Scientific Code Generation

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2 papers in the last four weeks, with none the four weeks before. 0.0% of all new papers.

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Latest papers 36

Oct 5, 2026cs.LG

SimAuthor: Harnessing Foundation Models for Persistent Scientific Simulator Authoring

Foundation models can generate scientific code, but authoring a scientific simulator (an executable program encoding hypotheses about how mechanisms generate observable signals) requires iterative refinement. Scientific adequacy rarely admits a unique implementation or exact test, so simulators must instead be judged against limited real observations. We study this setting as scientific simulator authoring under weak empirical feedback, where distributional comparisons between simulated and real signals guide revision, and the target is the simulator itself rather than only its generated samples. We introduce SimAuthor, a persistent authoring harness that retains and revises executable simulators, separates scalar search scores from structured discrepancy feedback, and accumulates reusable implementation mechanisms. We evaluate SimAuthor on six biomedical tasks spanning cardiac and respiratory audio, photoplethysmography (PPG), and electrocardiography (ECG). Under a fixed 100-attempt budget, SimAuthor outperforms PUCT score search on all six tasks, generally outperforms textual-strategy optimization, and achieves the highest endpoint score on five of six. The authored simulators also improve on unseen recordings, transfer to independent pretrained representations, and yield substantial out-of-distribution gains in downstream ECG classification. Finally, 111 of 138 audited revisions alter program structure and account for 86.1% of the signed score improvement. These results suggest that persistent revision can progressively convert foundation-model knowledge into better executable scientific simulators from limited empirical evidence.

Yishan Wang, Ran Piao, Mathias Funk +1

Eindhoven University of Technology

LLM-Based Program Synthesis Scientific Code Generation

Sep 28, 2026cs.AI

Towards Certificate-Driven Software Porting: A Self-Improving Agentic Harness for Scientific Program Optimization

The upgrade and rewriting of large scientific codebases has traditionally been a major challenge. While evolutionary search with large language models (LLMs) can port and accelerate legacy code, repair feedback in prompts alone does not prevent subsequent candidates from repeating the same errors. We introduce Certificate-Driven Evolutionary Search (CDES), which extends evolutionary search with enforceable restrictions derived from failed candidates, recorded as certificates of assumptions, checker evidence, and justified restrictions. Its control logic enforces these restrictions through rejection, backtracking, and targeted repair while preserving compatible edits. We apply CDES to CPU-to-GPU translation of two particle-simulation functions from the Geant4 toolkit, evaluated with a harness that goes beyond unit tests to combine formal checks, numerical comparisons, physics checks, and GPU safety tests. Generated implementations achieve 13.78x and 23.54x function-level speedups over CPU code, including data conversion and transfers; for one function, GPU throughput exceeds an expert implementation by 14.9%, reaching 16.1% when complementary components are combined. In an ablation over execution settings, certificate feedback increases the fraction of candidates passing required correctness checks from 55% to 90%.

Piyush Jha, Aishik Ghosh, Vijay Ganesh

School of Computer Science, Georgia Institute of Technology, USA · School of Physics, Georgia Institute of Technology, USA · Lawrence Berkeley National Laboratory, USA

Code Translation GPU Kernel Optimization Evolutionary Optimization Large Language Model-Guided Optimization Scientific Code Generation

Sep 24, 2026cs.AI

SciWalker: Synthesizing Scientific Coding Problems with Operator Graphs and Execution Feedback

Improving the scientific coding capabilities of large language models (LLMs) requires high-quality training data. However, such data remain scarce because manually authoring realistic problems is costly and time-consuming, while systematically covering diverse scientific domains and algorithmic combinations remains challenging. To address this, we introduce SciWalker, a framework for synthesizing scientific coding problems through operator-chain sampling and execution feedback. The framework combines scientific library interfaces with operation modes to instantiate operators, organizes them into operator graphs, and samples operator chains as computational workflow cues. Guided by these cues, we adopt LLMs to generate scientifically grounded problem statements, reference solutions, and tests, with failed generations iteratively repaired using execution feedback. By combining structured workflow composition with verification and quality review, SciWalker enables scalable task generation while promoting scientific grounding, computational diversity, and executability. Using this framework, we construct 8,178 high-quality problems spanning 5 scientific domains and 32 subdomains. To evaluate their training utility, we conduct reinforcement learning on Qwen3.5-9B using the GSPO algorithm. This training improves SciCode subproblem accuracy by 9.9 percentage points, from 29.3% to 39.2%, with gains across scientific code generation, code repair, and reasoning benchmarks. The code for SciWalker is available at https://github.com/lichenx1/SciWalker.

Chenxi Li, Wenxuan Zeng, Yun Luo +4

The Hong Kong University of Science and Technology · Shanghai AI Laboratory · Tsinghua University +1

Execution-Guided Code Generation Scientific Code Generation Synthetic Benchmark Generation Synthetic Data Generation for Language Models

Aug 9, 2026cs.LG

Idea Search: Guiding Tree Search with Ideas to Explore Diverse Scientific Methods

Tree Search-based test-time scaling of LLMs is a powerful tool for automated scientific coding. However, pure Tree Search sometimes struggles with systematic exploration, becoming trapped in local optima, or unproductive loops, especially in the vast search space of scientific methods. To address this limitation, we propose Idea Search, a framework that systematically integrates a dynamic "Idea Bank" into Tree Search. Idea Search involves three steps: (1) decomposing existing methods into atomic ideas, (2) sampling from this bank of ideas to guide branches of code mutations, and (3) dynamically updating the bank with new ideas discovered through execution. On single-cell RNA-sequencing (scRNA-seq) batch integration, Idea Search reliably breaks the plateau of a strong pure Tree Search baseline, improving the mean score from 0.678 to 0.697 and reaching a best score of 0.728. We then characterize which design choices drive these gains: bank augmentation helps bandit sampling but not random sampling, "Exploratory" prompting that prioritizes new ideas surfaces the rare best-performing solutions, while increasing sampling-level exploration is counterproductive.

