarks, MLE-Bench Lite and PostTrainBench. On MLE-Bench Lite, it improves medal rate by 32.27% over the initial score; on PostTrainBench, it surpasses the instruct model on GPQA (31.02% vs 30.35%).

Scientific discovery is fundamentally a resource-constrained process that requires navigating complex trade-offs between the quality and quantity of measurements due to physical and cost constraints. Measurements drive the scientific process by revealing novel phenomena to improve our understanding. Existing benchmarks for evaluating agents for scientific discovery focus on either static knowledge-based reasoning or unconstrained experimental design tasks, and do not capture the ability to make measurements and plan under constraints. To bridge this gap, we propose Measuring and Discovering Physics (MaD Physics), a benchmark to evaluate the ability of agents to make informative measurements and conclusions subject to constraints on the quality and quantity of measurements. The benchmark consists of three environments, each based on a distinct physical law. To mitigate contamination from existing knowledge, MaD Physics includes altered physical laws. In each trial, the agent makes measurements of the system until it exhausts an allotted budget and then the agent has to infer the underlying physical law to make predictions about the state of the system in the future. MaD Physics evaluates two fundamental capabilities of scientific agents: inferring models from data and planning under constraints. We also demonstrate how MaD Physics can be used to evaluate other capabilities such as multimodality and in-context learning. We benchmark agents on MaD Physics using four Gemini models (2.5 Flash Lite, 2.5 Flash, 2.5 Pro, and 3 Flash), identifying shortcomings in their structured exploration and data collection capabilities and highlighting directions to improve their scientific reasoning.

LLM-powered multi-agent systems can now automate the full research pipeline from ideation to paper writing, but a fundamental question remains: automation for whom? Researchers operate under different resource configurations, hold different methodological preferences, and target different output formats. A system that produces uniform outputs regardless of these differences will systematically under-serve every individual user, making personalization a precondition for research automation to be genuinely usable. However, achieving it requires three capabilities that current systems lack: accumulating reusable procedural knowledge across projects, retaining user-specific experience across sessions, and internalizing implicit preferences that resist explicit formalization. We propose NanoResearch, a multi-agent framework that addresses these gaps through tri-level co-evolution. A skill bank distills recurring operations into compact procedural rules reusable across projects. A memory module maintains user- and project-specific experience that grounds planning decisions in each user's research history. A label-free policy learning converts free-form feedback into persistent parameter updates of the planner, reshaping subsequent coordination. These three layers co-evolve: reliable skills produce richer memory, richer memory informs better planning, and preference internalization continuously realigns the loop to each user. Extensive experiments demonstrate that NanoResearch delivers substantial gains over state-of-the-art AI research systems, and progressively refines itself to produce better research at lower cost over successive cycles.

LLM-based foundation agents that perceive, reason, and act across thousands of reasoning steps are rapidly becoming the dominant paradigm for deploying artificial intelligence in open-ended, long-horizon complex tasks. Despite this significance, the field remains overwhelmingly engineering-driven. Engineering practice has converged on useful primitives (tool loops, memory banks, harnesses, reflection steps), yet these are assembled by empirical trial and error rather than from first principles. Fundamental questions remain open: under what conditions does a long-running agent remain on-task? How should an agent respond when its environment exceeds its representational capacity? What architectural properties are necessary for safe self-improvement? We argue that cybernetics, the mid-twentieth-century science of control and communication in complex systems, provides the missing theoretical scaffold for foundation agents. By mapping six canonical laws of classical cybernetics onto six agent design principles, and synthesizing those principles into three engineering desiderata (reliability, lifelong running, and self-Improvement), we arrive at a framework termed Agent Cybernetics. Three application domains, code generation, computer use and automated research, exemplify the analytical framework of agent cybernetics by identifying failure modes and concrete engineering recommendations. We hope that agent cybernetics opens a new research venue and establishes the scientific foundation that foundation agents need for principled, reliable real-world deployment.

Graph neural networks are increasingly adopted in trigger systems for collider experiments, where strict latency and throughput constraints render deployment on embedded platforms challenging. As detectors move towards higher granularity, the number of inputs per inference increase and FPGA-only solutions face resource bottlenecks. This work presents an end-to-end demonstrator for the real-time deployment of a dynamic Graph Neural Network for the Belle II electromagnetic calorimeter hardware trigger on the AMD Versal VCK190, leveraging both FPGA fabric and AI Engine tiles. We develop a Python-based semi-automated design flow covering operator fusion, partitioning, mapping, spatial parallelization, and kernel-level optimization. Our design achieves a throughput of 2.94 million events per second at an end-to-end latency of 7.15 microseconds. Compared to the FPGA-only baseline, this represents a 53% throughput improvement while reducing DSP utilization from 99% to 19% at 29% AI Engine tile utilization. To validate the deployment, an interactive visualization pipeline enables real-time monitoring of inference results on the physical demonstrator.

We demonstrate LLARS (LLM Assisted Research System), an open-source platform that bridges the gap between domain experts and developers for building LLM-based systems. It integrates three tightly connected modules into an end-to-end pipeline: Collaborative Prompt Engineering for real-time co-authoring with version control and instant LLM testing, Batch Generation for configurable output production across user-selected prompts $\times$ models $\times$ data with cost control, and Hybrid Evaluation where human and LLM evaluators jointly assess outputs through diverse assessment methods, with live agreement metrics and provenance analysis to identify the best model-prompt combination for a given use case. New prompts and models are automatically available for batch generation and completed batches can be turned into evaluation scenarios with a single click. Interviews with six domain experts and three developers in online counselling confirmed that LLARS feels intuitive, saves considerable time by keeping everything in one place and makes interdisciplinary collaboration seamless.

AI systems can now cheaply generate plausible scientific artifacts such as papers, reviews, and surveys. This creates a risk of \emph{epistemic pollution} in our scientific systems, where unreliable but plausible-looking artifacts can accumulate faster than the system can filter them out. The problem is structural: the epistemic infrastructure of science was calibrated to a world where producing a plausible artifact required substantial expertise, labor, and time, so generation cost itself served as a rough filter; AI weakens that filter without comparably lowering verification cost. We argue that \textbf{AI-era science should treat this as an engineering problem: redesigning epistemic infrastructure to rebalance the costs of generation and verification}. The current paper-centered system makes verification expensive: papers compress long-context scientific logic into prose, forcing reviewers, human or AI, to reconstruct underlying argument structure before they can evaluate it. As one step in this direction, we propose \textbf{blueprints} as preliminary epistemic infrastructure: structured, decomposed research artifacts that represent claims, evidence, assumptions, and definitions as typed graph components. Blueprints are designed to trade an upfront generation cost for cheaper, more local, more distributed verification downstream. We have instantiated the proposal in a proof-of-concept prototype.

A LaTeX manuscript that compiles without error is not necessarily publication-ready. The resulting PDFs frequently suffer from misplaced floats, overflowing equations, inconsistent table scaling, widow and orphan lines, and poor page balance, forcing authors into repetitive compile-inspect-edit cycles. Rule-based tools are blind to rendered visuals, operating only on source code and log files. Text-only LLMs perform open-loop text editing, unable to predict or verify the two-dimensional layout consequences of their changes. Reliable typesetting optimization therefore requires a visual closed loop with verification after every edit. We formalize this problem as Visual Typesetting Optimization (VTO), the task of transforming a compilable LaTeX paper into a visually polished, page-budget-compliant PDF through iterative visual verification and source-level revision, and introduce a five-category taxonomy of typesetting defects to guide diagnosis. We present PaperFit, a vision-in-the-loop agent that iteratively renders pages, diagnoses defects, and applies constrained repairs. To benchmark VTO, we construct PaperFit-Bench with 200 papers across 10 venue templates and 13 defect types at different difficulty. Extensive experiments show that PaperFit outperforms all baselines by a large margin, establishing that bridging the gap from compilable source to publication-ready PDF requires vision-in-the-loop optimization and that VTO constitutes a critical missing stage in the document automation pipeline.

