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Update supported_datasets.py based on Table 6 naming #48

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Update supported_datasets.py based on Table 6 naming
ptamarp Apr 8, 2026
1e2c5a2
Merge branch 'main' into patch-2
nrafaili May 11, 2026
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176 changes: 82 additions & 94 deletions src/protify/data/supported_datasets.py
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Original file line number Diff line number Diff line change
@@ -1,51 +1,52 @@

supported_datasets = {
'EC': 'GleghornLab/EC_reg',
'GO-CC': 'GleghornLab/CC_reg',
'GO-BP': 'GleghornLab/BP_reg',
'GO-MF': 'GleghornLab/MF_reg',
'MB': 'GleghornLab/MB_reg',
'DeepLoc-2': 'GleghornLab/DL2_reg',
'DeepLoc-10': 'GleghornLab/DL10_reg',
'Subcellular': 'GleghornLab/SL_13',
'DeepLoc-10': 'GleghornLab/DL10_reg',
'SL13': 'GleghornLab/SL_13',
'enzyme-kcat': 'GleghornLab/enzyme_kcat',
'solubility': 'GleghornLab/solubility_prediction',
'localization': 'GleghornLab/localization_prediction',
'temperature-stability': 'GleghornLab/temperature_stability',
'peptide-HLA-MHC-affinity': 'GleghornLab/peptide_HLA_MHC_affinity_ppi',
'optimal-temperature': 'GleghornLab/optimal_temperature',
'temp-stability': 'GleghornLab/temperature_stability',
'optimal-temp': 'GleghornLab/optimal_temperature',
'optimal-ph': 'GleghornLab/optimal_ph',
'optimal-ph-rigor': 'GleghornLab/optimal_ph_rigor',
'material-production': 'GleghornLab/material_production',
'fitness-prediction': 'GleghornLab/fitness_prediction',
'mat-production': 'GleghornLab/material_production',
'fitness-pred': 'GleghornLab/fitness_prediction',
'number-of-folds': 'GleghornLab/fold_prediction',
'cloning-clf': 'GleghornLab/cloning_clf',
'stability-prediction': 'GleghornLab/stability_prediction',
'human-ppi-saprot': 'GleghornLab/HPPI',
'SecondaryStructure-3': 'GleghornLab/SS3',
'SecondaryStructure-8': 'GleghornLab/SS8',
'fluorescence-prediction': 'GleghornLab/fluorescence_prediction',
'plastic': 'GleghornLab/plastic_degradation_benchmark',
'gold-ppi': 'Synthyra/bernett_gold_ppi',
'human-ppi-pinui': 'GleghornLab/HPPI_PiNUI',
'yeast-ppi-pinui': 'GleghornLab/YPPI_PiNUI',
'shs27-ppi-raw': 'Synthyra/SHS27k',
'shs148-ppi-raw': 'Synthyra/SHS148k',
'shs27-ppi-random': 'GleghornLab/ppi_SHS27k_random_2025',
'shs148-ppi-random': 'GleghornLab/ppi_SHS148k_random_2025',
'shs27-ppi-dfs': 'GleghornLab/ppi_SHS27k_dfs_2025',
'shs148-ppi-dfs': 'GleghornLab/ppi_SHS148k_dfs_2025',
'shs27-ppi-bfs': 'GleghornLab/ppi_SHS27k_bfs_2025',
'stability-pred': 'GleghornLab/stability_prediction',
'ec-active': 'lhallee/ec_active',
'ecoli_expression': 'GleghornLab/ecoli_expression',
'soluprot': 'GleghornLab/soluprot',
'KSMoFinder-clustered': 'GleghornLab/ksmo_clustered',
'KSMoFinder': 'GleghornLab/KSmo_fixed',
'shs148-ppi-bfs': 'GleghornLab/ppi_SHS148k_bfs_2025',
