test

README.md

@@ -42,12 +42,16 @@ DeepKE 提供了多种知识抽取模型。
 
 1.NER
 
+```
+REGULAR
+```
+
 2.RE 
 
     1.REGULAR
-
+    
     2.FEW-SHOT
-
+    
     3.DOCUMENT
 
 3.AE
@@ -66,6 +70,8 @@ Deepke包含了以下功能：（各子块导航到各模块的readme）
 
 1.NER
 
+**[REGULAR](https://github.com/zjunlp/deepke/blob/test_new_deepke/example/ner/regular/README.md)**
+
 2.RE 其中RE包括了以下三个子功能
 
 **[REGULAR](https://github.com/zjunlp/deepke/blob/test_new_deepke/example/re/regular/README.md)**

README_ENGLISH.md

@@ -44,12 +44,16 @@ demo 's urls
 
 1.NER
 
+```
+REGULAR
+```
+
 2.RE 
 
     1.REGULAR
-
+    
     2.FEW-SHOT
-
+    
     3.DOCUMENT
 
 3.AE
@@ -68,6 +72,8 @@ Deepke contains these models:
 
 1.NER
 
+**[REGULAR](https://github.com/zjunlp/deepke/blob/test_new_deepke/example/ner/regular/README.md)**
+
 2.RE 
 
 **[REGULAR](https://github.com/zjunlp/deepke/blob/test_new_deepke/example/re/regular/README.md)**

example/ner/regular/README.md

@@ -0,0 +1,41 @@
+# 快速上手
+
+## 克隆代码
+
+```
+git clone git@github.com:zjunlp/DeepKE.git
+```
+
+
+
+## 配置环境
+
+创建python虚拟环境（python>=3.7）
+
+安装依赖库
+
+```
+pip install -r requirements.txt
+```
+
+
+
+## 使用工具
+
+先进行训练，训练后的模型参数保存在out_ner文件夹中
+
+```
+python run.py --data_dir=data/ --bert_model=bert-base-cased --task_name=ner --output_dir=out_ner --max_seq_length=128 --do_train --num_train_epochs 5 --do_eval --warmup_proportion=0.1
+```
+
+再进行预测<br>
+
+执行以下命令运行示例
+
+```
+python predict.py
+```
+如果需要指定NER的文本，可以利用--text参数指定
+```
+python predict.py --text="Irene, a master student in Zhejiang University, Hangzhou, is traveling in Warsaw for Chopin Music Festival."
+```

example/ner/regular/predict.py

@@ -0,0 +1,174 @@
+"""BERT NER Inference."""
+
+from __future__ import absolute_import, division, print_function
+
+import json
+import os
+
+import torch
+import torch.nn.functional as F
+from nltk import word_tokenize
+from pytorch_transformers import (BertConfig, BertForTokenClassification,
+                                  BertTokenizer)
+from collections import OrderedDict
+import argparse
+
+import nltk
+nltk.data.path.insert(0,'./data/nltk_data')
+
+
+class BertNer(BertForTokenClassification):
+
+    def forward(self, input_ids, token_type_ids=None, attention_mask=None, valid_ids=None):
+        sequence_output = self.bert(input_ids, token_type_ids, attention_mask, head_mask=None)[0]
+        batch_size,max_len,feat_dim = sequence_output.shape
+        valid_output = torch.zeros(batch_size,max_len,feat_dim,dtype=torch.float32,device='cuda' if torch.cuda.is_available() else 'cpu')
+        for i in range(batch_size):
+            jj = -1
+            for j in range(max_len):
+                    if valid_ids[i][j].item() == 1:
+                        jj += 1
+                        valid_output[i][jj] = sequence_output[i][j]
+        sequence_output = self.dropout(valid_output)
+        logits = self.classifier(sequence_output)
+        return logits
+
+class Ner:
+
+    def __init__(self,model_dir: str):
+        self.model , self.tokenizer, self.model_config = self.load_model(model_dir)
+        self.label_map = self.model_config["label_map"]
+        self.max_seq_length = self.model_config["max_seq_length"]
+        self.label_map = {int(k):v for k,v in self.label_map.items()}
+        self.device = "cuda" if torch.cuda.is_available() else "cpu"
+        self.model = self.model.to(self.device)
+        self.model.eval()
+
+    def load_model(self, model_dir: str, model_config: str = "model_config.json"):
+        model_config = os.path.join(model_dir,model_config)
+        model_config = json.load(open(model_config))
+        model = BertNer.from_pretrained(model_dir)
+        tokenizer = BertTokenizer.from_pretrained(model_dir, do_lower_case=model_config["do_lower"])
+        return model, tokenizer, model_config
+
+    def tokenize(self, text: str):
+        """ tokenize input"""
+        words = word_tokenize(text)
+        tokens = []
+        valid_positions = []
+        for i,word in enumerate(words):
+            token = self.tokenizer.tokenize(word)
+            tokens.extend(token)
+            for i in range(len(token)):
+                if i == 0:
+                    valid_positions.append(1)
+                else:
+                    valid_positions.append(0)
+        return tokens, valid_positions
+
+    def preprocess(self, text: str):
+        """ preprocess """
+        tokens, valid_positions = self.tokenize(text)
+        ## insert "[CLS]"
+        tokens.insert(0,"[CLS]")
+        valid_positions.insert(0,1)
+        ## insert "[SEP]"
+        tokens.append("[SEP]")
+        valid_positions.append(1)
+        segment_ids = []
+        for i in range(len(tokens)):
+            segment_ids.append(0)
+        input_ids = self.tokenizer.convert_tokens_to_ids(tokens)
+        input_mask = [1] * len(input_ids)
+        while len(input_ids) < self.max_seq_length:
+            input_ids.append(0)
+            input_mask.append(0)
+            segment_ids.append(0)
+            valid_positions.append(0)
+        return input_ids,input_mask,segment_ids,valid_positions
+
+    def predict(self, text: str):
+        input_ids,input_mask,segment_ids,valid_ids = self.preprocess(text)
+        input_ids = torch.tensor([input_ids],dtype=torch.long,device=self.device)
+        input_mask = torch.tensor([input_mask],dtype=torch.long,device=self.device)
+        segment_ids = torch.tensor([segment_ids],dtype=torch.long,device=self.device)
+        valid_ids = torch.tensor([valid_ids],dtype=torch.long,device=self.device)
+        with torch.no_grad():
+            logits = self.model(input_ids, segment_ids, input_mask,valid_ids)
+        logits = F.softmax(logits,dim=2)
+        logits_label = torch.argmax(logits,dim=2)
+        logits_label = logits_label.detach().cpu().numpy().tolist()[0]
+
+        logits_confidence = [values[label].item() for values,label in zip(logits[0],logits_label)]
+
+        logits = []
+        pos = 0
+        for index,mask in enumerate(valid_ids[0]):
+            if index == 0:
+                continue
+            if mask == 1:
+                logits.append((logits_label[index-pos],logits_confidence[index-pos]))
+            else:
+                pos += 1
+        logits.pop()
+
+        labels = [(self.label_map[label],confidence) for label,confidence in logits]
+        words = word_tokenize(text)
+        assert len(labels) == len(words)
+
+        result = []
+        for word, (label, confidence) in zip(words, labels):
+            if label!='O':
+                result.append((word,label))
+        tmp = []
+        tag = OrderedDict()
+        tag['PER'] = []
+        tag['LOC'] = []
+        tag['ORG'] = []
+        tag['MISC'] = []
+        
+        for i, (word, label) in enumerate(result):
+            if label=='B-PER' or label=='B-LOC' or label=='B-ORG' or label=='B-MISC':
+                if i==0:
+                    tmp.append(word)
+                else:
+                    wordstype = result[i-1][1][2:]
+                    tag[wordstype].append(' '.join(tmp))
+                    tmp.clear()
+                    tmp.append(word)
+            elif i==len(result)-1:
+                tmp.append(word)
+                wordstype = result[i][1][2:]
+                tag[wordstype].append(' '.join(tmp))
+            else:
+                tmp.append(word)
+
+        return tag
+
+
+if __name__ == "__main__":
+    model = Ner("out_ner/")
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--text",
+                  default="Irene, a master student in Zhejiang University, Hangzhou, is traveling in Warsaw for Chopin Music Festival.",
+                  type=str,
+                  help="The text to be NERed")
+    text = parser.parse_args().text
+
+    print("The text to be NERed:")
+    print(text)
+    print('Results of NER:')
+
+    result = model.predict(text)
+    for k,v in result.items():
+        if v:
+            print(v,end=': ')
+            if k=='PER':
+                print('Person')
+            elif k=='LOC':
+                print('Location')
+            elif k=='ORG':
+                print('Organization')
+            elif k=='MISC':
+                print('Miscellaneous')

