Merge branch 'version-linker' of...

Merge branch 'version-linker' of https://gitlab.irit.fr/pnria/global-helper/deepgrail-linker into version-linker

# Conflicts:
#	Configuration/config.ini
#	train.py

Configuration/config.ini

@@ -12,15 +12,14 @@ max_atoms_in_one_type=250
 dim_encoder = 768
 
 [MODEL_DECODER]
-dim_decoder = 16
-num_rnn_layers=1
+dim_decoder = 32
 dropout=0.1
 teacher_forcing=0.05
 
 [MODEL_LINKER]
 nhead=4
 dim_feedforward=246
-dim_embedding_atoms=16
+dim_embedding_atoms=32
 dim_polarity_transfo=128
 layer_norm_eps=1e-5
 dropout=0.1
@@ -31,4 +30,4 @@ device=cpu
 batch_size=16
 epoch=20
 seed_val=42
-learning_rate=2e-5
+learning_rate=2e-5
\ No newline at end of file

Linker/Linker.py

@@ -9,6 +9,7 @@ import sys
 
 from torch.optim import AdamW
 from torch.utils.data import TensorDataset, random_split
+from torch.utils.tensorboard import SummaryWriter
 from transformers import get_cosine_schedule_with_warmup
 
 from Configuration import Configuration
@@ -23,6 +24,19 @@ from Linker.eval import mesure_accuracy, SinkhornLoss
 from utils import pad_sequence
 
 
+def output_create_dir():
+    """
+    Create le output dir for tensorboard and checkpoint
+    @return: output dir, tensorboard writter
+    """
+    from datetime import datetime
+    outpout_path = 'TensorBoard'
+    training_dir = os.path.join(outpout_path, 'Tranning_' + datetime.today().strftime('%d-%m_%H-%M'))
+    logs_dir = os.path.join(training_dir, 'logs')
+    writer = SummaryWriter(log_dir=logs_dir)
+    return training_dir, writer
+
+
 class Linker(Module):
     def __init__(self, supertagger):
         super(Linker, self).__init__()
@@ -67,20 +81,20 @@ class Linker(Module):
 
         self.device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
 
-    def __preprocess_data(self, batch_size, df_axiom_links, sentences_tokens, sentences_mask, validation_rate=0.0):
+    def __preprocess_data(self, batch_size, df_axiom_links, validation_rate=0.0):
         r"""
         Args:
             batch_size : int
             df_axiom_links pandas DataFrame
-            sentences_tokens
-            sentences_mask
             validation_rate
         Returns:
             the training dataloader and the validation dataloader. They contains the list of atoms, their polarities, the axiom links, the sentences tokenized, sentence mask
         """
+        sentences_batch = df_axiom_links["Sentences"].tolist()
+        sentences_tokens, sentences_mask = self.Supertagger.sent_tokenizer.fit_transform_tensors(sentences_batch)
+
         atoms_batch = get_atoms_batch(df_axiom_links["sub_tree"])
-        atom_tokenizer = AtomTokenizer(atom_map, self.max_atoms_in_sentence)
-        atoms_batch_tokenized = atom_tokenizer.convert_batchs_to_ids(atoms_batch)
+        atoms_batch_tokenized = self.atoms_tokenizer.convert_batchs_to_ids(atoms_batch)
 
         atoms_polarity_batch = find_pos_neg_idexes(self.max_atoms_in_sentence, df_axiom_links["sub_tree"])
 
@@ -153,29 +167,56 @@ class Linker(Module):
 
         return F.log_softmax(link_weights_per_batch, dim=3)
 
-    def train_linker(self, df_axiom_links, sentences_tokens, sentences_mask, validation_rate=0.1, epochs=20,
-                     batch_size=32, checkpoint=True, validate=True):
+    def train_linker(self, df_axiom_links, validation_rate=0.1, epochs=20,
+                     batch_size=32, checkpoint=True, tensorboard=False):
         r"""
         Args:
             df_axiom_links : pandas dataFrame containing the atoms anoted with _i
-            sentences_tokens : sentences tokenized by BERT
-            sentences_mask : mask of tokens
             validation_rate : float
             epochs : int
             batch_size : int
             checkpoint : boolean
-            validate : boolean
+            tensorboard : boolean
         Returns:
             Final accuracy and final loss
         """
         training_dataloader, validation_dataloader = self.__preprocess_data(batch_size, df_axiom_links,
-                                                                            sentences_tokens, sentences_mask,
                                                                             validation_rate)
         self.to(self.device)
-        for epoch_i in range(0, epochs):
-            epoch_acc, epoch_loss = self.train_epoch(training_dataloader, validation_dataloader, checkpoint, validate)
 
