Scientific Workflows

The economic value of inference depends on how capacity and task information are distributed across stages of AI production. We study these organizational margins using controlled workflow experiments on externally verified software-engineering tasks. In two matched resource panels, direct execution records the same success rate of 59.6 percent at logical-token ceilings of 12,000 and 24,000, while success under information-constrained planning rises from 36.2 to 51.2 percent. The planning disadvantage narrows by 15.0 percentage points (95 percent task-cluster bootstrap interval: 4.2 to 25.8). A strict read-only planning campaign varies whether the planner sees the task issue. At 12,000 tokens, issue access raises success by about 16 percentage points over issue-hidden planning. Compared with direct execution, task-informed planning is about 10 points lower at 12,000 tokens; at 24,000 tokens, it shows a 29.6-point advantage. In the resource panels, direct execution uses substantially less than either ceiling, while the planning workflow's binding rate falls from 46.2 to 0.8 percent and downstream execution accounts for 89.9 percent of the increase in total use. Scale determines the capacity available to a system; workflow and information structure shape the productive value

Modern LLMs and AI agents increasingly support data engineering workflows that integrate evidence from unstructured sources. Such pipelines typically do data retrieval, integration, and ranking before proceeding to more complex agentic reasoning or actions, e.g., for scientific discovery. The core retrieval problem in these workflows jointly executes multi-attribute filtering, multi-vector search, exact relational joins, and thresholded embedding-similarity joins. Given a planned query and monotone scoring function, our DASE query engine constructs and ranks candidate evidence tuples. It comprises (i) a multi-step reasoning query model over structured predicates, multiple vectors, and relational links; (ii) SemJI, a sparse materialized embedding-similarity join index for rare near-neighbor pairs; and (iii) a co-designed execution layer that combines predicate-aware ANN traversal, batched access, and threshold-based score aggregation. On scientific-discovery workloads, DASE retrieves candidate evidence for multi-step reasoning queries 6x to 46x faster than strong RDBMS, rerank, and vector-database baselines at comparable recall; and for tasks that require semantic-operator post-processing, DASE acts as a high-recall prefilter that makes downstream LLM evaluation both cheaper and more accurate -- e.g., on SemBench E-Commerce it improves BigQuery quality from 0.67 to 0.80 while cutting cost from $2.42 to$0.54.

Scientific research increasingly relies on large, heterogeneous data sources, motivating interest in retrieval-augmented generation (RAG) systems that provide natural language access to scientific knowledge and research workflows. Researchers are exploring the viability of these systems as natural language interfaces for document search and for generating analysis code and pipeline components. At the same time, concerns about data privacy and control over research infrastructure have motivated interest in open-weight models and open-source deployments hosted within research institutions. In astronomy, this development follows a long history of computational infrastructure development, from archival databases and Structured Query Language (SQL)-based systems to large language model (LLM)-assisted research tools. This paper presents a domain-expert evaluation of faithfulness for AquiLLM, an open-weight, offline RAG-LLM platform designed to support scientific research groups in the use and preservation of tacit and formal knowledge. We define faithfulness as the extent to which generated responses remain grounded in retrieved scientific context without unsupported claims or omissions. We report results from an astronomy case study evaluating AquiLLM across retrieval and scientific analysis tasks. AquiLLM performs most reliably on explicit retrieval-oriented questions grounded in the RAG collection, while faithfulness degrades for queries requiring synthesis or ambiguity resolution. These results highlight both the promise and limitations of open-weight RAG-LLM systems for scientific research and demonstrate the importance of domain-expert evaluation beyond standard benchmark leaderboards.

AI co-scientists could accelerate computational research, but over a long-running study the workflow also has to stay inspectable, resumable and reproducible, which requires persistent computational state and provenance. Here we present OpenAI4S, an open-source scientific research agent built around the principle of \emph{Code as Action, Science as Sessions}. OpenAI4S combines a persistent computing runtime with research-session management: orchestration is handled through structured tool calls, while scientific actions are represented as complete code cells executed in persistent Python and R kernels. An append-only Action Ledger, per-cell execution records, versioned artifacts, environment records, and workspace checkpoints preserve how results were produced and support session recovery, branching, and extension. Configurable sandboxing, permission controls, and code and trajectory screening provide complementary safeguards. We evaluate OpenAI4S on 36 research scenarios spanning retrosynthesis, molecular dynamics, protein binder design, protein mutation, catalyst screening, and mineral spectroscopy, measuring scientific task accuracy, workflow completeness, and reproducibility of the resulting repositories. OpenAI4S achieves an overall score of 7.83, compared with 5.7--6.4 for a general-purpose coding harness evaluated with three frontier models, with the largest gains on long-horizon and computation-intensive workflows. These results suggest that integrating persistent execution with session-level provenance can improve the reliability of AI-assisted scientific workflows. Environment specification and full rerunnability remain weak for every evaluated system, ours included, so reproducibility is still an open problem for scientific agents. The system is available under the MIT license at \href{https://github.com/PKU-YuanGroup/OpenAI4S}{github.com/PKU-YuanGroup/OpenAI4S}.

Scientific workflow management (WMSs) systems automate execution, yet orchestrate using fixed, hand-tuned rules. LLM agents promise more autonomous orchestration, but it remains unclear where to introduce agentic reasoning, how to bound its risk, and when it actually helps. We present Avatar, an actor-based architecture comprising an orchestrator, an executor, and a provenance monitor. Each actor's decision policy is pluggable (rule-based or LLM-backed) via a single adapter-validated action catalog, so conventional and agentic control run on the same core across different WMSs. We present an implementation using the Academy framework and evaluate Avatar across three workloads. We observe that Avatar's rule mode reproduces native execution, with a single unchanged core running all three. Moreover, LLM-backed Avatar reports a reduction of compute wastage by $55\%$ and cuts GPU-busy time by $40\%$. Overall, we envision Avatar as a step toward workflow systems that reason about their own orchestration rather than follow pre-fixed rules.

Making science computable requires representations of both scientific knowledge and the physical world in which scientific claims are tested. A computable representation of the physical laboratory is established through typed research objects, capability-bound operations and a compositional workflow algebra. It provides the physical-world counterpart to machine-readable knowledge, expressing workflows as programs over evolving laboratory states with explicit dependencies, decisions, iteration and concurrency. The representation was implemented in a modular agentic robotic laboratory by binding formal operations to executable Function Skills. For diverse scientific intents, capability-relative workflows were generated, while stateful simulation propagated object transformations and verified operation preconditions and laboratory constraints before dispatch. The proposed representation and its engineering framework jointly establish a general computational interface between agent reasoning and capability-bound physical transformations, providing a foundation for end-to-end autonomous scientific discovery.