src/deepke/ner/regular/README.md

@@ -1,38 +0,0 @@
-# 快速上手
-
-## 克隆代码
-
-```
-git clone git@github.com:xxupiano/BERTNER.git
-```
-
-
-
-## 配置环境
-
-创建python虚拟环境（python>=3.7）
-
-安装依赖库
-
-```
-pip install -r requirements.txt
-```
-
-
-
-## 使用工具
-
- 先进行训练
-
-```
-python run_ner.py --data_dir=data/ --bert_model=bert-base-cased --task_name=ner --output_dir=out_ner --max_seq_length=128 --do_train --num_train_epochs 5 --do_eval --warmup_proportion=0.1
-```
-
-再进行预测
-
-- 修改main.py中text为需要进行NER的句子
-
-- ```
-  python main.py
-  ```
-

src/deepke/ner/regular/models/BERTNER.py

@@ -12,7 +12,7 @@ from pytorch_transformers import (BertConfig, BertForTokenClassification,
                                   BertTokenizer)
 from collections import OrderedDict
 import nltk
-nltk.data.path.insert(0,'./data/nltk_data')
+nltk.data.path.insert(0,os.path.dirname(os.getcwd())+'/module/data/nltk_data')
 
 
 class BertNer(BertForTokenClassification):

src/deepke/ner/regular/models/NER.py

@@ -0,0 +1,51 @@
+from __future__ import absolute_import, division, print_function
+
+import argparse
+import csv
+import json
+import logging
+import os
+import random
+import sys
+import numpy as np
+import torch
+import torch.nn.functional as F
+from pytorch_transformers import (WEIGHTS_NAME, AdamW, BertConfig,
+                                  BertForTokenClassification, BertTokenizer,
+                                  WarmupLinearSchedule)
+from torch import nn
+from torch.utils.data import (DataLoader, RandomSampler, SequentialSampler,
+                              TensorDataset)
+from torch.utils.data.distributed import DistributedSampler
+from tqdm import tqdm, trange
+from seqeval.metrics import classification_report
+
+class Ner(BertForTokenClassification):
+
+    def forward(self, input_ids, token_type_ids=None, attention_mask=None, labels=None,valid_ids=None,attention_mask_label=None):
+        sequence_output = self.bert(input_ids, token_type_ids, attention_mask,head_mask=None)[0]
+        batch_size,max_len,feat_dim = sequence_output.shape
+        valid_output = torch.zeros(batch_size,max_len,feat_dim,dtype=torch.float32,device='cuda')
+        for i in range(batch_size):
+            jj = -1
+            for j in range(max_len):
+                    if valid_ids[i][j].item() == 1:
+                        jj += 1
+                        valid_output[i][jj] = sequence_output[i][j]
+        sequence_output = self.dropout(valid_output)
+        logits = self.classifier(sequence_output)
+
+        if labels is not None:
+            loss_fct = nn.CrossEntropyLoss(ignore_index=0)
+            # Only keep active parts of the loss
+            #attention_mask_label = None
+            if attention_mask_label is not None:
+                active_loss = attention_mask_label.view(-1) == 1
+                active_logits = logits.view(-1, self.num_labels)[active_loss]
+                active_labels = labels.view(-1)[active_loss]
+                loss = loss_fct(active_logits, active_labels)
+            else:
+                loss = loss_fct(logits.view(-1, self.num_labels), labels.view(-1))
+            return loss
+        else:
+            return logits

src/deepke/ner/regular/module/data/nltk_data/tokenizers/punkt/PY3/README

@@ -0,0 +1,98 @@
+Pretrained Punkt Models -- Jan Strunk (New version trained after issues 313 and 514 had been corrected)
+
+Most models were prepared using the test corpora from Kiss and Strunk (2006). Additional models have
+been contributed by various people using NLTK for sentence boundary detection.
+
+For information about how to use these models, please confer the tokenization HOWTO:
+http://nltk.googlecode.com/svn/trunk/doc/howto/tokenize.html
+and chapter 3.8 of the NLTK book:
+http://nltk.googlecode.com/svn/trunk/doc/book/ch03.html#sec-segmentation
+
+There are pretrained tokenizers for the following languages:
+
+File                Language            Source                             Contents                Size of training corpus(in tokens)           Model contributed by
+=======================================================================================================================================================================
+czech.pickle        Czech               Multilingual Corpus 1 (ECI)        Lidove Noviny                   ~345,000                             Jan Strunk / Tibor Kiss
+                                                                           Literarni Noviny
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+danish.pickle       Danish              Avisdata CD-Rom Ver. 1.1. 1995     Berlingske Tidende              ~550,000                             Jan Strunk / Tibor Kiss
+                                        (Berlingske Avisdata, Copenhagen)  Weekend Avisen
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+dutch.pickle        Dutch               Multilingual Corpus 1 (ECI)        De Limburger                    ~340,000                             Jan Strunk / Tibor Kiss
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+english.pickle      English             Penn Treebank (LDC)                Wall Street Journal             ~469,000                             Jan Strunk / Tibor Kiss
+                    (American)
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+estonian.pickle     Estonian            University of Tartu, Estonia       Eesti Ekspress                  ~359,000                             Jan Strunk / Tibor Kiss
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+finnish.pickle      Finnish             Finnish Parole Corpus, Finnish     Books and major national        ~364,000                             Jan Strunk / Tibor Kiss
+                                        Text Bank (Suomen Kielen           newspapers
+                                        Tekstipankki)
+                                        Finnish Center for IT Science
+                                        (CSC)
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+french.pickle       French              Multilingual Corpus 1 (ECI)        Le Monde                        ~370,000                             Jan Strunk / Tibor Kiss
+                    (European)
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+german.pickle       German              Neue Zürcher Zeitung AG            Neue Zürcher Zeitung            ~847,000                             Jan Strunk / Tibor Kiss
+                    (Switzerland)       CD-ROM
+                    (Uses "ss"
+                     instead of "ß")
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+greek.pickle        Greek               Efstathios Stamatatos              To Vima (TO BHMA)               ~227,000                             Jan Strunk / Tibor Kiss
