dvc.lock

schema: '2.0'
stages:
  train_aqueous:
    cmd: python3 scripts/train_aqueous.py
    deps:
    - path: data/AqueousSolu.csv
      md5: a971c59bbbee6dbe768d3bdb60c7f7f6
      size: 2415802
    - path: scripts/aqueous_config.json
      hash: md5
      md5: 66f47df394ae6d8503d09515aac74604
      size: 224
    - path: scripts/train_aqueous.py
      hash: md5
      md5: eaf16b78e9f121955e7ef92896e272f7
      size: 2662
    - path: src/dataloader.py
      hash: md5
      md5: c78dea881a7a20d636ebbfed2a740f19
      size: 14418
    - path: src/model.py
      hash: md5
      md5: fac78b8d4e90126a943cea6cffe23015
      size: 23302
    outs:
    - path: results/aqueous/models/
      hash: md5
      md5: 5958776518eb1ec667c1fbedce0ea163.dir
      size: 309150
      nfiles: 3
  plot_aqueous:
    cmd: python3 scripts/explain_aqueous.py
    deps:
    - path: data/AqueousSolu.csv
      md5: a971c59bbbee6dbe768d3bdb60c7f7f6
      size: 2415802
    - path: results/aqueous/models/
      hash: md5
      md5: 5958776518eb1ec667c1fbedce0ea163.dir
      size: 309150
      nfiles: 3
    - path: scripts/aqueous_config.json
      hash: md5
      md5: 66f47df394ae6d8503d09515aac74604
      size: 224
    - path: scripts/explain_aqueous.py
      hash: md5
      md5: a0c83ba0da650697f3c4d4a1b0cdc66d
      size: 5682
    - path: src/dataloader.py
      hash: md5
      md5: c78dea881a7a20d636ebbfed2a740f19
      size: 14418
    - path: src/model.py
      hash: md5
      md5: fac78b8d4e90126a943cea6cffe23015
      size: 23302
    outs:
    - path: results/aqueous/viz/
      hash: md5
      md5: 81964e9504e973d1a118c38431454c42.dir
      size: 56031866
      nfiles: 1171
  predict_aqueous:
    cmd: python3 scripts/predict_aqueous.py
    deps:
    - path: data/AqueousSolu.csv
      md5: a971c59bbbee6dbe768d3bdb60c7f7f6
      size: 2415802
    - path: results/aqueous/models/
      hash: md5
      md5: 6d3dcf4d6bff9e3d422e61d6982fc202.dir
      size: 944065298
      nfiles: 7
    - path: scripts/aqueous_config.json
      hash: md5
      md5: b95d1100d38e9ba4aa1bbcd3f268a059
      size: 227
    - path: scripts/predict_aqueous.py
      hash: md5
      md5: 70cbf54a4802d4b8cc49c5b69052b98a
      size: 3097
    - path: src/dataloader.py
      hash: md5
      md5: 22dbac31abf08d1f115bcf176d14aca5
      size: 14019
    - path: src/model.py
      hash: md5
      md5: ad6282bdc4a676d392e21749e6229c9d
      size: 23301
    outs:
    - path: results/aqueous/AqueousSolu_predictions.csv
      hash: md5
      md5: 305770ec55ebb07ab7a47d0d711ec6d9
      size: 5200032
  aqueous:
    cmd: echo "Finished full aqueous solubility pipeline"
    deps:
    - path: results/aqueous/AqueousSolu_predictions.csv
      hash: md5
      md5: 2df2dc9267963edf1b991e6aa962a808
      size: 5126643
    - path: results/aqueous/models/
      hash: md5
      md5: 4fe432db7302f9c9897df33944594d11.dir
      size: 2828979740
      nfiles: 12
    - path: results/aqueous/viz/
      hash: md5
      md5: 12f3e38a70d4972a916c690077352226.dir
      size: 80450038
      nfiles: 1722
  train_combi:
    cmd: python3 scripts/train_combi.py
    deps:
    - path: data/CombiSolu-Exp.csv
      md5: b249b75582a9ca5e7a374648b81993be
      size: 1623266
    - path: scripts/combi_config.json
      md5: c16f95d9d61dff44470face9e47952ac
      size: 123
    - path: scripts/train_combi.py
      md5: 28c24006da34b1bc755765c628a325f7
      size: 1899