'string-ppi-random': 'GleghornLab/ppi_STRING_random_2025',
'string-ppi-dfs': 'GleghornLab/ppi_STRING_dfs_2025',
'shs27-ppi-bfs': 'GleghornLab/ppi_SHS27k_bfs_2025',
'string-ppi-bfs': 'GleghornLab/ppi_STRING_bfs_2025',
'gold-ppi': 'Synthyra/bernett_gold_ppi',
'plm-interact': 'GleghornLab/plm_interact_human_train_cross_ppi',
'ppi-mutation-effect': 'GleghornLab/ppi_mutation_effect', # requires multi_column
'PPA-ppi': 'Synthyra/ppi_affinity',
'million_full': 'GleghornLab/millionfull_round_1_oct_2025',
'taxon_species': 'GleghornLab/taxonomy_species_0.4_clusters',
'diff_phylogeny': 'GleghornLab/diff_phylo',
'localization': 'GleghornLab/localization_prediction',
'peptide-HLA-MHC-affinity': 'GleghornLab/peptide_HLA_MHC_affinity_ppi',
'optimal-ph-rigor': 'GleghornLab/optimal_ph_rigor',
'SS3': 'GleghornLab/SS3',
'SS8': 'GleghornLab/SS8',
'foldseek-fold': 'lhallee/foldseek_dataset', # prostt5
'foldseek-inverse': 'lhallee/foldseek_dataset', # prostt5
'ec-active': 'lhallee/ec_active',
'plddt': 'GleghornLab/af2_plddt',
'shs27-ppi-random': 'GleghornLab/ppi_SHS27k_random_2025',
'shs27-ppi-dfs': 'GleghornLab/ppi_SHS27k_dfs_2025',
'shs27-ppi-raw': 'Synthyra/SHS27k',
'shs148-ppi-random': 'GleghornLab/ppi_SHS148k_random_2025',
'shs148-ppi-dfs': 'GleghornLab/ppi_SHS148k_dfs_2025',
'shs148-ppi-raw': 'Synthyra/SHS148k',
'string-ppi-random': 'GleghornLab/ppi_STRING_random_2025',
'string-ppi-dfs': 'GleghornLab/ppi_STRING_dfs_2025',
'proteingym_zs': 'proteingym_zs', # not a path, data loading for this is currently handled in benchmarks/proteingym/data_loader.py
'proteingym_supervised': 'proteingym_supervised', # not a path, data loading for this is currently handled in benchmarks/proteingym/data_loader.py
'taxon_domain': 'GleghornLab/taxonomy_domain_0.4_clusters',
Expand All @@ -55,59 +56,64 @@
'taxon_order': 'GleghornLab/taxonomy_order_0.4_clusters',
'taxon_family': 'GleghornLab/taxonomy_family_0.4_clusters',
'taxon_genus': 'GleghornLab/taxonomy_genus_0.4_clusters',
'taxon_species': 'GleghornLab/taxonomy_species_0.4_clusters',
'diff_phylogeny': 'GleghornLab/diff_phylo',
'plddt': 'GleghornLab/af2_plddt',
'human-ppi-saprot': 'GleghornLab/HPPI',
'human-ppi-pinui': 'GleghornLab/HPPI_PiNUI',
'yeast-ppi-pinui': 'GleghornLab/YPPI_PiNUI',
'ppi-mutation-effect': 'GleghornLab/ppi_mutation_effect', # requires multi_column
'fluorescence': 'GleghornLab/fluorescence_prediction',
'realness': 'GleghornLab/realness_dataset',
'million_full': 'GleghornLab/millionfull_round_1_oct_2025',
'soluprot': 'GleghornLab/soluprot',
'ecoli_expression': 'GleghornLab/ecoli_expression',
'KSMoFinder-clustered': 'GleghornLab/ksmo_clustered',
'KSMoFinder': 'GleghornLab/KSmo_fixed',
# bom-pooling paper (Hoang & Singh 2025) datasets
'FLUO': 'GleghornLab/bom_fluorescence',
'BLAC': 'GleghornLab/bom_blac',
'remote_homology': 'GleghornLab/bom_remote_homology',
'DPI': 'GleghornLab/bom_dpi',
}