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+italian.pickle      Italian             Multilingual Corpus 1 (ECI)        La Stampa, Il Mattino           ~312,000                             Jan Strunk / Tibor Kiss
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+norwegian.pickle    Norwegian           Centre for Humanities              Bergens Tidende                 ~479,000                             Jan Strunk / Tibor Kiss
+                    (Bokmål and         Information Technologies,
+                     Nynorsk)           Bergen
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+polish.pickle       Polish              Polish National Corpus             Literature, newspapers, etc.  ~1,000,000                             Krzysztof Langner
+                                        (http://www.nkjp.pl/)
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+portuguese.pickle   Portuguese          CETENFolha Corpus                  Folha de São Paulo              ~321,000                             Jan Strunk / Tibor Kiss
+                    (Brazilian)         (Linguateca)
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+slovene.pickle      Slovene             TRACTOR                            Delo                            ~354,000                             Jan Strunk / Tibor Kiss
+                                        Slovene Academy for Arts
+                                        and Sciences
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+spanish.pickle      Spanish             Multilingual Corpus 1 (ECI)        Sur                             ~353,000                             Jan Strunk / Tibor Kiss
+                    (European)
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+swedish.pickle      Swedish             Multilingual Corpus 1 (ECI)        Dagens Nyheter                  ~339,000                             Jan Strunk / Tibor Kiss
+                                                                           (and some other texts)
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+turkish.pickle      Turkish             METU Turkish Corpus                Milliyet                        ~333,000                             Jan Strunk / Tibor Kiss
+                                        (Türkçe Derlem Projesi)
+                                        University of Ankara
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+
+The corpora contained about 400,000 tokens on average and mostly consisted of newspaper text converted to
+Unicode using the codecs module.
+
+Kiss, Tibor and Strunk, Jan (2006): Unsupervised Multilingual Sentence Boundary Detection.
+Computational Linguistics 32: 485-525.
+
+---- Training Code ----
+
+# import punkt
+import nltk.tokenize.punkt
+
+# Make a new Tokenizer
+tokenizer = nltk.tokenize.punkt.PunktSentenceTokenizer()
+
+# Read in training corpus (one example: Slovene)
+import codecs
+text = codecs.open("slovene.plain","Ur","iso-8859-2").read()
+
+# Train tokenizer
+tokenizer.train(text)
+
+# Dump pickled tokenizer
+import pickle
+out = open("slovene.pickle","wb")
+pickle.dump(tokenizer, out)
+out.close()
+
+---------

src/deepke/ner/regular/module/data/nltk_data/tokenizers/punkt/README

@@ -0,0 +1,98 @@
+Pretrained Punkt Models -- Jan Strunk (New version trained after issues 313 and 514 had been corrected)
+
+Most models were prepared using the test corpora from Kiss and Strunk (2006). Additional models have
+been contributed by various people using NLTK for sentence boundary detection.
+
+For information about how to use these models, please confer the tokenization HOWTO:
+http://nltk.googlecode.com/svn/trunk/doc/howto/tokenize.html
+and chapter 3.8 of the NLTK book:
+http://nltk.googlecode.com/svn/trunk/doc/book/ch03.html#sec-segmentation
+
+There are pretrained tokenizers for the following languages:
+
+File                Language            Source                             Contents                Size of training corpus(in tokens)           Model contributed by
+=======================================================================================================================================================================
+czech.pickle        Czech               Multilingual Corpus 1 (ECI)        Lidove Noviny                   ~345,000                             Jan Strunk / Tibor Kiss
+                                                                           Literarni Noviny
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+danish.pickle       Danish              Avisdata CD-Rom Ver. 1.1. 1995     Berlingske Tidende              ~550,000                             Jan Strunk / Tibor Kiss
+                                        (Berlingske Avisdata, Copenhagen)  Weekend Avisen
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+dutch.pickle        Dutch               Multilingual Corpus 1 (ECI)        De Limburger                    ~340,000                             Jan Strunk / Tibor Kiss
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+english.pickle      English             Penn Treebank (LDC)                Wall Street Journal             ~469,000                             Jan Strunk / Tibor Kiss
+                    (American)
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+estonian.pickle     Estonian            University of Tartu, Estonia       Eesti Ekspress                  ~359,000                             Jan Strunk / Tibor Kiss
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+finnish.pickle      Finnish             Finnish Parole Corpus, Finnish     Books and major national        ~364,000                             Jan Strunk / Tibor Kiss
+                                        Text Bank (Suomen Kielen           newspapers
+                                        Tekstipankki)
+                                        Finnish Center for IT Science
+                                        (CSC)
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+french.pickle       French              Multilingual Corpus 1 (ECI)        Le Monde                        ~370,000                             Jan Strunk / Tibor Kiss
+                    (European)
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+german.pickle       German              Neue Zürcher Zeitung AG            Neue Zürcher Zeitung            ~847,000                             Jan Strunk / Tibor Kiss
+                    (Switzerland)       CD-ROM
+                    (Uses "ss"
+                     instead of "ß")
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+greek.pickle        Greek               Efstathios Stamatatos              To Vima (TO BHMA)               ~227,000                             Jan Strunk / Tibor Kiss