Large language models can fail in critic interaction not only by answering incorrectly, but also by abandoning an initially correct scientific solution after user criticism. This is especially risky in scientific reasoning, where user criticism can turn a valid answer into an incorrect one. We frame critic interaction as an inter-turn correctness-transition problem rather than a final-answer accuracy problem, and identify three challenges: transition awareness, decoupling useful correction from harmful sycophancy, and scalable rollout. We propose ReCrit, a transition-aware reinforcement learning framework that decomposes Initial-to-Critic behavior into four quadrants: Correction, Sycophancy, Robustness, and Boundary. ReCrit rewards correction and robustness, penalizes sycophancy, and treats persistent errors as weak boundary signals. To make interaction training practical, ReCrit further uses dynamic asynchronous rollout with tail-adaptive completion to reduce rollout waiting. On three scientific reasoning benchmarks, ChemBench, TRQA, and EarthSE, ReCrit improves average Critic accuracy from 38.15 to 51.49 on Qwen3.5-4B and from 45.40 to 55.59 on Qwen3.5-9B. Ablations show that final-answer rewards provide little interaction-level gain, while transition-aware rewards and quadrant weighting produce more distinguishable training signals and larger net Critic-stage improvement. The code is available at https://github.com/black-yt/ReCrit .

AI scientist systems are increasingly deployed for autonomous research, yet their academic integrity has never been systematically evaluated. We introduce SCIINTEGRITY-BENCH, the first benchmark designed around a dilemmatic evaluation paradigm: each of its 33 scenarios across 11 trap categories is constructed so that honest acknowledgment of failure is the only correct response, while task completion requires misconduct. Across 231 evaluation runs spanning 7 state-of-the-art LLMs, the overall integrity problem rate reaches 34.2%, and no model achieves zero failures. Most strikingly, across missing-data scenarios, all seven models generate synthetic data rather than acknowledging infeasibility, differing only in whether they disclose the substitution. A further prompt ablation study separates two drivers: removing explicit completion pressure sharply reduces undisclosed fabrication from 20.6% to 3.2%, while the underlying synthesis rate remains unchanged, revealing an intrinsic completion bias that persists independent of prompt-level instructions. These findings point to the absence of honest refusal as a trained disposition as the primary driver of observed failures. We release SCIINTEGRITY-BENCH at https://github.com/liuxingtong/Sci-Integrity-Bench.

Current AI-powered research systems adopt a direct search-then-summarize paradigm that treats hypotheses as end products of scientific discovery. We argue this leaves a critical gap: hypotheses can serve a far more powerful role as organizational instruments that structure the research process itself. We propose the Hypothesis-Driven Deep Research (HDRI) methodology - the first framework using hypotheses to organize general-purpose deep research across arbitrary domains, rather than merely validating claims within specific domains. This transforms research from reactive information retrieval into proactive, verifiable, and iterative knowledge discovery. HDRI is formalized with six core principles and an eight-stage pipeline. A central innovation is the gap-driven iterative research mechanism - a closed-loop quality assurance system that automatically identifies informational and logical gaps, triggering targeted supplementary investigation. We further introduce a fact reasoning framework with traceable reasoning chains and quantified confidence propagation, a subject locking mechanism to prevent entity confusion, and a multi-dimensional quality assessment scheme. The methodology is realized in the INFOMINER system. Experiments demonstrate improvements of 22.4% in fact density, 90% subject matching accuracy, 0.92 multi-source verification confidence, and 14% completeness gain from gap-driven supplementation. Five case studies validate its practical applicability, achieving an average quality rating of 4.46/5.0.

Scientific reasoning is a key aspect of human intelligence, requiring the integration of multimodal inputs, domain expertise, and multi-step inference across various subjects. Existing benchmarks for multimodal large language models (MLLMs) often fail to capture the complexity and traceability of reasoning processes necessary for rigorous evaluation. To fill this gap, we introduce SciVQR, a multimodal benchmark covering 54 subfields in mathematics, physics, chemistry, geography, astronomy, and biology. SciVQR includes domain-specific visuals, such as equations, charts, and diagrams, and challenges models to combine visual comprehension with reasoning. The tasks range from basic factual recall to complex, multi-step inferences, with 46% including expert-authored solutions. SciVQR not only evaluates final answers but also examines the reasoning process, providing insights into how models reach their conclusions. Our evaluation of leading MLLMs, including both proprietary and open-source models, reveals significant limitations in handling complex multimodal reasoning tasks, underscoring the need for improved multi-step reasoning and better integration of interdisciplinary knowledge in advancing MLLMs toward true scientific intelligence. The dataset and evaluation code are publicly available at https://github.com/CASIA-IVA-Lab/SciVQR.

Artificial intelligence (AI) tools are being incorporated into scientific research workflows with the potential to enhance efficiency in tasks such as document analysis, question answering (Q&A), and literature search. However, system outputs are often difficult to verify, lack transparency in their generation and remain prone to errors. Suitable benchmarks are needed to document and evaluate arising issues. Nevertheless, existing benchmarking approaches are not adequately capturing human-centered criteria such as usability, interpretability, and integration into research workflows. To address this gap, the present work proposes and applies a benchmarking framework combining human-centered and computer-centered metrics to evaluate AI-based Q&A and literature review tools for research use. The findings suggest that Q&A tools can offer valuable overviews and generally accurate summaries; however, they are not always reliable for precise information extraction. Explainable AI (xAI) accuracy was particularly low, meaning highlighted source passages frequently failed to correspond to generated answers. This shifted the burden of validation back onto the researcher. Literature review tools supported exploratory searches but showed low reproducibility, limited transparency regarding chosen sources and databases, and inconsistent source quality, making them unsuitable for systematic reviews. A comparison of these tool groups reveals a similar pattern: while AI tools can enhance efficiency in the early stages of the research workflow and shallow tasks, their outputs still require human verification. The findings underscore the importance of explainability features to enhance transparency, verification efficiency and careful integration of AI tools into researchers' workflows. Further, human-centered evaluation remains an important concern to ensure practical applicability.

The implicit policy of maintaining relatively stable acceptance rates at top AI conferences, despite exponentially growing submissions, introduces a critical structural vulnerability. This position paper characterizes a new systemic threat we term Agentic Denominator Gaming, in which a malicious actor deploys AI agents to generate and submit a large volume of superficially plausible but low-quality papers. Crucially, their objective is not the acceptance of low-quality papers, but rather to inflate the submission denominator and overwhelm reviewing capacity. Under a relatively stable acceptance rate, this dilution can systematically increase the publication probability of a small, targeted set of legitimate papers. We analyze the practical feasibility of this threat and its broader consequences, including intensified reviewer burnout, degraded review quality, and the emergence of industrialized automated agent mills. Finally, we propose and evaluate a range of mitigation strategies, and argue that durable protection will require system-level policy and incentive reforms, rather than relying primarily on technical detection alone.

