Merge pull request #117 from jyaacoub/development

resolves #113

.gitignore

@@ -214,12 +214,15 @@ slurm_out*/
 *.swp
 *.swo
 /*.sh
-results/model_checkpoints/ours/*.model_tmp
-results/model_checkpoints/ours/*.model
+results/**/model_checkpoints/*/*.model_tmp
+results/**/model_checkpoints/*/*.model
 *.swp
 *.swo
 
 results/model_media/*/train_log/*
 results/model_media/*/train_set_pred/*
 results/model_media/*/test_set_pred/*
-results/model_media/test_set_pred
+results/model_media/test_set_pred
+
+splits/**/*.csv
+results/v113/model_media/*/train_log/*.json

playground.py

@@ -1,5 +1,7 @@
-#%%
 # %%
+########################################################################
+########################## VIOLIN PLOTTING #############################
+########################################################################
 import logging
 from typing import OrderedDict
 
@@ -9,137 +11,82 @@
 
 from src.analysis.figures import prepare_df, custom_fig, fig_combined
 
-df = prepare_df()
-# %%
 models = {
     'DG': ('nomsa', 'binary', 'original', 'binary'),
+    # 'esm': ('ESM', 'binary', 'original', 'binary'), # esm model
     'aflow': ('nomsa', 'aflow', 'original', 'binary'),
-    # 'aflow_ring3': ('nomsa', 'aflow_ring3', 'original', 'binary'),
     # 'gvpP': ('gvp', 'binary', 'original', 'binary'),
-    # 'gvpL': ('nomsa', 'binary', 'gvp', 'binary'),
-    'gvpL_aflow': ('nomsa', 'aflow', 'gvp', 'binary'),
     'gvpL': ('nomsa', 'binary', 'gvp', 'binary'),
+    # 'aflow_ring3': ('nomsa', 'aflow_ring3', 'original', 'binary'),
+    'gvpL_aflow': ('nomsa', 'aflow', 'gvp', 'binary'),
     # 'gvpL_aflow_rng3': ('nomsa', 'aflow_ring3', 'gvp', 'binary'),
+    #GVPL_ESMM_davis3D_nomsaF_aflowE_48B_0.00010636872718329864LR_0.23282479481785903D_2000E_gvpLF_binaryLE
+    # 'gvpl_esm_aflow': ('ESM', 'aflow', 'gvp', 'binary'),
 }
 
-# %%
-fig, axes = fig_combined(df, datasets=['davis','PDBbind'], fig_callable=custom_fig,
+df = prepare_df('/cluster/home/t122995uhn/projects/MutDTA/results/v113/model_media/model_stats.csv')
+fig, axes = fig_combined(df, datasets=['davis'], fig_callable=custom_fig,
              models=models, metrics=['cindex', 'mse'],
-             fig_scale=(8,5))
+             fig_scale=(10,5), add_stats=True, title_postfix=" test set performance")
 plt.xticks(rotation=45)
 
+df = prepare_df('/cluster/home/t122995uhn/projects/MutDTA/results/v113/model_media/model_stats_val.csv')
+fig, axes = fig_combined(df, datasets=['davis'], fig_callable=custom_fig,
+             models=models, metrics=['cindex', 'mse'],
+             fig_scale=(10,5), add_stats=True, title_postfix=" validation set performance")
+plt.xticks(rotation=45)
 
-# %%
-########################################################################
-########################## PLATINUM ANALYSIS ###########################
-########################################################################
-import torch, os
-import pandas as pd
 