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+italian.pickle      Italian             Multilingual Corpus 1 (ECI)        La Stampa, Il Mattino           ~312,000                             Jan Strunk / Tibor Kiss
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+norwegian.pickle    Norwegian           Centre for Humanities              Bergens Tidende                 ~479,000                             Jan Strunk / Tibor Kiss
+                    (Bokmål and         Information Technologies,
+                     Nynorsk)           Bergen
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+polish.pickle       Polish              Polish National Corpus             Literature, newspapers, etc.  ~1,000,000                             Krzysztof Langner
+                                        (http://www.nkjp.pl/)
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+portuguese.pickle   Portuguese          CETENFolha Corpus                  Folha de São Paulo              ~321,000                             Jan Strunk / Tibor Kiss
+                    (Brazilian)         (Linguateca)
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+slovene.pickle      Slovene             TRACTOR                            Delo                            ~354,000                             Jan Strunk / Tibor Kiss
+                                        Slovene Academy for Arts
+                                        and Sciences
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+spanish.pickle      Spanish             Multilingual Corpus 1 (ECI)        Sur                             ~353,000                             Jan Strunk / Tibor Kiss
+                    (European)
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+swedish.pickle      Swedish             Multilingual Corpus 1 (ECI)        Dagens Nyheter                  ~339,000                             Jan Strunk / Tibor Kiss
+                                                                           (and some other texts)
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+turkish.pickle      Turkish             METU Turkish Corpus                Milliyet                        ~333,000                             Jan Strunk / Tibor Kiss
+                                        (Türkçe Derlem Projesi)
+                                        University of Ankara
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+
+The corpora contained about 400,000 tokens on average and mostly consisted of newspaper text converted to
+Unicode using the codecs module.
+
+Kiss, Tibor and Strunk, Jan (2006): Unsupervised Multilingual Sentence Boundary Detection.
+Computational Linguistics 32: 485-525.
+
+---- Training Code ----
+
+# import punkt
+import nltk.tokenize.punkt
+
+# Make a new Tokenizer
+tokenizer = nltk.tokenize.punkt.PunktSentenceTokenizer()
+
+# Read in training corpus (one example: Slovene)
+import codecs
+text = codecs.open("slovene.plain","Ur","iso-8859-2").read()
+
+# Train tokenizer
+tokenizer.train(text)
+
+# Dump pickled tokenizer
+import pickle
+out = open("slovene.pickle","wb")
+pickle.dump(tokenizer, out)
+out.close()
+
+---------

src/deepke/ner/regular/module/dataset.py

@@ -0,0 +1,75 @@
+class InputExample(object):
+    """A single training/test example for simple sequence classification."""
+
+    def __init__(self, guid, text_a, text_b=None, label=None):
+        """Constructs a InputExample.
+
+        Args:
+            guid: Unique id for the example.
+            text_a: string. The untokenized text of the first sequence. For single
+            sequence tasks, only this sequence must be specified.
+            text_b: (Optional) string. The untokenized text of the second sequence.
+            Only must be specified for sequence pair tasks.
+            label: (Optional) string. The label of the example. This should be
+            specified for train and dev examples, but not for test examples.
+        """
+        self.guid = guid
+        self.text_a = text_a
+        self.text_b = text_b
+        self.label = label
+
+class InputFeatures(object):
+    """A single set of features of data."""
+
+    def __init__(self, input_ids, input_mask, segment_ids, label_id, valid_ids=None, label_mask=None):
+        self.input_ids = input_ids
+        self.input_mask = input_mask
+        self.segment_ids = segment_ids
+        self.label_id = label_id
+        self.valid_ids = valid_ids
+        self.label_mask = label_mask
+
+def readfile(filename):
+    '''
+    read file
+    '''
+    f = open(filename)
+    data = []
+    sentence = []
+    label= []
+    for line in f:
+        if len(line)==0 or line.startswith('-DOCSTART') or line[0]=="\n":
+            if len(sentence) > 0:
+                data.append((sentence,label))
+                sentence = []
+                label = []
+            continue
+        splits = line.split(' ')
+        sentence.append(splits[0])
+        label.append(splits[-1][:-1])
+
+    if len(sentence) >0:
+        data.append((sentence,label))
+        sentence = []
+        label = []
+    return data
+
+class DataProcessor(object):
+    """Base class for data converters for sequence classification data sets."""
+
+    def get_train_examples(self, data_dir):
+        """Gets a collection of `InputExample`s for the train set."""
+        raise NotImplementedError()
+
+    def get_dev_examples(self, data_dir):
+        """Gets a collection of `InputExample`s for the dev set."""
+        raise NotImplementedError()
+
+    def get_labels(self):
+        """Gets the list of labels for this data set."""
+        raise NotImplementedError()
+
+    @classmethod
+    def _read_tsv(cls, input_file, quotechar=None):
+        """Reads a tab separated value file."""
+        return readfile(input_file)

src/deepke/ner/regular/module/finetune.py

@@ -0,0 +1,358 @@
+from __future__ import absolute_import, division, print_function
+
+import argparse
+import csv
+import json
+import logging
+import os
+import random
+import sys
+import numpy as np
+import torch
+import torch.nn.functional as F
+from pytorch_transformers import (WEIGHTS_NAME, AdamW, BertConfig,
+                                  BertForTokenClassification, BertTokenizer,
+                                  WarmupLinearSchedule)
+from torch import nn
+from torch.utils.data import (DataLoader, RandomSampler, SequentialSampler,
+                              TensorDataset)
+from torch.utils.data.distributed import DistributedSampler
+from tqdm import tqdm, trange
+from seqeval.metrics import classification_report
+
+from dataset import *
+from preprocess import *
+sys.path.append("..")
+from models.NER import Ner
+
+
+def main():
+    parser = argparse.ArgumentParser()
+
+    ## Required parameters