Xuefei Julie Wang, Hao Cui, Michael P. Brenner +1

California Institute of Technology · *Work done during an internship at Google Research. · Google Research +1

Inference-Time Search Automated Algorithm Discovery Scientific Code Generation Large Language Model-Guided Scientific Discovery

Aug 5, 2026cs.SE

SciCode-Verified: How Benchmark Defects Underestimated the Scientific-Coding Ability of Language Models

SciCode is the standard measure of the scientific-coding ability of language models: research-level problems that demand both frontier scientific theory and its implementation as working numerical code. It is a component of the Artificial Analysis Intelligence Index and a standing evaluation in government and national-laboratory suites. Yet its scores have recently plateaued: the strongest 2026 models cluster tightly around 60% subproblem accuracy, and a successor model ties its predecessor. We trace this stagnation to defects in the benchmark itself. A per-problem, domain-expert audit of all 65 test problems uncovers 263 defects; 192 of them, spread across 91% of the main problems, cause correct, instruction-following solutions to be wrongly rejected---through non-reproducible gold answers, over-tight tolerances, or self-contradictory specifications. Critically, 78% of these score-suppressing defects require specialized physics or mathematics knowledge to detect, not mere clerical proofreading. We corrected every confirmable defect to produce SciCode-Verified. The corrections add only the specifications a well-posed problem requires, repair grading, and tighten the tests that were too lenient; every change is recorded with its justification and independently re-checked by a second domain expert. We re-evaluate twelve frontier model snapshots on the corrected benchmark and find a substantial recovery: subproblem accuracy rises from 45--60% to 84--98%, and main-problem accuracy from 9--27% to 69--92%. State-of-the-art models are far more proficient in scientific coding than SciCode has suggested---the bottleneck was not model capability, but the quality of the evaluation instrument. We release SciCode-Verified with its complete audit trail as the corrected public standard.

Sihan Hu, Lyuhan Huang, Youjin Deng +1

Hefei National Laboratory College of Mechanical and Electrical Engineering University of Science and Technology of China · Hefei National Laboratory Institute of Theoretical Physics University of Science and Technology of China Chinese Academy of Sciences Hefei 230026, China · Chinese Academy of Sciences Beijing 100190, China

LLM Evaluation Scientific Code Generation Benchmark Validity Code Generation Benchmarks

Jul 31, 2026physics.chem-ph

MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows

Accelerating scientific discovery is among the most consequential applications of AI, and computational biomolecular simulation stands out as a particularly promising target within this broader effort. Coding agents promise to automate significant portions of this workflow, yet their reliability on realistic molecular dynamics (MD) tasks remains poorly characterized. To address this issue, we introduce MDArena, a benchmark of 50 containerized tasks drawn from active biomolecular simulation projects, spanning 29 molecular systems and 14 broad research protocols, including trajectory analysis, complex system preparation, free-energy protocols, and enhanced sampling. We evaluate six model/harness configurations spanning Codex and OpenCode. Among the evaluated configurations, Codex GPT-5.5 at extra-high reasoning effort performs best, reaching 24/50 Strict-Pass@1 successes (48%), followed by Codex GPT-5.5 Medium with 21/50, and OpenCode Gemini Flash 3.5 with 20/50. Average correctness and process rewards are substantially higher than strict success rates across all configurations, indicating that agents frequently make meaningful partial progress but fail on the fine-grained details required for reproducible scientific workflows. Hard tasks remain largely unsolved, particularly membrane-protein system preparation and alchemical free-energy setup, both unsolved or near-unsolved by every evaluated configuration. MDArena thus exposes a substantial gap between the usefulness of coding agents as supervised assistants and their reliability as autonomous MD researchers, while providing a reproducible and extensible platform for tracking progress toward closing it.

Nithishwer Mouroug Anand, Wei-Tse Hsu, Kyle Vaccaro +6

Department of Biochemistry, University of Oxford · Scripps Research Institute

Coding Agents Scientific Code Generation AI Agent Benchmarks Scientific Workflow Automation Molecular Dynamics Simulation

Jul 27, 2026cs.AI

From Execution to Capability: Scientific Experience Consolidation via Procedural Knowledge Synthesis

