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Cristofary run 2022 10#5

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minjaf wants to merge 82 commits intoarlapin:masterarlapin/selene:masterfrom AIRI-Institute:cristofary_run_2022-10AIRI-Institute/selene:cristofary_run_2022-10Copy head branch name to clipboard

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Commits on Feb 27, 2021

• Ignore downloaded data and local VS Code config

  

  Alex Lapin

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Commits on Mar 4, 2021

• Merge pull request FunctionLab#159 from arlapin/arlapin/gitignore

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  kathyxchen

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Commits on Mar 5, 2021

• Add SamplesBatch class

  

  Alex Lapin

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• Utilize SamplesBatch class

  

  Alex Lapin

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Commits on Mar 11, 2021

• Let EvaluateModel accept a list of metrics

  

  Alex Lapin

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Commits on Mar 12, 2021

• Log average train loss over nth_step_report_stats

  

  Alex Lapin

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• Add tqdm to train loop

  

  Alex Lapin

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Commits on Mar 13, 2021

• Add tensorboard

  

  Alex Lapin

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• Publish train metrics to tensorboard

  

  Alex Lapin

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Commits on Mar 17, 2021

• Add tqdm to evaluation

  

  Alex Lapin

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• Use tqdm in sampler

  

  Alex Lapin

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• Don't filter features in evaluation

  

  Alex Lapin

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Commits on Mar 18, 2021

• Log config to tensorboard

  

  Alex Lapin

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Commits on Mar 19, 2021

• Log model to tensorboard

  

  Alex Lapin

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Commits on Mar 22, 2021

• Update setup.py

  arlapin

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• Add tqdm to requirements

  arlapin

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• Update setup.py

  arlapin

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Commits on Mar 24, 2021

• Write config and model on "train" mode only

  

  Alex Lapin

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• Log lr

  

  Alex Lapin

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• Log hparams and post-train evaluation metrics

  

  Alex Lapin

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Commits on Mar 25, 2021

• Black-format code and small refactoring

  

  Alex Lapin

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• Plot confusion matrix and publish it to TB

  

  Alex Lapin

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• Fix publising of config and model

  

  Alex Lapin

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• Fix plot confusion matrix

  

  Alex Lapin

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Commits on Apr 19, 2021

• add dataset training & masked metric logging

  

  Maria Sindeeva

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  Maria Sindeeva

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• Merge pull request #1 from sberbank-ai-lab/msindeeva/dataset_train

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  msindeeva

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Commits on Apr 22, 2021

• add transform config parsing

  

  Maria Sindeeva

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  msindeeva

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Commits on Apr 23, 2021

• add LR scheduler config parsing

  

  Maria Sindeeva

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  msindeeva

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Commits on Jun 17, 2021

• add dataset evaluation option

  

  Maria Sindeeva

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  msindeeva

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• add separate val/test transform support

  

  Maria Sindeeva

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  msindeeva

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• fix val/test transform instantiation

  

  Maria Sindeeva

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  msindeeva

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Commits on Jun 30, 2021

• Add handler for bigWig files

  sb-vsfishman

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Commits on Jul 1, 2021

• Fix bug in write_multi_ct_handler.py

  sb-vsfishman

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Commits on Jul 15, 2021

• Merge pull request #6 from sberbank-ai-lab/AddPredictionMode

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  sb-vsfishman

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• Add support for quantitative features

  sb-vsfishman

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Commits on Jul 29, 2021

• Add support for quantitative features

  labdevgen

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Commits on Aug 1, 2021

• Merge branch 'arlapin/dev' of https://github.com/sberbank-ai-lab/selene into quantitative_features

  sb-vsfishman

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• Add more flexible config for samplers

  sb-vsfishman

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Commits on Aug 2, 2021

• Update docstrings and fix typos

  labdevgen

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  6170461

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• resolve merge conflict

  sb-vsfishman

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  d3ba760

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• fix typos

  

  labdevgen

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  sb-vsfishman

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  2f1e3ef

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• Merge pull request #7 from sberbank-ai-lab/quantitative_features

