Scientific Workflow Automation

Large language models (LLMs) can now translate a researcher's plain-language goal into executable computation, yet scientific workflows demand determinism, provenance, and governance that are difficult to guarantee when an LLM decides what runs. Semi-structured interviews with 18 experts across 10 industrial R&D stakeholders surface 2 competing requirements--deterministic, constrained execution and conversational flexibility without workflow rigidity--together with boundary properties (human-in-the-loop control and transparency) that any resolution must satisfy. We propose schema-gated orchestration as the resolving principle: the schema becomes a mandatory execution boundary at the composed-workflow level, so that nothing runs unless the complete action--including cross-step dependencies--validates against a machine-checkable specification. We operationalize the 2 requirements as execution determinism (ED) and conversational flexibility (CF), and use these axes to review 20 systems spanning 5 architectural groups along a validation-scope spectrum. Scores are assigned via a multi-model protocol--15 independent sessions across 3 LLM families--yielding substantial-to-near-perfect inter-model agreement (Krippendorff a=0.80 for ED and a=0.98 for CF), demonstrating that multi-model LLM scoring can serve as a reusable alternative to human expert panels for architectural assessment. The resulting landscape reveals an empirical Pareto front--no reviewed system achieves both high flexibility and high determinism--but a convergence zone emerges between the generative and workflow-centric extremes. We argue that a schema-gated architecture, separating conversational from execution authority, is positioned to decouple this trade-off, and distill 3 operational principles--clarification-before-execution, constrained plan-act orchestration, and tool-to-workflow-level gating--to guide adoption.

Density Functional Theory (DFT) is a cornerstone of materials science, yet executing DFT in practice requires coordinating a complex, multi-step workflow. Existing tools and LLM-based solutions automate parts of the steps, but lack support for full workflow automation, diverse task adaptation, and accuracy-cost trade-off optimization in DFT configuration. To this end, we present TritonDFT, a multi-agent framework that enables efficient and accurate DFT execution through an expert-curated, extensible workflow design, Pareto-aware parameter inference, and multi-source knowledge augmentation. We further introduce DFTBench, a benchmark for evaluating the agent's multi-dimensional capabilities, spanning science expertise, trade0off optimization, HPC knowledge, and cost efficiency. TritonDFT provides an open user interface for real-world usage. Our website is at https://www.tritondft.com. Our source code and benchmark suite are available at https://github.com/Leo9660/TritonDFT.git.

Automated paper reproduction -- generating executable code from academic papers -- is bottlenecked not by information retrieval but by the tacit knowledge that papers inevitably leave implicit. We formalize this challenge as the progressive recovery of three types of tacit knowledge -- relational, somatic, and collective -- and propose \method, a graph-based agent framework with a dedicated mechanism for each: node-level relation-aware aggregation recovers relational knowledge by analyzing implementation-unit-level reuse and adaptation relationships between the target paper and its citation neighbors; execution-feedback refinement recovers somatic knowledge through iterative debugging driven by runtime signals; and graph-level knowledge induction distills collective knowledge from clusters of papers sharing similar implementations. On an extended ReproduceBench spanning 3 domains, 10 tasks, and 40 recent papers, \method{} achieves an average performance gap of 10.04% against official implementations, improving over the strongest baseline by 24.68%. The code will be publicly released upon acceptance; the repository link will be provided in the final version.

While large language models accelerate scientific discovery, existing agents face severe limitations in adaptability, domain generalization, and multimodal scalability, often struggling to autonomously process raw, domain-specific experimental data. To overcome these barriers, we introduce SciDER, a multi-agent system designed to flexibly automate the entire research lifecycle. This framework employs a novel data-centric approach and integrates a dynamic multimodal skill system across four specialized sub-agents. Specifically, an ideation agent generates novel hypotheses via Evolutionary Idea Search, a data analysis agent systematically structures raw data, an experimentation agent synthesizes executable code grounded in dataset characteristics, and a critic agent drives iterative self-refinement. To democratize open-source scientific discovery, we release OpenSciDER-SFT-8K, a high-quality execution trajectory dataset, alongside the OpenSciDER-27B fine-tuned model. Across six benchmarks, SciDER and OpenSciDER obtain competitive or leading results, with especially strong gains on data-centric analysis, end-to-end research execution, and multimodal scientific visualization. By integrating data analysis with experimental execution, SciDER bridges the gap between abstract scientific reasoning and reproducible experimentation synthesis.