+# %%
+from src.data_prep.init_dataset import create_datasets
 from src import cfg
-from src import TUNED_MODEL_CONFIGS
+
+splits = '/cluster/home/t122995uhn/projects/MutDTA/splits/davis/'
+create_datasets(cfg.DATA_OPT.davis, 
+                feat_opt=cfg.PRO_FEAT_OPT.nomsa, 
+                edge_opt=cfg.PRO_EDGE_OPT.aflow,
+                ligand_features=[cfg.LIG_FEAT_OPT.original, cfg.LIG_FEAT_OPT.gvp], 
+                ligand_edges=cfg.LIG_EDGE_OPT.binary,
+                k_folds=5, 
+                test_prots_csv=f'{splits}/test.csv',
+                val_prots_csv=[f'{splits}/val{i}.csv' for i in range(5)])
+
+# %%
 from src.utils.loader import Loader
-from src.train_test.training import test
-from src.analysis.figures import predictive_performance, tbl_stratified_dpkd_metrics, tbl_dpkd_metrics_overlap, tbl_dpkd_metrics_in_binding
-
-device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
-
-INFERENCE = True
-VERBOSE = True
-out_dir = f'{cfg.MEDIA_SAVE_DIR}/test_set_pred/'
-os.makedirs(out_dir, exist_ok=True)
-cp_dir = cfg.CHECKPOINT_SAVE_DIR
-RAW_PLT_CSV=f"{cfg.DATA_ROOT}/PlatinumDataset/raw/platinum_flat_file.csv"
-
-#%% load up model:
-for KEY, CONFIG in TUNED_MODEL_CONFIGS.items():
-    MODEL_KEY = lambda fold: Loader.get_model_key(CONFIG['model'], CONFIG['dataset'], CONFIG['feature_opt'], CONFIG['edge_opt'], 
-                                    CONFIG['batch_size'], CONFIG['lr'], CONFIG['architecture_kwargs']['dropout'],
-                                    n_epochs=2000, fold=fold, 
-                                    ligand_feature=CONFIG['lig_feat_opt'], ligand_edge=CONFIG['lig_edge_opt'])
-    print('\n\n'+ '## ' + KEY)
-    OUT_PLT = lambda i: f'{out_dir}/{MODEL_KEY(i)}_PLATINUM.csv'
-    db_p = f"{CONFIG['feature_opt']}_{CONFIG['edge_opt']}_{CONFIG['lig_feat_opt']}_{CONFIG['lig_edge_opt']}"
-
-    if CONFIG['dataset'] in ['kiba', 'davis']:
-        db_p = f"DavisKibaDataset/{CONFIG['dataset']}/{db_p}"
-    else:
-        db_p = f"{CONFIG['dataset']}Dataset/{db_p}"
-
-    train_p = lambda set: f"{cfg.DATA_ROOT}/{db_p}/{set}0/cleaned_XY.csv"
-
-    if not os.path.exists(OUT_PLT(0)) and INFERENCE:
-        print('running inference!')
-        cp = lambda fold: f"{cp_dir}/{MODEL_KEY(fold)}.model"
-
-        model = Loader.init_model(model=CONFIG["model"], pro_feature=CONFIG["feature_opt"],
-                                    pro_edge=CONFIG["edge_opt"],**CONFIG['architecture_kwargs'])
-
-        # load up platinum test db
-        loaders = Loader.load_DataLoaders(cfg.DATA_OPT.platinum,
-                                    pro_feature    = CONFIG['feature_opt'], 
-                                    edge_opt       = CONFIG['edge_opt'],
-                                    ligand_feature = CONFIG['lig_feat_opt'], 
-                                    ligand_edge    = CONFIG['lig_edge_opt'],
-                                    datasets=['test'])
-
-        for i in range(5):
-            model.safe_load_state_dict(torch.load(cp(i), map_location=device))
-            model.to(device)
-            model.eval()
-
-            loss, pred, actual = test(model, loaders['test'], device, verbose=True)
-
-            # saving as csv with columns code, pred, actual
-            # get codes from test loader
-            codes, pid = [b['code'][0] for b in loaders['test']], [b['prot_id'][0] for b in loaders['test']]
