1. MPS still does not work (torch incompatibility)

2. Train function transferred (needs to be checked)
3. Minor changes

.gitignore

@@ -2,3 +2,4 @@
 /pretrained_models
 *.tsv
 *.fasta
+*.sh
\ No newline at end of file

senseppi/__main__.py

 import argparse
+import logging
 from .commands import *
 from senseppi import __version__
 
@@ -22,6 +23,13 @@ def main():
         sp.set_defaults(func=module.main)
 
     params = parser.parse_args()
+
+    #WARNING: due to some internal issues of torch, the mps backend is temporarily disabled
+    if params.device == 'mps':
+        logging.warning('WARNING: due to some internal issues of torch, the mps backend is temporarily disabled.'
+                        'The cpu backend will be used instead.')
+        params.device = 'cpu'
+
     params.func(params)
 
 

senseppi/commands/predict.py

@@ -11,7 +11,7 @@ from ..esm2_model import add_esm_args, compute_embeddings
 
 
 def predict(params):
-    test_data = PairSequenceData(emb_dir=params.output_dir_esm, actions_file=params.pairs,
+    test_data = PairSequenceData(emb_dir=params.output_dir_esm, actions_file=params.pairs_file,
                                  max_len=params.max_len, labels=False)
 
     pretrained_model = SensePPIModel(params)
@@ -34,7 +34,7 @@ def predict(params):
     preds = [pred for batch in trainer.predict(pretrained_model, test_loader) for pred in batch.squeeze().tolist()]
     preds = np.asarray(preds)
 
-    data = pd.read_csv(params.pairs, delimiter='\t', names=["seq1", "seq2"])
+    data = pd.read_csv(params.pairs_file, delimiter='\t', names=["seq1", "seq2"])
     data['preds'] = preds
 
     return data
@@ -66,16 +66,19 @@ def add_args(parser):
     predict_args = parser.add_argument_group(title="Predict args")
     parser._action_groups[0].add_argument("model_path", type=str,
                               help="A path to .ckpt file that contains weights to a pretrained model.")
-    predict_args.add_argument("--pairs", type=str, default=None,
-                              help="A path to a .tsv file with pairs of proteins to test (Optional). If not provided, all-to-all pairs will be generated.")
+    predict_args.add_argument("--pairs_file", type=str, default=None,
+                              help="A path to a .tsv file with pairs of proteins to test (Optional). If not provided, "
+                                   "all-to-all pairs will be generated.")
     predict_args.add_argument("-o", "--output", type=str, default="predictions",
-                              help="A path to a file where the predictions will be saved. (.tsv format will be added automatically)")
+                              help="A path to a file where the predictions will be saved. "
+                                   "(.tsv format will be added automatically)")
     predict_args.add_argument("--with_self", action='store_true',
                               help="Include self-interactions in the predictions."
                                    "By default they are not included since they were not part of training but"
                                    "they can be included by setting this flag to True.")
     predict_args.add_argument("-p", "--pred_threshold", type=float, default=0.5,
-                              help="Prediction threshold to determine interacting pairs that will be written to a separate file. Range: (0, 1).")
+                              help="Prediction threshold to determine interacting pairs that "
+                                   "will be written to a separate file. Range: (0, 1).")
 
     parser = SensePPIModel.add_model_specific_args(parser)
     remove_argument(parser, "--lr")
@@ -88,9 +91,9 @@ def main(params):
     logging.info("Device used: ", params.device)
 
     process_string_fasta(params.fasta_file, min_len=params.min_len, max_len=params.max_len)
-    if params.pairs is None:
+    if params.pairs_file is None:
         generate_pairs(params.fasta_file, 'protein.pairs.tsv', with_self=params.with_self)
-        params.pairs = 'protein.pairs.tsv'
+        params.pairs_file = 'protein.pairs.tsv'
 
     compute_embeddings(params)
 