+    parser.add_argument("--data_dir",
+                        default=None,
+                        type=str,
+                        required=True,
+                        help="The input data dir. Should contain the .tsv files (or other data files) for the task.")
+    parser.add_argument("--bert_model", default=None, type=str, required=True,
+                        help="Bert pre-trained model selected in the list: bert-base-uncased, "
+                        "bert-large-uncased, bert-base-cased, bert-large-cased, bert-base-multilingual-uncased, "
+                        "bert-base-multilingual-cased, bert-base-chinese.")
+    parser.add_argument("--task_name",
+                        default=None,
+                        type=str,
+                        required=True,
+                        help="The name of the task to train.")
+    parser.add_argument("--output_dir",
+                        default=None,
+                        type=str,
+                        required=True,
+                        help="The output directory where the model predictions and checkpoints will be written.")
+
+    ## Other parameters
+    parser.add_argument("--cache_dir",
+                        default="",
+                        type=str,
+                        help="Where do you want to store the pre-trained models downloaded from s3")
+    parser.add_argument("--max_seq_length",
+                        default=128,
+                        type=int,
+                        help="The maximum total input sequence length after WordPiece tokenization. \n"
+                             "Sequences longer than this will be truncated, and sequences shorter \n"
+                             "than this will be padded.")
+    parser.add_argument("--do_train",
+                        action='store_true',
+                        help="Whether to run training.")
+    parser.add_argument("--do_eval",
+                        action='store_true',
+                        help="Whether to run eval or not.")
+    parser.add_argument("--eval_on",
+                        default="dev",
+                        help="Whether to run eval on the dev set or test set.")
+    parser.add_argument("--do_lower_case",
+                        action='store_true',
+                        help="Set this flag if you are using an uncased model.")
+    parser.add_argument("--train_batch_size",
+                        default=32,
+                        type=int,
+                        help="Total batch size for training.")
+    parser.add_argument("--eval_batch_size",
+                        default=8,
+                        type=int,
+                        help="Total batch size for eval.")
+    parser.add_argument("--learning_rate",
+                        default=5e-5,
+                        type=float,
+                        help="The initial learning rate for Adam.")
+    parser.add_argument("--num_train_epochs",
+                        default=3.0,
+                        type=float,
+                        help="Total number of training epochs to perform.")
+    parser.add_argument("--warmup_proportion",
+                        default=0.1,
+                        type=float,
+                        help="Proportion of training to perform linear learning rate warmup for. "
+                             "E.g., 0.1 = 10%% of training.")
+    parser.add_argument("--weight_decay", default=0.01, type=float,
+                        help="Weight deay if we apply some.")
+    parser.add_argument("--adam_epsilon", default=1e-8, type=float,
+                        help="Epsilon for Adam optimizer.")
+    parser.add_argument("--max_grad_norm", default=1.0, type=float,
+                        help="Max gradient norm.")
+    parser.add_argument("--no_cuda",
+                        action='store_true',
+                        help="Whether not to use CUDA when available")
+    parser.add_argument("--local_rank",
+                        type=int,
+                        default=-1,
+                        help="local_rank for distributed training on gpus")
+    parser.add_argument('--seed',
+                        type=int,
+                        default=42,
+                        help="random seed for initialization")
+    parser.add_argument('--gradient_accumulation_steps',
+                        type=int,
+                        default=1,
+                        help="Number of updates steps to accumulate before performing a backward/update pass.")
+    parser.add_argument('--fp16',
+                        action='store_true',
+                        help="Whether to use 16-bit float precision instead of 32-bit")
+    parser.add_argument('--fp16_opt_level', type=str, default='O1',
+                        help="For fp16: Apex AMP optimization level selected in ['O0', 'O1', 'O2', and 'O3']."
+                             "See details at https://nvidia.github.io/apex/amp.html")
+    parser.add_argument('--loss_scale',
+                        type=float, default=0,
+                        help="Loss scaling to improve fp16 numeric stability. Only used when fp16 set to True.\n"
+                             "0 (default value): dynamic loss scaling.\n"
+                             "Positive power of 2: static loss scaling value.\n")
+    parser.add_argument('--server_ip', type=str, default='', help="Can be used for distant debugging.")
+    parser.add_argument('--server_port', type=str, default='', help="Can be used for distant debugging.")
+    args = parser.parse_args()
+
+    if args.server_ip and args.server_port:
+        # Distant debugging - see https://code.visualstudio.com/docs/python/debugging#_attach-to-a-local-script
+        import ptvsd
+        print("Waiting for debugger attach")
+        ptvsd.enable_attach(address=(args.server_ip, args.server_port), redirect_output=True)
+        ptvsd.wait_for_attach()
+
+    processors = {"ner":NerProcessor}
+
+    if args.local_rank == -1 or args.no_cuda:
+        device = torch.device("cuda" if torch.cuda.is_available() and not args.no_cuda else "cpu")
+        n_gpu = torch.cuda.device_count()
+    else:
+        torch.cuda.set_device(args.local_rank)
+        device = torch.device("cuda", args.local_rank)
+        n_gpu = 1
+        # Initializes the distributed backend which will take care of sychronizing nodes/GPUs
+        torch.distributed.init_process_group(backend='nccl')
+
+    if args.gradient_accumulation_steps < 1:
+        raise ValueError("Invalid gradient_accumulation_steps parameter: {}, should be >= 1".format(
+                            args.gradient_accumulation_steps))
+
+    args.train_batch_size = args.train_batch_size // args.gradient_accumulation_steps
+
+    random.seed(args.seed)
