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Datasets:
qingxin1999
/
pepforge-training-data

Tasks:
Text Generation
Languages:
English
Size:
100K<n<1M
Tags:
peptide
HELM
chemistry
drug-discovery
antimicrobial-peptide
License:
Dataset card Data Studio Files
xet
 Community
qingxin1999 commited on
Commit
9ecf584
·
verified ·
1 Parent(s): 21df888

feat: upload training data (HELM CSVs, processed JSONL, tokenizers, embeddings)

Browse files
Files changed (26) hide show
  1. .gitattributes +8 -0
  2. Data/all_peptides/HELM.csv +3 -0
  3. Data/amp_peptides/HELM.csv +0 -0
  4. Embeddings/monomer_embeddings.manifest.json +445 -0
  5. Embeddings/monomer_embeddings.pt +3 -0
  6. Generation/processed/hierarchical/test_content.jsonl +0 -0
  7. Generation/processed/hierarchical/test_hierarchical_stats.json +5 -0
  8. Generation/processed/hierarchical/test_layout.jsonl +0 -0
  9. Generation/processed/hierarchical/train_content.jsonl +3 -0
  10. Generation/processed/hierarchical/train_hierarchical_stats.json +5 -0
  11. Generation/processed/hierarchical/train_layout.jsonl +3 -0
  12. Generation/processed/hierarchical/val_content.jsonl +0 -0
  13. Generation/processed/hierarchical/val_hierarchical_stats.json +5 -0
  14. Generation/processed/hierarchical/val_layout.jsonl +0 -0
  15. Generation/processed/stats.json +6 -0
  16. Generation/processed/test.jsonl +3 -0
  17. Generation/processed/train.jsonl +3 -0
  18. Generation/processed/val.jsonl +3 -0
  19. Monomer/HELMLibrary.json +0 -0
  20. Prediction/processed/test.jsonl +0 -0
  21. Prediction/processed/train.jsonl +3 -0
  22. Prediction/processed/train_active.jsonl +0 -0
  23. Prediction/processed/unlabeled_pool.jsonl +3 -0
  24. Prediction/processed/val.jsonl +0 -0
  25. Tokenizers/content_vocab.json +510 -0
  26. Tokenizers/layout_vocab.json +80 -0
.gitattributes CHANGED
@@ -58,3 +58,11 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
58
  # Video files - compressed
59
  *.mp4 filter=lfs diff=lfs merge=lfs -text
60
  *.webm filter=lfs diff=lfs merge=lfs -text
 
 
 
 
 
 
 
 
 
58
  # Video files - compressed
59
  *.mp4 filter=lfs diff=lfs merge=lfs -text
60
  *.webm filter=lfs diff=lfs merge=lfs -text
61
+ Data/all_peptides/HELM.csv filter=lfs diff=lfs merge=lfs -text
62
+ Generation/processed/hierarchical/train_content.jsonl filter=lfs diff=lfs merge=lfs -text
63
+ Generation/processed/hierarchical/train_layout.jsonl filter=lfs diff=lfs merge=lfs -text
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+ Generation/processed/test.jsonl filter=lfs diff=lfs merge=lfs -text
65
+ Generation/processed/train.jsonl filter=lfs diff=lfs merge=lfs -text
66
+ Generation/processed/val.jsonl filter=lfs diff=lfs merge=lfs -text
67
+ Prediction/processed/train.jsonl filter=lfs diff=lfs merge=lfs -text
68
+ Prediction/processed/unlabeled_pool.jsonl filter=lfs diff=lfs merge=lfs -text
Data/all_peptides/HELM.csv ADDED
@@ -0,0 +1,3 @@
 
 
 