Large language models increasingly solve scientific-computing tasks, but executable feedback from one problem rarely becomes durable capability on subsequent problems. We study scientific-computing experience consolidation: converting verified runtime experience into transferable procedural knowledge and persistent model improvement. This setting presents two challenges: trajectory-derived artifacts may encode source-specific repairs rather than cross-task computational mechanisms; and a weaker target model may be unable to operationalize an otherwise valid abstract procedure - an abstraction-execution gap. We introduce SciConsolidate, which contrasts verified successes and failures to induce cross-task procedures, selects them through a development-validation gate, and uses failure-informed, answer-free query synthesis to expand the consolidation data without requiring pre-existing reference answers. Because the target model may not directly execute these abstractions, a stronger model concretizes them into executable code supervision for standard, procedure-free SFT; a matched no-procedure teacher branch isolates the value of procedural guidance. On SciCode, runtime procedure injection improves Qwen3.6-27B by +3.85/+6.26 sub-step/main-problem points, but yields almost no aggregate main-problem gain for Qwen3.5-9B, providing operational evidence of the abstraction-execution gap. After procedure-guided concretization, the 9B student improves under procedure-free deployment by +3.89/+6.25 points over the no-procedure SFT control and by +5.62/+11.25 over the original 9B model. These results establish an experience-to-capability pathway for scientific computing and provide a practical starting point for scaling self-improving scientific assistance.

Liwei Dong, Jiahao Zhao, Nan Xu

ScienceOne AI

Continual Learning for LLMs Scientific Code Generation

Jul 23, 2026cs.SE

Enhancing SLMs for Sustainable Code Optimization in Radio-Astronomy

Recent Large Language Models (LLMs) can produce and optimize complex code. We investigate the use of LLMs to generate and optimize code for large-scale sciences, focusing on radio astronomy and sustainability. The LOFAR telescope is currently being upgraded, significantly increasing the sky area observed, while simultaneously processing more data faster. However, this is expected to increase the computational requirements 40-fold. This upgrade thus critically depends on rigorous performance optimization of existing software and widespread adoption of accelerators. The code base is very large, making this a daunting task. We therefore investigate and demonstrate an AI-driven approach meant to assist developers in evaluating and optimizing their code, including porting to hardware accelerators. The LOFAR community is committed to sustainable solutions, and needs to achieve these improvements without increasing the energy budget. We thus need to optimize existing codes or port them to accelerators, while making sure that the optimization process itself is also energy efficient. This poses a challenge, since LLMs are energy-intensive. We therefore propose to use Small Language Models (SLMs) instead to limit environmental impact. In this paper, we show how to enhance SLMs through the use of agentic AI. We extend the SLMs in two ways to improve code generation quality and performance: first with a multi-sampling generation strategy and second with incorporating compiler feedback. We demonstrate that multi-sampling SLMs can match or surpass larger single-generation models with fewer computational resources and that feeding compiler output back into the SLMs leads to consistent improvements across all tested models. Our approach is generic, and can also use Retrieval Augmented Generation (RAG) as well as static and dynamic analysis tools in the code generation pipeline.

Elisa Chiarotto, Jingbo Li, P. Chris Broekema +1

LIACS, Leiden University · NWO-I ASTRON

Large Language Model-Guided Optimization Code Generation Small Language Models Scientific Code Generation

Jul 23, 2026cs.LG

Automated Synthesis and Adversarial Validation of Executable Causal Research Pipelines

While automated research systems promise to accelerate empirical analysis, they are prone to silent failures: instances in which analysis code executes successfully yet relies on invalid causal assumptions. We present the Artificial Intelligence (AI)-based Epidemiology Research Assistant (ARA), a framework that makes these failures visible by explicitly encoding causal design principles, study-specific assumptions, and methodological constraints. ARA integrates protocol construction, synthetic data generation, and adversarial validation into a unified pipeline. The framework translates natural language research questions into structured causal protocols and executable analysis code by first constructing a protocol and then generating synthetic datasets using Structural Causal Models (SCMs) with known ground-truth effects. This synthetic-data step can also support pipeline development when access to confidential data, such as medical data, is restricted. The generated analysis is then evaluated under controlled violations of identification assumptions. We evaluate ARA on the Automated Causal Reasoning Benchmark, assessing recovery of identification strategies, causal quantities, treatment and outcome variables, and consistency between generated code and approved protocol. Protocol construction and adversarial validation did not consistently improve numerical agreement with benchmark estimates compared with standard LLM-based generation. However, they changed the failure mode: instead of silently returning causal estimates, ARA often surfaced protocol concerns, diagnostic failures, incomplete inference, or downgraded non-causal interpretations. These findings suggest that validity-first automated science systems should be evaluated not only by answer accuracy, but also by whether they indicate when causal claims are unwarranted.

Irena Girshovitz, Dan Zeltzer, Ran Gilad-Bachrach

School of Biomedical Engineering Tel Aviv University Tel Aviv, Israel · School of Public Health University of California, Berkeley Berkeley, CA, USA

AI-Assisted Scientific Research Scientific Code Generation Causal Inference

Jul 21, 2026cs.SE

SciCodePile: A 128GB Corpus and Executable Benchmark for Challenging Scientific Code Generation

Large language models (LLMs) excel at general-purpose code generation, yet how well they handle scientific code remains an open question. Existing datasets and benchmarks are limited in scale, domain coverage, or executable verification, leaving the true gap between current LLMs and reliable scientific code generators inadequately assessed. To address these limitations, we present SciCodePile, the largest scientific code corpus to date, constructed from 37,737 public repositories and collectively comprising 128GB of code that spans multiple computational science disciplines. From this corpus, we further curate an executable benchmark of 200 tasks, each equipped with a sandboxed execution environment and an automated test harness for functional verification. We evaluate 15 LLMs from both open-source and closed-source families on three tasks: prefix-to-suffix completion, fill-in-the-middle infilling, and executable code generation. Results show that scientific code generation remains highly challenging: The best CodeBLEU reaches only 38.13 and 38.37 on the two completion tasks, while the strongest model achieves just 12.30% Pass@1 on the executable benchmark, underscoring how far current models remain from reliable scientific code generation. To demonstrate the training utility of SciCodePile, we further show that continued pretraining on our corpus improves CodeBLEU by

\times

2.84 on scientific code completion, and instruction tuning on our data improves Pass@1 by

\times

4.79 on the executable benchmark. All code and data are available at https://huggingface.co/SciCodePile.