+    np.random.seed(args.seed)
+    torch.manual_seed(args.seed)
+
+    if not args.do_train and not args.do_eval:
+        raise ValueError("At least one of `do_train` or `do_eval` must be True.")
+
+    if os.path.exists(args.output_dir) and os.listdir(args.output_dir) and args.do_train:
+        raise ValueError("Output directory ({}) already exists and is not empty.".format(args.output_dir))
+    if not os.path.exists(args.output_dir):
+        os.makedirs(args.output_dir)
+
+    task_name = args.task_name.lower()
+
+    if task_name not in processors:
+        raise ValueError("Task not found: %s" % (task_name))
+
+    processor = processors[task_name]()
+    label_list = processor.get_labels()
+    num_labels = len(label_list) + 1
+
+    tokenizer = BertTokenizer.from_pretrained(args.bert_model, do_lower_case=args.do_lower_case)
+
+    train_examples = None
+    num_train_optimization_steps = 0
+    if args.do_train:
+        train_examples = processor.get_train_examples(args.data_dir)
+        num_train_optimization_steps = int(
+            len(train_examples) / args.train_batch_size / args.gradient_accumulation_steps) * args.num_train_epochs
+        if args.local_rank != -1:
+            num_train_optimization_steps = num_train_optimization_steps // torch.distributed.get_world_size()
+
+    if args.local_rank not in [-1, 0]:
+        torch.distributed.barrier()  # Make sure only the first process in distributed training will download model & vocab
+
+    # Prepare model
+    config = BertConfig.from_pretrained(args.bert_model, num_labels=num_labels, finetuning_task=args.task_name)
+    model = Ner.from_pretrained(args.bert_model,
+              from_tf = False,
+              config = config)
+
+    if args.local_rank == 0:
+        torch.distributed.barrier()  # Make sure only the first process in distributed training will download model & vocab
+
+    model.to(device)
+
+    param_optimizer = list(model.named_parameters())
+    no_decay = ['bias','LayerNorm.weight']
+    optimizer_grouped_parameters = [
+        {'params': [p for n, p in param_optimizer if not any(nd in n for nd in no_decay)], 'weight_decay': args.weight_decay},
+        {'params': [p for n, p in param_optimizer if any(nd in n for nd in no_decay)], 'weight_decay': 0.0}
+        ]
+    warmup_steps = int(args.warmup_proportion * num_train_optimization_steps)
+    optimizer = AdamW(optimizer_grouped_parameters, lr=args.learning_rate, eps=args.adam_epsilon)
+    scheduler = WarmupLinearSchedule(optimizer, warmup_steps=warmup_steps, t_total=num_train_optimization_steps)
+    if args.fp16:
+        try:
+            from apex import amp
+        except ImportError:
+            raise ImportError("Please install apex from https://www.github.com/nvidia/apex to use fp16 training.")
+        model, optimizer = amp.initialize(model, optimizer, opt_level=args.fp16_opt_level)
+
+    # multi-gpu training (should be after apex fp16 initialization)
+    if n_gpu > 1:
+        model = torch.nn.DataParallel(model)
+
+    if args.local_rank != -1:
+        model = torch.nn.parallel.DistributedDataParallel(model, device_ids=[args.local_rank],
+                                                          output_device=args.local_rank,
+                                                          find_unused_parameters=True)
+
+    global_step = 0
+    nb_tr_steps = 0
+    tr_loss = 0
+    label_map = {i : label for i, label in enumerate(label_list,1)}
+    if args.do_train:
+        train_features = convert_examples_to_features(
+            train_examples, label_list, args.max_seq_length, tokenizer)
+        all_input_ids = torch.tensor([f.input_ids for f in train_features], dtype=torch.long)
+        all_input_mask = torch.tensor([f.input_mask for f in train_features], dtype=torch.long)
+        all_segment_ids = torch.tensor([f.segment_ids for f in train_features], dtype=torch.long)
+        all_label_ids = torch.tensor([f.label_id for f in train_features], dtype=torch.long)
+        all_valid_ids = torch.tensor([f.valid_ids for f in train_features], dtype=torch.long)
+        all_lmask_ids = torch.tensor([f.label_mask for f in train_features], dtype=torch.long)
+        train_data = TensorDataset(all_input_ids, all_input_mask, all_segment_ids, all_label_ids,all_valid_ids,all_lmask_ids)
+        if args.local_rank == -1:
+            train_sampler = RandomSampler(train_data)
+        else:
+            train_sampler = DistributedSampler(train_data)
+        train_dataloader = DataLoader(train_data, sampler=train_sampler, batch_size=args.train_batch_size)
+
+        model.train()
+        for _ in trange(int(args.num_train_epochs), desc="Epoch"):
+            tr_loss = 0
+            nb_tr_examples, nb_tr_steps = 0, 0
+            for step, batch in enumerate(tqdm(train_dataloader, desc="Iteration")):
+                batch = tuple(t.to(device) for t in batch)
+                input_ids, input_mask, segment_ids, label_ids, valid_ids,l_mask = batch
+                loss = model(input_ids, segment_ids, input_mask, label_ids,valid_ids,l_mask)
+                if n_gpu > 1:
+                    loss = loss.mean() # mean() to average on multi-gpu.
+                if args.gradient_accumulation_steps > 1:
+                    loss = loss / args.gradient_accumulation_steps
+
+                if args.fp16:
+                    with amp.scale_loss(loss, optimizer) as scaled_loss:
+                        scaled_loss.backward()
+                    torch.nn.utils.clip_grad_norm_(amp.master_params(optimizer), args.max_grad_norm)
+                else:
+                    loss.backward()
+                    torch.nn.utils.clip_grad_norm_(model.parameters(), args.max_grad_norm)
+
+                tr_loss += loss.item()
+                nb_tr_examples += input_ids.size(0)
+                nb_tr_steps += 1
+                if (step + 1) % args.gradient_accumulation_steps == 0:
+                    optimizer.step()
+                    scheduler.step()  # Update learning rate schedule
+                    model.zero_grad()
+                    global_step += 1
+
+        # Save a trained model and the associated configuration
+        model_to_save = model.module if hasattr(model, 'module') else model  # Only save the model it-self
+        model_to_save.save_pretrained(args.output_dir)
+        tokenizer.save_pretrained(args.output_dir)
+        label_map = {i : label for i, label in enumerate(label_list,1)}
+        model_config = {"bert_model":args.bert_model,"do_lower":args.do_lower_case,"max_seq_length":args.max_seq_length,"num_labels":len(label_list)+1,"label_map":label_map}
+        json.dump(model_config,open(os.path.join(args.output_dir,"model_config.json"),"w"))
+        # Load a trained model and config that you have fine-tuned
