Software increasingly functions as part of the scientific instrument itself, making failures in scientific code capable of compromising not only program behavior but also the evidence underlying scientific conclusions. Yet existing evaluations of coding agents largely emphasize aggregate task success, providing limited insight into why agents fail when repairing scientific software. We introduce \textbf{SWE-bench Science}, a repository-level benchmark for scientific software engineering comprising 119 tasks from 98 GitHub repositories across 20 scientific domains. Each task is organized into one of three paradigms: Issue-driven, Expert-exploratory, and Engineering-integration. Even the best-performing agent, \textbf{Claude Code with Opus-5 (max), achieves a pass@1 below 50\%}, highlighting the substantial challenges posed by scientific software engineering. We identify four recurring failure mechanisms: deficits in scientific knowledge or abstraction, misguided exploration or surface-level repair, incomplete repair coverage or system integration, and failures to generalize scientific knowledge beyond observed cases in our analysis. We further conduct a paired ablation that removes explicit scientific guidance while preserving the repository and executable engineering context. The results show that scientific knowledge is not uniformly beneficial: well-grounded information can constrain repair and improve average performance and token efficiency, whereas poorly aligned guidance can induce anchoring and does not necessarily improve exact repair success. Together, SWE-bench Science provides a broad testbed for studying both the capabilities and failure mechanisms of coding agents in scientific software engineering.
Modernizing legacy Fortran is a problem of volume: the transformations are individually routine, but the codebases can be enormous, and across much of computational science the work simply goes undone. We propose an agentic workflow that takes this work on at production scale, and we set out to measure how far such delegation can reach. In this work, three prompt-specialized agent roles operate under a version-controlled specification that the agents themselves authored and revised, while humans hold a small number of gates. The arrangement is kept safe by an exact verification oracle inherited from the domain, and the boundary of safe delegation lies exactly where that oracle stops seeing. We apply the proposed workflow in a case study, converting the two-electron-integral routines of GAMESS (General Atomic and Molecular Electronic Structure System), a mature quantum-chemistry package with a 48-year development history, from fixed-form Fortran 77 to free-form Fortran 2008. The scope of this work was twelve source files, 56,448 lines, and 225 subroutines for computing electron repulsion integrals. The agents ran as three Claude Code roles in isolated worktrees, and the work spanned four Claude model generations. Because the GAMESS group ships a standard test suite whose printed energies its user community treats as canonical, we could adopt bit-for-bit reproduction of those energies as the merge criterion, where a deviation in the twelfth decimal place counts as a failure rather than drift. All twelve source files pass a 51-test validation battery comprising the 49 standard GAMESS tests and two additional calculations, and across 612 test runs the number of chemistry-relevant differences is zero, and every file also passes the Jenkins tests that are used for continuous integration.
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.
Aya Lahlou, Linnia Hawkins, Pierre Gentinecs.SE cs.AI cs.CE cs.MA
Differentiable programming offers transformative capabilities for scientific modeling, enabling gradient-based parameter estimation, sensitivity analysis, and data assimilation. Yet, migrating legacy codebases into differentiable frameworks remains a challenge. We present a five-phase LLM-based agentic pipeline that translates legacy Fortran into JAX: static dependency analysis determines module translation order from the full call graph; iterative compile-repair loops correct errors autonomously; and a Fortran reference oracle enforces numerical parity at the module level before integration and gradient verification. We instantiate and evaluate the pipeline on CLM-ml-v2, a 19,000-line Fortran land surface model, and analyze agent behavior across 73 module translation tasks. The resulting differentiable model computes the complete Jacobian in a single backward pass, recovers physical parameters in eight times fewer steps than gradient-free optimization, and achieves a 24 times wall-clock speedup over sequential Fortran at ensemble size N=2,048. Both the translated model and pipeline infrastructure are released as a reusable framework for differentiating other Earth system model components.