    - path: src/dataloader.py
      md5: 93db22cf89b1216e0372a8c1987de690
      size: 7477
    - path: src/model.py
      md5: dd61320f74f218659e501d58e46ef4f2
      size: 13068
    outs:
    - path: results/combi/models/
      md5: 49d97cb1b6c7c7909b63f212eddd991d.dir
      size: 235939805
      nfiles: 2
  plot_combi:
    cmd: python3 scripts/explain_combi.py
    deps:
    - path: data/CombiSolu-Exp.csv
      md5: b249b75582a9ca5e7a374648b81993be
      size: 1623266
    - path: results/combi/models/
      md5: 49d97cb1b6c7c7909b63f212eddd991d.dir
      size: 235939805
      nfiles: 2
    - path: scripts/combi_config.json
      md5: c16f95d9d61dff44470face9e47952ac
      size: 123
    - path: scripts/explain_combi.py
      md5: e8179f9e59c2381bc18703d741e881ab
      size: 5001
    - path: src/dataloader.py
      md5: 93db22cf89b1216e0372a8c1987de690
      size: 7477
    - path: src/model.py
      md5: dd61320f74f218659e501d58e46ef4f2
      size: 13068
    outs:
    - path: results/combi/viz/
      md5: 5e1fb28bb5fa0312af78438394adf8ff.dir
      size: 29300564
      nfiles: 494
  combi:
    cmd: echo "Finished full combi solubility pipeline"
    deps:
    - path: results/combi/models/
      md5: 49d97cb1b6c7c7909b63f212eddd991d.dir
      size: 235939805
      nfiles: 2
    - path: results/combi/viz/
      md5: 5e1fb28bb5fa0312af78438394adf8ff.dir
      size: 29300564
      nfiles: 494
  train_shap:
    cmd: python3 scripts/train_aqueous.py
    deps:
    - path: data/AqueousSolu.csv
      md5: a971c59bbbee6dbe768d3bdb60c7f7f6
      size: 2415802
    - path: scripts/aqueous_config.json
      md5: ad60becfccc50a2cd9761056997aeafb
      size: 119
    - path: scripts/train_aqueous.py
      md5: c6a4179a1a6007b93ef420b9a00568c1
      size: 1970
    - path: src/dataloader.py
      md5: 93db22cf89b1216e0372a8c1987de690
      size: 7477
    - path: src/model.py
      md5: 7e5343a96d7684960206ec2c277c8c70
      size: 14260
    outs:
    - path: results/shap/models/
      md5: efa6710e3112aebc873601e15a39a20f.dir
      size: 235939037
      nfiles: 1
  shap:
    cmd: echo "Finished full SHAP aqueous solubility pipeline"
    deps:
    - path: results/shap/models/
      md5: efa6710e3112aebc873601e15a39a20f.dir
      size: 235939037
      nfiles: 1
    - path: results/shap/viz/
      md5: bcfa35117ce3dc3b5d56a8c4b349c04a.dir
      size: 27310046
      nfiles: 574
  plot_shap:
    cmd: python3 scripts/explain_shap.py
    deps:
    - path: data/AqueousSolu.csv
      md5: a971c59bbbee6dbe768d3bdb60c7f7f6
      size: 2415802
    - path: results/shap/models/
      md5: efa6710e3112aebc873601e15a39a20f.dir
      size: 235939037
      nfiles: 1
    - path: scripts/explain_shap.py
      md5: a642fa70b3c13245c4e832c004f89104
      size: 4514
    - path: src/explainer.py
      md5: f8c2026326c3139ef120cfbd79c5f6fe
      size: 6419
    - path: src/model.py
      md5: 7e5343a96d7684960206ec2c277c8c70
      size: 14260
    outs:
    - path: results/shap/viz/
      md5: bcfa35117ce3dc3b5d56a8c4b349c04a.dir
      size: 27310046
      nfiles: 574
  train_logp:
    cmd: python3 scripts/train_logp.py
    deps:
    - path: data/opera_logp.csv
      md5: 2b10b2d996b900b9fb9027a78b736853
      size: 1372348
    - path: scripts/logp_config.json
      md5: aafe4564dfa9e70d14653161dc93f341
      size: 100
    - path: scripts/train_logp.py
      md5: 1ea7f4ea03a3afa3ff1102dd933cd8c3