Internet measurement faces twin challenges: complex analyses require expert-level orchestration of tools, yet even syntactically correct implementations can have methodological flaws and can be difficult to verify. Democratizing measurement capabilities thus demands automating both workflow generation and verification against methodological standards established through decades of research. We present Airavat, the first agentic framework for Internet measurement workflow generation with systematic verification and validation. Airavat coordinates a set of agents mirroring expert reasoning: three agents handle problem decomposition, solution design, and code implementation, with assistance from a registry of existing tools. Two specialized engines ensure methodological correctness: a Verification Engine evaluates workflows against a knowledge graph encoding five decades of measurement research, while a Validation Engine identifies appropriate validation techniques grounded in established methodologies. Through four Internet measurement case studies, we demonstrate that Airavat (i) generates workflows matching expert-level solutions, (ii) makes sound architectural decisions, (iii) addresses novel problems without ground truth, and (iv) identifies methodological flaws missed by standard execution-based testing.

Infrared radiation computing underpins advances in climate science, remote sensing and spectroscopy but remains constrained by manual workflows. We introduce InfEngine, an autonomous intelligent computational engine designed to drive a paradigm shift from human-led orchestration to collaborative automation. It integrates four specialized agents through two core innovations: self-verification, enabled by joint solver-evaluator debugging, improves functional correctness and scientific plausibility; self-optimization, realized via evolutionary algorithms with self-discovered fitness functions, facilitates autonomous performance optimization. Evaluated on InfBench with 200 infrared-specific tasks and powered by InfTools with 270 curated tools, InfEngine achieves a 92.7% pass rate and delivers workflows 21x faster than manual expert effort. More fundamentally, it illustrates how researchers can transition from manual coding to collaborating with self-verifying, self-optimizing computational partners. By generating reusable, verified and optimized code, InfEngine transforms computational workflows into persistent scientific assets, accelerating the cycle of scientific discovery. Code: https://github.com/kding1225/infengine

Large-scale facilities increasingly face analysis and reporting latency as the limiting step in scientific throughput, particularly for structurally and magnetically complex samples that require iterative reduction, integration, refinement, and validation. To improve time-to-result and analysis efficiency, NeuDiff Agent is introduced as a governed, tool-using AI workflow for TOPAZ at the Spallation Neutron Source that takes instrument data products through reduction, integration, refinement, and validation to a validated crystal structure and a publication-ready CIF. NeuDiff Agent executes this established pipeline under explicit governance by restricting actions to allowlisted tools, enforcing fail-closed verification gates at key workflow boundaries, and capturing complete provenance for inspection, auditing, and controlled replay. Performance is assessed using a fixed prompt protocol and repeated end-to-end runs with two large language model backends, with user and machine time partitioned and intervention burden and recovery behaviors quantified under gating. In a reference-case benchmark, NeuDiff Agent reduces wall time from 435 minutes (manual) to 86.5(4.7) to 94.4(3.5) minutes (4.6-5.0x faster) while producing a validated CIF with no checkCIF level A or B alerts. These results establish a practical route to deploy agentic AI in facility crystallography while preserving traceability and publication-facing validation requirements.

