Code

Adding simulation stuff#41

Code

Merged

roman-bushuiev merged 73 commits intopluskal-lab:mainpluskal-lab/MassSpecGym:mainfrom adamoyoung:adamo5adamoyoung/MassSpecGym:adamo5Copy head branch name to clipboardFeb 10, 2025

+6,861-1,743

Commits

Commits on May 27, 2024

• adding preprocessing for the spectrum simulation subset

  adamoyoung

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  dd80123

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• initial dataset/transform changes, still WIP

  adamoyoung

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  dc757e9

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Commits on May 28, 2024

• adding dataset stuff for simulation models

  adamoyoung

  committed
  532272e

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• fixing minor bugs

  adamoyoung

  committed
  8c6514c

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Commits on May 29, 2024

• temporary commit, WIP

  adamoyoung

  committed
  0b8d346

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• attempting merge

  adamoyoung

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  5921920

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• updating dataset stuff to work with new data

  adamoyoung

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  71ad27c

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Commits on May 30, 2024

• adding model stuff, WIP

  adamoyoung

  committed
  da0bcfe

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• more model stuff, still WIP

  adamoyoung

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  4fe1d32

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• more pl model stuff, still WIP

  adamoyoung

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Commits on May 31, 2024

• first model runs, still need to debug training

  adamoyoung

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  f846ac3

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• minor dataset rework, eval metrics still not functional

  adamoyoung

  committed
  d473f57

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• NEIMS model now works in notebook, does not perform well on validation data

  adamoyoung

  committed
  cbb1ad0

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Commits on Jun 1, 2024

• adding runner.py script, proper epoch metric accumulation

  adamoyoung

  committed
  8006a2c

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• adding precursor only baseline, fixing some bugs

  adamoyoung

  committed
  5d081e0

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Commits on Jun 2, 2024

• refactoring into runner/config format, fixing intensity bug, other small changes

  adamoyoung

  committed
  52666d5

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• integrating newer dataset (v4), misc small changes

  adamoyoung

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  a6dfbea

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• implemented GNN models

  adamoyoung

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  e3eb328

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Commits on Jun 3, 2024

• changing old dataset filters to checks

  adamoyoung

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Commits on Jul 23, 2024

• final commit before original submission

  adamoyoung

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  5cf673d

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• finished merge

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  4153a2f

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Commits on Aug 4, 2024

• major updates

  adamoyoung

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  1123bad

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Commits on Aug 8, 2024

• removing cache_feats

  adamoyoung

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  950245a

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• merging changes from main

  adamoyoung

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  368978f

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Commits on Aug 9, 2024

• fixing import bugs, inheritance bugs

  adamoyoung

  committed
  0f5adf1

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• fixing metric calculation and logging functions to comply with parent class

  adamoyoung

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  3f13624

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Commits on Aug 11, 2024

• reworking models to not use save_hyperparameters

  adamoyoung

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  3304b64

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• reworking SimulationDataset

  adamoyoung

  committed
  163c37b

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Commits on Aug 14, 2024

• initial simulation retrieval implementation, support for dataset subsampling

  adamoyoung

  committed
  8c1cc68

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• more retrieval changes, fixing some bugs

  adamoyoung

  committed
  0ccea3f

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• fixing cos_sim bug

  adamoyoung

  committed
  95a6299

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• removing pdb statements

  adamoyoung

  committed
  c3e3f7a

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Commits on Aug 15, 2024

• adding random noise to break ties

  adamoyoung

  committed
  0e3b681

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• merging changes

  adamoyoung

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  50d55a5

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• properly integrating new changes (retrieval, hparams, bootstrapping)

  adamoyoung

  committed
  b364076

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• fixing GNN model, refactoring cos sim calculations to work with bootstrap

  adamoyoung

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  ab9c56e

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• adding checkpoint loading for test evaluation

  adamoyoung

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  f9f5ad1

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• fixing improperly processed mol data

  adamoyoung

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  12718e7

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Commits on Aug 16, 2024

• updating retrieval configs

  adamoyoung

  committed
  e0d4749

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• adding mz_bin_res configs

  adamoyoung

  committed
  0c547df

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• adding additional metrics

  adamoyoung

  committed
  63e634a

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• reducing max_epochs back down to 20

  adamoyoung

  committed
  3c8be7b

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• returning max_epochs to 100

  adamoyoung

  committed
  c2ec360

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• minor config changes

  adamoyoung

  committed
  8db29c8

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• adding df_test and ckpt uploading

  adamoyoung

  committed
  bd67369

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• adding notebook to calculate bootstrap

  adamoyoung

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  81cb98a

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• updating notebook

  adamoyoung

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Commits on Aug 26, 2024

• merged with new changes

  adamoyoung

  committed
  54e5782

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• config cleanup

  adamoyoung

  committed
  82ea88c

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• fixing bootstrap sig figs

  adamoyoung

  committed
  2777f8a

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• minor bug fix

  adamoyoung

  committed
  de016ce

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• reorganizing configs

  adamoyoung

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Commits on Oct 28, 2024

• Merge branch 'main' into adamo5

  adamoyoung

  committed
  1ccc233

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• removing wandb information

  adamoyoung

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  bd2e486

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• removing bin res ablations

  adamoyoung

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Commits on Oct 29, 2024

• reworking data stuff

  adamoyoung

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  988d343

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Commits on Jan 6, 2025

• merging with more recent changes

  adamoyoung

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  1daf6f0

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• removing old notebook

  adamoyoung

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  ee31e86

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Commits on Jan 10, 2025

• fixing jss metric

  adamoyoung

  committed
  73c3adc

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• reorganizing run files

  adamoyoung

  committed
  b70d544

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• minor updates to SpecToMzsInts transform

  adamoyoung

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  d77b965

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Commits on Jan 12, 2025

• Merge branch 'main' into adamo5

  adamoyoung

  committed
  73328f4

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• redefining jss such that it is between 0 and 1

  adamoyoung

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Commits on Jan 17, 2025

• minor fix to datasets

  adamoyoung

  committed
  9fdb5c8

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• adding updated version of demo notebook

  adamoyoung

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Commits on Feb 4, 2025

• reworking configs, removing old notebooks

  adamoyoung

  committed
  2dc5bf3

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• adding script for fixing JSS from original version

  adamoyoung

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  aaafca6

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• removing user-specific info from template config

  adamoyoung

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  059d0fe

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• updating demo stuff

  adamoyoung

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  4b7589f

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• updating boostrap notebook

  adamoyoung

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  7a03118

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• fixing some notebook stuff

  adamoyoung

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  5a68754

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Commits on Feb 10, 2025

• removing debug configs

  adamoyoung

  committed
  01508d2

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• Merge branch 'main' into adamo5

  roman-bushuiev

  authored
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