+    else:
+        # Load a trained model and vocabulary that you have fine-tuned
+        model = Ner.from_pretrained(args.output_dir)
+        tokenizer = BertTokenizer.from_pretrained(args.output_dir, do_lower_case=args.do_lower_case)
+
+    model.to(device)
+
+    if args.do_eval and (args.local_rank == -1 or torch.distributed.get_rank() == 0):
+        if args.eval_on == "dev":
+            eval_examples = processor.get_dev_examples(args.data_dir)
+        elif args.eval_on == "test":
+            eval_examples = processor.get_test_examples(args.data_dir)
+        else:
+            raise ValueError("eval on dev or test set only")
+        eval_features = convert_examples_to_features(eval_examples, label_list, args.max_seq_length, tokenizer)
+        all_input_ids = torch.tensor([f.input_ids for f in eval_features], dtype=torch.long)
+        all_input_mask = torch.tensor([f.input_mask for f in eval_features], dtype=torch.long)
+        all_segment_ids = torch.tensor([f.segment_ids for f in eval_features], dtype=torch.long)
+        all_label_ids = torch.tensor([f.label_id for f in eval_features], dtype=torch.long)
+        all_valid_ids = torch.tensor([f.valid_ids for f in eval_features], dtype=torch.long)
+        all_lmask_ids = torch.tensor([f.label_mask for f in eval_features], dtype=torch.long)
+        eval_data = TensorDataset(all_input_ids, all_input_mask, all_segment_ids, all_label_ids,all_valid_ids,all_lmask_ids)
+        # Run prediction for full data
+        eval_sampler = SequentialSampler(eval_data)
+        eval_dataloader = DataLoader(eval_data, sampler=eval_sampler, batch_size=args.eval_batch_size)
+        model.eval()
+        eval_loss, eval_accuracy = 0, 0
+        nb_eval_steps, nb_eval_examples = 0, 0
+        y_true = []
+        y_pred = []
+        label_map = {i : label for i, label in enumerate(label_list,1)}
+        for input_ids, input_mask, segment_ids, label_ids,valid_ids,l_mask in tqdm(eval_dataloader, desc="Evaluating"):
+            input_ids = input_ids.to(device)
+            input_mask = input_mask.to(device)
+            segment_ids = segment_ids.to(device)
+            valid_ids = valid_ids.to(device)
+            label_ids = label_ids.to(device)
+            l_mask = l_mask.to(device)
+
+            with torch.no_grad():
+                logits = model(input_ids, segment_ids, input_mask,valid_ids=valid_ids,attention_mask_label=l_mask)
+
+            logits = torch.argmax(F.log_softmax(logits,dim=2),dim=2)
+            logits = logits.detach().cpu().numpy()
+            label_ids = label_ids.to('cpu').numpy()
+            input_mask = input_mask.to('cpu').numpy()
+
+            for i, label in enumerate(label_ids):
+                temp_1 = []
+                temp_2 = []
+                for j,m in enumerate(label):
+                    if j == 0:
+                        continue
+                    elif label_ids[i][j] == len(label_map):
+                        y_true.append(temp_1)
+                        y_pred.append(temp_2)
+                        break
+                    else:
+                        temp_1.append(label_map[label_ids[i][j]])
+                        temp_2.append(label_map[logits[i][j]])
+
+        report = classification_report(y_true, y_pred,digits=4)
+#         logger.info("\n%s", report)
+        output_eval_file = os.path.join(args.output_dir, "eval_results.txt")
+        with open(output_eval_file, "w") as writer:
+#             logger.info("***** Eval results *****")
+#             logger.info("\n%s", report)
+            writer.write(report)
+
+
+if __name__ == "__main__":
+    main()

src/deepke/ner/regular/module/predict.py

@@ -1,4 +1,6 @@
-from bert import Ner
+import sys
+sys.path.append("..")
+from models.BERTNER import Ner
 model = Ner("out_ner/")
 
 text= "Irene, a master student in Zhejiang University, Hangzhou, is traveling in Warsaw for Chopin Music Festival."
@@ -17,4 +19,4 @@ for k,v in result.items():
         elif k=='ORG':
             print('Organization')
         elif k=='MISC':
-            print('Miscellaneous')
+            print('Miscellaneous')

src/deepke/ner/regular/module/preprocess.py

@@ -0,0 +1,117 @@
+from dataset import *
+
+import argparse
+import csv
+import json
+import logging
+import os
+import random
+import sys
+import numpy as np
+
+class NerProcessor(DataProcessor):
+    """Processor for the CoNLL-2003 data set."""
+
+    def get_train_examples(self, data_dir):
+        """See base class."""
+        return self._create_examples(
+            self._read_tsv(os.path.join(data_dir, "train.txt")), "train")
+
+    def get_dev_examples(self, data_dir):
+        """See base class."""
+        return self._create_examples(
+            self._read_tsv(os.path.join(data_dir, "valid.txt")), "dev")
+
+    def get_test_examples(self, data_dir):
+        """See base class."""
+        return self._create_examples(
+            self._read_tsv(os.path.join(data_dir, "test.txt")), "test")
+
+    def get_labels(self):
+        return ["O", "B-MISC", "I-MISC",  "B-PER", "I-PER", "B-ORG", "I-ORG", "B-LOC", "I-LOC", "[CLS]", "[SEP]"]
+
+    def _create_examples(self,lines,set_type):
+        examples = []
+        for i,(sentence,label) in enumerate(lines):
+            guid = "%s-%s" % (set_type, i)
+            text_a = ' '.join(sentence)
+            text_b = None
+            label = label
+            examples.append(InputExample(guid=guid,text_a=text_a,text_b=text_b,label=label))
+        return examples
+
+def convert_examples_to_features(examples, label_list, max_seq_length, tokenizer):
+    """Loads a data file into a list of `InputBatch`s."""
+
+    label_map = {label : i for i, label in enumerate(label_list,1)}
+
+    features = []
+    for (ex_index,example) in enumerate(examples):
+        textlist = example.text_a.split(' ')
+        labellist = example.label
+        tokens = []
+        labels = []
+        valid = []
+        label_mask = []
+        for i, word in enumerate(textlist):
+            token = tokenizer.tokenize(word)
+            tokens.extend(token)
+            label_1 = labellist[i]
+            for m in range(len(token)):
+                if m == 0:
+                    labels.append(label_1)
+                    valid.append(1)
+                    label_mask.append(1)
+                else:
+                    valid.append(0)
+        if len(tokens) >= max_seq_length - 1:
+            tokens = tokens[0:(max_seq_length - 2)]
+            labels = labels[0:(max_seq_length - 2)]
+            valid = valid[0:(max_seq_length - 2)]
+            label_mask = label_mask[0:(max_seq_length - 2)]
+        ntokens = []
+        segment_ids = []
+        label_ids = []
+        ntokens.append("[CLS]")
+        segment_ids.append(0)
