Scientific Code Generation

Large language models can write scientific code, but direct paper-to-program translation remains fragile when correctness depends on tacit conventions rather than explicit equations. We frame this as a knowledge-externalization problem: index choices, gauges, fermionic signs, contraction order, validation gates, and scaling constraints must be made explicit before code generation. We evaluate a multi-stage, human-in-the-loop workflow on two quantum many-body tasks. DMRG from Schollwoeck's pedagogical review serves as calibration: specification-guided implementations pass in all 16 model pairings, compared with 6/13 direct attempts, and a prose-specification ablation shows that externalized content, not LaTeX form, is the active ingredient. Pfaffian conversion of HFB states to MPS from the five-page Letter by Jin et al. serves as the stress test: the archived runs use a closed-world NumPy/SciPy/Matplotlib protocol, with no TeNPy, TeMFpy, or external implementation code supplied to the agents, so success depends on reconstructing tacit sign, gauge, ordering, and scalability conventions within a restricted dependency setting. Here the workflow yields 11/26 audited passes, while direct prompting yields none. Cross-specification transfer is asymmetric: non-GPT specifications implemented by GPT 5.5 pass 4/4, whereas GPT 5.5 specifications implemented by the tested non-GPT models fail 4/4. The contrast supports a two-bottleneck picture. Externalization resolves the first bottleneck -- paper-to-code ambiguity -- well enough to make DMRG reproducible and Pfaffian-MPS auditable. The remaining failures expose a second bottleneck in implementation-model capability. Iterative meta-specification moves this boundary but does not eliminate it. The resulting Paper-to-Program Many-Body skill is both a reusable implementation protocol and a diagnostic instrument for AI-assisted many-body programming.

The increasing adoption of Large Language Models (LLMs) has enabled AI scientists to perform complex end-to-end scientific discovery tasks requiring coordination of specialized roles, including idea generation and experimental execution. However, most state-of-the-art AI scientist systems rely on static, hand-designed pipelines and fail to adapt based on accumulated interaction histories. As a result, these systems overlook promising research directions, repeat failed experiments, and pursue infeasible ideas. To address this, we introduce EvoScientist, an evolving multi-agent AI scientist framework that continuously improves research strategies through persistent memory and self-evolution. EvoScientist comprises three specialized agents: a Researcher Agent (RA) for scientific idea generation, an Engineer Agent (EA) for experiment implementation and execution, and an Evolution Manager Agent (EMA) that distills insights from prior interactions into reusable knowledge. EvoScientist contains two persistent memory modules: (i) an ideation memory, which summarizes feasible research directions from top-ranked ideas while recording previously unsuccessful directions; and (ii) an experimentation memory, which captures effective data processing and model training strategies derived from code search trajectories and best-performing implementations. These modules enable the RA and EA to retrieve relevant prior strategies, improving idea quality and code execution success rates over time. Experiments show that EvoScientist outperforms 7 open-source and commercial state-of-the-art systems in scientific idea generation, achieving higher novelty, feasibility, relevance, and clarity via automatic and human evaluation. EvoScientist also substantially improves code execution success rates through multi-agent evolution, demonstrating persistent memory's effectiveness for end-to-end scientific discovery.

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.

Despite long-standing efforts in accelerating scientific discovery with AI, building AI co-scientists remains challenging due to limited high-quality data for training and evaluation. To tackle this data scarcity issue, we present AutoSDT, an automatic pipeline that collects high-quality coding tasks in real-world data-driven discovery workflows. AutoSDT leverages the coding capabilities and parametric knowledge of LLMs to search for diverse sources, select ecologically valid tasks, and synthesize accurate task instructions and code solutions. Using our pipeline, we construct AutoSDT-5K, a dataset of 5,404 coding tasks for data-driven discovery that covers four scientific disciplines and 756 unique Python packages. To the best of our knowledge, AutoSDT-5K is the only automatically collected and the largest open dataset for data-driven scientific discovery. Expert feedback on a subset of 256 tasks shows the effectiveness of AutoSDT: 93% of the collected tasks are ecologically valid, and 92.2% of the synthesized programs are functionally correct. Trained on AutoSDT-5K, the Qwen2.5-Coder-Instruct LLM series, dubbed AutoSDT-Coder, show substantial improvement on two challenging data-driven discovery benchmarks, ScienceAgentBench and DiscoveryBench. Most notably, AutoSDT-Coder-32B reaches the same level of performance as GPT-4o on ScienceAgentBench with a success rate of 7.8%, doubling the performance of its base model. On DiscoveryBench, it lifts the hypothesis matching score to 8.1, bringing a 17.4% relative improvement and closing the gap between open-weight models and GPT-4o.

While LLMs have accelerated scientific code generation, comprehensively evaluating generated code remains challenging. Many benchmarks emphasize functional correctness or task completion, which is insufficient for code built on production HPC libraries, where solver selection, API conventions, memory management, parallel awareness, and performance also matter. We introduce PETSCAgent-Bench, a multidimensional benchmark and agent-based framework for assessing whether AI-generated scientific code uses a production HPC library as an expert would. A tool-augmented evaluator compiles, executes, and measures code and combines deterministic checks with LLM-based assessments in a 14-evaluator pipeline spanning five categories: correctness, performance, code quality, algorithmic appropriateness, and library-specific conventions. A2A and MCP enable black-box evaluation of compatible coding agents. Across realistic PETSc problems, frontier models generate readable, well-structured code but struggle with correctness on challenging problems and with library-specific conventions even when code compiles and runs---limitations that conventional pass/fail evaluation does not capture.

Translating natural-language descriptions of physical phenomena into executable simulation code requires both programming expertise and physical reasoning. Current large language models (LLMs) lack this combination: they frequently produce code that runs but simulates the wrong physics. We introduce PhysCodeBench, the first benchmark for this task, with 1,200 expert-validated examples spanning four physical domains. Its evaluation suite, PhysCodeEval, goes beyond executability and visual fidelity to measure physical correctness directly from the engine state via conservation-law residuals and expert-written assertions, and supports cross-engine evaluation to disentangle physics reasoning from API fluency. As a reference method, we propose the Self-Corrective Multi-Agent Refinement Framework (SMRF), which decouples physics-aware error correction from code generation through specialized agents. This design is motivated by our finding that targeted correction, rather than generic iterative refinement, is the key driver of physical accuracy. SMRF nearly triples the physical-assertion pass rate of the best proprietary baseline (70.6% vs.\ 23.8%) and retains its advantage under cross-engine transfer.