bench: add Polars streaming vs in-memory loader benchmark#871
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AhmedAli58 wants to merge 2 commits intosunlabuiuc:masterfrom
Closed
bench: add Polars streaming vs in-memory loader benchmark#871AhmedAli58 wants to merge 2 commits intosunlabuiuc:masterfrom
AhmedAli58 wants to merge 2 commits intosunlabuiuc:masterfrom
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InMemorySampleDataset is primarly designed for unittest, it is not as battle tested as the SampleDataset. And also I think InMemorySampleDataset lacks a few functionality compare with SampleDataset. |
Collaborator
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Hey we did run some tests across a variety of things to make our decision: https://pyhealth.readthedocs.io/en/latest/why_pyhealth.html Will be closing this PR. Would love to talk more if you want to discuss benchmarking PyHealth 2.0 in general on the discord |
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What this does
Adds a benchmarking script that compares PyHealth's new Polars streaming data loader
against the legacy in-memory loader across RAM usage, wall-clock time, and throughput
at 3 dataset scales (100, 1k, 5k patients).
Why it matters
The new streaming loader was added without systematic benchmarks. This PR gives
maintainers and users data to make informed decisions about which loader to use
based on dataset size and available memory.
How to run
python benchmarks/loader_benchmark.py
Results
See benchmarks/results.csv and benchmarks/benchmark_chart.png for outputs.