A language-model agent asked to analyse an experiment will usually return working code. Whether the analysis is defensible is a different question. A defensible analysis depends on procedural choices: which test the field accepts, which identifier namespace is authoritative, and which caveats must accompany a result. We present Scientific Agent Skills, an open library of 163 such procedures in 16 areas of practice, including genomics, cheminformatics, medical imaging, study design and scientific communication. Each skill is a directory built around a versioned, human-readable instruction file. An agent loads the file only when a task calls for it; the directory often also contains reference material and runnable scripts. We report no task-level evaluation and no host selection rate. We measure two properties of the documentation corpus: the always-resident descriptions of all 163 skills cost 7.1% of a 200,000-token window, and the median documented workflow fits within 23.9% of it, although 29 of 46 would overflow if every reference file were loaded. Openly licensed and available at https://github.com/K-Dense-AI/scientific-agent-skills.

Scientific agents increasingly analyze data, execute code, and produce research artifacts, yet most benchmarks emphasize final answers, isolated programs, or a single domain. We introduce FrontierChallenge, a cross-domain benchmark comprising 300 end-to-end scientific workflows. In this paper, we release and evaluate 97 of these tasks, spanning quantum chemistry, molecular dynamics, materials characterization, analytical chemistry, life science, and electrochemistry/environment. Each task provides fixed inputs and specifies a bundle of required scientific deliverables. We evaluate twelve frontier models with three agent scaffolds. Pass Rate measures the fraction of tasks satisfying the full-completion criterion, while Avg. Score captures partial progress. Each of the best-performing configurations completed only 20 of the 97 released tasks, yielding a Pass Rate of 20.6%. Partial progress translated especially poorly into complete delivery in analytical chemistry and electrochemistry/environment: Avg. Scores reached 87.6 and 94.9, but the highest Pass Rates were only 4% and 0%. Among non-passing Claude Code trajectories, 75.5% still ended with language claiming completion. Complementary HDS6 process scores correlate strongly with task outcomes, supporting FrontierChallenge as a benchmark of Heavy Duty Solver capabilities. These findings show that neither high partial scores nor confident claims of completion reliably indicate that a scientific task has been fully delivered, highlighting the need to evaluate end-to-end workflow execution and the completeness of scientific deliverables together.

Real-world data science involves long-horizon workflows that span data wrangling, exploration, modeling, visualization, and validation, and require coordinated use of tools such as notebooks, IDEs, terminals, browsers, and databases within real operating environments. Yet existing benchmarks lack real-computer interaction and do not evaluate whether agents can execute complete end-to-end data-science workflows in realistic computing environments, failing to capture the multi-stage, multi-tool nature of data-science practice. We introduce DSAgentBench, the first benchmark to evaluate whether agents can automate full data-science workflows inside real computer environments. DSAgentBench contains 275 diverse tasks covering the entire data-science life-cycle, reflecting the complexity and tool coordination required in practice. Each task requires grounding decisions in intermediate outputs and coordinated tool use, and includes a deterministic evaluator that verifies analytical correctness, visual outputs, and model performance rather than code-only execution. Our extensive experiments with 15 closed- and open-source models show that even the strongest agent, Claude-4.6-Sonnet, achieves only 56.70% task success, while all open-source agents remain below 1%, frequently failing at tool orchestration, OS grounding, and multi-step reasoning. These results reveal a substantial capability gap between current agentic systems and real data-science workflows, positioning DSAgentBench as a foundation for developing grounded, verifiable, autonomous data-science agents. We release DSAgentBench at https://github.com/vis-nlp/DSAgentBench.

CheMLFlow is an open-source platform for building and executing end-to-end, high-throughput, and agentic workflows for scientific and technological applications. CheMLFlow targets a common bottleneck in scientific machine learning development, where researchers often need to assemble data acquisition, curation, representation, model training, validation, screening, interpretation, and reporting into a reproducible pipeline, even when their primary research contribution concerns only one stage. CheMLFlow provides modular workflow components, ready-to-run reference pipelines, standardized artifacts, and evaluation outputs that reduce orchestration overhead and support benchmarking across methods and datasets. The platform is designed to be extensible, reproducible, and automation friendly, with pluggable representations and models, deterministic splits, explicit run artifacts, batch execution, and report generation. As scientific software increasingly moves toward agent assisted experimentation, CheMLFlow's configuration driven workflows and structured outputs also provide a practical interface for coding agents to help users construct experiments, inspect results, and summarize findings under human supervision. This article describes the system architecture, core workflows, and benchmarks that reach literature performance for quantum mechanical, physicochemical and bioactivity property prediction, and use cases involving time series datasets demonstrating applications beyond molecular chemistry datasets.

Recent advances in large language models (LLMs) have enabled AI systems to assist scientific research and peer review. However, an essential capability for reliable AI-assisted scientific workflows remains underexplored: verifying whether reviewer feedback leads to meaningful and evidence-supported manuscript improvements. We introduce AutoSupervision, which evaluates whether scientific manuscript revisions genuinely address reviewer concerns through grounded evidence. AutoSupervision leverages transparent peer-review records as a natural source of supervision, where reviewer comments specify scientific concerns, author responses describe claimed resolutions, and revised manuscripts provide evidence of changes. Given reviewer comments, author responses, and revised manuscripts, models must characterize reviewer concerns, determine whether concerns have been addressed, and identify supporting manuscript evidence. We construct AutoSupervision from 56,000 Nature Communications articles and corresponding review records. Then we conducted experiments on LLMs, the ablation study, and the case study. Our results show that while LLMs perform well in characterizing reviewer concerns, with GPT-5.5 achieving a score of 0.754, evidence-based verification remains the primary bottleneck, with the best-performing model reaching only 0.501.

Large language model agents increasingly plan, execute, and interpret biological analyses, yet fluent responses, successful tool calls, and benchmark performance alone do not establish scientific credibility. Existing reviews primarily organize biological agents by application, architecture, and agentic capability, but do not jointly operationalize the accountability of agent-generated workflows. We address this gap by treating the inspectable workflow trajectory, rather than architecture or final output alone, as the primary unit of analysis. We introduce the Function--Evidence--Validation (FEV) framework, which separates demonstrated workflow operations, traceable support for actions and claims, and use-case-specific validation. Using FEV, we map 109 agentic or agent-adjacent systems and 28 benchmark or evaluation resources, representing 128 unique publications across genomics, single-cell and spatial omics, protein science, drug discovery, computational pathology, and general bioinformatics automation. Across domains, planning and tool-mediated execution have advanced more rapidly than replayability, provenance, robust scientific assessment, external validation, and prospective empirical testing. We therefore argue that agentic bioinformatics should be assessed through workflow correctness rather than final-answer correctness alone. FEV provides a practical basis for comparing systems and designing transparent, auditable, and scientifically accountable bioinformatics workflows.

