Implement fine-tuning BERT on CoNLL-2003 named entity recognition task

examples/run_ner.py

@@ -55,7 +55,7 @@ def set_seed(args):
         torch.cuda.manual_seed_all(args.seed)
 
 
-def train(args, train_dataset, model, tokenizer, labels, pad_token_label_id):
+def train(args, train_dataset, model, tokenizer, pad_token_label_id):
     """ Train the model """
     if args.local_rank in [-1, 0]:
         tb_writer = SummaryWriter()
@@ -148,7 +148,7 @@ def train(args, train_dataset, model, tokenizer, labels, pad_token_label_id):
                 if args.local_rank in [-1, 0] and args.logging_steps > 0 and global_step % args.logging_steps == 0:
                     # Log metrics
                     if args.local_rank == -1 and args.evaluate_during_training:  # Only evaluate when single GPU otherwise metrics may not average well
-                        results, _ = evaluate(args, model, tokenizer, labels, pad_token_label_id)
+                        results = evaluate(args, model, tokenizer, pad_token_label_id)
                         for key, value in results.items():
                             tb_writer.add_scalar("eval_{}".format(key), value, global_step)
                     tb_writer.add_scalar("lr", scheduler.get_lr()[0], global_step)
@@ -160,7 +160,8 @@ def train(args, train_dataset, model, tokenizer, labels, pad_token_label_id):
                     output_dir = os.path.join(args.output_dir, "checkpoint-{}".format(global_step))
                     if not os.path.exists(output_dir):
                         os.makedirs(output_dir)
-                    model_to_save = model.module if hasattr(model, "module") else model  # Take care of distributed/parallel training
+                    model_to_save = model.module if hasattr(model,
+                                                            "module") else model  # Take care of distributed/parallel training
                     model_to_save.save_pretrained(output_dir)
                     torch.save(args, os.path.join(output_dir, "training_args.bin"))
                     logger.info("Saving model checkpoint to %s", output_dir)
@@ -178,8 +179,8 @@ def train(args, train_dataset, model, tokenizer, labels, pad_token_label_id):
     return global_step, tr_loss / global_step
 
 
-def evaluate(args, model, tokenizer, labels, pad_token_label_id, mode, prefix=""):
-    eval_dataset = load_and_cache_examples(args, tokenizer, labels, pad_token_label_id, mode=mode)
+def evaluate(args, model, tokenizer, pad_token_label_id, prefix=""):
+    eval_dataset = load_and_cache_examples(args, tokenizer, pad_token_label_id, evaluate=True)
 
     args.eval_batch_size = args.per_gpu_eval_batch_size * max(1, args.n_gpu)
     # Note that DistributedSampler samples randomly
@@ -219,7 +220,7 @@ def evaluate(args, model, tokenizer, labels, pad_token_label_id, mode, prefix=""
     eval_loss = eval_loss / nb_eval_steps
     preds = np.argmax(preds, axis=2)
 
-    label_map = {i: label for i, label in enumerate(labels)}
+    label_map = {i: label for i, label in enumerate(get_labels())}
 
     out_label_list = [[] for _ in range(out_label_ids.shape[0])]
     preds_list = [[] for _ in range(out_label_ids.shape[0])]
@@ -241,15 +242,15 @@ def evaluate(args, model, tokenizer, labels, pad_token_label_id, mode, prefix=""
     for key in sorted(results.keys()):
         logger.info("  %s = %s", key, str(results[key]))
 
-    return results, preds_list
+    return results
 
 
-def load_and_cache_examples(args, tokenizer, labels, pad_token_label_id, mode):
+def load_and_cache_examples(args, tokenizer, pad_token_label_id, evaluate=False):
     if args.local_rank not in [-1, 0] and not evaluate:
         torch.distributed.barrier()  # Make sure only the first process in distributed training process the dataset, and the others will use the cache
 
     # Load data features from cache or dataset file
-    cached_features_file = os.path.join(args.data_dir, "cached_{}_{}_{}".format(mode,
+    cached_features_file = os.path.join(args.data_dir, "cached_{}_{}_{}".format("dev" if evaluate else "train",
         list(filter(None, args.model_name_or_path.split("/"))).pop(),
         str(args.max_seq_length)))
     if os.path.exists(cached_features_file):
@@ -257,8 +258,9 @@ def load_and_cache_examples(args, tokenizer, labels, pad_token_label_id, mode):
         features = torch.load(cached_features_file)
     else:
         logger.info("Creating features from dataset file at %s", args.data_dir)
-        examples = read_examples_from_file(args.data_dir, mode)
-        features = convert_examples_to_features(examples, labels, args.max_seq_length, tokenizer,
+        label_list = get_labels()
+        examples = read_examples_from_file(args.data_dir, evaluate=evaluate)
+        features = convert_examples_to_features(examples, label_list, args.max_seq_length, tokenizer,
                                                 cls_token_at_end=bool(args.model_type in ["xlnet"]),
                                                 # xlnet has a cls token at the end
                                                 cls_token=tokenizer.cls_token,
@@ -303,8 +305,6 @@ def main():
                         help="The output directory where the model predictions and checkpoints will be written.")
 
