update benchmark examples and pypi ver. #771
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Logiquo
approved these changes
Jan 6, 2026
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This pull request adds comprehensive benchmarking tools and updates documentation for the PyHealth project, focusing on drug recommendation tasks using the MIMIC-IV dataset. The main changes include the addition of two new benchmarking scripts for performance analysis and an update to the installation documentation to clarify Python version requirements and improve installation instructions.
Benchmarking tools for drug recommendation:
benchmark_pandas_drug_rec.py, a standalone script that benchmarks drug recommendation preprocessing using pandas on MIMIC-IV data, including cumulative history construction and peak memory tracking.benchmark_workers_n_drug_recommendation.py, a script to benchmark the PyHealthDrugRecommendationMIMIC4task across differentnum_workerssettings, measuring wall time, cache sizes, and peak memory usage, and writing results to CSV for further analysis.Documentation improvements:
docs/install.rstto clarify that PyHealth 2.0 requires Python 3.12 or higher (up to 3.13), updated installation instructions for both alpha and legacy versions, and improved version-specific recommendations.