      size: 1906
    - path: src/model.py
      md5: 7e5343a96d7684960206ec2c277c8c70
      size: 14260
    - path: src/prop_loader.py
      md5: 06ce4fcf7cba3571ce0a62b313e4d599
      size: 1984
    outs:
    - path: results/logp/models/
      md5: b63c8f9ba5e97833e1427452153539c9.dir
      size: 471878074
      nfiles: 2
  plot_logp:
    cmd: python3 scripts/explain_logp.py
    deps:
    - path: data/opera_logp.csv
      md5: 2b10b2d996b900b9fb9027a78b736853
      size: 1372348
    - path: results/logp/models/
      md5: b63c8f9ba5e97833e1427452153539c9.dir
      size: 471878074
      nfiles: 2
    - path: scripts/explain_logp.py
      md5: 1e50bad7188de0a169be4a25cceda5a6
      size: 7468
    - path: scripts/logp_config.json
      md5: aafe4564dfa9e70d14653161dc93f341
      size: 100
    - path: src/explainer.py
      md5: 178193b2961e9cce86bc8fee08a19514
      size: 6829
    - path: src/model.py
      md5: 7e5343a96d7684960206ec2c277c8c70
      size: 14260
    - path: src/prop_loader.py
      md5: 06ce4fcf7cba3571ce0a62b313e4d599
      size: 1984
    outs:
    - path: results/logp/logp_predictions.csv
      md5: 31ffcf88fc0de56856327ddc86177b4f
      size: 2115034
    - path: results/logp/viz_crippen/
      md5: e694658da9480e3726973930e73a5bef.dir
      size: 36029637
      nfiles: 731
    - path: results/logp/viz_ours/
      md5: 595462959f6bf37f6d1d668c6ee496b2.dir
      size: 35751902
      nfiles: 731
  logp:
    cmd: echo "Finished full logP + crippen explainability pipeline"
    deps:
    - path: results/logp/models/
      md5: 92611c76440c2b9dd87e6438b58091c6.dir
      size: 471878074
      nfiles: 2
    - path: results/logp/viz_crippen/
      md5: 1c30afed6ba264e835c8df03facc725d.dir
      size: 23100055
      nfiles: 731
    - path: results/logp/viz_ours/
      md5: 03486896f91aefb80d9b0de9fb735e48.dir
      size: 23053456
      nfiles: 731
  shap_logp:
    cmd: python3 scripts/explain_shap_logp.py
    deps:
    - path: data/logp_dataset.csv
      md5: 75b14bb0a736a67a5f89508e8420c415
      size: 246951
    - path: results/logp/models/
      md5: 6a65348a8355a84575341a55ecd13fcb.dir
      size: 707817111
      nfiles: 3
    - path: scripts/explain_shap_logp.py
      md5: ea261e35ed9c3d26616dc8514cd76697
      size: 4463
    - path: scripts/logp_config.json
      md5: f7de1a7f5cefe925558db9f4ec6c013b
      size: 100
    - path: src/explainer.py
      md5: dd65fb3ccd43f56d3a95a98dc60899fe
      size: 6821
    - path: src/model.py
      md5: 7e5343a96d7684960206ec2c277c8c70
      size: 14260
    - path: src/prop_loader.py
      md5: 27f739a707f74622a13a5b04fe4dc5a4
      size: 1907
    outs:
    - path: results/logp/logp_shap_predictions.csv
      md5: 801fd61211205905cbd3ae940abba0ff
      size: 148871
    - path: results/logp/viz_shap/
      md5: f7979bc24ae772c2a60c8e353f5cf323.dir
      size: 23288533
      nfiles: 730
  train_cmc:
    cmd: python3 scripts/train_cmc.py
    deps:
    - path: data/cmc_dataset_1235.csv
      md5: fdef3b6e89bff73a93f9501b73d5a49a
      size: 558577
    - path: scripts/cmc_config.json
      md5: cfa9016dcbbb66c7064ec004b7a20288
      size: 97
    - path: scripts/train_cmc.py
      md5: 0414cab9f181f686b44983b82316e0ba
      size: 1978
    - path: src/model.py
      md5: e4b80e905dc13b2d4750d823b83073da
      size: 14598
    - path: src/prop_loader.py
      md5: 8954c0f62ea4396f044b6beee336d981
      size: 2159