Scientific research involves complex information-seeking and reasoning workflows across heterogeneous sources. However, existing benchmarks primarily emphasize general-domain retrieval or static scientific question answering, and therefore fail to assess key capabilities required in realistic scientific research workflows. We introduce SciExplore, a benchmark designed to evaluate scientific information-seeking and reasoning capabilities of LLMs and agents. SciExplore comprises four task types covering 103 expert-curated tasks across more than ten scientific disciplines: scientific database navigation, ambiguous literature retrieval, missing reference completion, and cross-source structured knowledge synthesis, which probe progressively higher-level abilities from entity-level reasoning and document-level identification to evidence-level grounding and domain-level synthesis. We evaluate over ten state-of-the-art LLMs and autonomous agents on SciExplore, revealing substantial performance gaps with performance degrading sharply as task complexity increases and extremely low accuracy on the most challenging structured synthesis tasks. These results highlight significant limitations of current models and agents in realistic scientific information-seeking scenarios.

Deep learning frameworks like nnU-Net achieve state-of-theart brain lesion segmentation performance but remain difficult to deploy in clinical research environments due to, among other reasons, software dependencies and computational requirements. We introduce StrokeSeg2, a lightweight, modular, cross-platform C++/Qt framework designed to adapt resource-intensive 3D stroke segmentation pipelines into portable and reproducible applications. To improve compatibility with standard clinical workstations, we investigate the combined effect of architectural compression through knowledge distillation and inference optimisation using ONNX Runtime with Float16 quantisation. Across heterogeneous hardware configurations (CPU, integrated GPU, and dedicated GPU) architectural distillation emerged as the primary contributor to efficiency gains, contributing to over 90% reduction in energy consumption and an average 84% reduction in inference time. Specifically, we identify a 0.84M-parameter student model as the most favourable trade-off, reducing the original 102.3M-parameter teacher architecture to a 2.1 MB disk footprint while preserving robust lesion localisation and competitive segmentation performance. This small footprint supports the development of a self-contained installer for clinical workstation targets. Finally, StrokeSeg2 packages these optimisations into standalone installers for Windows, macOS, and Linux. By providing both graphical and commandline interfaces without Docker or external environment dependencies, StrokeSeg2 facilitates deployment of high-performance segmentation workflows for routine clinical research pipelines.

As pathogen genomic surveillance scales, the bottleneck is shifting from data generation to analysis. We present BioSecBench-Surveillance, a verifiable benchmark of 100 evaluations testing whether AI agents can infer the right analysis pipeline from raw sequencing data and surveillance context. Each evaluation gives an agent only the data and context a human analyst would have, then grades its structured answer deterministically. The tasks span seven categories, from taxonomic classification to genetic-engineering detection, across diverse sample types and sequencing technologies. Across 3,962 gradable attempts from sixteen model-harness pairs, the strongest configuration cleared only about half. Opus 4.8 with PI led at 50.2 percent, with a 95 percent confidence interval of 40.1 to 60.3 percent across 83 evaluations, tied with GPT-5.5 with Codex at 50.2 percent, with a 95 percent confidence interval of 40.8 to 59.6 percent, followed by Opus 4.7 with PI at 49.6 percent, with a 95 percent confidence interval of 40.0 to 59.2 percent, and Sonnet 4.6 with PI at 48.6 percent, with a 95 percent confidence interval of 38.9 to 58.3 percent. Even when agents invoked the correct workflows, their mistakes came from the choices around them, such as which references, thresholds, filters, and normalization to apply. BioSecBench-Surveillance provides a standard for measuring whether agents can be trusted to perform genomic surveillance when the next outbreak arrives.

Large language model (LLM) agents are starting to take on routine work in high-performance computing (HPC), including monitoring Slurm jobs, diagnosing failed builds, inspecting simulation output, and coordinating scientific workflows. To do this work, an agent commonly acts under its user's credentials and inherits the user's access to files and the scheduler. This arrangement creates a failure mode that ordinary account-level controls do not capture. Adversarial instructions in a log, tool description, shared file, or peer-agent message may redirect the agent beyond the task the user assigned, even though every resulting command is authenticated and permitted for that account. We refer to this as the hijacked authorized agent problem. Existing agent-security studies explain relevant mechanisms, such as indirect prompt injection and tool misuse, but generally evaluate them in web, enterprise, or personal-assistant settings. HPC security, by contrast, has mature controls for identity and isolation but does not ordinarily represent the intent of a particular task. This paper defines the threat model in the HPC setting, identifies attack surfaces created by schedulers, shared storage, multi-project accounts, and scientific workflows, and examines where current controls fall short. It concludes with a research agenda and a plan for an empirical benchmark, TaskBound.

Lattice quantum chromodynamics (LQCD) provides a first-principles framework for computing hadronic observables, but its practical use remains limited by the substantial expertise required to turn research motivation into reliable computing workflows. Here we present \textsc{LQCDMaster}, a tool-augmented, skill-guided and domain-specialized scientific computing agent that converts natural-language LQCD research tasks into executable PyQUDA computing workflows, including measurement scripts, job-submission artifacts, execution logs and numerical outputs. The system combines agentic planning, expert-annotated LQCD skills and a deterministic Wick-contraction tool to constrain the algebraically fragile components of code generation. We evaluate \textsc{LQCDMaster} on a benchmark at the forefront of scientific research, comprising 70 LQCD computing tasks, with observables covering local and nonlocal two-point functions, Wilson loops, meson and baryon three-point functions. The generated workflows exactly reproduce expert-written implementations in 63 of 70 tasks at machine precision, with three additional discrepancies attributable to convention mismatches. Across representative observables, the agent reduces implementation time from hours to minutes while preserving end-to-end numerical validation. Further, we present a typical case of \textsc{LQCDMaster}-driven exploration: a lattice computation of light-cone distribution amplitudes with diagonal Wilson-line, a quantity accessible with standard methods but never before computed, and computation of the spectrum of proton, deuteron, triton, hyperon, hyperdeuteron and hypertriton. This work pioneers the paradigm of agentic scientific computing by automating the end-to-end scientific computing workflows in lattice QCD research, lowering its barrier and facilitating the exploration and verification of non-standard scientific ideas.

Agentic coding tools present new opportunities to transform research workflows. The performance of agent systems built depends on both large language models (LLMs) and the harness around LLMs, which is the orchestration code that determines an agent's behavior. We present ToFu, an agentic harness for researchers that reads your codebase, edits files, runs commands, and integrates with your development tools. ToFu plays a dual role in research. As a research assistant, it supports practical research workflows with superior token efficiency, lower cost, and multilingual capability compared with existing agentic harnesses. Its release under the MIT License further enables local deployment for privacy-sensitive users. As a research object, ToFu provides a white-box agentic harness that allows researchers to inspect, modify, and evaluate its orchestration logic, tool-use behavior, and harness design, while retaining strong benchmark performance and an application-level user experience.