AI is transforming life sciences research at unprecedented speed, accelerating discovery across protein structure prediction, genome modeling, and drug development (Jumper et al., 2021; Mak et al., 2024). Yet this rapid advancement, coupled with the open science movement, introduces significant dual-use research concerns that have received limited empirical scrutiny. Here we present the first systematic analysis of dual-use research of concern (DURC) content on open preprint servers. We screened ~52,000 bioRxiv preprints (2024-2025) using a hybrid pipeline of lexical filtering and large language model (LLM) evaluation, scoring metadata across nine DURC, three PEPP, and five governance categories aligned with U.S. and Australia Group oversight frameworks. Our analysis reveals that dual-use-adjacent knowledge is routinely present in openly accessible titles and abstracts, often exceeding established risk thresholds even in studies with legitimate public health objectives. While this mapping captures surface-level information diffusion, it does not measure operational capability, downstream misuse potential, or the substantial technical and biosafety barriers that constrain harmful application. We argue that institutional review processes, funding requirements, and preprint platform policies must evolve to incorporate proactive, metadata-level monitoring without compromising scientific transparency. Ultimately, harmonizing controlled-access mechanisms for high-risk methodologies with open summaries of scientific contributions offers a pragmatic framework for governing AI-accelerated biology at scale.

A growing body of work pursues AI scientists capable of end-to-end autonomous scientific discovery. This position paper argues that although they already function as co-scientists, agentic AI scientists are not built for autonomous scientific discovery. We identify the following challenges in building and deploying autonomous AI scientists: (1) Problem selection is influenced by the McNamara fallacy; (2) Agents are built on large language models (LLMs) whose training corpora omit tacit procedural and failure knowledge of laboratory practice; (3) Preference optimisation during post-training compresses output diversity toward consensus; and (4) Most scientific benchmarks measure single-turn prediction accuracy and lack feedback from physical experiments back to the computational model. These challenges are not just questions of scale and scaffolding; they require revisiting fundamental design choices. To build truly autonomous AI scientists, we recommend the use of scientific simulations as verifiers for training, the design of persistent world models that represent the shifting objectives governing real investigations, the establishment of a centralized preregistration repository for all AI-generated hypotheses, and application driven by scientific need rather than tool affordance.

The promise of AI-driven scientific discovery hinges on whether AI agents can autonomously design and execute the computational workflows that underpin modern science. Molecular dynamics (MD) simulation presents a natural test bed to stress-test this claim; it requires translating physical intuition into syntactically and semantically correct input scripts, reasoning about initial and boundary conditions, diagnosing numerically unstable trajectories, and interpreting outputs against known physical behavior and laws. We introduce MDGYM, a benchmark of 169 expert-curated MD simulations spanning LAMMPS and GROMACS, two widely used MD packages, across three increasing difficulty levels. We evaluate three agentic frameworks -- Claude Code, Codex, and OpenHands -- with four LLMs, and find that all perform poorly: even the strongest agent solves only 21% of easy-level tasks, with less than 10% at higher difficulties. Trajectory analysis reveals a characteristic pattern of failure -- agents successfully invoke simulation machinery but produce physically unstable configurations, fabricate numerical outputs without executing the underlying computation, or abandon tasks prematurely rather than iterating through simulation-specific errors. These failure modes are qualitatively distinct from those observed in general software engineering benchmarks, indicating that fluent code generation does not transfer to grounded physical reasoning.

The increasing complexity of modern computational environments often burdens researchers with infrastructure management, authentication protocols, and container deployments. We present Sci-Orchestra, a layered orchestration framework designed to fully automate experimental workflows, allowing scientists to prioritize scientific discovery over backend operations. By abstracting execution through an API-driven interface, the system assumes responsibility for secure authentication, resource management, and scalable deployment across diverse high-performance computing environments using Kubernetes architectures. A key innovation of Sci-Orchestra is its autonomous marketplace, which serves as a catalyst for cross-institutional collaboration. Through an intuitive user interface, researchers can rapidly deploy and share specialized services via simple selections, eliminating the need for complex installations and technical setups. This modular infrastructure is specifically designed to facilitate industry partnerships as it provides a secure execution environment and allows external collaborators to test and validate proprietary tools without the need for source-code exchange. This ``black-box'' interoperability protects intellectual property while enabling seamless integration into broader scientific pipelines, ultimately accelerating the transition from laboratory prototypes to industrial-scale applications.

Balancing exploration and exploitation is a core challenge in sequential decision-making and black-box optimization. We introduce POETS ($\textbf{Po}$licy $\textbf{E}$nsembles for $\textbf{T}$hompson $\textbf{S}$ampling), a novel framework that bridges uncertainty quantification and policy optimization. Our approach is grounded in the insight that policies trained with Kullback-Leibler (KL) regularization implicitly encode an underlying reward function. Building on this, POETS bypasses the complex, nested process of training an uncertainty-aware reward model and separately fitting a policy to this model. Instead, we directly train a policy ensemble to capture epistemic uncertainty by matching implicitly encoded reward functions to online, bootstrapped data. To overcome the prohibitive compute and memory constraints of ensembling Large Language Models (LLMs), POETS utilizes an efficient architecture: the ensemble shares a pre-trained backbone while maintaining diversity through independent Low-Rank Adaptation (LoRA) branches. Theoretically, we prove that POETS implicitly conducts KL-regularized Thompson sampling and thus inherits strong cumulative regret bounds of ${\mathcal O}(\sqrt{T γ_T})$. Empirically, we demonstrate that POETS achieves state-of-the-art sample efficiency across diverse scientific discovery domains, including protein search and quantum circuit design. Furthermore, it improves the optimization trajectories of reinforcement learning, proving particularly robust in off-policy settings with experience replay or in small dataset regimes.

Large language models (LLMs) are known to generate plausible but false information across a wide range of contexts, yet the real-world magnitude and consequences of this hallucination problem remain poorly understood. Here we leverage a uniquely verifiable object - scientific citations - to audit 111 million references across 2.5 million papers in arXiv, bioRxiv, SSRN, and PubMed Central. We find a sharp rise in non-existent references following widespread LLM adoption, with a conservative estimate of 146,932 hallucinated citations in 2025 alone. These errors are diffusely embedded across many papers but especially pronounced in fields with rapid AI uptake, in manuscripts with linguistic signatures of AI-assisted writing, and among small and early-career author teams. At the same time, hallucinated references disproportionately assign credit to already prominent and male scholars, suggesting that LLM-generated errors may reinforce existing inequities in scientific recognition. Preprint moderation and journal publication processes capture only a fraction of these errors, suggesting that the spread of hallucinated content has outpaced existing safeguards. Together, these findings demonstrate that LLM hallucinations are infiltrating knowledge production at scale, threatening both the reliability and equity of future scientific discovery as human and AI systems draw on the existing literature.

When applying Bayesian optimization (BO) to scientific workflow, a major yet often overlooked source of uncertainty is the task itself -- namely, what to optimize and how to evaluate it -- which can evolve as evidence accumulates. We introduce Generate-Select-Refine (GSR), a open-ended BO framework that alternates between task generation and task optimization. Starting from a user-provided seed task, GSR generates new tasks in a coarse-to-fine manner while a task-acquisition function schedules optimization. Asymptotically, it concentrates evaluations on the best task, incurring only logarithmic regret overhead relative to single-task BO. We apply GSR to new product development, chemical synthesis scaling, algorithm analysis, and patent repurposing, where it outperforms existing LLM-based optimizers.