    outs:
    - path: results/cmc/models/
      md5: b6a7d7b25c269abbd83eeb0af8c7c967.dir
      size: 1649743563
      nfiles: 7
  plot_cmc:
    cmd: python3 scripts/explain_cmc.py
    deps:
    - path: data/cmc_dataset_1235.csv
      md5: fdef3b6e89bff73a93f9501b73d5a49a
      size: 558577
    - path: results/cmc/models/
      hash: md5
      md5: b6a7d7b25c269abbd83eeb0af8c7c967.dir
      size: 1649743563
      nfiles: 7
    - path: scripts/cmc_config.json
      hash: md5
      md5: cfa9016dcbbb66c7064ec004b7a20288
      size: 97
    - path: scripts/explain_cmc.py
      hash: md5
      md5: cbcf1de9093a7d25398980be8c3dadbd
      size: 7537
    - path: src/explainer.py
      md5: 178193b2961e9cce86bc8fee08a19514
      size: 6829
    - path: src/model.py
      hash: md5
      md5: e4b80e905dc13b2d4750d823b83073da
      size: 14598
    - path: src/prop_loader.py
      md5: 8954c0f62ea4396f044b6beee336d981
      size: 2159
    outs:
    - path: results/cmc/cmc_predictions.csv
      hash: md5
      md5: 663adddd2382632531939574e3ad743c
      size: 352666
    - path: results/cmc/viz_ours/
      hash: md5
      md5: 79bf5754d341f78fb22c6c2963628cbf.dir
      size: 4913998
      nfiles: 115
  aq:
    cmd: echo "Finished full aqueous solubility pipeline"
    deps:
    - path: out/aq/accurate/
      hash: md5
      md5: 064953f982ca98c67b9b5ac7ff181dec.dir
      size: 27071668
      nfiles: 578
    - path: out/aq/accurate/mmb-hier/best.pt
      hash: md5
      md5: a27bbdd3a56f5378ac83d52c5b6d07a9
      size: 154575
    - path: out/aq/accurate/mmb-hier/viz
      hash: md5
      md5: 68615c9d10b9b3bf980ca75fab540b2b.dir
      size: 26105388
      nfiles: 571
  split_data:
    cmd:
    - pwd
    - echo "SPLIT DATA --task aq --property aq --loader AqSolDataset --filepath /workspace/data/AqueousSolu.csv
      --propname logS_aq_avg --smilesname 'smiles solute' --plot_title 'Aqueous solubility'
      --plot_propname 'log(S)' --split scaffold --n_splits 5 --split_frac 0.9 --data_seed
      42 --scaffold_k 0 --color r"
    - mkdir -p data/aq/scaffold/
    - python3 scripts/split_data.py
    deps:
    - path: scripts/split_data.py
      hash: md5
      md5: ef207805679def351f00edeeb7c61b59
      size: 3022
    - path: src/dataloader.py
      hash: md5
      md5: 926fbd1e4cded22e6ba50cbfee23cfd9
      size: 23030
    params:
      params.yaml:
        split:
          split: scaffold
          n_splits: 5
          split_frac: 0.9
          data_seed: 42
          scaffold_k: 0
          color: r
          scale: false
        task:
          task: aq
          property: aq
          loader: AqSolDataset
          filepath: /workspace/data/AqueousSolu.csv
          propname: logS_aq_avg
          smilesname: smiles solute
          plot_title: Aqueous solubility
          plot_propname: log(S)
    outs:
    - path: data/aq/scaffold/
      hash: md5
      md5: 5e2663c51b6e6b175ece4459fdf31136.dir
      size: 2881218
      nfiles: 12
  train_model:
    cmd:
    - mkdir -p out/aq/scaffold/mmb-ft-avg-hier/{viz,model}
    - echo "TRAIN --model mmb-ft-avg --finetune --n_batch 48 --seed 42 --n_epochs
      1 --head hier --fit model"
    - python3 scripts/train_model.py
    deps:
    - path: data/aq/scaffold/
      hash: md5
      md5: 5e2663c51b6e6b175ece4459fdf31136.dir
      size: 2881218
      nfiles: 12
    - path: scripts/train_model.py
      hash: md5
      md5: bfbfd6c042eeb900f227cae3a11e83e3