Agentic research systems are emerging as a new paradigm for coordinating scientific workflows beyond isolated model inference, code generation, or statistical analysis. However, deployment in institutional biomedical environments requires governed mechanisms for research planning, data access, workflow orchestration, evidence tracking, reproducibility, and human oversight. We present NVAITC AI Scientist (NAIS), a governed end-to-end agentic research system designed to support domain-general scientific workflows while keeping protected data within institutional privacy boundaries. NAIS integrates proposal review, execution planning, governed computational routing, reproducible workflow orchestration, evidence generation, and scientist-in-the-loop oversight. We validate NAIS in a real-world hypertension genome-wide association study (GWAS) using hospital-linked genotype and electronic health record (EHR) data from 286,422 individuals under an aggregate-only data policy. The agent planned cohort extraction, orchestrated GWAS execution, generated quality-control summaries, and drafted publication-oriented outputs. Human-AI review identified phenotype discrepancies and enabled iterative refinement of the hypertension definition. After reconciliation, the agent-orchestrated GWAS reproduced established hypertension loci, including FGF5, ATP2B1, CNNM2, FTO, and GRB14, with the strongest signal at FGF5 reaching $-\log_{10}(p) \sim 70$. As a secondary demonstration, NAIS also supported a drug-induced liver injury prediction workflow, achieving a multimodal graph neural network AUC of 0.842. These results demonstrate that governed agentic research systems can support scalable AI-assisted biomedical discovery while producing outputs comparable to expert-led workflows.

We present a clinically deployed end-to-end auto-contouring system for cervical cancer radiotherapy planning, anchored by the Boundary-Aware Transformer with Region-Aware Mamba (BAT-RM), a hybrid architecture that integrates Sobel-gated boundary attention, a linear-time, multi-directional Mamba module for long-range context, and a boundary-skeleton-guided fusion gate. This design achieves linear-time complexity for long-range context modeling, avoiding the quadratic cost of full spatial self-attention. The full pipeline spans multi-institutional data collection, rigorous inter-rater quality assurance, external validation in an independent cohort, and a web-based clinical interface natively compatible with Varian, RayStation, and Monaco. Against four baselines, BAT-RM achieves superior performance across seven anatomical classes, with statistically significant improvements in target volumes, including GTV and CTV, and in organs at risk such as the rectum and bladder. A prospective multi-center reader study involving 13 radiation oncologists demonstrated that AI assistance elevates junior oncologists' IoU from 0.899 to 0.965, approaching senior-level accuracy, while reducing contouring time by more than 80%. The system also reduced expert consultation rates and improved inter-reader consistency, reflecting gains in both efficiency and quality assurance. Following clinical deployment at a partner hospital, the system reduced patient wait times from days to hours without additional staffing, enabling same-day or next-day initiation of treatment for routine cases. BAT-RM demonstrates that a rigorous research pipeline, from data curation to clinical deployment, can translate directly into measurable patient benefit in resource-constrained settings where the demand for radiotherapy far exceeds specialist capacity.

As AI agents are incorporated into life science workflows, the capabilities that speed discovery might also enable misuse. We present BioSecBench-Refusal, a benchmark for risk identification and refusal behavior for biological research tasks. The benchmark pairs 61 Routine tasks, legitimate analyses adapted from the published literature, with 46 Red-Team tasks, fictional scenarios that resemble real research but conceal a biosecurity hazard. Across 16 model-harness configurations, refusal rates ranged from 7% to 74% on Routine tasks and 1% to 62% on Red-Team tasks, with many configurations refusing legitimate Routine work at comparable or higher rates than concealed hazards. Refusals were most often triggered by provider API filters applied prior to agentic reasoning. However, models given room to reason showed the potential to identify more real threats. We release BioSecBench-Refusal as a tool for model developers to calibrate capability and caution for agentic biotech R&D.

We propose PRECEDE, a precedent-guided co-scientist for side-effect-aware drug redesign that revises a parent compound to mitigate a specified side effect while preserving therapeutic function. Rather than isolated molecular generation, PRECEDE frames redesign as evidence-grounded reasoning over drug--side-effect associations, biomedical knowledge graphs, and precedents of safety-driven optimization, coordinated by an LLM orchestrator with explicit policies and human-review checkpoints. We position PRECEDE as a human-supervised AI-for-science workflow in which hypotheses remain auditable, falsifiable, and bounded by prior pharmacology.

Leadership computing facilities steward large-scale scientific datasets that routinely require substantial transformation before serving as AI training data. However, no existing framework fully unifies automated transformation, readiness assessment, provenance tracking, and agent-native deployment. We present REDI, an open-source framework that addresses this gap through a unified five-stage pipeline (ingest, preprocess, transform, structure, and output) with per-stage instrumentation for reproducibility and deployment as an agent-callable skill; companion tool SetGo automates FAIR compliance and catalog publication. Evaluated across climate, proteomics, materials science, and nuclear fusion, REDI transforms all datasets from raw to AI-ready, with outputs validated against domain-expert references, and preliminary results show near-ideal parallel scaling to 100 nodes on Frontier for the climate case. Provenance-instrumented profiling reveals file I/O as the dominant pipeline cost, with format selection a first-order optimization lever. These results establish REDI as a cross-domain platform providing automated data readiness for scientific AI, transforming data preparation bottlenecks into reproducible, reusable community assets.

Scientific discovery workflows often depend on structured curation from the literature. This is difficult for current agents because the key evidence is scattered across long text, dense tables, and figures, and the final records often require reasoning across multiple evidence fragments rather than copying a single span. We study scientific curation from multimodal sources and introduce Beaver, an agent harness that extracts structured information from scientific papers while preserving provenance to the supporting evidence. Beaver combines a frontier agent with multimodal evidence tooling, task scaffolding, and artifact-grounded autoresearch. These components turn curation into a staged, auditable workflow and enable an iterative evaluate--diagnose--revise loop, where persistent run artifacts expose stage-localized failures and guide harness updates. Experiments show that Beaver reaches 81.0 on Gold-Referenced Attribute Score (GRAS), an attribute-level measure of agreement with gold curated records, outperforming frontier agents by over 23 absolute points. Ablations show that task scaffolding, multimodal evidence tooling, and provenance traces each contribute meaningfully to performance, while attribute-level analysis shows the largest gains on high-value attributes that require cross-modal reasoning and normalization. These results show that, for scientific curation from papers with multimodal evidence, harness design is a central determinant of agent performance.

Federated learning over medical images is a demanding workflow application. Each round fans out across parallel client jobs and converges on an aggregation step that feeds the next round. At scale this yields 101 sub-workflows and 2,679 jobs on GPUs at four sites, which takes an expert months to build, mostly on workflow mechanics rather than science. We ask how far AI assistance can automate such workflows. An LLM agent, grounded in a released plugin of Pegasus-specific skills, first produces a reviewable specification of checkable constraints and acceptance criteria, then generates the executable workflow. A validation loop repairs runtime failures, checks code against those constraints, and regenerates the implementation from the specification alone. We evaluate three LLM agents, report end-to-end runs on the FABRIC testbed, and show how conformance checking against the specification caught three silent errors that failure-driven debugging missed, including one that trained 1,700 jobs on random tensors.

