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Functions176 in github.com/dmis-lab/bern

↓ 58 callersFunctionCoNLL_tokenizer
(text)
biobert_ner/ops.py:91
↓ 26 callersFunctionsoftmax
(logits)
biobert_ner/ops.py:82
↓ 15 callersMethodclose
(self)
biobert_ner/run_ner.py:859
↓ 10 callersFunctioncreate_initializer
Creates a `truncated_normal_initializer` with the given range.
biobert_ner/modeling.py:381
↓ 9 callersFunctionget_shape_list
Returns a list of the shape of tensor, preferring static dimensions. Args: tensor: A tf.Tensor object to find the shape of. expected_
biobert_ner/modeling.py:908
↓ 8 callersFunctionget_stats
(lst, batch_size=None)
service_checker.py:174
↓ 6 callersFunctionget_bestplus_spans
(mutations, title_space_abstract)
convert.py:428
↓ 5 callersFunctionconvert_to_unicode
Converts `text` to Unicode (if it's not already), assuming utf-8 input.
biobert_ner/tokenization.py:79
↓ 5 callersFunctionget_pub_annotation
(bern_dict, is_raw_text, elapsed_time_dict=None)
convert.py:467
↓ 5 callersFunctionpreprocess
(text)
convert.py:301
↓ 4 callersFunctionconvert_by_vocab
Converts a sequence of [tokens|ids] using the vocab.
biobert_ner/tokenization.py:137
↓ 4 callersMethodconvert_single_example
(self, example, max_seq_length, req_id, mode)
biobert_ner/run_ner.py:785
↓ 4 callersFunctiondelete_files
(dirname)
server.py:576
↓ 4 callersFunctiondropout
Perform dropout. Args: input_tensor: float Tensor. dropout_prob: Python float. The probability of dropping out a value (NOT of
biobert_ner/modeling.py:349
↓ 4 callersFunctionget_pubtator
(bern_dict_list)
convert.py:559
↓ 4 callersFunctionpubtator_biocxml2dict_list
(pmids)
convert.py:201
↓ 3 callersMethodget_err_dict
()
server.py:505
↓ 3 callersFunctionis_get_good
(pmid, output_format, num_type_set, normal_id_cnt)
utils.py:213
↓ 3 callersFunctionlayer_norm
Run layer normalization on the last dimension of the tensor.
biobert_ner/modeling.py:367
↓ 3 callersMethodnormalize
(self, base_name, doc_dict_list, cur_thread_name, is_raw_text)
normalize.py:168
↓ 3 callersFunctionreshape_to_matrix
Reshapes a >= rank 2 tensor to a rank 2 tensor (i.e., a matrix).
biobert_ner/modeling.py:945
↓ 3 callersFunctionsentence_split
(text)
biobert_ner/ops.py:98
↓ 3 callersMethodtag
(self, text)
normalizers/miRNA_normalizer.py:135
↓ 3 callersFunctionwhitespace_tokenize
Runs basic whitespace cleaning and splitting on a piece of text.
biobert_ner/tokenization.py:153
↓ 2 callersMethod_create_example
(self, lines, set_type)
biobert_ner/run_ner.py:228
↓ 2 callersMethod_read_data
Reads a BIO data.
biobert_ner/run_ner.py:158
↓ 2 callersMethodbiobert_recognize
(self, dict_list, is_raw_text, cur_thread_name)
server.py:486
↓ 2 callersFunctiondownload_ftp
(url, output_dir, overwrite=True)
download.py:517
↓ 2 callersFunctionget_tmchem_name
(name)
normalizers/chemical_normalizer.py:64
↓ 2 callersFunctioninput_form
sent_data: dict of sentence, key=pmid {pmid:[sent,sent, ...], pmid: ...}
biobert_ner/ops.py:37
↓ 2 callersFunctionjson_to_sent
data: list of json file [{pmid,abstract,title}, ...]
biobert_ner/ops.py:8
↓ 2 callersFunctionload_auxiliary_dict
(path)
normalizers/gene_auxiliary_normalizer.py:36
↓ 2 callersFunctionquery
(pmid, url='https://bern.korea.ac.kr/pubmed', output_format='json', verbose=False)
utils.py:15
↓ 2 callersMethodrecognize
(self, input_dl, is_raw_text=False, thread_id=None, indent=None)
biobert_ner/run_ner.py:447
↓ 2 callersFunctionreplace_wspaces
(t)
download.py:654
↓ 2 callersFunctionreshape_from_matrix
Reshapes a rank 2 tensor back to its original rank >= 2 tensor.
biobert_ner/modeling.py:959
↓ 2 callersFunctiontell_inputfile
(host, port, inputfile)
server.py:541
↓ 2 callersFunctiontranspose_for_scores
(input_tensor, batch_size, num_attention_heads, seq_length, width)
biobert_ner/modeling.py:637
↓ 2 callersFunctionwrite_auxiliary_dict
(aux_dict, output_path)
normalizers/gene_auxiliary_normalizer.py:30
↓ 1 callersMethod_clean_text
Performs invalid character removal and whitespace cleanup on text.
biobert_ner/tokenization.py:287
↓ 1 callersFunction_decode_record
(record, name_to_features)
biobert_ner/run_ner.py:248
↓ 1 callersMethod_is_chinese_char
Checks whether CP is the codepoint of a CJK character.