+        valid.insert(0,1)
+        label_mask.insert(0,1)
+        label_ids.append(label_map["[CLS]"])
+        for i, token in enumerate(tokens):
+            ntokens.append(token)
+            segment_ids.append(0)
+            if len(labels) > i:
+                label_ids.append(label_map[labels[i]])
+        ntokens.append("[SEP]")
+        segment_ids.append(0)
+        valid.append(1)
+        label_mask.append(1)
+        label_ids.append(label_map["[SEP]"])
+        input_ids = tokenizer.convert_tokens_to_ids(ntokens)
+        input_mask = [1] * len(input_ids)
+        label_mask = [1] * len(label_ids)
+        while len(input_ids) < max_seq_length:
+            input_ids.append(0)
+            input_mask.append(0)
+            segment_ids.append(0)
+            label_ids.append(0)
+            valid.append(1)
+            label_mask.append(0)
+        while len(label_ids) < max_seq_length:
+            label_ids.append(0)
+            label_mask.append(0)
+        assert len(input_ids) == max_seq_length
+        assert len(input_mask) == max_seq_length
+        assert len(segment_ids) == max_seq_length
+        assert len(label_ids) == max_seq_length
+        assert len(valid) == max_seq_length
+        assert len(label_mask) == max_seq_length
+
+        features.append(
+                InputFeatures(input_ids=input_ids,
+                              input_mask=input_mask,
+                              segment_ids=segment_ids,
+                              label_id=label_ids,
+                              valid_ids=valid,
+                              label_mask=label_mask))
+    return features

src/deepke/ner/regular/tutorial.ipynb

@@ -1,157 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "id": "08e09d48",
-   "metadata": {},
-   "source": [
-    "# BERT based NER using CoNLL-2003\n",
-    "> Author: Xin Xu <xxucs@zju.edu.cn>"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "14365b62",
-   "metadata": {},
-   "source": [
-    "## Overview\n",
-    "- **Named-entity recognition (NER)** (also known as named entity identification, entity chunking, and entity extraction) is a subtask of information extraction that seeks to locate and classify named entities mentioned in unstructured text into pre-defined categories such as person names, organizations, locations, medical codes, time expressions, quantities, monetary values, percentages, etc.\n",
-    "- [**CoNLL-2003**](https://www.clips.uantwerpen.be/conll2003/ner/) is a dataset for NER, concentrating on four types of named entities related to persons, locations, organizations, and names of miscellaneous entities. The dataset is in 'data' folder, containing *train.txt*, *valid.txt* and *test.txt*\n",
-    "- [**Bidirectional Encoder Representations from Transformers (BERT)**](https://github.com/google-research/bert) is a transformer-based machine learning technique for natural language processing (NLP) pre-training developed by Google."
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "733b418c",
-   "metadata": {},
-   "source": [
-    "## Clone Repository\n",
-    "The 1st step is to clone DeepKE Github Repository."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "65822b98",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "!git clone https://github.com/xxupiano/BERTNER.git"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "eb6b8798",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "!cd BERTNER"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "c3b0cf3f",
-   "metadata": {},
-   "source": [
-    "## Prepare the runtime environment"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "3e46f572",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "!pip install -r requirements.txt"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "4b2319dc",
-   "metadata": {},
-   "source": [
-    "## Fine-Tune\n",
-    "- Finetune or train the **bert-base** model run the 'run_ner.py'\n",
-    "- In below command we have to pass different arguments:\n",
-    "  - '--data_dir' argument required to collect dataset. Pass 'data/' as argument which we can see as directory inside 'BERT-NER' folder for the previous comment and command for 'BERT-NER files'.\n",
-    "  - '--bert_model' used to download pretrained bert base model of Hugging Face transformers. There are different model-names as suggested by hugging face for argument, here we select 'bert-base-cased'.\n",
-    "  - '--task_name' argument used for task to perform. Enter 'ner' as we will train the model for Named Entity Recogintion(NER).\n",
-    "  - '--output_dir' argument is for where to store fine-tuned model. We give name 'out_base' for directory where fine-tuned model stored.\n",
-    "  - Other arguments like '--max_seq_length', '--num_train_epochs' and '--warmup_proportion', just give values as suggested in repository.\n",
-    "  - For training pass argument '--do_train' and after that evaluating for results pass argument '--do_eval'."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "1cdd7e86",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "!python run_ner.py --data_dir=data/ --bert_model=bert-base-cased --task_name=ner --output_dir=out_ner --max_seq_length=128 --do_train --num_train_epochs 5 --do_eval --warmup_proportion=0.1"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "6c0f79a8",
-   "metadata": {},
-   "source": [
-    "## Prediction\n",
-    "- Set the variable *text* in the following cell as the sentence to be NERed\n",
-    "- Run the following cell to get the NER result"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "0da6a2f6",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from bert import Ner\n",
-    "model = Ner(\"out_ner/\")\n",
-    "\n",
-    "text= \"Irene, a master student in Zhejiang University, Hangzhou, is traveling in Warsaw for Chopin Music Festival.\"\n",
-    "print(\"Text to predict Entity:\")\n",
-    "print(text)\n",
-    "print('Results of NER:')\n",
-    "\n",
-    "result = model.predict(text)\n",
-    "for k,v in result.items():\n",
-    "    if v:\n",
-    "        print(v,end=': ')\n",
-    "        if k=='PER':\n",
-    "            print('Person')\n",
-    "        elif k=='LOC':\n",
-    "            print('Location')\n",
-    "        elif k=='ORG':\n",
-    "            print('Organization')\n",
-    "        elif k=='MISC':\n",
-    "            print('Miscellaneous')"
-   ]
-  }
- ],
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-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
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-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
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-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
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