We introduce EpiBench, a verifiable benchmark for short-horizon epigenomics analysis. EpiBench evaluates whether agents can make well-defined analysis decisions from realistic workflow states and return deterministically gradable answers. The benchmark includes 106 evaluations across CUT&Tag/CUT&RUN, ATAC-seq, ChIP-seq, and DNA methylation workflows. Across 5,088 valid trajectories from 16 model-harness pairs, no system passed a majority of attempts: GPT-5.5 / Pi led at 45.0% (143/318 attempts; 95% confidence interval (CI), 36.3--53.7), followed by GPT-5.5 / OpenAI Codex at 39.9% (127/318 attempts; 95% CI, 31.6--48.3). Claude Opus 4.8 Max / Pi and GPT-5.4 / Pi each passed 39.0% (124/318 attempts; 95% CI, 30.2--47.8 and 31.0--47.0, respectively). Performance varies across assay types, and many failed runs still contain parts of the correct answer. Agents often found the right files and computed useful intermediate results, but failed when the task required deeper, assay-specific scientific judgment.

Scientific laboratories increasingly rely on AI systems to reason about experiments, but the physical act of doing science remains largely outside their reach. AI can help read literature, generate hypotheses, and plan protocols, yet the execution of those protocols at the bench still requires a human operator. Vision-Language-Action (VLA) models provide one possible interface between written protocols and robot execution, but existing policies are trained mostly on household and tabletop demonstrations and rarely encounter the instruments, transparent liquids, or fixed protocol workflows found in scientific laboratories. Closing this gap requires both laboratory-specific supervision and a unified learning framework that can accommodate the diverse robot embodiments used to execute experimental protocols. We therefore identify data and embodiment as central bottlenecks alongside model design. To address the data side, we build RoboGenesis, a simulation-based workflow and data engine that composes configured laboratory workflows from atomic skills, validates and filters rollouts, and exports structured demonstrations across supported robot profiles. On the policy side, we present LabVLA, trained with a two-stage recipe: FAST action token pretraining first makes the Qwen3-VL-4B-Instruct backbone action aware before any continuous control is learned, and flow matching posttraining then attaches a DiT action expert under knowledge insulation. On the LabUtopia benchmark, LabVLA achieves the highest average success rate among all evaluated baselines under both in-distribution and out-of-distribution settings.

As scientific workflows shift from deterministic executables to LLM-based agents, the development practices on offer, such as fine-tuning, reinforcement learning, and prompt-and-go, bury the scientist's judgment. We propose treating agent construction as a workflow stage and introduce AgentBuild, which builds a scientific agent from a contract the scientist authors. The contract is a version-controlled rubric, a difficulty-graded curriculum, and a curated external knowledge base. A rubric-driven judge gates a meta-optimizer coding agent that edits the agent within a declared boundary, so the build compiles the agent, not the scientist's judgment. We instantiate this for Rietveld refinement of X-ray diffraction data through GSAS-II behind MCP and A2A, where a blank-harness construction run progresses through a lithium lanthanum zirconium oxide (LLZO) signal-to-noise ladder, reaches the 4 hour scan as a frontier case, and exposes the workflow-scope limits that remain. The same rubric that rewards credible fits also scores trajectory scope, making the frontier a contract failure rather than a pattern-fitting failure. As base models evolve, re-running AgentBuild is a re-tune, not a rebuild, and the scientist's authored contract remains the durable asset.

Scientific discovery workflows rely heavily on lab notes, where researchers record observations, interpret uncertain results, and plan follow-up experiments. Unlike polished publications, lab notes preserve evolving scientific reasoning, tacit scientific knowledge, and author uncertainty, giving AI agents access to the process of science. However, most prior work on scientific text focuses on papers, protocols, or structured databases, leaving informal laboratory notes underexplored as inputs to AI agents for science. This gap matters because tacit knowledge in lab notes is not written as a clean set of instructions: validated observations, tentative judgments, and possible experimental next steps often appear in the same passage. If these signals are conflated, an AI agent may mistake uncertain scientific judgments for confirmed conclusions or executable actions. To this end, we present Notes2Skills, a two-stage framework for turning lab notebooks into verifiable skills for scientific AI agents while preserving the author's certainty. Across three wet-lab sessions and seven original downstream configurations, Notes2Skills is the only tested configuration that avoids both observed regime-level failures: over-acting on uncertain notes and missing firm directives. We show that certainty preservation is a key missing piece between lab notebooks and reliable agent skills, opening a path toward safer AI co-scientist systems.

LLM-based scientific agents have shown strong capacity for autonomous research, yet their safety layers remain structurally divorced from core reasoning: they inspect pipeline outputs rather than shaping the deliberation that produces them. This separation opens two failure modes: safety signals accumulated at one stage are discarded before the next, and sequences of individually benign tool calls can compose into harmful outcomes that no single-step filter detects. To address these challenges, we introduce \textbf{SciTrace}, a framework that weaves safety reasoning into every stage of the scientific agent pipeline. SciTrace couples two complementary mechanisms: a \textit{Safety-Intrinsic Reasoning Loop} (SIR) that maintains a cumulative risk state across the Thinker, Experimenter, Writer, and Reviewer stages through joint task-and-safety deliberation, and a \textit{Compositional Tool-Chain Verifier} (CTV) that performs trajectory-aware safety checks before execution, catching risks that surface only across multi-step tool sequences. Evaluated on 240 high-risk research tasks and 120 tool-related risk tasks spanning six scientific domains, SciTrace achieves state-of-the-art (\textbf{SOTA}) safety among compared frameworks across four backbone models: it consistently improves tool call safety and adversarial robustness while preserving scientific output quality, and it uncovers \textbf{78.8%} of the compositional tool-chain escapes that single-step monitors miss. The project website is available at https://opensciagent.github.io/SciTrace/.

Large language models (LLMs) are increasingly used in academic research workflows, but scholarly tasks require high factual precision and therefore expose a key weakness: overconfidence. Here, overconfidence is defined behaviorally as the tendency to produce confident, assertive, and well-formatted outputs even when the underlying knowledge is incomplete or unverifiable, rather than as a calibration gap between stated confidence and accuracy. To examine this issue, we introduce GIScholarBench, a benchmark built from 10,865 papers published in 25 core GIScience journals between 2020 and 2025. The benchmark covers three tasks with increasing cognitive complexity: metadata retrieval, literature linking, and research direction generation. We evaluate Claude Sonnet 4.5, Gemini 3, and ChatGPT 5.3 through their native web interfaces under real-world user-facing conditions. Results show consistent overconfidence across all tasks. In metadata retrieval, ChatGPT 5.3 achieves the highest accuracy, but all models still generate definitive titles and DOIs when predictions are wrong. In literature linking, Claude Sonnet 4.5 recovers the most references, but all models show a clear gap between top-ranked retrieval and longer citation lists, suggesting that references are extended beyond reliable retrieval capacity. In research direction generation, AI-generated directions show lower topic coverage, higher novel miss rates, and lower semantic diversity than real future-citing papers. These findings suggest that LLM overconfidence is task-invariant but takes different forms: factual overgeneration in retrieval, unreliable citation expansion in literature linking, and overconfidence in output completeness during research ideation.