Weifeng Sun, Ye Fan, Yuchen Chen +6

Singapore Management University · Nanjing University · SUN YAT-SEN University +1

Scientific Code Generation Code Generation Evaluation Code Generation Benchmarks

Jul 18, 2026cs.AI

From Overload to Insights: How AI Agents Can Support Scientists in Analyzing Complex Data

Scientists at European XFEL conduct experiments that generate very large and complex datasets. The subsequent data analysis is challenging as scientists must combine their domain expertise with facility- and software-specific knowledge scattered across documentation, tools, and support channels. To address this problem, we designed and evaluated an agentic AI system tailored to the scientists' needs and integrated with the high-performance computing environment of European XFEL. Using a design science research approach, we conducted a rapid literature review, a systematic evaluation of 16 AI tools, multiple interviews, a focus group, and a user study with experts at European XFEL to develop and evaluate two prototypes. Our study identifies key knowledge challenges in scientific data analysis, derives requirements for an AI agent that supports knowledge retrieval and source code generation, and proposes design recommendations for a specialized system adaptable to the evolving AI tool landscape. These findings provide guidance for developing maintainable AI support in highly specialized scientific environments.

Tim Fuchs, Luca Gelisio, Steffen Hauf +1

University of Hamburg Hamburg, Germany · European XFEL Schenefeld, Germany · Hasso Plattner Institute University of Potsdam Potsdam, Germany

AI for Science AI-Assisted Scientific Research Scientific Code Generation Information Retrieval

Jul 16, 2026hep-lat

LQCDMaster: Agentic Scientific Computing for Lattice Quantum Chromodynamics Research

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.

Haofei Gao, Tingjia Miao, Wenkai Jin +12

School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, 200240, China. · Tsung-Dao Lee Institute, Shanghai Jiao Tong University, Shanghai, 200240, China. · State Key Laboratory of Dark Matter Physics, Shanghai Jiao Tong University, Shanghai, 200240, China. +6

Scientific Code Generation High-Energy Physics Scientific Workflow Automation

Jul 11, 2026cs.LG

Reinforcement Learning with Verifiable Physics: Post-training LLMs with Continuous Rewards

Partial differential equations (PDEs) are foundational to modeling in science and engineering, but constructing reliable numerical solvers remains labor-intensive, demanding expert knowledge of discretization schemes, stability conditions, and boundary treatments. Recent work has begun to frame PDE solving as a code-generation task for large language models (LLMs), yet existing approaches operate primarily at inference time: relying on prompting, debugging, self-refinement, and test-time scaling rather than adapting the model itself. In parallel, reinforcement learning with verifiable rewards has emerged as a post-training paradigm for code and math reasoning, but its verifiers are typically binary: a compiler runs, or a test passes. Such signals discard the graded structure of scientific correctness, where two solvers may both execute and yet differ in solution accuracy by orders of magnitude. In this work, we introduce RLVP: Reinforcement Learning with Verifiable Physics, an RL post-training framework for multi-PDE solver code generation. RLVP addresses this verifiability gap with a hybrid verifier: hard program-validity checks ensure executability, while continuous physics rewards score function-space accuracy and PDE-residual consistency. A single policy is post-trained across diverse PDE families spanning hyperbolic, parabolic, elliptic, and incompressible-flow systems. RLVP improves over both pre-trained and supervised-only baselines on PDE benchmarks, and shows zero-shot improvement transfer to held-out PDEs. We show that a smaller LLM post-trained with RLVP can outperform prompting a frontier model on in-distribution PDE solver generation. The trained policy shows evidence of compositionality in numerical motifs: it recombines stencils, time-stepping schemes, and boundary-handling primitives learned from the PDEs used in training into generated solvers for unseen PDE problems.

Pengfei Cai, Utkarsh Utkarsh, Alan Edelman +2

Massachusetts Institute of Technology

RL for Code Generation Scientific Code Generation Reinforcement Learning with Verifiable Rewards RL Post-Training Reward Design for RL

Jul 7, 2026cs.HC

Plainbook: Data Science, in Plain Language

Jupyter Notebooks have become widely adopted in data science, as they allow the sharing of reproducible computational analysis. They are, however, accessible only to people who understand computer code. To reach the broader audience of scientists interested in data analysis and computation, but unfamiliar with code, we introduce Plainbook, notebooks centered on natural language rather than code. Plainbook is based on two principles: promote the natural language descriptions, and verify the values. In plainbook, the natural language descriptions are preserved, rather than the resulting code; the code is generated automatically from the cell descriptions. As natural language is read top to bottom, Plainbook adopts a linear execution semantics, in which cells are guaranteed to be executed in the order in which they appear; there is no "hidden state" or out-of-order execution as in Jupyter. To allow users who may not understand code to verify the correctness of the computation, we have built into Plainbook verification mechanisms centered on values and value inspection. These include mechanisms that focus on individual cells, akin to unit tests, as well as global mechanisms. Both the linear execution semantics, and the verification mechanisms, are underpinned by a snapshot kernel that caches execution states and makes execution and verification efficient.