-            df = pd.DataFrame({'prot_id': pid, 'pred': pred, 'actual': actual}, index=codes)
-            df.index.name = 'code'
-            df.to_csv(OUT_PLT(i))
-
-    # run platinum eval:
-    print('\n### 1. predictive performance')
-    mkdown = predictive_performance(OUT_PLT, train_p, verbose=VERBOSE, plot=False)
-    print('\n### 2 Mutation impact analysis')
-    print('\n#### 2.1 $\Delta pkd$ predictive performance')
-    mkdn = tbl_dpkd_metrics_overlap(OUT_PLT, train_p, verbose=VERBOSE, plot=False)
-    print('\n#### 2.2 Stratified by location of mutation (binding pocket vs not in binding pocket)')
-    m = tbl_dpkd_metrics_in_binding(OUT_PLT, RAW_PLT_CSV, verbose=VERBOSE, plot=False)
-
+
+db_aflow = Loader.load_dataset('../data/DavisKibaDataset/davis/nomsa_aflow_original_binary/full')
+db = Loader.load_dataset('../data/DavisKibaDataset/davis/nomsa_binary_original_binary/full')
+
 # %%
-dfr = pd.read_csv(RAW_PLT_CSV, index_col=0)
-
-# add in_binding info to df
-def get_in_binding(df, dfr):
-    """
-    df is the predicted csv with index as <raw_idx>_wt (or *_mt) where raw_idx 
-    corresponds to an index in dfr which contains the raw data for platinum including 
-    ('mut.in_binding_site')
-        - 0: wildtype rows
-        - 1: close (<8 Ang)
-        - 2: Far (>8 Ang)
-    """
-    pocket = dfr[dfr['mut.in_binding_site'] == 'YES'].index   
-    pclass = []
-    for code in df.index:
-        if '_wt' in code:
-            pclass.append(0)
-        elif int(code.split('_')[0]) in pocket:
-            pclass.append(1)
-        else:
-            pclass.append(2)
-    df['pocket'] = pclass
-    return df
-
-df = get_in_binding(pd.read_csv(OUT_PLT(0), index_col=0), dfr)
-if VERBOSE: 
-    cnts = df.pocket.value_counts()
-    cnts.index = ['wt', 'in pocket', 'not in pocket']
-    cnts.name = "counts"
-    print(cnts.to_markdown(), end="\n\n")
-
-tbl_stratified_dpkd_metrics(OUT_PLT, NORMALIZE=True, n_models=5, df_transform=get_in_binding,
-                            conditions=['(pocket == 0) | (pocket == 1)', '(pocket == 0) | (pocket == 2)'], 
-                            names=['in pocket', 'not in pocket'], 
-                            verbose=VERBOSE, plot=True, dfr=dfr)
+# 5-fold cross validation + test set
+import pandas as pd
+from src import cfg
+from src.train_test.splitting import balanced_kfold_split
+from src.utils.loader import Loader
+test_df = pd.read_csv('/cluster/home/t122995uhn/projects/MutDTA/splits/pdbbind_test.csv')
+test_prots = set(test_df.prot_id)
+db = Loader.load_dataset(f'{cfg.DATA_ROOT}/PDBbindDataset/nomsa_binary_original_binary/full/')
 
+train, val, test = balanced_kfold_split(db,
+                k_folds=5, test_split=0.1, val_split=0.1, 
+                test_prots=test_prots, random_seed=0, verbose=True
+                )
+
+#%%
+db.save_subset_folds(train, 'train')
+db.save_subset_folds(val, 'val')
+db.save_subset(test, 'test')
+
+#%%
+import shutil, os
+
+src = "/cluster/home/t122995uhn/projects/data/PDBbindDataset/nomsa_binary_original_binary/"
+dst = "/cluster/home/t122995uhn/projects/MutDTA/splits/pdbbind"
+os.makedirs(dst, exist_ok=True)
+
+for i in range(5):
+    sfile = f"{src}/val{i}/XY.csv"
+    dfile = f"{dst}/val{i}.csv"
+    shutil.copyfile(sfile, dfile)
+
+# %%