High-performance computing (HPC) clusters remain the backbone of large-scale scientific computation, traditionally executing deterministic, linear pipelines optimised for predictable performance. However, the pervasive integration of artificial intelligence (AI) and foundation models into scientific research has introduced a fundamentally new computational paradigm. AI-driven workflows are characteristically iterative, data-driven, and probabilistic, introducing unique challenges regarding data gravity, heterogeneous resource management, and complex workflow orchestration. This guide provides twelve practical tips designed to help researchers design efficient, scalable, and reproducible AI-driven HPC workflows. By addressing critical system-level bottlenecks - such as containerisation for environment portability, strategic deployment of job arrays, explicit feedback loop mechanics, and I/O optimisation for small files - this article offers a framework for transitioning from rigid execution pipelines to adaptive, intelligent computational environments. While these architectural principles are broadly applicable across distributed environments, they are particularly tailored to the resource-intensive throughput demands of modern computational biology.

Agentic AI tools offer a promising path to automating software development bottlenecks in scientific research pipelines, particularly for stages that take domain experts days to months to build, where scientists care about correctness and robustness, not implementation details. We present an empirical study of general-purpose coding agents on a fly optogenetics data-to-discovery pipeline. We assess agents on tasks substantially larger than existing benchmarks, datasets orders of magnitude bigger, and evaluation criteria grounded in domain expert standards. We show that agents can solve several individual pipeline stages, suggesting stage-level automation is tractable. By analyzing agents' code iterations, we show that they struggle most when there is not a pre-defined criterion to iterate on, and they must instead use their scientific judgment to assess their current solution, a key open challenge. Mirroring scientific practice, they sometimes attempt visual inspection of intermediate outputs for self-evaluation, but largely fail to interpret what they see or act on it appropriately. Solving the end-to-end pipeline correctly requires stringing together successes across all pipeline stages, and this is beyond agents' current abilities. We identify challenges largely absent from existing benchmarks, including computational resource management and generalization to large held-out data collections. Finally, we distill principles for constructing scientific tasks and rigorous evaluation criteria for open-ended problems.

Scientific workflows increasingly generate structured JSON data that is easy to exchange but difficult to interpret consistently across systems due to lacking semantic interoperability. While JSON Schema ensures structural validation, it provides no native support for Linked Data semantics. This paper presents an RDF Authoring View extending the open-source JSON Schema editor MetaConfigurator, enabling researchers to transform existing JSON, YAML, or CSV data into RDF using AI-assisted RML mappings, refine triples, execute SPARQL queries, visualize knowledge graphs, and export RDF serializations within a single integrated web interface. This workflow is supported by ontology-aware IRI auto-completion, bidirectional synchronization between JSON-LD text views and RDF triple tables, and AI-assisted SPARQL query generation from natural language hints. We demonstrate the workflow using laboratory data from metal-organic framework (MOF) synthesis experiments. Protocol data describing reagents, procedure steps, and quantities is converted from JSON to ontology-based JSON-LD via RML mappings. We then refine the semantic representation, query relationships between experimental conditions and outcomes, and explore the resulting knowledge graph interactively. This integrated environment bridges conventional structured data management with Semantic Web technologies while preserving experimental context and lowering technical barriers through AI assistance.

We present Archi, an open-source, end-to-end framework for scientific collaborations that combines the systematic ingestion and organization of heterogeneous data sources with the deployment of configurable, private, and extensible agents that retrieve and reason over them. An instance of Archi has been deployed for the Computing Operations team of the CMS experiment at CERN's LHC since February 2026 as a support agent for technical operators, offering retrieval and analysis capabilities by combining documentation, historical data, and live monitoring systems. We evaluate the system on operator feedback and a question set collected from production usage, graded by human and automated panels. The system proves effective at operational tasks, resolving real-world queries posed by CMS operators. We also observe that locally-hosted, open-weight models perform competitively, enabling fully private management of sensitive data.

Scientific research has traditionally been human-intensive, requiring researchers to coordinate literature, ideas, experiments, manuscripts, and review responses across long project cycles. The rise of LLM-based scientific agents creates an opportunity to automate this process. Such a system must support the full research lifecycle, maintain structured persistent memory across projects, and improve its own research procedures over time. However, existing systems either partially satisfy or fail to satisfy these requirements, leaving a gap for a unified automated scientific research system. As a result, we present AutoSci, a memory-centric agentic system for the full scientific research lifecycle. AutoSci is organized around four modules. SciMem provides schema-governed research memory, separating Long-Term Knowledge Memory for reusable scientific knowledge from Active Research Memory for project-level artifacts such as ideas, experiments, manuscripts, and reviews. SciFlow executes a five-stage lifecycle from literature understanding to rebuttal through a harness that controls state, context, verification, feedback, and orchestration. SciDAG augments difficult skills with DAG-shaped multi-agent operators and reusable stage-specific templates. SciEvolve converts feedback signals from users, experiments, reviews, and external environments into versioned updates to SciMem organization, SciFlow skills, and SciDAG templates. Together, these modules make AutoSci a persistent research environment that can execute, remember, and evolve across research projects. The code repository is available at https://github.com/skyllwt/AutoSci.

This paper details two novel frameworks for developing autonomous, agentic AI in scientific workflows. Both systems leverage a hybrid Local Body, Remote Brain architecture via Google Colab, utilizing Python-based local orchestrators to invoke large language model (LLM) cloud backends. The first agent, DeepTS/DeepCollector, automates the large-scale curation, extraction, and deduplication of time-series datasets. The second, DeepScribe, is an autonomous presentation analyzer that converts visually dense, mathematically complex physics lectures into structured scientific reports. Through practical systems engineering-such as granular attribute extraction (Cellular RAG), remote data inspection, and distributed concurrency controls-we demonstrate how agentic AI can overcome the context and reasoning limitations of current state-of-the-art systems to rigorously support scientific workflows. Finally, we outline a generalization of DeepTS to support deep knowledge graphs and discuss the application of this conceptual approach to high-energy physics (DeepQCD).

