update benchmark examples and pypi ver. #762
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Jan 1, 2026
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This pull request adds two new benchmarking scripts for drug recommendation tasks using the MIMIC-IV dataset and updates the installation documentation to clarify Python version requirements and recommended package versions. The new scripts provide reproducible performance measurements for both single-threaded pandas processing and parallelized PyHealth task processing with configurable worker counts, including detailed tracking of memory usage and cache sizes.
Benchmarking scripts for drug recommendation:
examples/benchmark_perf/benchmark_pandas_drug_rec.py, a standalone pandas-based benchmark for the MIMIC-IV drug recommendation task, including cumulative visit history construction, memory tracking, and result reporting.examples/benchmark_perf/benchmark_workers_n_drug_recommendation.py, a benchmarking script that measures PyHealth's drug recommendation task performance across multiplenum_workersvalues. It tracks dataset/task cache sizes, peak memory usage (including child processes), and supports repeated runs for robust statistics. Results are written to CSV for analysis.Documentation updates:
docs/install.rstto clarify that PyHealth 2.0 requires Python 3.12 or higher (up to 3.13), reflecting a hard dependency on modern Python features. Also updated recommended and legacy version installation instructions and notes.