internal_datasets = {
'plastic': 'GleghornLab/plastic_degradation_benchmark',
}

# TODO update
possible_with_vector_reps = [
### multi-label
'EC',
# GO
'GO-CC',
'GO-BP',
'GO-MF',
'Subcellular',
# ppi
'shs27-ppi-random',
'shs27-ppi-dfs',
'shs27-ppi-bfs',
'shs148-ppi-random',
'shs148-ppi-dfs',
'shs148-ppi-bfs',
'string-ppi-random',
'string-ppi-dfs',
'string-ppi-bfs',
'SL13',
### classification
'MB',
'DeepLoc-2',
'DeepLoc-10',
'solubility',
'temperature-stability',
'material-production',
'fitness-prediction',
'temp-stability',
'mat-production',
'fitness-pred',
'number-of-folds',
'cloning-clf',
'stability-prediction',
'stability-pred',
'ec-active',
'localization',
# taxonomy
### regression
'enzyme-kcat',
'optimal-temp',
'optimal-ph',
'million_full',
### ppi
'shs148-ppi-bfs',
'shs27-ppi-bfs',
'string-ppi-bfs',
'gold-ppi',
'plm-interact',
'PPA-ppi',
'shs27-ppi-raw',
'shs148-ppi-raw',
'shs27-ppi-random',
'shs27-ppi-dfs',
'shs148-ppi-random',
'shs148-ppi-dfs',
'string-ppi-random',
'string-ppi-dfs',
'human-ppi-saprot',
'human-ppi-pinui',
'yeast-ppi-pinui',
### taxonomy
'taxon_domain',
'taxon_kingdom',
'taxon_phylum',
Expand All @@ -117,22 +123,6 @@
'taxon_genus',
'taxon_species',
'diff_phylogeny',
# ppi
'shs27-ppi-raw',
'shs148-ppi-raw',
'plm-interact',
'gold-ppi',
'string-ppi-bfs',
'human-ppi-saprot',
'human-ppi-pinui',
'yeast-ppi-pinui',
### regression
'enzyme-kcat',
'optimal-temperature',
'optimal-ph',
'million_full',
# ppi
'PPA-ppi',
]

# TODO update
Expand All @@ -146,9 +136,9 @@
'DeepLoc-2',
'DeepLoc-10',
'enzyme-kcat',
'optimal-temperature',
'opt-temp',
'optimal-ph',
'fitness-prediction',
'fitness-pred',
]


Expand All @@ -159,37 +149,35 @@
'GO-CC', # SaProt
'GO-BP', # SaProt
'GO-MF', # SaProt
'Subcellular', # Custom - Tamar
# ppi
'shs27-ppi-bfs', # MGPPI + SHS27k + SHS148k + STRING
'shs148-ppi-bfs', # MGPPI + SHS27k + SHS148k + STRING
'string-ppi-bfs', # MGPPI + SHS27k + SHS148k + STRING
'SL13', # Custom - Tamar
### classification
'MB', # SaProt
'DeepLoc-2', # SaProt
'DeepLoc-10', # SaProt
'solubility', # Biomap
'temperature-stability', # Biomap
'material-production', # Biomap
'fitness-prediction', # Biomap
'temp-stability', # Biomap
'mat-production', # Biomap
'fitness-pred', # Biomap
'number-of-folds', # Biomap
'cloning-clf', # Biomap
'stability-prediction', # Biomap
'stability-pred', # Biomap
'ec-active', # Custom - Logan
'soluprot', # Custom - SoluProt
# taxonomy
### taxonomy
'taxon_species', # Accidental taxonomists
'diff_phylogeny', # Accidental taxonomists
# ppi
### ppi
'shs27-ppi-bfs', # MGPPI + SHS27k + SHS148k + STRING
'shs148-ppi-bfs', # MGPPI + SHS27k + SHS148k + STRING
'string-ppi-bfs', # MGPPI + SHS27k + SHS148k + STRING
'plm-interact', # PLM-Interact
'gold-ppi', # Bernett
### regression
'PPA-ppi', # Custom - Logan - Bindwell
# regression
'enzyme-kcat', # Custom - Logan - Biomap
'optimal-temperature', # Biomap
'opt-temp', # Biomap
'optimal-ph', # Biomap
'million_full', # Millionfull
# ppi
'PPA-ppi', # Custom - Logan - Bindwell
]


Expand All @@ -200,5 +188,5 @@
'enzyme-kcat', # regression
'human-ppi', # ppi
'plddt', # tokenwise regression
'SecondaryStructure-3', # tokenwise classification
]
'SS3', # tokenwise classification
]