scicode-lint: Detecting Methodology Bugs in Scientific Python Code with LLM-Generated Patterns

Abstract

Methodology bugs in scientific Python code produce plausible but incorrect results that traditional linters and static analysis tools cannot detect. Several research groups have built ML-specific linters, demonstrating that detection is feasible. Yet these tools share a sustainability problem: dependency on specific pylint or Python versions, limited packaging, and reliance on manual engineering for every new pattern. As AI-generated code increases the volume of scientific software, the need for automated methodology checking (such as detecting data leakage, incorrect cross-validation, and missing random seeds) grows. We present scicode-lint, whose two-tier architecture separates pattern design (frontier models at build time) from execution (small local model at runtime). Patterns are generated, not hand-coded; adapting to new library versions costs tokens, not engineering hours. On Kaggle notebooks with human-labeled ground truth, preprocessing leakage detection reaches 65% precision at 100% recall; on 38 published scientific papers applying AI/ML, precision is 62% (LLM-judged) with substantial variation across pattern categories; on a held-out paper set, precision is 54%. On controlled tests, scicode-lint achieves 97.7% accuracy across 66 patterns.