      size: 6344
    - path: scripts/train_sklearn.py
      hash: md5
      md5: 965c34ea380b3caf505849c75a38719b
      size: 4271
    - path: src/model.py
      hash: md5
      md5: e7b58ba72bb006addebd9becc588e612
      size: 22951
    params:
      params.yaml:
        head:
          head: hier
          fit: model
        model:
          model: mmb-ft-avg
          finetune: true
          n_batch: 48
          seed: 42
          n_epochs: 1
        split:
          split: scaffold
          n_splits: 5
          split_frac: 0.9
          data_seed: 42
          scaffold_k: 0
          color: r
          scale: false
        task:
          task: aq
          property: aq
          loader: AqSolDataset
          filepath: /workspace/data/AqueousSolu.csv
          propname: logS_aq_avg
          smilesname: smiles solute
          plot_title: Aqueous solubility
          plot_propname: log(S)
    outs:
    - path: out/aq/scaffold/mmb-ft-avg-hier/best.pt
      hash: md5
      md5: 87b692f48e3d3caacd36c4dc8229bff6
      size: 154575
    - path: out/aq/scaffold/mmb-ft-avg-hier/metrics.json
      hash: md5
      md5: 9ca5c2f43202f54eca81fed9aa9d747e
      size: 917
    - path: out/aq/scaffold/mmb-ft-avg-hier/model/
      hash: md5
      md5: f2dfa8737b15110a4bd561d7bebca426.dir
      size: 476968575
      nfiles: 11
  explain_model:
    cmd:
    - mkdir -p out/aq/scaffold/mmb-ft-avg-hier/viz
    - python3 scripts/explain_shap.py
    deps:
    - path: data/aq/scaffold/test.pkl
      hash: md5
      md5: d950d274cfd670f7f49adcecef523c77
      size: 53396
    - path: out/aq/scaffold/mmb-ft-avg-hier/best.pt
      hash: md5
      md5: 87b692f48e3d3caacd36c4dc8229bff6
      size: 154575
    - path: scripts/explain_shap.py
      hash: md5
      md5: 072efdcef0cc6f1cda0cac300b42f23d
      size: 8638
    - path: src/explainer.py
      hash: md5
      md5: 66ff3736c22485db0817ce9ef9bf2815
      size: 13047
    - path: src/maskedhead.py
      hash: md5
      md5: e51c7a5310350d0e2607cfac6375cab7
      size: 6830
    params:
      params.yaml:
        head:
          head: hier
          fit: model
        model:
          model: mmb-ft-avg
          finetune: true
          n_batch: 48
          seed: 42
          n_epochs: 1
        split:
          split: scaffold
          n_splits: 5
          split_frac: 0.9
          data_seed: 42
          scaffold_k: 0
          color: r
          scale: false
        task:
          task: aq
          property: aq
          loader: AqSolDataset
          filepath: /workspace/data/AqueousSolu.csv
          propname: logS_aq_avg
          smilesname: smiles solute
          plot_title: Aqueous solubility
          plot_propname: log(S)
        xai:
          model: mmb-avg
          xai: shap
          mask: false
          cmap: div
    outs:
    - path: out/aq/scaffold/mmb-ft-avg-hier/attributions.csv
      hash: md5
      md5: 8d3cbbb0439e2fe5885bf08ac2425da8
      size: 1111063
    - path: out/aq/scaffold/mmb-ft-avg-hier/viz
      hash: md5
      md5: e882736880e4b01cda760240927939fa.dir
      size: 44435575
      nfiles: 926
  predict_model:
    cmd:
    - mkdir -p out/aq/scaffold/mmb-ft-avg-hier/viz
    - python3 scripts/predict_model.py
    - python3 scripts/plot_datasplit.py
    deps:
    - path: data/aq/scaffold/
      hash: md5
      md5: 5e2663c51b6e6b175ece4459fdf31136.dir
      size: 2881218
