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Chunked model evaluation #91

Merged
merged 9 commits into from
Dec 4, 2024
Merged

Chunked model evaluation #91

merged 9 commits into from
Dec 4, 2024

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willdumm
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@willdumm willdumm commented Dec 4, 2024

Companion PR for https://github.com/matsengrp/dnsm-experiments-1/pull/46

  • Batches evaluation of ModelBase.evaluate_sequences. Adds a method wrapper in netam.common which can easily be re-used on similar methods in the future (such as the equivalent method on AbstractBinarySelectionModel, if it ever gets vectorized). This is useful for avoiding loading the whole input vector's worth of intermediate results into memory, which was causing memory errors on the GPU when evaluating neutral models on large datasets.
  • fixes branch length setter
  • documents Crepe.__call__ and enforces type of argument.

@willdumm willdumm requested a review from matsen December 4, 2024 19:09
@matsen matsen changed the title Batch model evaluation Chunked model evaluation Dec 4, 2024
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WOOT

@willdumm willdumm merged commit b59adbd into main Dec 4, 2024
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@willdumm willdumm deleted the dnsmex45-uncertainty branch December 4, 2024 20:09
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2 participants