Virtual Cell Modeling (VCM) requires models that not only predict perturbation responses, but also support targeted revision when predictions fail. Current LLM-assisted modeling workflows face a refinement-routing problem: prediction discrepancies are observed through executable implementations, but the relevant revision may involve the modeling assumption, representation design, implementation, or task constraint. Without structured feedback propagation across these levels, iterative refinement may repair code while failing to revise the assumption responsible for the discrepancy. We propose CellScientist, a dual-space hierarchical framework that couples a high-level hypothesis space with a low-level executable implementation space. CellScientist represents modeling decisions as structured states, realizes them as admissible programs under task and interface constraints, and routes execution discrepancies back to targeted hypothesis or implementation updates. This enables a closed Hypothesis -> Implementation -> Hypothesis loop where failures become structured signals for model refinement rather than debugging events. Across morphology and transcriptomic benchmarks, with additional single-cell perturbation evaluations, the final executable models selected by CellScientist improve over reference baselines under fixed split and evaluation protocols, while the workflow produces auditable refinement traces.

Autonomous research agents can already run machine learning experiments without human supervision, but many rely on a narrow search strategy: they repeatedly modify one program and keep changes only when they improve the current best result. This can cause them to discard useful partial ideas, alternative promising directions, and insights from failed or incomplete experiments. GEAR, or Genetic AutoResearch, replaces this single-path search with a population-based search over multiple research states. It keeps a set of strong candidate solutions, selects parents based on productivity, novelty, and coverage, and explores new ideas through mutation and crossover. Each research state stores its code changes, reflections, and performance data, allowing future decisions to build on past discoveries. The paper studies three versions of GEAR: one controlled through prompting, one using a fixed programmatic search controller, and one where the controller itself can evolve during the run. Under the same compute budget and environment, all three versions outperform the AutoResearch baseline. More importantly, while the baseline tends to settle into one local optimum, GEAR continues finding improvements over longer runs. Overall, the results suggest that autonomous research agents become more effective when they maintain multiple promising directions and can adapt their search strategy over time.

Large Language Models (LLMs) have shown good performance on various science educational benchmarks, demonstrating their potential for use in science and mathematics education. Yet, LLMs tend to be evaluated on science and mathematical educational datasets from the Western world, with an underrepresentation of datasets from the Global South. Furthermore, they tend to have multiple-choice answer options that are trivial to evaluate. In this work, we present NSMQ Riddles, a novel benchmark of Scientific and Mathematical Riddles from Ghana's National Science and Maths Quiz (NSMQ) competition to evaluate LLMs. The NSMQ is an annual live TV competition for senior secondary school students in Ghana that brings together the smartest high school students in Ghana who compete in teams of 2 by answering questions in biology, chemistry, physics, and math over five rounds and five stages until a winning team is crowned for that year. NSMQ Riddles consists of 11 years of riddle questions (n=1.8K) from the 5th round, with each riddle containing a minimum of 3 clues. Students compete to be the first to guess the answer on any of the clues, with earlier clues being vague and also fetching more points. The answers are usually a number, word, or short phrase, allowing for automatic evaluation. We evaluated state-of-the-art models: closed (GPT-5.4, Gemini 3.1 Pro, Claude Opus 4.6) and open models (Kimi-K2.5, DeepSeek-V3.1, GPT-OSS-120B) with high and low reasoning settings. Our evaluation shows that the dataset is challenging even for state-of-the-art LLMs, which performed worse than the best student contestants. This work contributes a novel and challenging benchmark for scientific and mathematical reasoning from the Global South towards enabling a true global benchmarking of LLMs' capabilities for science and mathematics education.

Autonomous experimentation has transformed microscopy and materials discovery by enabling closed-loop optimization including imaging and spectroscopy tuning, strucutre property relationship discovery, and exploration of combinatorial libraries. However, most current workflows remain limited to selecting measurements within fixed objective or hypothesis spaces, rather than generating new physical models from experimental data. Here, we introduce an open hypothesis-learning framework that combines symbolic regression with large-language-model-based physical evaluation and implement it for autonomous scanning probe microscopy. Symbolic regression generates candidate analytical relationships directly from sparse measurements, while the language-model evaluator ranks these candidates according to physical plausibility, scaling behavior, and consistency with known mechanisms. We demonstrate the approach on autonomous piezoresponse force microscopy measurements of ferroelectric domain switching in a PZT thin film. Starting from five seed measurements, the workflow evolves from physically incomplete candidate expressions toward interpretable voltage-time growth laws consistent with kinetic domain-wall motion. This work extends autonomous microscopy from closed-loop optimization toward open hypothesis discovery, where candidate physical laws emerge from the experiment itself rather than being specified in advance. More broadly, the framework establishes a route for integrating symbolic regression, physical reasoning, and adaptive experimentation into hierarchical autonomous scientific workflows.

As large language models (LLMs) show increasing promise on research-level physics reasoning tasks and agentic AI becomes more common, a practical question emerges: How does the interaction between researchers and agents affect the results? We study this using SCALAR (Structured Critic--Actor Loop for AI Reasoning), an Actor--Critic--Judge pipeline applied to quantum field theory and string theory problems. The Actor proposes solutions, the Critic provides iterative feedback, and an independent Judge evaluates the transcript against reference solutions. We vary the Actor persona, the Critic feedback strategy, and the Actor model family and scale. Multi-turn dialogue improves over single-shot attempts throughout, but both the mechanism of improvement and the value of different prompting choices depend strongly on the Actor--Critic pairing. Increasing the scale within one model family (e.g. from the 8B-parameter DeepSeek-R1 variant to DeepSeek-R1 70B) improves some easier-problem behavior, but does not remove the hardest bottleneck we observe. Critic feedback strategy matters most clearly in the asymmetric Actor--Critic setting (e.g., a lightweight Haiku Actor guided by a stronger Sonnet Critic), where constructive feedback improves mean-score outcomes. In same-family Actor--Critic settings, strategy effects are weaker: lenient feedback is sometimes favored, while strict and adversarial feedback are not beneficial. Taken together, SCALAR provides a controlled testbed for evaluating which interaction structures help or hinder AI-driven scientific discovery.

Recent LLM-based agents have closed substantial portions of the scientific discovery loop in software-only machine-learning research, in chemistry, and in biology. Extending the same loop to high-fidelity physical simulators is harder, because solver completion does not imply physical validity and many failure modes appear only in field-level imagery rather than in solver logs. We present AI CFD Scientist, an open-source AI scientist for computational fluid dynamics (CFD) that, to our knowledge, is the first to span literature-grounded ideation, validated execution, vision-based physics verification, source-code modification, and figure-grounded writing within a single inspectable workflow. Three coupled pathways cover parameter sweeps within a fixed solver, case-local C++ library compilation for new physical models, and open-ended hypothesis search against a reference comparator, all running on OpenFOAM through Foam-Agent. At the center of the framework is a vision-language physics-verification gate that inspects rendered flow fields before any result is accepted, rerun, or written into a manuscript. On five tasks under a shared GPT-5.5 backbone, AI CFD Scientist autonomously discovers a Spalart-Allmaras runtime correction that reduces lower-wall Cf RMSE against DNS by 7.89% on the periodic hill at Reh=5600; under matched LLM cost, two strong general AI-scientist baselines (ARIS, DeepScientist) execute partial CFD workflows but lack the domain-specific validity gates needed to convert runs into defensible scientific claims; and a controlled planted-failure ablation shows that the vision-language gate detects 14 of 16 silent failures missed by solver-level checks. Code, prompts, and run artifacts are released at https://github.com/csml-rpi/cfd-scientist.