      nfiles: 12
    - path: out/aq/scaffold/mmb-ft-avg-hier/best.pt
      hash: md5
      md5: 87b692f48e3d3caacd36c4dc8229bff6
      size: 154575
    - path: scripts/plot_datasplit.py
      hash: md5
      md5: 67df0b5de0b523caccd498d817163775
      size: 6155
    - path: scripts/predict_model.py
      hash: md5
      md5: 23ff467aea9b73822284078601c370ec
      size: 8048
    - path: src/model.py
      hash: md5
      md5: e7b58ba72bb006addebd9becc588e612
      size: 22951
    params:
      params.yaml:
        head:
          head: hier
          fit: model
        model:
          model: mmb-ft-avg
          finetune: true
          n_batch: 48
          seed: 42
          n_epochs: 1
        split:
          split: scaffold
          n_splits: 5
          split_frac: 0.9
          data_seed: 42
          scaffold_k: 0
          color: r
          scale: false
        task:
          task: aq
          property: aq
          loader: AqSolDataset
          filepath: /workspace/data/AqueousSolu.csv
          propname: logS_aq_avg
          smilesname: smiles solute
          plot_title: Aqueous solubility
          plot_propname: log(S)
    outs:
    - path: out/aq/scaffold/mmb-ft-avg-hier/latent_viz.png
      hash: md5
      md5: 92daad24dd3ad13e15b0494e76b8e1e6
      size: 268505
    - path: out/aq/scaffold/mmb-ft-avg-hier/parity_plot.png
      hash: md5
      md5: 4ca34fd7848306b071be0215f71ae1f1
      size: 46127
    - path: out/aq/scaffold/mmb-ft-avg-hier/predictions.csv
      hash: md5
      md5: ece2bdd4c30516f8aeee45f240ad8dfe
      size: 546031
  all:
    cmd:
    - pwd
    - mkdir -p /workspace/final/aq/scaffold/mmb-ft-avg-hier/{model,viz}
    - cp -r out/aq/scaffold/mmb-ft-avg-hier/ /workspace/final/aq/scaffold/
    - cp -r dvc.lock /workspace/final/aq/scaffold/mmb-ft-avg-hier/dvc.lock
    - cp -r params.yaml /workspace/final/aq/scaffold/mmb-ft-avg-hier/params.yaml
    - python3 scripts/plot_similarity.py
    - python3 scripts/plot_models.py
    - echo "Finished full aq scaffold pipeline with mmb-ft-avg-hier"
    deps:
    - path: out/aq/scaffold/
      hash: md5
      md5: a1685bd0b0802873badaa279e0ac6aa7.dir
      size: 602904241
      nfiles: 945
    - path: out/aq/scaffold/mmb-ft-avg-hier/attributions.csv
      hash: md5
      md5: 8d3cbbb0439e2fe5885bf08ac2425da8
      size: 1111063
    - path: out/aq/scaffold/mmb-ft-avg-hier/best.pt
      hash: md5
      md5: 87b692f48e3d3caacd36c4dc8229bff6
      size: 154575
    - path: out/aq/scaffold/mmb-ft-avg-hier/latent_viz.png
      hash: md5
      md5: 92daad24dd3ad13e15b0494e76b8e1e6
      size: 268505
    - path: out/aq/scaffold/mmb-ft-avg-hier/model
      hash: md5
      md5: f2dfa8737b15110a4bd561d7bebca426.dir
      size: 476968575
      nfiles: 11
    - path: out/aq/scaffold/mmb-ft-avg-hier/parity_plot.png
      hash: md5
      md5: 4ca34fd7848306b071be0215f71ae1f1
      size: 46127
    - path: out/aq/scaffold/mmb-ft-avg-hier/predictions.csv
      hash: md5
      md5: ece2bdd4c30516f8aeee45f240ad8dfe
      size: 546031
    - path: out/aq/scaffold/mmb-ft-avg-hier/viz
      hash: md5
      md5: e882736880e4b01cda760240927939fa.dir
      size: 44435575
      nfiles: 926
    - path: scripts/plot_models.py
      hash: md5
      md5: 26cd98667331cd1b47ab0d2fa81b0ea4
      size: 6188
    - path: scripts/plot_similarity.py
      hash: md5
      md5: e0f8dbf182973c6704998119cc1d3708
      size: 3690