     ## Other parameters
-    parser.add_argument("--labels", default="", type=str,
-                        help="Path to a file containing all labels. If not specified, CoNLL-2003 labels are used.")
     parser.add_argument("--config_name", default="", type=str,
                         help="Pretrained config name or path if not the same as model_name")
     parser.add_argument("--tokenizer_name", default="", type=str,
@@ -318,8 +318,6 @@ def main():
                         help="Whether to run training.")
     parser.add_argument("--do_eval", action="store_true",
                         help="Whether to run eval on the dev set.")
-    parser.add_argument("--do_predict", action="store_true",
-                        help="Whether to run predictions on the test set.")
     parser.add_argument("--evaluate_during_training", action="store_true",
                         help="Whether to run evaluation during training at each logging step.")
     parser.add_argument("--do_lower_case", action="store_true",
@@ -408,8 +406,8 @@ def main():
     set_seed(args)
 
     # Prepare CONLL-2003 task
-    labels = get_labels(args.labels)
-    num_labels = len(labels)
+    label_list = get_labels()
+    num_labels = len(label_list)
     # Use cross entropy ignore index as padding label id so that only real label ids contribute to the loss later
     pad_token_label_id = CrossEntropyLoss().ignore_index
 
@@ -435,8 +433,8 @@ def main():
 
     # Training
     if args.do_train:
-        train_dataset = load_and_cache_examples(args, tokenizer, labels, pad_token_label_id, mode="train")
-        global_step, tr_loss = train(args, train_dataset, model, tokenizer, labels, pad_token_label_id)
+        train_dataset = load_and_cache_examples(args, tokenizer, pad_token_label_id, evaluate=False)
+        global_step, tr_loss = train(args, train_dataset, model, tokenizer, pad_token_label_id)
         logger.info(" global_step = %s, average loss = %s", global_step, tr_loss)
 
     # Saving best-practices: if you use defaults names for the model, you can reload it using from_pretrained()
@@ -468,7 +466,7 @@ def main():
             global_step = checkpoint.split("-")[-1] if len(checkpoints) > 1 else ""
             model = model_class.from_pretrained(checkpoint)
             model.to(args.device)
-            result, _ = evaluate(args, model, tokenizer, labels, pad_token_label_id, mode="dev", prefix=global_step)
+            result = evaluate(args, model, tokenizer, pad_token_label_id, prefix=global_step)
             if global_step:
                 result = {"{}_{}".format(global_step, k): v for k, v in result.items()}
             results.update(result)
@@ -477,32 +475,6 @@ def main():
             for key in sorted(results.keys()):
                 writer.write("{} = {}\n".format(key, str(results[key])))
 
-    if args.do_predict and args.local_rank in [-1, 0]:
-        tokenizer = tokenizer_class.from_pretrained(args.output_dir, do_lower_case=args.do_lower_case)
-        model = model_class.from_pretrained(args.output_dir)
-        model.to(args.device)
-        result, predictions = evaluate(args, model, tokenizer, labels, pad_token_label_id, mode="test")
-        # Save results
-        output_test_results_file = os.path.join(args.output_dir, "test_results.txt")
-        with open(output_test_results_file, "w") as writer:
-            for key in sorted(result.keys()):
-                writer.write("{} = {}\n".format(key, str(result[key])))
-        # Save predictions
-        output_test_predictions_file = os.path.join(args.output_dir, "test_predictions.txt")
-        with open(output_test_predictions_file, "w") as writer:
-            with open(os.path.join(args.data_dir, "test.txt"), "r") as f:
-                example_id = 0
-                for line in f:
-                    if line.startswith("-DOCSTART-") or line == "" or line == "\n":
-                        writer.write(line)
-                        if not predictions[example_id]:
-                            example_id += 1
-                    elif predictions[example_id]:
-                        output_line = line.split()[0] + " " + predictions[example_id].pop(0) + "\n"
-                        writer.write(output_line)
-                    else:
-                        logger.warning("Maximum sequence length exceeded: No prediction for '%s'.", line.split()[0])
-
     return results
 
 

examples/utils_ner.py

@@ -51,8 +51,13 @@ class InputFeatures(object):
         self.label_ids = label_ids
 
 
-def read_examples_from_file(data_dir, mode):
-    file_path = os.path.join(data_dir, "{}.txt".format(mode))
+def read_examples_from_file(data_dir, evaluate=False):
+    if evaluate:
+        file_path = os.path.join(data_dir, "dev.txt")
+        guid_prefix = "dev"
+    else:
+        file_path = os.path.join(data_dir, "train.txt")
+        guid_prefix = "train"
     guid_index = 1
     examples = []
     with open(file_path, encoding="utf-8") as f:
@@ -61,7 +66,7 @@ def read_examples_from_file(data_dir, mode):
         for line in f:
             if line.startswith("-DOCSTART-") or line == "" or line == "\n":
                 if words:
-                    examples.append(InputExample(guid="{}-{}".format(mode, guid_index),
+                    examples.append(InputExample(guid="{}-{}".format(guid_prefix, guid_index),
                                                  words=words,
                                                  labels=labels))
                     guid_index += 1
@@ -70,13 +75,9 @@ def read_examples_from_file(data_dir, mode):
             else:
                 splits = line.split(" ")
                 words.append(splits[0])
-                if len(splits) > 1:
-                    labels.append(splits[-1].replace("\n", ""))
-                else:
-                    # Examples could have no label for mode = "test"
-                    labels.append("O")
+                labels.append(splits[-1][:-1])
         if words:
-            examples.append(InputExample(guid="%s-%d".format(mode, guid_index),
+            examples.append(InputExample(guid="%s-%d".format(guid_prefix, guid_index),
                                          words=words,
                                          labels=labels))
     return examples
@@ -201,12 +202,5 @@ def convert_examples_to_features(examples,
     return features
 
 
-def get_labels(path):
-    if path:
-        with open(path, "r") as f:
-            labels = f.read().splitlines()
-        if "O" not in labels:
-            labels = ["O"] + labels
-        return labels
-    else:
+def get_labels():
     return ["O", "B-MISC", "I-MISC",  "B-PER", "I-PER", "B-ORG", "I-ORG", "B-LOC", "I-LOC"]