AI for Science (AI4Science) workflows often treat the released dataset as a fixed interface to the underlying system. However, in domains relying on \emph{indirect observation}, the learner observes a derivative representation produced by multi-stage measurement, reconstruction, and preprocessing pipelines. \textbf{We argue that these measurement-to-dataset pipelines are inference components: treating their outputs as given data'' freezes an observation model and obscures uncertainty over feasible pipeline choices.} We identify three failure modes arising from this frozen lens'': \textbf{(C1) hidden hypothesis space}, where the released dataset does not specify the pipeline configuration or its validity conditions; \textbf{(C2) uncertified transportability}, where a pipeline may be documented but its regime of validity is untested, so failures under distribution shift cannot be adjudicated; \textbf{(C3) ungoverned multiplicity}, where many defensible pipelines exist and dispersion is real but not propagated into uncertainty-aware evidence. We stress-test these claims with a large-scale neuroscience empirical audit, finding a survival rate of $\approx 0.0004\%$ under a cross-dataset stability criterion. We call on the AI4Science community to make pipelines \emph{computable} inference objects via domain-specific Computable Observation Frameworks. This shift enables quantifying pipeline adequacy and stability, converting implicit implementation choices into auditable, reproducible, and cumulative scientific evidence.

Autonomous research systems increasingly make the scientific workflow executable: agents can propose ideas, run code, inspect results, and draft papers. But executable workflows do not by themselves produce research judgment. We analyze where current systems lose trial experience: weak evidence becomes prose, pilot signals become broad claims, memory remains textual, and recurring process failures do not change later behavior. We introduce Sibyl-AutoResearch, a self-evolving AutoResearch framework built around Scientific Trial-and-Error Harnesses. A harness lets agents run bounded trials, preserve positive and negative outcomes, and route lessons into later planning, validation, claim scope, scheduling, critique, writing, and harness repair. We formalize this through two auditable conversion units: trial-to-behavior conversion, which links trial signals to later research actions, and trial-to-harness-behavior conversion, which links recurring process failures to system updates. We implement the framework in SIBYL, a file-backed autonomous research system that exposes the state, roles, memory, gates, and artifact traces needed to inspect these conversion paths. A retrospective audit identifies eight high-confidence conversion events, with a median latency of one iteration and a maximum latency of three iterations. A recovered-failure registry further shows how five naturally occurring failure classes, including duplicate results, stale numbers, and unsupported statistics, were blocked, downgraded, or routed into later repair. These traces do not establish a comparative performance claim; they show that the proposed conversion units are recoverable from realistic autonomous-research workspaces. The SIBYL framework and system are available at https://github.com/Sibyl-Research-Team/AutoResearch-SibylSystem.

The Materials Genome Initiative catalyzed the proliferation of centralized platforms--SaaS, PaaS, and IaaS--that aggregate computational and experimental resources for accelerated materials discovery. In parallel, breakthroughs in large language models (LLMs) and autonomous agents have created powerful new reasoning capabilities for scientific research. Yet a critical "last mile" problem remains: while we possess world-class models and vast repositories of materials data, we lack the organizational infrastructure to compose these capabilities securely across institutional boundaries. The development of structural and functional materials for harsh service environments--high-temperature alloys, radiation resistant steels, corrosion-resistant coatings--remains characterized by long-term iteration, mechanistic complexity, and high domain expertise--demands that exceed both monolithic agent systems and traditional centralized platforms. To address this gap we propose OpenAaaS, an open-source hierarchical and distributed Agent-as-a-Service framework that enables organized multi-agent collaboration for intelligent materials design. OpenAaaS is built on a single foundational principle: code flows, data stays still. A Master Agent plans and decomposes complex research tasks without requiring direct access to subordinate agents' managed data and computational resources. Sub-agents, deployed as near-data execution nodes, retain full sovereignty over local datasets, proprietary algorithms, and specialized hardware. This architecture guarantees that raw data never leaves its domain of origin while enabling cross-scale, cross-domain secure integration of previously isolated materials intelligence silos. We validate the framework through two representative case studies: (i) AlphaAgent, an evidence-grounded materials literature analysis executor that achieves 4.66/5.0 on deep analytical questions against single-pass RAG baselines; and (ii) an ultra-large-scale hexa-high-entropy alloy descriptor database service that demonstrates secure near-data execution and domain-specific scientific workflows under strict data-sovereignty constraints. OpenAaaS establishes a principled pathway toward "organized research" via agent collectives, offering a scalable foundation for next-generation materials intelligent design platforms. All source code is available at https://github.com/Wolido/OpenAaaS.

Self-driving laboratories (SDLs) have attracted increasing attention as a means of accelerating scientific discovery; however, developing SDL software remains technically demanding. To improve accessibility, orchestration software frameworks have been proposed to coordinate SDL components. Nevertheless, existing frameworks are primarily designed for human interaction and do not provide standardized interfaces suitable for AI agents. In this work, we propose an SDL software architecture based on the Model Context Protocol (MCP), in which all SDL functionalities are exposed through MCP servers. Following this design principle, we introduce an MCP-based SDL orchestrator, named NIMO Controller. It provides a visual programming interface automatically generated through MCP-based tool discovery, allowing human users to design experimental workflows without writing code. The same MCP backend can also be accessed by AI agents, providing a unified interface for both human users and AI agents. We demonstrate the proposed system through a case study on a color-matching SDL. The results validate the usability of the proposed MCP-based SDL architecture.

Language models can produce convincing scientific analyses, but repeated generations on the same data do not guarantee the same result. A researcher may regenerate an identical query and receive a different fit, a different peak position or a different analysis procedure, without an obvious way to decide which output to trust. We propose typed mediation, a pattern in which the model orchestrates deterministic tools rather than generating analytical code. Each tool encodes one researcher's exact procedure for one instrument, ported through structured interviews. The model selects which tool to call and with what parameters. The tool produces the result. Regeneration does not change it. We evaluate this claim by running the same photoluminescence analysis on four platforms, including three commercial foundation models, four times each with the same prompt. The typed tool produces identical results across all runs. The commercial platforms either vary in numerical output and analytical methodology across runs, or fail to produce valid results on the task. We deploy this pattern on two instruments serving users over approximately six months, with very positive user feedback. Both cases are very challenging: they involve proprietary binary formats and per-seat licensed software, which force the tool to remain on local infrastructure alongside the data and the instrument it operates. We argue that deployment topology is not just a preference, but a structural requirement of scientific tool mediation. The result is a practical pattern for deploying language models in scientific workflows where reproducibility is mandatory, reducing analysis time from weeks to minutes while guaranteeing identical outputs across runs.

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 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.

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.

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.

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.

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.

Existing multi-agent Large Language Model (LLM) frameworks for code generation typically use execution feedback and improve iteratively using Input/Output (I/O) test cases. However, this does not work for scientific workflows, where I/O test cases do not exist, and generating them requires solving the very problem at hand. To address this, we introduce MOSAIC, a training-free multi-agent framework for scientific code generation without I/O supervision. Instead of execution feedback, MOSAIC employs a student-teacher knowledge distillation framework that grounds generation through domain-specific examples and structured problem decomposition. To further mitigate hallucinations across chained subproblems, we introduce a Consolidated Context Window (CCW) for maintaining consistent reasoning across agents. Experiments on the SciCode benchmark show that MOSAIC improves accuracy, executability, and numerical precision over existing approaches while relying on lightweight models.