@@ -104,7 +107,8 @@ def main(params):
 
 
 if __name__ == '__main__':
-    parser = add_args()
+    parser = argparse.ArgumentParser()
+    parser = add_args(parser)
     params = parser.parse_args()
 
     main(params)

senseppi/commands/train.py

-import os
-from pathlib import Path
-import torch
 import pytorch_lightning as pl
-import sys
 from pytorch_lightning.callbacks import TQDMProgressBar, ModelCheckpoint
 from ..model import SensePPIModel
 from ..dataset import PairSequenceData
@@ -10,72 +6,63 @@ from ..utils import *
 from ..esm2_model import add_esm_args, compute_embeddings
 
 
-
-# training_th.py
 def main(params):
     if params.seed is not None:
         pl.seed_everything(params.seed, workers=True)
 
-    dataset = PairSequenceData(emb_dir=params.output_dir_esm, actions_file=params.pairs,
-                               max_len=params.max_len, labels=False)
+    compute_embeddings(params)
 
-    model = SensePPIModel(params)
+    dataset = PairSequenceData(emb_dir=params.output_dir_esm, actions_file=params.pairs_file,
+                               max_len=params.max_len, labels=True)
 
-    model.load_data(dataset=dataset, valid_size=0.1)
+    model = SensePPIModel(params)
 
+    model.load_data(dataset=dataset, valid_size=params.valid_size)
     train_set = model.train_dataloader()
     val_set = model.val_dataloader()
 
-    logger = pl.loggers.TensorBoardLogger("logs", name='SENSE-PPI')
+    # logger = pl.loggers.TensorBoardLogger("logs", name='SENSE-PPI')
+    logger = None
 
     callbacks = [
-        TQDMProgressBar(refresh_rate=250),
+        # TQDMProgressBar(refresh_rate=250),
         ModelCheckpoint(filename='chkpt_loss_based_{epoch}-{val_loss:.3f}-{val_BinaryF1Score:.3f}', verbose=True,
                         monitor='val_loss', mode='min', save_top_k=1)
     ]
 
-    trainer = pl.Trainer(accelerator="gpu" if torch.cuda.is_available() else "cpu", devices=params.devices, num_nodes=params.num_nodes, max_epochs=100,
-                         logger=logger, callbacks=callbacks, strategy=params.strategy)
+    trainer = pl.Trainer(accelerator=params.device, devices=params.num_devices, num_nodes=params.num_nodes,
+                         max_epochs=params.num_epochs, logger=logger, callbacks=callbacks)
 
     trainer.fit(model, train_set, val_set)
 
 
-def esm_check(fasta_file, output_dir, params):
-    params.model_location = 'esm2_t36_3B_UR50D'
-    params.fasta_file = fasta_file
-    params.output_dir = output_dir
-
-    with open(params.fasta_file, 'r') as f:
-        seq_ids = [line.strip().split(' ')[0].replace('>', '') for line in f.readlines() if line.startswith('>')]
-
-    if not os.path.exists(params.output_dir):
-        print('Computing ESM embeddings...')
-        esm2_model.run(params)
-    else:
-        for seq_id in seq_ids:
-            if not os.path.exists(os.path.join(params.output_dir, seq_id + '.pt')):
-                print('Computing ESM embeddings...')
-                esm2_model.run(params)
-                break
-
 def add_args(parser):
     parser = add_general_args(parser)
 
-    predict_args = parser.add_argument_group(title="Training args")
+    train_args = parser.add_argument_group(title="Training args")
+    parser._action_groups[0].add_argument("pairs_file", type=str,
+                                          help="A path to a .tsv file containing training pairs. "
+                                               "Required format: 3 tab separated columns: first protein, "
+                                               "second protein (protein names have to be present in fasta_file), "
+                                               "label (0 or 1).")
+    train_args.add_argument("--valid_size", type=float, default=0.1,
+                            help="Fraction of the training data to use for validation.")
+    train_args.add_argument("--seed", type=int, default=None, help="Global training seed.")
+    train_args.add_argument("--num_epochs", type=int, default=100, help="Number of training epochs.")
+    train_args.add_argument("--num_devices", type=int, default=1,
+                            help="Number of devices to use for multi GPU training.")
+    train_args.add_argument("--num_nodes", type=int, default=1,
+                            help="Number of nodes to use for training on a cluster.")
 