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  sb-vsfishman

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• Merge branch 'arlapin/dev' of https://github.com/sberbank-ai-lab/selene into vsfisman/AddSubsetSampler

  sb-vsfishman

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Commits on Aug 4, 2021

• Merge branch 'arlapin/dev' of https://github.com/sberbank-ai-lab/selene into vsfisman/AddSubsetSampler

  sb-vsfishman

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• Merge branch 'vsfisman/AddSubsetSampler' of https://github.com/sberbank-ai-lab/selene into vsfisman/AddSubsetSampler

  sb-vsfishman

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• Merge pull request #8 from sberbank-ai-lab/vsfisman/AddSubsetSampler

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  sb-vsfishman

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• Update setup.py

  

  msindeeva

  authored and

  Maria Sindeeva

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Commits on Aug 26, 2021

• add support for sequential targets

  

  Maria Sindeeva

  authored and

  msindeeva

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Commits on Sep 27, 2021

• Code cleanup in q_genomic_features

  sb-vsfishman

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• Update performance metrics to allow more flexible transforms

  sb-vsfishman

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• Allow more flexible intervals sampling

  sb-vsfishman

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Commits on Oct 1, 2021

• Merge pull request #10 from sberbank-ai-lab/minja/dev

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  sb-vsfishman

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• add sequential memmap targets

  

  Maria Sindeeva

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  Maria Sindeeva

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• add dataloader pin_memory

  

  Maria Sindeeva

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  Maria Sindeeva

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• fix samples intervals loading

  

  Maria Sindeeva

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  Maria Sindeeva

  committed
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• remove shape assertion in metrics

  

  Maria Sindeeva

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  Maria Sindeeva

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Commits on Oct 11, 2021

• update loader args parsing

  

  Maria Sindeeva

  authored and

  Maria Sindeeva

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Commits on Nov 10, 2021

• add metrics log for each track

  sb-vsfishman

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Commits on Nov 15, 2021

• add ct_masked_train logic

  

  thurs8

  authored and

  msindeeva

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• add get_full_dataset

  

  thurs8

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  msindeeva

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Commits on Nov 21, 2021

• More detailed log from perormance metrix errors

  sb-vsfishman

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Commits on Dec 8, 2021

• Allow flexible aggregation functions for q_genmic_features

  sb-vsfishman

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• Define random samples as default sampler

  sb-vsfishman

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Commits on Dec 11, 2021

• make q_genomic_features compatible with Masha's enformer brach

  sb-vsfishman

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• merge origin/msindeeva/seq_targets

  sb-vsfishman

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Commits on Dec 15, 2021

• Code cleanup

  sb-vsfishman

  committed
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• inverse the axes of memmap array

  sb-vsfishman

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Commits on Dec 27, 2021

• add ct_masked_train logic

  

  thurs8

  authored and

  msindeeva

  committed
  6920438

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• add get_full_dataset

  

  thurs8

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  msindeeva

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• fix sampler creation for split loaders

  msindeeva

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Commits on Dec 30, 2021

• Add license

  sb-vsfishman

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Commits on Jan 23, 2022

• Update license

  sb-vsfishman

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• Update license

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• Update license

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Commits on Apr 25, 2022

• Update license and add tsv annotation support

  sb-vsfishman

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• Update Readme

  sb-vsfishman

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• Update Readme

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Commits on May 3, 2022

• Create LICENSE

  minjaf

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Commits on Oct 12, 2022

• Chage mode of memmap files to 'r'

  sb-vsfishman

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Commits on Oct 23, 2022

• Add verbosity for errors in q_genomic_features

  sb-vsfishman

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Commits on Dec 7, 2022

• Merge branch 'ct_masked_train' into arlapin/dev

  msindeeva

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Commits on Mar 12, 2023

• Merge branch 'arlapin/dev' into cristofary_run_2022-10

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