Luca de Alfaro, Mathis Aubert, Ranjit Jhala +2

University of California · Santa Cruz, California, USA · San Diego, California, USA +2

Scientific Code Generation Scientific Reproducibility

Jul 2, 2026cs.SE

LLMoxie: Exploring Agentic AI for Scientific Software Development

In this paper, we describe LLMoxie, an institutional AI platform whose three-tiered architecture supports multi-cloud and on-premise inference, a LiteLLM/MLflow control plane for authentication, budgeting, PII masking, and observability, and an application augmentation layer for AI coding agents. Layered on top, an open-source RSE-Plugins ecosystem encodes accumulated RSE knowledge as a Plugin-Agent-Skill hierarchy spanning scientific Python practice, domain-specific knowledge, a six-phase research-and-implement workflow, and project lifecycle management. Scientific software is judged less by raw code quality than by whether it can be cited, audited, reproduced, and extended. Off-the-shelf AI coding agents, optimized against commercial software benchmarks, are poorly calibrated for this setting: they ignore the conventions of the scientific Python libraries they invoke, mishandle sensitive or embargoed data, and leave decision trails that are difficult to reconstruct after the fact. We report on twenty months of practice at a university-based research software engineering (RSE) center, where RSEs embedded across astronomy, earth and climate science, agriculture, and health projects worked to close this gap. We characterize the recurring infrastructure, governance, and process challenges of adopting Agentic AI inside a multi-domain RSE center, describe the platform and plugin design, and distill operational lessons from real scientific software deployments. Together, the platform and plugins shift AI coding agents from generic code generators into domain-aware collaborators that respect community norms and produce auditable provenance of technical reasoning.

Landung Setiawan, Anant Mittal, Cordero Core +5

eScience Institute University of Washington Seattle, Washington, USA · eScience Institute Dept of Chemical Engineering University of Washington Seattle, Washington, USA · eScience Institute Dept of Astronomy University of Washington Seattle, Washington, USA

Scientific Code Generation AI Agent Governance LLM Agent Harnesses

Jun 30, 2026cs.AI

A Self-Evolving Agentic System for Automated Generation and Execution of Biological Protocols

Autonomous wet-lab experimentation requires more than plausible protocol text: biological intent, quantitative procedures, device constraints and experimental feedback must remain aligned from protocol and SOP design to code and physical execution. We developed ProtoPilot, a self-evolving multi-agent system, together with an expert-grounded benchmark and evaluation framework for testing this conversion as an experimental automation problem. The framework spans 294 synthetic-biology and molecular-biology tasks derived from 98 gold-standard protocols, wet-lab expert rubrics, device-level validity gates and real experimental tests. ProtoPilot incorporates layer-wise verifiability, multi-agent orchestration and a runtime-updated skill library to generate protocols, expand SOPs, synthesize SDK-compliant code and revise workflows from wet-lab feedback. It achieved a Top@3 expert-preference rate of 90.2%, an overall protocol-to-code gate pass rate of 89.5% and an Opentrons pass rate of 88.24%, compared with 32.35% for OpenTrons-AI. Wet-lab validation produced interpretable readouts, Sanger-confirmed products and feedback-corrected PCA-assembled DNA targets, establishing a verifiable route to autonomous experimentation. Together, these results show that the evaluation framework captures execution-relevant requirements for autonomous wet-lab automation, and that ProtoPilot can meet them by converting protocol and code generation into validated execution and feedback-guided revision.

Yankai Jiang, Weiting Tang, Haoran Sun +11

1Shanghai Artificial Intelligence Laboratory, Shanghai, China · 2Genoria AI, Shenzhen, China

Scientific Code Generation Laboratory Automation Scientific Workflow Automation Autonomous Experimentation Self-Evolving Agents

Jun 8, 2026cs.AI

Auto-Configuring Scientific Simulators with Lightweight Coding-Agent Adapters

Configuring an advanced scientific simulator, translating a modeling goal into a valid, runnable input deck, is a persistent bottleneck that costs domain scientists hours to days. Input decks are executable interfaces: simulator-specific vocabulary, cross-file references, schema constraints, and validation rules must align before a simulation can run. We show that this bottleneck can be substantially reduced with a lightweight adapter around an off-the-shelf coding agent, rather than a bespoke simulator agent. Coding agents already navigate files, edit code, run commands, and repair outputs; what they lack is the simulator's executable contract, and rebuilding the agent loop risks discarding harness-calibrated tool-use and self-correction behavior. We introduce SIGA, a coding-agent adapter that supplies this contract through retrieval, procedural memory, agent-callable validation, and validation-gated termination while leaving the model and loop frozen. Because this contract is small and external, SIGA also supports adapter self-evolution: prior trajectories can rewrite the adapter contents without modifying the underlying agent. On GEOS, a multiphysics subsurface simulator, SIGA's main gain is reliability: on harder held-out tasks it improves TreeSim from 0.720 to 0.789 and reduces across-run standard deviation by about 16x by preventing empty or invalid decks. In a human calibration, SIGA reaches in about five minutes the deck quality a domain expert reached in about three hours. Transfers to OpenFOAM and LAMMPS show the recipe is portable but interface-dependent: completion gates help when structural completeness is the bottleneck, while memory and retrieval help when value correctness is.

