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TCR chain type special tokens#127

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floccinauc merged 96 commits intomainBiomedSciAI/fuse-drug:mainfrom PPI_t5BiomedSciAI/fuse-drug:PPI_t5Copy head branch name to clipboardJun 2, 2024

+507-2

Commits

Commits on May 18, 2023

• from_file for modular tokenizer

  

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• from_file for modular tokenizer

  

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Commits on May 24, 2023

• add EOS token to modulartokenizer

  

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Commits on May 25, 2023

• modular tokenizer ops for t5 PPI

  

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Commits on May 28, 2023

• modular tokenizer ops adjustments

  

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Commits on May 29, 2023

• modular tokenizer additions: ops

  

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Commits on May 30, 2023

• adding special tokens to existing ModularTokenizer

  

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• adding special tokens to existing ModularTokenizer

  

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Commits on May 31, 2023

• modular tokenizer ops bug fix

  

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• mod tokenizer additions

  

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Commits on Jun 1, 2023

• pr comments

  

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Commits on Jun 4, 2023

• modulartokenizer fixes, special tokens added

  

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• modulartokenizer fixes, special tokens added

  

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• modulartokenizer fixes, special tokens added

  

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• formatting fixes

  

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Commits on Jun 5, 2023

• PR fixes

  

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• readme update

  

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Commits on Jun 6, 2023

• relative links test

  

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• relative links test

  

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  72e731a

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• Merge branch 'main' into PPI_t5

  floccinauc

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• code cleanup

  

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• Merge branch 'PPI_t5' of https://github.com/BiomedSciAI/fuse-drug into PPI_t5

  

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  2de1cec

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• cleanup

  

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• cleanup

  

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Commits on Jun 7, 2023

• Merge branch 'main' into PPI_t5

  floccinauc

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• PR fix

  

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• PR fix

  

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• added special token

  

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Commits on Jun 8, 2023

• remove unused FastModularTokenizerOp operator

  

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• Merge branch 'main' of https://github.com/BiomedSciAI/fuse-drug into PPI_t5

  

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Commits on Jun 14, 2023

• adding dti_binding_dataset_combined

  

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• Merge branch 'main' of https://github.com/BiomedSciAI/fuse-drug into PPI_t5

  

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• adding dti_binding_dataset_combined

  

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  1d180c5

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Commits on Jun 18, 2023

• Merge branch 'main' into PPI_t5

  floccinauc

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  3aab635

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• small fixes

  

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  639a400

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• Merge branch 'PPI_t5' of https://github.com/BiomedSciAI/fuse-drug into PPI_t5

  

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  f03c4b2

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• small fixes

  

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  7a00d65

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• Merge branch 'main' of https://github.com/BiomedSciAI/fuse-drug into PPI_t5

  

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  39ae971

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• black fixes

  

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• black fixes

  

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Commits on Jun 21, 2023

• setting and exposing consistent max_len logic

  

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• Merge branch 'main' of https://github.com/BiomedSciAI/fuse-drug into PPI_t5

  

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  363b6be

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• setting and exposing consistent max_len logic

  

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  f1f3817

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• Merge branch 'main' of https://github.com/BiomedSciAI/fuse-drug into PPI_t5

  

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  b9ab404

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• PR fixes

  

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Commits on Jun 25, 2023

• merging with string encode

  

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Commits on Jun 29, 2023

• Merge branch 'main' of https://github.com/BiomedSciAI/fuse-drug into PPI_t5

  

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Commits on Jul 16, 2023

• small tokenizer ops fix

  

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  e8d201c

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• Merge branch 'main' of https://github.com/BiomedSciAI/fuse-drug into PPI_t5

  

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  708e2e4

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• formatting

  

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Commits on Jul 19, 2023

• Merge branch 'main' of https://github.com/BiomedSciAI/fuse-drug into PPI_t5

  