 
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Data/amp_peptides/HELM.csv ADDED
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Embeddings/monomer_embeddings.manifest.json ADDED
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+ "created_at": "2026-02-26T12:14:23.977616",
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+ "symbols": [
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+ "C",
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+ "D",
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+ "dD",
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+ "dE",
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+ "dF",
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+ "dH",
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+ "dI",
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+ "dK",
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+ "dL",
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+ "dM",
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+ "dN",
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+ "dP",
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+ "dQ",
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+ "dR",
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+ "dV",
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+ "dW",
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+ "ac",
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+ "am",
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+ "-Me",
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+ "meA",
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+ "meD",
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+ "meV",
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+ "meE",
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+ "meG",
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+ "meI",
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+ "meK",
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+ "meM",
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+ "meN",
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+ "meQ",
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+ "meC",
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+ "meR",
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+ "meW",
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+ "meF",
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+ "meH",
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+ "meL",
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+ "Nle",
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+ "Nva",
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+ "Orn",
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+ "Iva",
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+ "aIle",
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+ "Hcy",
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+ "Hyp",
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+ "D-Nle",
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+ "D-hPhe",
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+ "D-Hyp",
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+ "D-Nva",
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+ "D-Orn",
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+ "Pyr",
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+ "D-Pyr",
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+ "Phe_3Cl",
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+ "Phe_4Cl",
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+ "Phe_4NH2",
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+ "Phg",
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+ "Ser_tBu",
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+ "Tyr_Bn",
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+ "Tza",
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+ "1Nal",
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+ "Cha",
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+ "Lys_Boc",
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+ "D-2Nal",
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+ "D-2Thi",
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+ "D-aHyp",
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+ "D-aIle",
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+ "D-Phg",
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+ "D-Ser_tBu",
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+ "Cya",
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+ "Lys_Me3",
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+ "Pen",
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+ "Phe_4Me",
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+ "Ser_Bn",
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+ "Tyr_tBu",
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+ "2Nal",
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+ "Thi",
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+ "aHyp",
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+ "Ala_tBu",
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+ "hPhe",
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+ "D-1Nal",
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+ "D-Cha",
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+ "D-Pen",
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+ "D-Phe_4Cl",
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+ "D-Ser_Bn",
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+ "Wil",
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+ "MsO",
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+ "Oic_3aS-7aS",
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+ "Pip",
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+ "3Pal",
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+ "4Pal",
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+ "Apm",
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+ "Chg",
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+ "Dab",
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+ "Dap",
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+ "D-3Pal",
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+ "D-aMeAbu",
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+ "D-Chg",
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+ "D-Cit",
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+ "D-Dab",
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+ "D-Pip",
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+ "D-Tic",
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+ "Aca",
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+ "Tic",
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+ "Aad",
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+ "Cit",
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+ "Aze",
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+ "Ac5c",
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+ "Aib",
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+ "D-2Pal",
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+ "D-Dap",
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+ "Asu",
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+ "Cbz",
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+ "-Et",
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+ "NHEt",
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+ "OEt",
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+ "-OMe",
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+ "OtBu",
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+ "Tos",
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+ "D-Thz",
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+ "fmoc",
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+ "Mpa",
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+ "Bua",
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+ "deamino-Cys",
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+ "deamino-Dab",
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+ "deamino-Gly_CN",
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+ "deamino-Gly_cPent",
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+ "deamino-Gly_thien2yl",
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+ "D-Trp_For",
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+ "deamino-Ncy",
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+ "deamino-Phe",
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+ "deamino-Phg_35diMe",
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+ "deamino-Leu",
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+ "D-OAla",
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+ "L-OAla",
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+ "L-OVal",
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+ "NHBn-",
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+ "Bz",
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+ "D-Tyr_Et",
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+ "Lys_Ac",
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+ "OMe-",
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+ "Asp_OMe",
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+ "NMe23Abz",
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+ "Phe_ab-dehydro",
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+ "Sta_3xi4xi",
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+ "Tyr_ab-dehydroMe",
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+ "App",
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+ "Cap",
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+ "Cys_SEt",
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+ "Dsu",
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+ "pnC",
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+ "pnG",
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+ "Pqa",
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+ "Pro_4Me3OH",
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+ "Ala-al",
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+ "Arg-al",
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+ "Asp-al",
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+ "Lys-al",
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+ "Pro-al",
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+ "-NHBn",
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+ "NHMe",
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+ "Met_O2",
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+ "Phe_2Me",
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+ "Phe_34diCl",
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+ "Phe_4Br",
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+ "Phe_4I",
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+ "Phe_4Sdihydroorotamido",
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+ "Pyl",
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+ "Ser_PO3H2",
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+ "Thr_PO3H2",
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+ "Thz",
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+ "Trp_Me",
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+ "Val_3OH",
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+ "xiIle",
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+ "NMe2Abz",
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+ "NMebAla",
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+ "aMePhe",
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+ "aMePro",
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+ "aMeTyr_3OH",
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+ "Cys_Bn",
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+ "Gla",
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+ "hHis",
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+ "His_1Me",
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+ "Gly_allyl",
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+ "Gly_cPr",
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+ "Hsl",
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+ "Asp_Ph2NH2",
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+ "Azi",
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+ "2Abz",
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+ "3Abz",
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+ "4Abz",
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+ "Ac3c",
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+ "Ac6c",
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+ "bAla",
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+ "D-hArg",
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+ "D-Phe_4F",
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+ "D-Trp_2Me",
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+ "D-Tyr_3OH",
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+ "D-Tyr_Me",
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+ "D-xiIle",
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+ "Lys_iPr",
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+ "-Bn",
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+ "-OBn",
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+ "Ph",
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+ "Boc",
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+ "Mba",
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+ "Hva",
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+ "deamino-Chg",
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+ "deamino-Dip",
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+ "deamino-Gly_tBu",
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+ "deamino-hPhe",
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+ "deamino-nTyr_Me",
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+ "deamino-Phg_4Cl",
243
+ "D-OVal",
244
+ "OLeu",
245
+ "OBn-",
246
+ "deamino-Lys",
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+ "NMe24Abz",
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+ "Phe_ab-dehydro_3NO2",
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+ "Sta_3S4S",
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+ "Bux",
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+ "Dpm",
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+ "pnA",
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+ "pnT",
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+ "seC",
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+ "Gly-al",
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+ "Leu-al",
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+ "Phe-al",
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+ "L-hArg(Et,Et)",
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+ "Met_O",
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+ "Oic_3aR-7aS",
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+ "Oic_3axi-7axi",
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+ "Phe_2F",
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+ "Phe_3F",
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+ "Phe_4F",
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+ "Phe_4NO2",
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+ "Phe_bbdiMe",
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+ "Trp_5OH",
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+ "Trp_Ome",
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+ "Tyr_3OH",
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+ "Tyr_Me",
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+ "Tyr_PO3H2",
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+ "xiHyp",
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+ "NMe4Abz",
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+ "Aoda",
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+ "Bpa",
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+ "Cys_Me",
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+ "Dip",
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+ "hArg",
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+ "His_1Bn",
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+ "Hyl_5xi",
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+ "Abu_23dehydro",
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+ "D-Dip",
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+ "D-hArg_Et2",
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+ "D-Met_S-O",
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+ "D-His_1Bn",
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+ "xiThr",
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+ "D-Ala-ol",
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+ "D-Phg-ol",
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+ "Gly-ol",
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+ "Ala-ol",
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+ "Lys-ol",
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+ "Phg-ol",
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+ "Pro-ol",
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+ "Y",
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+ "Tyr_3I",
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+ "Tyr_3NO2",
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+ "pep_token": "<PEP>",
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+ "chem_token": "<CHEM>"
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+ }