Scientific workflow systems automate execution -- scheduling, fault tolerance, resource management -- but not the semantic translation that precedes it. Scientists still manually convert research questions into workflow specifications, a task requiring both domain knowledge and infrastructure expertise. We propose an agentic architecture that closes this gap through three layers: an LLM interprets natural language into structured intents (semantic layer); validated generators produce reproducible workflow DAGs (deterministic layer); and domain experts author ``Skills'': markdown documents encoding vocabulary mappings, parameter constraints, and optimization strategies (knowledge layer). This decomposition confines LLM non-determinism to intent extraction: identical intents always yield identical workflows. We implement and evaluate the architecture on the 1000 Genomes population genetics workflow and Hyperflow WMS running on Kubernetes. In an ablation study on 150 queries, Skills raise full-match intent accuracy from 44% to 83%; skill-driven deferred workflow generation reduces data transfer by 92%; and the end-to-end pipeline completes queries on Kubernetes with LLM overhead below 15 seconds and cost under $0.001 per query.

Multi-agent systems built from teams of large language models (LLMs) are increasingly deployed for collaborative scientific reasoning and problem-solving. These systems require agents to coordinate under shared constraints, such as GPUs or credit balances, where cooperative behavior matters. Behavioral economics provides a rich toolkit of games that isolate distinct cooperation mechanisms, yet it remains unknown whether a model's behavior in these stylized settings predicts its performance in realistic collaborative tasks. Here, we benchmark 35 open-weight LLMs across six behavioral economics games and show that game-derived cooperative profiles robustly predict downstream performance in AI-for-Science tasks, where teams of LLM agents collaboratively analyze data, build models, and produce scientific reports under shared budget constraints. Models that effectively coordinate games and invest in multiplicative team production (rather than greedy strategies) produce better scientific reports across three outcomes, accuracy, quality, and completion. These associations hold after controlling for multiple factors, indicating that cooperative disposition is a distinct, measurable property of LLMs not reducible to general ability. Our behavioral games framework thus offers a fast and inexpensive diagnostic for screening cooperative fitness before costly multi-agent deployment.

We present pAI/MSc, an open-source, customizable, modular multi-agent system for academic research workflows. Our goal is not autonomous scientific ideation, nor fully automated research. It is narrower and more practical: to reduce by orders of magnitude the human steering required to turn a specified hypothesis into a literature-grounded, mathematically established, experimentally supported, submission-oriented manuscript draft. pAI/MSc is built with a current emphasis on machine learning theory and adjacent quantitative fields.

The rapid growth of scientific software has created practical barriers for bioinformatics research. Although powerful statistical, artificial intelligence (AI)-based methods are now widely available, their effective use is often hindered by fragmented distribution, inconsistent documentation, complex dependencies, and difficult-to-reproduce execution environments. As a result, reusing published tools and workflow adaptation to own date remains technically demanding and time-intensive, even for experienced users. Here, we present PoSyMed, an open and modular platform for the controlled integration, composition, and execution of bioinformatics tools and workflows. PoSyMed combines a backend-centered platform architecture with formal tool descriptions, controlled container-based build and execution processes, persistent workflow state, and a dialogue-based user interface. Large language models (LLM) are integrated not as autonomous decision-makers, but as human-computer interface with bounded semantic assistants that help identify tools, propose workflow steps, and support parameterization within a typed, validated, and human-supervised execution environment. PoSyMed is designed to improve reproducibility, traceability, and transparency in practical biomedical analysis within one platform. We describe the system architecture and evaluate its behavior across representative biological software scenarios with respect to workflow support, interaction design, and platform extensibility. PoSyMed is publicly available at https://apps.cosy.bio/posymed.

Motivation: The rapid growth of biological data has intensified the need for transparent, reproducible, and well-documented computational workflows. The ability to clearly connect the steps of a workflow in the code with their description in a paper would improve workflow comprehension, support reproducibility, and facilitate reuse. This task requires the linking of bioinformatics tools in workflow code with their mentions in a published workflow description. Results: We present CoPaLink, an automated approach that integrates three components: named entity recognition (NER) for identifying tool mentions in scientific text, NER for tool mentions in workflow code, and entity resolution based on word embedding similarity. We propose approaches for all three steps, achieving a high individual F1-measure (77 - 90) and a joint accuracy of 66 when evaluated on Nextflow workflows using Sentence-BERT. CoPaLink leverages corpora of scientific articles and workflow executable code with curated tool annotations to bridge the gap between narrative descriptions and workflow implementations. Availability: The code is available at https://gitlab.liris.cnrs.fr/sharefair/copalink-experiments and https://gitlab.liris.cnrs.fr/sharefair/copalink. The corpora are also available: CPL-Article (https://doi.org/10.5281/zenodo.20746904), CPL-Code (https://doi.org/10.5281/zenodo.20746970) and CPL-Gold-Entity-Resolution (https://doi.org/10.5281/zenodo.20746994).

Drug-induced toxicity is a leading cause of preclinical and early-clinical failure, making early detection critical. Histopathology is the gold standard for toxicity assessment but relies on expert pathologists, creating a bottleneck for large-scale screening. We introduce an AI-based anomaly detection framework for whole-slide images (WSIs) of rodent liver that identifies healthy tissue and known pathologies (anomalies) and flags samples without training data as out-of-distribution (OOD). We evaluate OOD detection on two held-out categories: apoptosis (single-cell, near-OOD) and staining/processing artifacts (heterogeneous, far-OOD). We build a novel pixelwise-annotated dataset and fine-tune a pre-trained Vision Transformer (DINOv2) via Low-Rank Adaptation (LoRA) for segmentation, then use the Mahalanobis distance for OOD detection with class-specific thresholds. Optimizing the false positive rate subject to a predefined constraint on the false negative rate yields only 0.16% of pathological tissue classified as healthy and 0.35% of healthy tissue classified as pathological. Our false negative rate does not penalise cross-type errors, reflecting the safety-first objective of never overlooking a lesion; under the stricter correct-class criterion our method assigns 93.93% of ID and 89.38% of OOD findings to their own class. The study demonstrates technical feasibility of pixel-level anomaly detection for mouse liver histopathology, indicating possible applications in improving preclinical workflows and drug development efficiency.

We present domain-adapted large language model agents designed to support Cherenkov Telescope Array operation and data analysis. The agents combine contextual knowledge with automated validation and iterative correction to produce more reliable outputs. This approach reduces manual effort, improves consistency, and helps accelerate operational and scientific workflows. The results demonstrate the potential of agentic systems as practical assistants in specialized research environments.