In many scientific domains, including experimentation, researchers rely on measurements of proxy outcomes to achieve faster and more frequent reads, especially when the primary outcome of interest is challenging to measure directly. While proxies offer a more readily accessible observation for inference, the ultimate goal is to draw statistical inferences about the primary outcome parameter and proxy data are typically imperfect in some ways. To correct for these imperfections, current statistical inference methods often depend on strict identifying assumptions (such as surrogacy, covariate/label shift, or missingness assumptions). These assumptions can be difficult to validate and may be violated by various additional sources of distribution shift, potentially leading to biased parameter estimates and miscalibrated uncertainty quantification. We introduce an estimate-level framework, inspired by domain adaptation techniques, to empirically calibrate proxy-based inference. This framework models the proxy-primary metric discrepancy as a random effect at the parameter level, estimating its distribution from aggregated historical observations across past domains (e.g., experiments, time periods, or distinct segments). This method avoids the requirement for retaining individual-level response data. Additionally, this adjustment can be layered on top of existing proxy-correction methods (such as prediction-powered inference or importance weighting) to account for additional biases not addressed by those corrections. To manage uncertainty when the number of historical domains is limited, we provide both a method-of-moments estimator and a domain bootstrap procedure. We further validate this approach using publicly available datasets and real-world experiments.

AI research agents have shown strong potential in automating literature search and manuscript refinement, yet most assume a clear and actionable initial input, operating only after a research question has been made explicit. In contrast, human research often begins with tacit friction, a sense of misalignment before a question can be formed. We introduce InciteResearch, a multi-agent framework designed to make a researcher's implicit understanding explicit, inspectable, and actionable. InciteResearch decomposes the logical chain of Socratic questioning and distributes it across the entire pipeline that: (1) Elicits a structured five-dimensional researcher profile state anchored by specific friction points from vague, even domain-unrelated inputs; (2) Violates hidden assumptions by maximizing the feasibility-novelty product with enforcing a 7-stage causal derivation trace; and (3) check whether the proposed method is a Necessary consequence of the reframed insight. We further introduce TF-Bench, the first benchmark for tacit-to-explicit research assistance that distinguishes domain-related from domain-unrelated inspirations across four scientific modes. On TF-Bench, InciteResearch achieves leapfrogging gains over a prompt-based baseline (novelty/impact from 3.671/3.806 to 4.250/4.397), shifting generated proposals from recombination to architectural insight. Our work demonstrates that AI can serve as an extension of thinking itself, rather than merely automating downstream execution.

The extent to which Artificial Intelligence (AI) technologies can trigger generalized paradigm shifts in science is unclear. Although these technologies have revolutionized data collection and analysis in specific fields, their overall impact depends on the scope and ways of adoption. We analyze over 227 million scholarly works from the OpenAlex collection (1960-2024) spanning four scientific domains and 46 fields. To distinguish the use of AI as research method (AI adoption) from mentioning AI-related terms (AI engagement), we developed a two-step AI-assisted semantic classification pipeline, validated through human coding of 911 abstracts and a robustness check on 348,000 full-text articles (PLOS One). We document differences in the timing and extent of AI adoption across domains, with generalized exponential growth after 2015. The transformative nature of this growth, however, is less apparent. AI-supported research is confined to a few topics with strong ties to Computer Science and conventional statistical frameworks, suggesting limited epistemological transformation. It is also associated with an unwarranted citation premium and substantially higher retraction rates than non-AI-supported. Geographically, while wealthy countries lead in AI publications per capita, global South countries in a belt from Indonesia to Algeria lead in AI adoption relative to their national output, signaling a distinctive resource concentration pattern. The transformative capacity of AI in science thus remains untapped, and its rapid adoption underlines challenges in research openness, transparency, reproducibility, and ethics. We discuss how best research practices could boost the benefits of AI adoption and highlight areas that warrant closer scrutiny.

Systematic reviews and meta-analyses frequently require numerical data that authors report only as figures, yet manual digitisation is slow and does not scale. We present PlotPick, an open-source tool that uses vision-language models (VLMs) to batch-extract structured tabular data from scientific figures. We evaluate six VLMs from three providers on two established chart-to-table benchmarks (ChartX and PlotQA) and compare against the dedicated chart-to-table model DePlot. All six VLMs outperform DePlot on both benchmarks. On ChartX (restricted to bar charts, line charts, box plots, and histograms; n=300), VLMs achieve 88-96% recall versus 71% for DePlot. On PlotQA (n=529), VLMs achieve 86-99% RMSF1 versus 94% for DePlot. The gap is largest on chart types absent from the dedicated models' training data: on box plots, DePlot achieves 24% RMSF1 while VLMs achieve 83-97%. PlotPick is available at https://plotpick.streamlit.app.

Artificial intelligence offers powerful new tools for scientific discovery, but the interaction paradigms required to effectively harness these systems remain underexplored. In this paper, we present findings from a formative user study with 11 expert mathematicians who used AlphaEvolve, an evolutionary coding agent, to tackle advanced problems in their fields of expertise. We identify and characterize a distinct workflow we term intentmaking, the iterative process of discovering, defining, and refining one's experimental goals through active system interaction. We frame this as a natural extension to sensemaking, the cognitive process of building an understanding of complex or novel data. We suggest that users enter a cycle of intentmaking (defining and updating their experiment) and sensemaking (interpreting the results) which repeats many times during the course of an investigation. Our documentation of these themes suggests an approach to designing AI tools for scientific discovery that goes beyond the existing question/answer model of many current systems, treating them as collaborative instruments rather than opaque black-box assistants.

The communication of scientific knowledge has become increasingly multimodal, spanning text, visuals, and speech through materials such as research papers, slides, and recorded presentations. These different representations collectively convey a study's reasoning, results, and insights, offering complementary perspectives that enrich understanding. However, despite their shared purpose, such materials are rarely connected in a structured way. The absence of explicit links across formats makes it difficult to trace how concepts, visuals, and explanations correspond, limiting unified exploration and analysis of research content. To address this gap, we introduce the Multimodal Conference Dataset (MCD), the first benchmark that integrates research papers, presentation videos, explanatory videos, and slides from the same works. We evaluate a range of embedding-based and vision-language models to assess their ability to discover fine-grained cross-format correspondences, establishing the first systematic benchmark for this task. Our results show that vision-language models are robust but struggle with fine-grained alignment, while embedding-based models capture text-visual correspondences well but equations and symbolic content form distinct clusters in the embedding space. These findings highlight both the strengths and limitations of current approaches and point to key directions for future research in multimodal scientific understanding. To ensure reproducibility, we release the resources for MCD at https://github.com/meghamariamkm2002/MCD

We study auto research as a closed empirical loop driven by external measurement. Each submitted trial carries a hypothesis, an executable code edit, an evaluator-owned outcome, and feedback that shapes the next proposal. The output is not a generated paper or a single model checkpoint, but an auditable trajectory of proposals, code diffs, experiments, scores, and failure labels. We instantiate this loop with specialist agents that partition recipe surfaces and share measured lineage across trials. The central empirical finding is that lineage feedback lets agents turn evaluator outcomes, including crashes, budget overruns, size failures, and accuracy-gate misses, into later program-level recipe edits rather than one-shot suggestions. Across 1,197 headline-run trials plus 600 Parameter Golf control trials after one-time setup and launch, humans did not choose proposals, edit recipes, override scores, or repair failed trials during the search. In the three headline runs, the same submitted-trial loop reduces Parameter Golf validation bpb by $0.81\%$, raises NanoChat-D12 CORE by $38.7\%$, and reduces CIFAR-10 Airbench96 wallclock by $4.59\%$, with each task measured by its own external evaluator and legality checks. The trace includes a strict architecture-domain audit of 157 headline-run submissions and program rewrites such as a NanoChat attention-kernel path change. Within this scope the loop autonomously writes code, submits experiments, absorbs feedback, applies and combines known techniques inside each environment, and improves public starting recipes.