-    def train_epoch(self, training_dataloader, validation_dataloader, checkpoint=True, validate=True):
+        if checkpoint or tensorboard:
+            checkpoint_dir, writer = output_create_dir()
+
+        for epoch_i in range(epochs):
+            avg_train_loss, avg_accuracy_train = self.train_epoch(training_dataloader)
+
+            print("Average Loss on train dataset : ", avg_train_loss)
+            print("Average Accuracy on train dataset : ", avg_accuracy_train)
+
+            if checkpoint:
+                self.__checkpoint_save(
+                    path=os.path.join("Output", 'linker' + datetime.today().strftime('%d-%m_%H-%M') + '.pt'))
+
+            if validation_rate > 0.0:
+                with torch.no_grad():
+                    loss_test, accuracy_test = self.eval_epoch(validation_dataloader, self.cross_entropy_loss)
+                    print("Average Loss on test dataset : ", loss_test)
+                    print("Average Accuracy on test dataset : ", accuracy_test)
+
+            if tensorboard:
+                writer.add_scalars(f'Accuracy', {
+                    'Train': avg_accuracy_train}, epoch_i)
+                writer.add_scalars(f'Loss', {
+                    'Train': avg_train_loss}, epoch_i)
+                if validation_rate > 0.0:
+                    writer.add_scalars(f'Accuracy', {
+                        'Validation': accuracy_test}, epoch_i)
+                    writer.add_scalars(f'Loss', {
+                        'Validation': loss_test}, epoch_i)
+
+            print('\n')
+
+    def train_epoch(self, training_dataloader):
         r""" Train epoch
 
         Args:
@@ -188,6 +229,7 @@ class Linker(Module):
 
         # Reset the total loss for this epoch.
         epoch_loss = 0
+        accuracy_train = 0
 
         self.train()
 
@@ -220,22 +262,13 @@ class Linker(Module):
             self.optimizer.step()
             self.scheduler.step()
 
-        avg_train_loss = epoch_loss / len(training_dataloader)
-        print("Average Loss on train dataset : ", avg_train_loss)
+            pred_axiom_links = torch.argmax(logits_predictions, dim=3)
+            accuracy_train += mesure_accuracy(batch_true_links, pred_axiom_links)
 
-        if checkpoint:
-            self.__checkpoint_save(
-                path=os.path.join("Output", 'linker' + datetime.today().strftime('%d-%m_%H-%M') + '.pt'))
-
-        if validate:
-            with torch.no_grad():
-                accuracy, average_test_loss = self.eval_epoch(validation_dataloader, self.cross_entropy_loss)
-                print("Average Loss on test dataset : ", average_test_loss)
-                print("Average Accuracy on test dataset : ", accuracy)
-
-        print('\n')
+        avg_train_loss = epoch_loss / len(training_dataloader)
+        avg_accuracy_train = accuracy_train / len(training_dataloader)
 
-        return accuracy, avg_train_loss
+        return avg_train_loss, avg_accuracy_train
 
     def predict(self, categories, sents_embedding, sents_mask=None):
         r"""Prediction from categories output by BERT and hidden_state from BERT
@@ -302,7 +335,7 @@ class Linker(Module):
         accuracy = mesure_accuracy(batch_true_links, axiom_links_pred)
         loss = cross_entropy_loss(logits_axiom_links_pred, batch_true_links)
 
-        return accuracy, loss
+        return loss, accuracy
 
     def eval_epoch(self, dataloader, cross_entropy_loss):
         r"""Average the evaluation of all the batch.
@@ -312,14 +345,12 @@ class Linker(Module):
         """
         accuracy_average = 0
         loss_average = 0
-        compt = 0
         for step, batch in enumerate(dataloader):
-            compt += 1
-            accuracy, loss = self.eval_batch(batch, cross_entropy_loss)
+            loss, accuracy = self.eval_batch(batch, cross_entropy_loss)
             accuracy_average += accuracy
-            loss_average += loss
+            loss_average += float(loss)
 
-        return accuracy_average / compt, loss_average / compt
+        return loss_average / len(dataloader), accuracy_average / len(dataloader)
 
     def load_weights(self, model_file):
         print("#" * 15)

train.py

@@ -6,7 +6,7 @@ from utils import read_csv_pgbar
 
 torch.cuda.empty_cache()
 batch_size = int(Configuration.modelTrainingConfig['batch_size'])
-nb_sentences = batch_size * 200
+nb_sentences = batch_size * 20
 epochs = int(Configuration.modelTrainingConfig['epoch'])
 
 file_path_axiom_links = 'Datasets/goldANDsilver_dataset_links.csv'