     parser = SensePPIModel.add_model_specific_args(parser)
-    remove_argument(parser, "--lr")
 
     add_esm_args(parser)
     return parser
 
+
 if __name__ == '__main__':
     parser = argparse.ArgumentParser()
     parser = add_args(parser)
     params = parser.parse_args()
 
-    esm_check(Path(os.path.join('Data', 'Dscript', 'human.fasta')),
-                Path(os.path.join('Data', 'Dscript', 'esm_emb_3B_human')),
-                params)
-
     main(params)
\ No newline at end of file

senseppi/dataset.py

@@ -10,7 +10,7 @@ class PairSequenceData(Dataset):
     def __init__(self,
                  actions_file,
                  emb_dir,
-                 max_len=800,
+                 max_len,
                  pad_inputs=True,
                  labels=True):
 
@@ -34,9 +34,8 @@ class PairSequenceData(Dataset):
         try:
             emb = torch.load(f)
         except FileNotFoundError as _:
-            raise Exception(
-                'Embedding file {} not found. Check your fasta file and make sure it contains all the sequences used in training/testing.'.format(
-                    f))
+            raise Exception('Embedding file {} not found. Check your fasta file and make sure it contains '
+                            'all the sequences used in training/testing.'.format(f))
 
         tensor_emb = emb['representations'][36]  # [33]
         tensor_len = tensor_emb.size(0)

senseppi/model.py

@@ -47,7 +47,6 @@ class DynamicLSTM(pl.LightningModule):
 
     def forward(self, x, seq_lens):
         # sort input by descending length
-
         _, idx_sort = torch.sort(seq_lens, dim=0, descending=True)
         _, idx_unsort = torch.sort(idx_sort, dim=0)
         x_sort = torch.index_select(x, dim=0, index=idx_sort)
@@ -163,12 +162,12 @@ class BaselineModel(pl.LightningModule):
         self.valid_metrics.reset()
         self.log_dict(result, on_epoch=True, sync_dist=self.hparams.sync_dist)
 
-    def load_data(self, dataset, valid_size=0.2, indices=None):
+    def load_data(self, dataset, valid_size=0.1, indices=None):
         if indices is None:
             dataset_length = len(dataset)
             valid_length = int(valid_size * dataset_length)
             train_length = dataset_length - valid_length
-            self.train_set, self.val_set = data.random_split(dataset, [train_length, valid_length])  # , test_size])
+            self.train_set, self.val_set = data.random_split(dataset, [train_length, valid_length])
             print('Data has been randomly divided into train/val sets with sizes {} and {}'.format(len(self.train_set),
                                                                                                    len(self.val_set)))
         else:
@@ -216,7 +215,7 @@ class SensePPIModel(BaselineModel):
     def __init__(self, params):
         super(SensePPIModel, self).__init__(params)
 
-        self.encoder_features = self.hparams.encoder_features  # 2560
+        self.encoder_features = self.hparams.encoder_features
         self.hidden_dim = 256
 
         self.lstm = DynamicLSTM(self.encoder_features, hidden_size=128, num_layers=3, dropout=0.5, bidirectional=True)

senseppi/utils.py

@@ -15,10 +15,10 @@ def add_general_args(parser):
     )
     parser.add_argument("--min_len", type=int, default=50,
                         help="Minimum length of the protein sequence. "
-                             "The sequences with smaller length will not be considered. Default: 50")
+                             "The sequences with smaller length will not be considered.")
     parser.add_argument("--max_len", type=int, default=800,
                         help="Maximum length of the protein sequence. "
-                             "The sequences with larger length will not be considered. Default: 800")
+                             "The sequences with larger length will not be considered.")
     parser.add_argument("--device", type=str, default=determine_device(), choices=['cpu', 'gpu', 'mps'],
                         help="Device to used for computations. Options include: cpu, gpu, mps (for MacOS)."
                              "If not selected the device is set by torch automatically.")

setup.py

@@ -23,7 +23,7 @@ setup(
         "matplotlib",
         "tqdm",
         "scikit-learn",
-        "pytorch-lightning",
+        "pytorch-lightning==1.9.0",
         "torchmetrics",
         "biopython",
         "fair-esm"