Code

Merge refactor to main#88

Code

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braceal merged 140 commits intomainramanathanlab/genslm:mainfrom developramanathanlab/genslm:developCopy head branch name to clipboardFeb 13, 2023

+570-533

Commits

Commits on Jan 27, 2023

• output callback can do multiple options

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Commits on Jan 28, 2023

• inference dataset for improved efficiency

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• remove inference logic from train script

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• typing

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• scalable inference output script

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• scalable inference output script

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• scalable inference output script

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• scalable inference output script

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• scalable inference output script

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• scalable inference output script

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• scalable inference output script

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• scalable inference output script

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• scalable inference output script

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• scalable inference output script

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Commits on Jan 30, 2023

• ragged

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• Testing h5 distributed inference

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• Testing h5 distributed inference

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• Testing h5 distributed inference

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• Testing h5 distributed inference

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• Testing h5 distributed inference

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• Testing h5 distributed inference

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Commits on Jan 31, 2023

• Testing h5 distributed inference

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• Testing h5 distributed inference

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• Testing h5 distributed inference

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• Testing h5 distributed inference

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• write indices to h5

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• layer bounds

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• compression

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• compression

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• bug fix. node local storgae

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• no compress

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• dbg

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• dbg

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• dbg

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• dbg

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• Removing unused code

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• Testing gather h5

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• Testing h5 distributed inference

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• Testing gather h5

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• Setting seed to already existing embeddings

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• Testing gather h5

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Commits on Feb 1, 2023

• Testing gather h5

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• testing seq hashes

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• testing seq hashes, speedtest

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• testing logits, speedtest

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Commits on Feb 2, 2023

• testing logits, speedtest

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• counter speed test

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• counter speed test

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• testing layer bounds

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• testing layer bounds

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• revising gather

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• revising gather

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• revising gather

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• need to squeeze embeddings

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• adding hash directly to dataset

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• adding hash directly to dataset

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• adding hash directly to dataset

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• adding hash directly to dataset

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• adding hash directly to dataset

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• raw seq hash

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• Silence read fasta

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• See if model can be warmed

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• See if model can be warmed

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• Testing bulk inference

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• Testing bulk inference

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Commits on Feb 3, 2023

• Need to see env vars

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• Note that this script does not work as intended (at all)

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Commits on Feb 6, 2023

• Adding logic for gathering logits

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Commits on Feb 7, 2023

• Update logit glob pattern

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• Update logit outfile name

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• Exposing verbosity

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Commits on Feb 8, 2023

• moving h5 to after predict start

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• silence logging

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• silence logging

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Commits on Feb 10, 2023

• Testing failures

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• FIXING SEQ LEN

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• Squeeze the life out of me

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• Double checking sequence lengths

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• Verifying that the dataset (tokenizer) is and forever shall be correct

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Commits on Feb 13, 2023

• Refactor/cleanup for inference at scale

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• Merge branch 'patch/output-callback' of github.com:ramanathanlab/gene_transformer into patch/output-callback

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• Remove bogus utils :)

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• Linting and documentation

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• Remove mean reduction references

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• Merge pull request #85 from ramanathanlab/patch/output-callback

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• Increase version corresponding to recent refactor

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