scientific software engineers

Abstract: Large language models and agents have shown significant power in advanced physical research. In this paper, We introduce PHYRD, a living benchmark for theoretical-physics reasoning with 63 Reproduce and 43 Discover problems. Reproduce tests derivation of published results; Discover tests consequences of modified theoretical conditions. FormulaForest constructs the tasks with reference solutions and subquestion-level rubrics. Across five models, whole-problem accuracy ranges from 49.21% to 68.25% on Reproduce and from 18.60% to 74.42% on closed-book Discover. With tools, four models complete more Discover problems, but conceptual errors and missing arguments persist. Besides, our experimental results demonstrate the value of FormulaForest as synthetic data. On FrontierScience, a benchmark developed by OpenAI, it raises the accuracy of a Qwen-35B-A3B model from 61% to 72%.

Abstract: 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%.

Abstract: Galaxy is a widely used, community-driven scientific workflow system whose sustainability depends on continuous maintenance across its software, tools, workflows, infrastructure, documentation, and user-support ecosystem. However, maintenance knowledge in Galaxy is distributed across development and community-support spaces, making it difficult to understand what is maintained, how maintenance artifacts are resolved, and how user-facing concerns connect to repository-level development. We conduct a large-scale empirical study of Galaxy using 11,762 GitHub issues, 52,203 pull requests, and 6,235 Community Forum discussions. We characterize maintenance and support concerns, examine factors associated with resolution outcomes and resolution time, and investigate explicit and candidate connections among maintenance artifacts across these spaces. Using BERTopic modeling, we identify nine issue topics, 14 pull-request topics, and 14 forum topics, revealing a maintenance landscape spanning workflow execution, data management, tools and dependencies, infrastructure, testing, scientific resources, documentation, and user support. Resolution analyses show that coordination, diagnostic, contributor, automation, and engagement characteristics exhibit different associations with whether artifacts are resolved and how quickly resolution occurs. We further find limited explicit traceability between development and support spaces: 97.77\% of 16,426 resolved explicit relationships occur within GitHub, while only 294 connect GitHub artifacts with Community Forum discussions, despite additional semantic and technical relatedness across these spaces. Together, these findings characterize Galaxy maintenance as a distributed ecosystem-level process and identify opportunities to improve diagnostic reporting, lifecycle-aware triage, cross-space traceability, and the reuse of community-support knowledge.