This paper reflects on a AI research project carried out by a team of high-school and early-undergraduate students under the mentorship of graduate researchers and ably assisted by AI tools. We share our experience in not only on the learning experience for the high school students, but also on how AI tools accelerated the process that enabled the high school students to focus on higher order problem formulation and solution. Although the participants entered the project with limited background in both AI and finance, they showed strong enthusiasm for technical market analysis and ETF price prediction. Traditional learning settings would first teach the necessary methods in a classroom setting and only later let students apply them. In contrast, our project emphasized workflow design: students identified the sequence of steps needed to address the problem and then used AI-driven tools to execute each step. We note that the high school students developed the necessary code through iterating with the AI tools, and we used our daily stand-ups to debug and answer conceptual questions. Each of the student was able to dig deeper into their area of interest whether computer science or finance, while collaboratively making a significant advance over the summer of 2025. This project was an important pedagogical exercise on how AI tools can be used for mentoring high school students, allowing them to focus on their specific interests and using the daily stand-ups to focus on problem definition and conceptual understanding. Despite their limited technical qualifications, the students were able to leverage AI tools to build meaningful models with real-world application.

Students at all levels of higher education face a significant barrier in the form of information overload, which often paralyzes the initial stages of the research process and suppresses motivation. In response, this article introduces a pedagogical framework that leverages AI SciBrief, a platform powered by a Large Language Model (LLM) designed to automatically generate digests of scientific trends. We describe how this multidisciplinary tool - with initial coverage in finance, medicine, and education - can be integrated into the curriculum to overcome this "entry barrier." The framework provides concrete methodologies for utilizing these digests to facilitate topic selection for term papers, accelerate literature reviews for dissertations, and enable postgraduate students to continuously monitor emerging trends. We conclude that AI SciBrief functions as a "gateway to research" effectively reducing students' cognitive load and empowering them to transition more rapidly from information searching to knowledge creation.

Plant breeding underpins global food security through incremental, accumulating improvements in crop yield, quality and sustainability, achieved via repeated cycles of crop ranking, selection and crossing. Climate change disrupts this process by altering local growing conditions, thereby shifting the relative performance of crop genotypes. Predicting these relative changes in yield is critical for food security. Yet, this problem remains an open challenge in plant breeding, and relatively unexplored within the AI community. We propose MixINN, an approach that first isolates high-quality genotype-environment interaction labels using mixed models, and then predicts these interactions for new crop varieties in future environmental conditions with a deep neural network. We evaluate our method on a corn multi-environment trial across the continental United States and show improved prediction of genotype ranking over current plant breeding methods. MixINN demonstrated superior performance in identifying the 20% most productive corn genotypes, leading to a 5.8% higher average yield, which further improved to 7.2% when targeting specific growing environments. These are competitive results for real-world breeding programs, demonstrating the potential of AI research in accelerating the development of climate-adapted crops, and improving future food security under climate change.

To unleash the full potential of AI for Science, we must untether the agents from a purely digital environment. The agent's ability to control and explore in real-world labs is essential because the physical lab remains foundational to scientific discovery. While some tasks can be performed on a computer (e.g., data analysis, running simulated experiments), Eureka moments could occur at any time while operating lab instruments (e.g., when a scientist notices unexpected clues, intuition may prompt a real-time course change). Although autonomous labs are on the rise, which expose programmable APIs to control scientific instruments via software, bridging the gap between increasingly powerful AI agents and automated lab equipment requires innovation that draws insights from computer systems. We propose a new paradigm called ``Experiment-as-Code (EaC) Labs,'' where a core concept is to encode experiments as declarative configurations that can be compiled down to device-level APIs. AI agents come up with hypotheses and experiments, written as an ensemble of declarative configurations. The systems layer performs program analysis, safety checks, resource assignment, and job orchestration. Finally, programmatic experimentation occurs via actuating the device APIs. This is a general stack that is science-, lab-, and instrument-independent, representing a novel synthesis across the physical, systems, and intelligence layers to unleash the next breakthrough in AI for Science.

Materials science workflows rely on structured and unstructured data from the vast body of available scientific literature. However, most of the experimental details remain buried in text, tables, graphs and figures. Thus, constructing databases that incorporate this data is a manual, time-consuming, and hard-to-scale process. Multimodal large language models have made it feasible to extract information from text and scientific figures with high speed and accuracy. This opens the possibility of an AI system that can create production-scale material databases. Material Database Agent (MDA) is a modular, multi-agent system architecture for converting research literature into structured databases. MDA accepts article PDFs as input, which are subsequently processed in parallel into markdown files and figures. Multiple sub-agents read these markdown files and figures in parallel to assemble sub-databases for each paper. These sub-databases are then compiled into a single tabular database by an agent. As opposed to using either a rule-based approach or a single-pass pipeline for extracting information, MDA is a specialized architecture for transforming the literature into a database in the field of materials science. More generally, this study provides a basis for positioning multimodal agentic information extraction as a viable means for constructing next-generation scientific databases from the primary literature.

Mirroring its ubiquity in popular media and all human activities, the use of deep learning (DL) is rapidly growing in scientific imaging modalities. However, unlike everyday RGB pictures, pixels encode precise physicochemical properties in scientific imaging across potentially thousands of channels. While DL is well validated on human-centric RGB perceptual tasks, its effectiveness for scientific imaging remains uncertain. Here, we show that the naive application of DL frameworks to scientific images can lead to critical failures. We evaluate the use of DL for pathology, comparing RGB images of stained tissue with the quantitative and information-rich biochemical signatures of infrared (IR) imaging. Despite this informational advantage, DL models trained on IR data paradoxically underperform. We investigate this discrepancy to find that IR data priors interact poorly with the simplicity bias of DL, causing models to collapse to one-dimensional predictions. This constitutes a catastrophic DL failure because the model's representational capacity remains largely unused, while furthermore raising AI safety concerns and undermining the advantages of such scientific modalities. Notably, this problem persists even with state-of-the-art DL robustification strategies, which are primarily designed and validated for RGB imagery and thus inherit the same prior-bias mismatch. This work establishes a framework for understanding the limitations of generic DL in science and advocates for the study of modality-specific failure modes to guide the development of specialized, safe AI algorithms.