Operational rigor determines whether human-agent collaboration succeeds or fails. Scientific data pipelines need the equivalent of DevOps -- SciOps -- yet common approaches fragment provenance across disconnected systems without transactional guarantees. DataJoint 2.0 addresses this gap through the relational workflow model: tables represent workflow steps, rows represent artifacts, foreign keys prescribe execution order. The schema specifies not only what data exists but how it is derived -- a single formal system where data structure, computational dependencies, and integrity constraints are all queryable, enforceable, and machine-readable. Four technical innovations extend this foundation: object-augmented schemas integrating relational metadata with scalable object storage, semantic matching using attribute lineage to prevent erroneous joins, an extensible type system for domain-specific formats, and distributed job coordination designed for composability with external orchestration. By unifying data structure, data, and computational transformations, DataJoint creates a substrate for SciOps where agents can participate in scientific workflows without risking data corruption.

The rapid growth of Artificial Intelligence and Machine Learning in scientific research has highlighted a gap between industry-standard MLOps tools and platforms, and the unique requirements of modern and Open Science, particularly regarding the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. This paper presents AI4EOSC, a federated, open-source platform designed to operationalize the full AI/ML lifecycle within the European Open Science Cloud (EOSC) ecosystem. Our methodology tackles the fragmentation of distributed research infrastructures by integrating a modular and distributed architecture comprising an AI development platform, a serverless AI-as-a-Service layer, and a federated orchestration model that is able to integrate heterogeneous compute and storage resources from distributed e-Infrastructures. AI4EOSC also introduces a ``FAIR-by-design'' approach that enforces metadata standardization (via MLDCAT-AP) and W3C PROV-compliant provenance tracking through a platform-integrated CI/CD pipeline. AI4EOSC added value is demonstrated through the delivery of a diverse set of community installations, showing consistent and seamless deployment across heterogeneous cloud providers. These installations are validated by a set of scientific cases, showing how our work reduces the manual burden on researchers while ensuring high levels of reproducibility and interoperability and providing an unified environment for development, training, and production of AI/ML models in the EOSC.

Progress in computational science depends on complex numerical workflows that must faithfully encode physical laws, yet translating conceptual insight into reliable code remains a major bottleneck. Although large language models can generate isolated code fragments, they lack the structured reasoning required to design, verify, and iteratively refine complete scientific pipelines. Here we introduce ATHENA, an agentic framework explicitly designed to emulate scientific research modeled as a knowledge-driven contextual bandit process. Its core loop separates conceptual policy from numerical realization through expert-derived conceptual scaffolding, enabling principled diagnosis, reformulation, and repair of computational strategies. Across scientific computing and scientific machine learning tasks, ATHENA autonomously derives and correctly applies exact analytical solutions, constructs stable numerical solvers, diagnoses ill-posed formulations, and orchestrates hybrid symbolic-numeric workflows. Quantitatively, ATHENA matches and frequently surpasses the accuracy of expert-authored reference solutions reported in the literature on canonical benchmarks. By reframing computation as an object of agentic reasoning, our framework enables autonomous orchestration of heterogeneous algorithms across scientific domains.

Climate science demands automated workflows to transform comprehensive questions into data-driven statements across massive, heterogeneous datasets. However, generic LLM agents and static scripting pipelines lack climate-specific context and flexibility and thus perform poorly in practice. We present ClimateAgent, an autonomous multi-agent framework that orchestrates end-to-end climate data analytic workflows. ClimateAgent decomposes user questions into executable subtasks coordinated by an Orchestrate-Agent and a Plan-Agent; acquires data via specialized Data-Agents that dynamically introspect APIs to synthesize robust download scripts; and completes analysis and reporting with a Coding-Agent that generates Python code, visualizations, and a final report with a built-in self-correction loop. To enable systematic evaluation, we introduce Climate-Agent-Bench-85, a benchmark of 85 real-world tasks spanning atmospheric rivers, drought, extreme precipitation, heat waves, sea surface temperature, and tropical cyclones. On Climate-Agent-Bench-85, ClimateAgent achieves 100% task completion and a report quality score of 8.32, outperforming GitHub Copilot (6.27) and a GPT-5 baseline (3.26). These results demonstrate that our multi-agent orchestration with dynamic API awareness and self-correcting execution substantially advances reliable, end-to-end automation for climate science analytic tasks. The source code of ClimateAgent is available at https://github.com/Relaxed-System-Lab/ClimateAgent.