Matthew Ho, Brian Liu, Jixuan Chen +2

University of California, San Diego

Coding Agents Scientific Code Generation LLM Agent Reliability

Jun 5, 2026cs.AI

A case study of evaluating AI agents on a neuroscience data-to-discovery pipeline

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.

Kai A. Horstmann, Ethan Lin, Alice A. Robie +2

Cornell University · HHMI Janelia Research Campus

AI Agent Evaluation Scientific Code Generation AI Agent Benchmarks Scientific Workflow Automation

May 23, 2026cs.AI

GRAIL: AI translation for scientists application workflow on satellite data

Domain scientists increasingly develop Python scripts to analyze satellite imagery but they lack scalability to large-scale data. This paper demonstrates GRAIL, an agentic translation system that converts Python geospatial workflows into executable Spark-based programs without requiring scientists to learn a new framework. Rather than fine-tuning a specialized LLM model, GRAIL adapts RDPro, a Scala library for satellite data analysis, to make it LLM-ready using structured documentation, API alias functions, and repair-oriented error logs. Translation is structured as a LangGraph pipeline that decomposes code generation into explicit sections with guided inputs and outputs, enabling targeted repair without regenerating the full program. We demonstrate GRAIL on real-world geospatial workflows and showcase the correctness and scalability of the translated code.

Zhuocheng Shang, Ahmed Eldawy

University of California, Riverside · Riverside, California

Code Translation Scientific Code Generation Scientific Workflow Automation

May 12, 2026cs.AI

CVEvolve: Autonomous Algorithm Discovery for Unstructured Scientific Data Processing

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

Ming Du, Xiangyu Yin, Yanqi Luo +4

Advanced Photon Source Argonne National Laboratory Lemont, IL, USA

Automated Algorithm Discovery Scientific Code Generation Autonomous Scientific Discovery Large Language Model-Guided Scientific Discovery

May 10, 2026cs.AI

PDEAgent-Bench: A Multi-Metric, Multi-Library Benchmark for PDE Solver Generation

PDE-to-solver code generation aims to automatically synthesize executable numerical solvers from partial differential equation (PDE) specifications. This task requires not only understanding the mathematical structure of PDEs, but also selecting appropriate discretization schemes and solver configurations, and correctly implementing the resulting formulations in finite-element method (FEM) libraries. Existing code generation benchmarks mainly evaluate syntactic correctness, or success on predefined test cases. To our knowledge, there is currently no publicly available benchmark specifically for PDE-to-solver code generation, and general-purpose code benchmarks do not fully capture the unique challenges of numerical PDE solution, such as ensuring solver accuracy, efficiency, and compatibility with professional FEM libraries. We introduce PDEAgent-Bench, to the best of our knowledge, the first multi-metric, multi-library benchmark for PDE-to-solver code generation. PDEAgent-Bench contains 645 instances across 6 mathematical categories and 11 PDE families, with common FEM libraries for DOLFINx, Firedrake, and deal.II. Each instance provides an agent-facing problem specification, a reference solution on a prescribed evaluation grid, and case-specific accuracy and runtime targets. PDEAgent-Bench adopts a staged evaluation framework in which generated solvers must sequentially pass executability, numerical accuracy, and computational efficiency checks. Experiments with representative LLMs and code agents show that models can often produce runnable code, but their pass rate drops substantially once accuracy and efficiency requirements are enforced. These results indicate that current agents remain limited in producing numerically reliable and efficient PDE solvers, and that PDEAgent-Bench provides a reproducible testbed grounded in the practical requirements of numerical PDE solving.

Zhen Hang, Yushan Yashengjiang, Junhui Li +21

University of Science and Technology of China · Beijing University of Posts and Telecommunications · Tencent +10

PDE Solving Benchmark Design Scientific Code Generation Finite Element Method Code Generation Benchmarks

May 10, 2026cs.LG

Your Simulation Runs but Solves the Wrong Physics: PDE-Grounded Intent Verification for LLM-Generated Multiphysics Simulation Code

Execution-based evaluation of LLM-generated code implicitly treats successful execution as a proxy for correctness. In scientific simulation, this proxy is insufficient: a generated input file can run, mesh, and converge while encoding governing equations that differ from the user's intent. We call this mismatch between intended physics and generated code the comprehension-generation gap. We instantiate this in MOOSE, where Kernel and BC objects map compositionally to weak-form residual terms, enabling deterministic reconstruction of the encoded PDE and comparison against an intended contract. We formalize this comparison as the Intent Fidelity Score (IFS), a structural metric covering governing terms, BCs, ICs, coefficients, and time scheme. Building on IFS, we develop a PDE-grounded refinement loop that uses deterministic violation reports to correct generated code iteratively. We evaluate on MooseBench, a 220-case multiphysics benchmark with PDE-level ground truth released with this work. On this benchmark, our method consistently improves mean IFS over direct generation, with gains concentrated on hard cases. On the subset where direct generation falls below IFS 0.7, refinement adds +0.22 to +0.41 absolute IFS. In the deployment audit, execution-only repair improves execution success while leaving 39-40% of all 220 cases runnable but still solving the wrong physics across the three main deployment-audit models, exposing executability and intent fidelity as separable failure modes. Static proof-of-concept experiments on four PDE-oriented DSLs (UFL/FEniCS, FreeFEM, FiPy, and Devito) suggest that the reconstruction-and-comparison pattern extends beyond MOOSE. These findings reinforce that executable simulation code should be verified against the mathematical structure it is intended to encode, not accepted on execution alone.