Agentic data science (ADS) systems are rapidly improving their capability to autonomously analyze, fit, and interpret data, potentially moving towards a future where agents conduct the vast majority of data-science work. However, current ADS systems use statistical tools designed to be interpretable by humans, rather than interpretable by agents. To address this, we introduce Agentic-imodels, an agentic autoresearch loop that evolves data-science tools designed to be interpretable by agents. Specifically, it develops a library of scikit-learn-compatible regressors for tabular data that are optimized for both predictive performance and a novel LLM-based interpretability metric. The metric measures a suite of LLM-graded tests that probe whether a fitted model's string representation is "simulatable" by an LLM, i.e. whether the LLM can answer questions about the model's behavior by reading its string output alone. We find that the evolved models jointly improve predictive performance and agent-facing interpretability, generalizing to new datasets and new interpretability tests. Furthermore, these evolved models improve downstream end-to-end ADS, increasing performance for Copilot CLI, Claude Code, and Codex on the BLADE benchmark by up to 73%

This paper analyzes the strategic education process aimed at transitioning traditional software development squads into hybrid structures centered on collaborative work between humans and Artificial Intelligence (AI). In a context where human-AI collaboration can significantly increase productivity, this study explores how the upskilling of XPTO professionals, referred to as AI Advocates, acts as a catalyst for cultural and technical transformation. The objective is to present an experience report on the education and enablement process of AI Advocates within a private Brazilian technology company, highlighting key lessons learned and identified challenges.

We present AdaGraph, a graph-native clustering algorithm born from the Structure-Centric Machine Learning (SC-ML) paradigm -- a new field of unsupervised learning that replaces geometry-centric (distance-based) computation with structure-centric (topology-based) computation, fundamentally dissolving the curse of dimensionality. AdaGraph operates entirely within the kNN graph topology, a representation that retains meaningful relational structure in arbitrarily high dimensions where Euclidean distance metrics become uninformative. AdaGraph requires no a priori specification of the number of clusters k, handles noise natively, and scales via the SLCD (Sample-Learn-Calibrate-Deploy) prototype-deployment framework. As its unsupervised tuning objective, AdaGraph pairs with Graph-SCOPE, the topology-based cluster validity index introduced as a separate SC-ML contribution. On 10 synthetic benchmarks spanning d=10 to d=5000, Graph-SCOPE achieves mean ARI=0.900 and correctly selects k on 9/10 datasets -- outperforming Silhouette, Davies-Bouldin, and Calinski-Harabasz -- while maintaining Kendall tau >= 0.92 with ground-truth cluster quality across all dimensionalities (Silhouette: tau ~= 0.46). We validate AdaGraph across three scientific domains: (1) gene co-expression discovery in hepatocellular carcinoma (GSE14520, 10,000 genes, 488 patients, no dimensionality reduction), where AdaGraph identifies condition-specific gene modules that WGCNA, ICA, NMF, and Spectral Biclustering fail to resolve; (2) natural language text clustering, where AdaGraph achieves ARI=0.751 on 20NG-6cat versus HDBSCAN's 0.464 (62% relative improvement); (3) materials science clustering of superconductors (145-dimensional Magpie features), perovskites, and JARVIS-DFT materials, where AdaGraph achieves the highest Graph-SCOPE on all three datasets.

This report describes ARIS (Auto-Research-in-sleep), an open-source research harness for autonomous research, including its architecture, assurance mechanisms, and early deployment experience. The performance of agent systems built on LLMs depends on both the model weights and the harness around them, which governs what information to store, retrieve, and present to the model. For long-horizon research workflows, the central failure mode is not a visible breakdown but a plausible unsupported success: a long-running agent can produce claims whose evidential support is incomplete, misreported, or silently inherited from the executor's framing. Therefore, we present ARIS as a research harness that coordinates machine-learning research workflows through cross-model adversarial collaboration as a default configuration: an executor model drives forward progress while a reviewer from a different model family is recommended to critique intermediate artifacts and request revisions. ARIS has three architectural layers. The execution layer provides more than 65 reusable Markdown-defined skills, model integrations via MCP, a persistent research wiki for iterative reuse of prior findings, and deterministic figure generation. The orchestration layer coordinates five end-to-end workflows with adjustable effort settings and configurable routing to reviewer models. The assurance layer includes a three-stage process for checking whether experimental claims are supported by evidence: integrity verification, result-to-claim mapping, and claim auditing that cross-checks manuscript statements against the claim ledger and raw evidence, as well as a five-pass scientific-editing pipeline, mathematical-proof checks, and visual inspection of the rendered PDF. A prototype self-improvement loop records research traces and proposes harness improvements that are adopted only after reviewer approval.

Research funding discovery remains fundamentally fragmented: researchers navigate disparate agency portals (e.g., in the United States, NSF, NIH, DARPA, Grants.gov, and many others) with heterogeneous interfaces, search capabilities, and data schemas. We present a compound AI system that unifies this landscape through two tightly coupled components: (1) an aggregation layer that autonomously collects, normalizes, and indexes almost 12,000 federal and nonprofit opportunities from fragmented sources via LLM-equipped browser agents, maintaining a biweekly-updated unified database; and (2) an agentic ReAct-based query processing layer that interprets research context (including from PDF documents) and employs hybrid search combining a structured index with selective web search to retrieve relevant opportunities - while avoiding LLM hallucination. The conversational interface supports iterative refinement through multi-turn interactions, allowing researchers to progressively apply constraints without reformulating their core research description. Results stream in real time with full transparency of intermediate reasoning, enabling appropriate calibration of user trust. Currently used by almost 3,000+ users, our approach demonstrates the feasibility of compound AI in reducing grant discovery time from 30--45 minutes (manual, fragmented portal searches) to under 10 minutes (unified, conversational search).

Automated research agents increasingly generate code, retrieve literature, and draft scientific artifacts, but they often fail to verify whether generated experiments execute correctly or whether cited sources support generated claims. We present AutoResearch, an execution-grounded multi-agent framework for reliable research workflow automation. AutoResearch couples sandboxed Python/PyTorch execution, iterative code repair, citation verification, claim-support auditing, decision control, and structured \LaTeX{} artifact generation. The system treats runtime errors, citation-verification failures, and review-agent feedback as practical filtering signals for generated research artifacts. In controlled evaluations on HumanEval, MBPP, a SciCode subset, citation-validation tasks, claim-support auditing, and small end-to-end workflow stress tests, AutoResearch improves execution success, citation validity, local claim support, and workflow completion relative to directly comparable baselines. Code-oriented agents are reported separately as partial comparisons. AutoResearch is intended as a reliability-oriented research assistant, not as a fully autonomous scientist or a standalone manuscript-quality benchmark. Source Code: https://github.com/raja21068/AutoResearch

The automation of scientific research workflows has emerged as a transformative frontier in artificial intelligence, yet existing autonomous research agents remain largely domain-agnostic, lacking the specialized reasoning, method selection, and data acquisition capabilities required for rigorous spatial data science. This paper introduces NORA (Night Owl Research Agent), a harness-engineered, multi-agent autonomous research system purpose-built for GIScience and spatial data science. NORA orchestrates the complete research lifecycle through a skills-first architecture comprising 21 domain-specialized workflow skills, 9 specialist sub-agents, and custom Model Context Protocol (MCP) servers. Central to the system's design are two novel domain-specialized skills: a spatial analysis skill unit that encodes decision frameworks for exploratory spatial data analysis, spatial regression, and diagnostics; and a spatial data download skill that supports reproducible acquisition from authoritative geospatial data sources. We formalize the concept of harness engineering for scientific research agents, demonstrating how lifecycle hooks, safety gates, generator-evaluator separation, human-in-the-loop, and state persistence ensure reliable and reproducible autonomous research. We evaluate NORA through case studies by 6 domain specialists and 3 LLM reviewers across seven dimensions (novelty, quality, rigor, etc). Results demonstrate that domain-specialized harness engineering substantially improves the efficiency and quality of research output compared to general-purpose agent configurations.

