Open-source Python library + no-code web dashboard for evaluating oncology AI models at clinical decision thresholds. [P]

Reddit r/MachineLearning Tools

Summary

This article introduces oncothresh, a Python library and web dashboard for evaluating oncology AI models at specific clinical decision thresholds, providing metrics like sensitivity, specificity, and decision-curve analysis to fill gaps in existing benchmarks.

Most classification metrics for oncology AI models (AUC, ICC, MAE) measure global agreement. They don't answer the question that actually matters at the point of care: how reliable is this model at the exact cutoff that decides whether a patient gets flagged, biopsied, or treated? I built oncothresh to evaluate models at a specific clinical threshold rather than in aggregate: sensitivity/specificity/PPV/NPV at the cutoff, bootstrap confidence intervals, threshold-sensitivity curves, boundary-weighted calibration, decision-curve net benefit, and number-needed-to-test. It's a small, dependency-light Python library (numpy/scipy/scikit-learn/pydantic) built for tasks like tumor cellularity, Ki-67, TMB, and PD-L1 scoring, where a continuous model output gets collapsed into a yes/no clinical decision at a fixed cutoff. Pathology-specific benchmarks like PathBench and PathBench-MIL evaluate foundation models globally but don't evaluate at predefined clinical thresholds with uncertainty quantification, which is the gap this fills. There's also a companion web dashboard (oncothresh-web) for people who want the same analysis without writing code: upload a CSV of predictions and labels, pick a threshold, get the full set of charts plus a downloadable PDF report. docker compose up and it's running locally, no cloud dependency. Library: github.com/omkaradhali/oncothresh Dashboard: github.com/omkaradhali/oncothresh-web Still v0.1, so I'd genuinely welcome feedback: use cases I haven't considered, edge cases in the DCA/calibration math, or places the API doesn't fit how people actually work with threshold-based models.
Original Article

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