Zhenghan Song, Yulong Liu, Cheng Wan +4

Cornell University · Columbia University · Harvard University & Nanyang Technological University

LLM Self-Correction Scientific Code Generation Code Generation Evaluation Physics-Based Simulation

May 4, 2026cs.CL

MolViBench: Evaluating LLMs on Molecular Vibe Coding

Molecular Vibe Coding, a paradigm where chemists interact with LLMs to generate executable programs for molecular tasks, has emerged as a flexible alternative to chemical agents with predefined tools, enabling chemists to express arbitrarily complex, customized workflows. Unlike general coding tasks, molecular coding imposes a distinctive challenge that LLMs should jointly equip programming, molecular understanding, and domain-specific reasoning capabilities. However, existing benchmarks remain disconnected. General code generation benchmarks such as HumanEval and SWE-bench require no chemistry knowledge, while chemistry-focused benchmarks such as S^2-Bench and ChemCoTBench evaluate knowledge recall or property prediction rather than executable code generation. To bridge this gap, we introduce MolViBench, the first benchmark tailored for Molecular Vibe Coding. MolViBench comprises 358 curated tasks across five cognitive levels, ranging from single-API recall to end-to-end virtual screening pipeline design, spanning 12 real-world drug discovery workflows. To rigorously assess generated code, we also propose a multi-layered evaluation framework that combines type-aware output comparison and AST-based API-semantic fallback analysis, which jointly measures executability and chemical correctness. We systematically evaluate 9 frontier coding LLMs and compare three real-world Molecular Vibe Coding paradigms, providing a practical and fine-grained testbed for diagnosing LLMs' coding capabilities in AI-accelerated molecular discovery.

Jiatong Li, Yuxuan Ren, Weida Wang +4

The Hong Kong Polytechnic University · National University of Singapore · Fudan University

AI-Assisted Scientific Research Scientific Code Generation Code Generation Evaluation Code Generation Benchmarks Drug Discovery

May 2, 2026hep-ex

HepScript: A Dual-Use DSL for Human-AI Collaborative Data Analysis Workflows in High-Energy Physics

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.

Junkun Jiao, Tong Liu, Ke Li +6

Jilin University, Changchun, Jilin, China · Institute of High Energy Physics, CAS, Beijing, China · University of Chinese Academy of Sciences, Beijing, China

Scientific Code Generation High-Energy Physics Scientific Workflow Automation Human-AI Collaboration

Apr 29, 2026cs.SE

Theory Under Construction: Orchestrating Language Models for Research Software Where the Specification Evolves

Large language models can now generate substantial code and draft research text, but research-software projects require more than either artifact alone. The mathematical thesis, executable system, benchmark surface, and public claims must mature together, yet often drift apart. We identify two LM-specific failure modes: hallucination accumulation, in which claims exceed what code or theory supports and unsupported assertions propagate across sessions; and desynchronization, in which code, theory, or the model's own world model fall out of alignment. We propose Comet-H, an iterative prompt automaton that orchestrates ideation, implementation, evaluation, grounding, and paper-writing as coupled coordinates of a single workspace state. At each step, a controller selects the next prompt by scoring it against what the workspace currently lacks, carries unfinished follow-up work forward with a half-life, and re-checks the paper and README against the code and benchmarks whenever documentation changes. We frame prompt selection as a small contextual bandit problem over prompt families, with prompts as arms, workspace deficits as context, and a hand-weighted linear score. This transparent scorer, paired with a fading record of unfinished work, bounds long-horizon follow-ups, requires no learned policy, and makes each prompt choice legible from the workspace. We created a portfolio of 46 research-software repositories across two dozen domains. We study A3 in depth, a Python static-analysis tool built entirely within the loop, which reaches (F1 = 0.768) on a 90-case benchmark, compared with a next-best baseline of 0.364. Across approximately 400 commits, we find that audit-and-contraction passes dominate the later phases of every successful trajectory.

Halley Young, Nikolaj Björner

Microsoft Research

Software Engineering LLM Prompting Scientific Code Generation Autonomous Research Agents

Apr 27, 2026astro-ph.CO

spectroxide: A code package for computing cosmic microwave background spectral distortions

We present spectroxide, a code package for computing cosmic microwave background spectral distortions in which all

{\sim}14{,}500

lines of Rust code, Python interface, and

{\sim}400

automated tests were written by an AI assistant (Claude Code) under human physicist supervision. The solver evolves the photon Boltzmann equation under Compton scattering, double Compton emission, and Bremsstrahlung from

z \sim 5 \times 10^6

to the present, computing spectral distortions from arbitrary heat and photon injection within this redshift range. No fully open-source code of this kind is publicly available; we validate against analytic limits, published spectra, and publicly available precomputed Green's function tables. We document the development as a case study in AI-assisted scientific computing, highlighting how domain expertise caught physics bugs (incorrect dimensional prefactors, near-cancellation errors) that evaded the full automated test suite, and provide recommendations for best practices in human--AI collaborative development of scientific software. We make spectroxide publicly available on GitHub.