Local factual edits in scientific manuscripts often create non-local revision obligations. If a dataset changes from 215 to 80 documents, claims such as 'medium-scale' or 'a few hundred items' may also become stale, even though they do not repeat the edited number. In an audit of recent arXiv cs.CL benchmark and dataset papers, we find fact-dependent qualitative claims in 37.2% of papers, suggesting that this dependency pattern is common in the target genre. We introduce EditPropBench, a benchmark for measuring whether LLM editors propagate factual edits through dependent manuscript claims. Each item contains an ML/NLP-style synthetic manuscript, a targeted edit, and a controlled fact graph with sentence-level labels for direct targets, required downstream updates, and unrelated text that should remain unchanged. We summarize cascade success with Edit-Ripple Adherence (ERA), the fraction of required downstream updates correctly revised, and validate the metric with adversarial probes and stress-test variants. On the hardest cases, where dependent claims use implicit or free-form wording rather than repeating the edited value, five LLM editing systems span ERA 0.148-0.705. Even the strongest misses roughly 30% of required cascade updates. This advantage persists in a mixed evaluation that includes easy cases solvable by deterministic substitution. EditPropBench shows that current LLM editors can repair many implicit consequences of factual edits, but reliable scientific revision still requires cascade-aware checking.

Frontier scientific reasoning is rapidly emerging as a key foundation for advancing AI agents in automated scientific discovery. Deep research agents offer a promising approach to this challenge. These models develop robust problem-solving capabilities through post-training on information-seeking tasks, which are typically curated via knowledge graph construction or iterative web browsing. However, these strategies face inherent limitations in frontier science, where domain-specific knowledge is scattered across sparse and heterogeneous academic sources, and problem solving requires sophisticated computation and reasoning far beyond factual recall. To bridge this gap, we introduce SciResearcher, a fully automated agentic framework for frontier-science data construction. SciResearcher synthesizes diverse conceptual and computational tasks grounded in academic evidence, while eliciting information acquisition, tool-integrated reasoning, and long-horizon capabilities. Leveraging the curated data for supervised fine-tuning and agentic reinforcement learning, we develop SciResearcher-8B, an agent foundation model that achieves 19.46% on the HLE-Bio/Chem-Gold benchmark, establishing a new state of the art at its parameter scale and surpassing several larger proprietary agents. It further achieves 13-15% absolute gains on SuperGPQA-Hard-Biology and TRQA-Literature benchmarks. Overall, SciResearcher introduces a new paradigm for automated data construction for frontier scientific reasoning and offers a scalable path toward future scientific agents.

The escalating data scale in High-Energy Physics (HEP) fuels a growing aspiration for higher analytical efficiency. While Large Language Models (LLMs) offer a path toward automation via agentic AI, they struggle with complex scientific workflows that require deep domain knowledge and are tightly coupled to experiment-specific codebases. To address this, we introduce a methodology centered on HepScript, a dual-use Domain-Specific Language (DSL) for HEP data analysis workflows. HepScript serves as a shared formal interface, abstracting HEP analysis logic into a constrained syntax that is both intuitive for human experts and reliably generable by AI agents. First developed for the Beijing Spectrometer III (BESIII) experiment, HepScript hides the complexity of the underlying software stack, translating high-level analysis intent into low-level, production-ready code. In our case studies, this abstraction reduces the required human-written code by 93%. Crucially, HepScript's constrained grammar defines a tractable action space, enabling AI agents to autonomously generate executable specifications for core analysis stages directly from published literature with a 95% success rate. Our work demonstrates a scalable pathway toward human-AI collaborative systems, where a formally specified DSL acts as an unambiguous translation layer between human expertise, AI automation, and production environment, rendering previously intractable automation problems solvable.

The Karlsruhe Tritium Neutrino Experiment (KATRIN) aims to measure the absolute neutrino mass with unprecedented sensitivity, requiring precise monitoring of the windowless gaseous tritium source, where tritium beta decay occurs. To track variations of the source activity, beta-induced X-ray spectroscopy provides real-time diagnostics. However, traditional drift detection methods struggle with the infrequent and transient nature of instability events in gaseous tritium. This study bridges the gap between state-of-the-art time-series forecasting models and real-world experimental applications by leveraging deep learning to predict the time to stability after instabilities. Unlike standard benchmarking approaches that emphasize algorithmic performance on fixed datasets, we apply forecasting models -- including LSTM, N-BEATS, TFT, NHITS, DLinear, NLinear, TSMixer, and Chronos-LLM -- to complex, large-scale experimental data. Our findings highlight two challenges: learning from sparse instability events and forecasting long time horizons (i.e., predicting hundreds of future points), both of which are ongoing challenges in time-series forecasting and remain active areas of research. This prediction task has direct experimental value by enabling better scheduling and maintenance planning. A reliable forecast of stability time allows for more efficient measurement and task management during stabilization periods. Through model selection, we identified N-BEATS as the top performer, excelling in accuracy and repeatability, demonstrating that deep learning can optimize large-scale physics experiments.

Single-agent systems (SAS) have become the default pattern for LLM-driven scientific workflows, but routing planning, tool use, and synthesis through a single context window comes with a well-known cost: as tool specifications and observational traces accumulate, the effective context available for each decision shrinks, and end-to-end reliability suffers. We present a multi-agent system (MAS) prototype for hydrodynamics in which specialized agents are coordinated through a Layer Execution Graph (LEG). A planner agent constructs query-specific execution topologies from natural-language routing heuristics that capture domain knowledge without hard-coding it as rigid control logic; specialist agents operate under strict tool allowlists and occupy complementary data-class roles. Between layers, consolidator agents fuse parallel outputs into concise briefs, and a reporter agent synthesizes the final response, while the runtime logs provenance for every tool invocation to support auditability. All benchmarks, ablations, and stress tests use Claude Sonnet~4.6 as the backbone model for both specialist and general-purpose agents. Evaluated on 37 queries spanning six complexity categories, the prototype achieves 93.6% factual precision with a 100% pass rate. Accuracy remains above 90% across runs from single-threaded to five independent parallel tracks, and under simulated loss of individual data sources the system degrades gracefully, still returning substantive partial answers. Together, these results suggest that planner-guided, graph-structured multi-agent orchestration can meaningfully alleviate the context-saturation bottlenecks that constrain monolithic single-agent architectures.

Earth system science is producing increasingly large, high-dimensional datasets from both physics-based and AI-driven models. While embedding-based representations make these data searchable and serve as foundational building blocks for AI-driven discovery engines, nearest neighbors in latent spaces are not automatically scientifically meaningful. They may reflect real meteorological structures, or simply artifacts of preprocessing, geography, or model bias. Researchers therefore need visual tools to inspect latent space organization, trace search results back to physical evidence, and evaluate candidate representations against one another. We present an open source visual analytics workbench designed to support this provenance-aware scientific retrieval workflow. The system links distinct embedding experiments to shared source data, metadata, spatial contexts, and model configurations. It enables interactive retrieval strategy design by allowing users to issue image-level and localized patch-level queries, apply multi-constraint filters, and inspect analogs through familiar meteorological views. This facilitates a discovery loop where scientists characterize a phenomenon in a well-understood dataset and use its latent signature to probe larger archives. While we demonstrate the workbench through a tropical cyclone retrieval scenario using a vision foundation model (DINOv3) on ERA5 data, the framework is model-agnostic and designed to integrate with other embedding architectures in the future. Finally, we evaluate its out-of-core retrieval backend, demonstrating that interactive visual search over tens of millions of embeddings is highly scalable on commodity hardware.