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  e147566

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Commits on Jul 20, 2023

• import fixes

  

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  6adb330

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Commits on Aug 3, 2023

• some special token annotations

  

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• Merge branch 'main' of https://github.com/BiomedSciAI/fuse-drug into PPI_t5

  

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• some special token annotations

  

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Commits on Aug 8, 2023

• Merge branch 'main' of https://github.com/BiomedSciAI/fuse-drug into PPI_t5

  

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Commits on Aug 16, 2023

• Merge branch 'main' of https://github.com/BiomedSciAI/fuse-drug into PPI_t5

  

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Commits on Aug 20, 2023

• readme correction

  

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• readme correction

  

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  e4323e4

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Commits on Aug 21, 2023

• adding special tokens and text table loader

  

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  d3a4d9d

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• adding special tokens and text table loader

  

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• adding special tokens and text table loader

  

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  6d69fe6

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Commits on Sep 3, 2023

• small changes

  

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  960ba28

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• small changes

  

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• small changes

  

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  df3abab

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Commits on Sep 12, 2023

• Adding sequence-related tokens (start,end,type,noop,backspace)

  

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• Merge branch 'main' of https://github.com/BiomedSciAI/fuse-drug into PPI_t5

  

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  03cfd35

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Commits on Sep 21, 2023

• adding a new token TARGETED_ANTIBODY_DESIGN_ENCODER_ONLY_MODE

  

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  61637b5

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• adding a new token TARGETED_ANTIBODY_DESIGN_ENCODER_ONLY_MODE

  

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  db7fc3f

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Commits on Jan 11, 2024

• tokenizer improvements

  

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Commits on Feb 6, 2024

• Merge branch 'main' of https://github.com/BiomedSciAI/fuse-drug into PPI_t5

  

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Commits on Feb 21, 2024

• add a warning/exception on encountering unknown tokens and a method to count them to modular tokenizer

  

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• add a warning/exception on encountering unknown tokens and a method to count them to modular tokenizer

  

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  9398cb7

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• PR fix

  

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  348df7f

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Commits on Feb 29, 2024

• update

  

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• update

  

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• update

  

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  4624474

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• detail level in unk token warnings during ModularTokenizer encode/encode_list

  

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• detail level in unk token warnings during ModularTokenizer encode/encode_list

  

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• detail level in unk token warnings during ModularTokenizer encode/encode_list

  

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• detail level in unk token warnings during ModularTokenizer encode/encode_list

  

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  52742da

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Commits on Mar 3, 2024

• add verbose 0 version to ModularTokenizer.encode

  

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• add verbose 0 version to ModularTokenizer.encode

  

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Commits on Mar 7, 2024

• main merge

  

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Commits on Mar 19, 2024

• Merge branch 'main' of https://github.com/BiomedSciAI/fuse-drug into PPI_t5

  

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Commits on Mar 20, 2024

• Merge branch 'main' of https://github.com/BiomedSciAI/fuse-drug into PPI_t5

  

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  746f750

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• save path compatibility fix for modular tokenizer

  

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  a4f309e

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• save path compatibility fix for modular tokenizer

  

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  4dc0e0f

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Commits on Apr 11, 2024

• Merge branch 'main' of https://github.com/BiomedSciAI/fuse-drug into PPI_t5

  

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  committed
  aedce8b

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• adding special tokens

  

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  d3348e4

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Commits on Apr 14, 2024

• add mutated token

  

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  407a9d1

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• travis fixes

  

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  4c87f49

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Commits on May 26, 2024

• Merge branch 'main' of https://github.com/BiomedSciAI/fuse-drug into PPI_t5

  

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  b98584a

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Commits on Jun 2, 2024

• TCR chain tokens

  

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  2a14ae4

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• TCR chain type tokens: alpha, gamma, delta and their CDR3 regions

  

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• TCR chain type tokens: alpha, gamma, delta and their CDR3 regions

  

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