Ethan Baker, Hongwan Liu, Siddharth Mishra-Sharma

Physics Department, Boston University, Boston, MA 02215, USA · Faculty of Computing & Data Sciences, Boston University, Boston, MA 02215, USA

AI-Assisted Scientific Research Scientific Code Generation AI-Assisted Software Development

Apr 25, 2026cs.SE

No Test Cases, No Problem: Distillation-Driven Code Generation for Scientific Workflows

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.

Siddeshwar Raghavan, Tanwi Mallick

Purdue University · Electrical and Computer Engineering · West Lafayette, USA +3

Multi-Agent LLM Systems Code Generation Scientific Code Generation Scientific Workflow Automation

Apr 23, 2026cs.SE

Agentic AI-assisted coding offers a unique opportunity to instill epistemic grounding during software development

The capabilities of AI-assisted coding are progressing at breakneck speed. Chat-based vibe coding has evolved into fully fledged AI-assisted, agentic software development using agent scaffolds where the human developer creates a plan that agentic AIs implement. One current trend is utilizing documents beyond this plan document, such as project and method-scoped documents. Here we propose GROUNDING

.

md, a community-governed, field-scoped epistemic grounding document, using mass spectrometry-based proteomics as an example. This explicit field-scoped grounding document encodes Hard Constraints (non-negotiable validity invariants empirically required for scientific correctness) and Convention Parameters (community-agreed defaults) that override all other contexts to enforce validity, regardless of what the user prompts. In practice, this will empower a non-domain expert to generate code, tools, and software that have best practices baked in at the ground level, providing confidence to the software developer but also to those reviewing or using the final product. Undoubtedly it is easier to have agentic AIs adhere to guidelines than humans, and this opportunity allows for organizations to develop epistemic grounding documents in such a way as to keep domain experts in the loop in a future of democratized generation of bespoke software solutions.

Magnus Palmblad, Jared M. Ragland, Benjamin A. Neely

Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands · National Institute of Standards and Technology - Charleston, Charleston, SC USA

LLM Grounding Scientific Code Generation Agentic Code Generation AI-Assisted Software Development

Apr 21, 2026cs.AI

On Accelerating Grounded Code Development for Research

A major challenge for niche scientific and technical domains in leveraging coding agents is the lack of access to up-to-date, domain- specific knowledge. Foundational models often demonstrate limited reasoning capabilities in specialized fields and cannot inherently incorporate knowledge that evolves through ongoing research and experimentation. Materials scientists exploring novel compounds, communication engineers designing and evaluating new protocols, and bioengineering researchers conducting iterative experiments all face this limitation. These experts typically lack the resources to fine-tune large models or continuously embed new findings, creating a barrier to adopting AI-driven coding agents. To address this, we introduce a framework that gives coding agents instanta- neous access to research repositories and technical documentation, enabling real-time, context-aware operation. Our open-source im- plementation allows users to upload documents via doc-search.dev and includes zed-fork, which enforces domain-specific rules and workflows. Together, these tools accelerate the integration of coding agents into specialized scientific and technical workflows

Santosh Ganji

Coding Agents Code Generation AI-Assisted Scientific Research Scientific Code Generation

Apr 16, 2026cs.AI

El Agente Forjador: Task-Driven Agent Generation for Quantum Simulation

AI for science promises to accelerate the discovery process. The advent of large language models (LLMs) and agentic workflows enables the expediting of a growing range of scientific tasks. However, most of the current generation of agentic systems depend on static, hand-curated toolsets that hinder adaptation to new domains and evolving libraries. We present El Agente Forjador, a multi-agent framework in which universal coding agents autonomously forge, validate, and reuse computational tools through a four-stage workflow of tool analysis, tool generation, task execution, and iterative solution evaluation. Evaluated across 24 tasks spanning quantum chemistry and quantum dynamics on five coding agent setups, we compare three operating modes: zero-shot generation of tools per task, reuse of a curriculum-built toolset, and direct problem-solving with the coding agents as the baseline. We find that our tool generation and reuse framework consistently improves accuracy over the baseline. We also show that reusing a toolset built by a stronger coding agent can reduce API cost and substantially raises the solution quality for weaker coding agents. Case studies further demonstrate that tools forged for different domains can be combined to solve hybrid tasks. Taken together, these results show that LLM-based agents can use their scientific knowledge and coding capabilities to autonomously build reusable scientific tools, pointing toward a paradigm in which agent capabilities are defined by the tasks they are designed to solve rather than by explicitly engineered implementations.

Zijian Zhang, Aiwei Yin, Amaan Baweja +4

Department of Computer Science, University of Toronto, 40 St George St., Toronto, ON M5S 2E4, Canada · Vector Institute for Artificial Intelligence, W1140-108 College St., Schwartz Reisman Innovation2026 Campus, Toronto, ON M5G 0C6, Canada · NVIDIA, 431 King St W #6th, Toronto, ON M5V 1K4, Canada +5

Multi-Agent LLM Systems AI for Science Scientific Code Generation Tool-Using Agents LLM Agents