biobert_ner/tokenization.py:265
↓ 1 callersFunction_is_control
Checks whether `chars` is a control character.
biobert_ner/tokenization.py:375
↓ 1 callersFunction_is_punctuation
Checks whether `chars` is a punctuation character.
biobert_ner/tokenization.py:387
↓ 1 callersFunction_is_whitespace
Checks whether `chars` is a whitespace character.
biobert_ner/tokenization.py:363
↓ 1 callersMethod_run_split_on_punc
Splits punctuation on a piece of text.
biobert_ner/tokenization.py:232
↓ 1 callersMethod_run_strip_accents
Strips accents from a piece of text.
biobert_ner/tokenization.py:221
↓ 1 callersMethod_tokenize_chinese_chars
Adds whitespace around any CJK character.
biobert_ner/tokenization.py:252
↓ 1 callersFunctionassert_rank
Raises an exception if the tensor rank is not of the expected rank. Args: tensor: A tf.Tensor to check the rank of. expected_rank: Py
biobert_ner/modeling.py:972
↓ 1 callersFunctionattention_layer
Performs multi-headed attention from `from_tensor` to `to_tensor`. This is an implementation of multi-headed attention based on "Attention is
biobert_ner/modeling.py:566
↓ 1 callersFunctionbern2pub_annotation
(entity_dict)
convert.py:507
↓ 1 callersFunctioncheck_bern
(from_gmail, to_email, from_google_account, from_google_password)
service_checker.py:13
↓ 1 callersMethodconvert_tokens_to_ids
(self, tokens)
biobert_ner/tokenization.py:179
↓ 1 callersFunctioncount_entities
(data)
server.py:526
↓ 1 callersFunctioncreate_attention_mask_from_input_mask
Create 3D attention mask from a 2D tensor mask. Args: from_tensor: 2D or 3D Tensor of shape [batch_size, from_seq_length, ...]. to_ma
biobert_ner/modeling.py:532
↓ 1 callersFunctioncreate_model
(bert_config, is_training, input_ids, input_mask, segment_ids, labels, num_labels, use_one_ho
biobert_ner/run_ner.py:272
↓ 1 callersFunctiondetokenize
(tokens, predicts, logits)
biobert_ner/ops.py:479
↓ 1 callersFunctionembedding_lookup
Looks up words embeddings for id tensor. Args: input_ids: int32 Tensor of shape [batch_size, seq_length] containing word ids.
biobert_ner/modeling.py:386
↓ 1 callersFunctionembedding_postprocessor
Performs various post-processing on a word embedding tensor. Args: input_tensor: float Tensor of shape [batch_size, seq_length, emb
biobert_ner/modeling.py:435
↓ 1 callersFunctionfilter_entities
(ner_results, is_raw_text)
utils.py:279
↓ 1 callersFunctionfind_best_plus_largest_index
(best_plus_dict_path)
normalizers/gene_auxiliary_normalizer.py:7
↓ 1 callersFunctionfind_largest_index
(uid_list)
normalizers/gene_auxiliary_normalizer.py:12
↓ 1 callersMethodfrom_dict
Constructs a `BertConfig` from a Python dictionary of parameters.
biobert_ner/modeling.py:82
↓ 1 callersMethodfrom_json_file
Constructs a `BertConfig` from a json file of parameters.
biobert_ner/modeling.py:90
↓ 1 callersFunctionget_activation
Maps a string to a Python function, e.g., "relu" => `tf.nn.relu`. Args: activation_string: String name of the activation function. Ret
biobert_ner/modeling.py:285
↓ 1 callersFunctionget_assignment_map_from_checkpoint
Compute the union of the current variables and checkpoint variables.
biobert_ner/modeling.py:322
↓ 1 callersMethodget_labels
(self)
biobert_ner/run_ner.py:225
↓ 1 callersFunctionget_pmc_archive
(non_comm_use_pdf, non_comm_output_dir, comm_use_file_list, comm_output_dir, overwrite=Fal
download.py:427
↓ 1 callersMethodget_sequence_output
Gets final hidden layer of encoder. Returns: float Tensor of shape [batch_size, seq_length, hidden_size] corresponding to
biobert_ner/modeling.py:242
↓ 1 callersMethodget_test_dict_list
(self, dict_list, is_raw_text=False)
biobert_ner/run_ner.py:212
↓ 1 callersMethodget_test_examples
(self, data_dir)
biobert_ner/run_ner.py:194
↓ 1 callersMethodinput_fn
(params)
biobert_ner/run_ner.py:733
↓ 1 callersFunctionis_good
(num_type_set=3, normal_id_cnt=13)
utils.py:155
↓ 1 callersFunctionlayer_norm_and_dropout
Runs layer normalization followed by dropout.
biobert_ner/modeling.py:374
↓ 1 callersFunctionload_vocab
Loads a vocabulary file into a dictionary.
biobert_ner/tokenization.py:122
↓ 1 callersFunctionmake_best_dict
(best_dict_path, start_index, type_code=2)
normalizers/gene_auxiliary_normalizer.py:15
↓ 1 callersFunctionmake_freq_dict
(total_sample_path, start_index, threshold, type_code=2)
normalizers/gene_auxiliary_normalizer.py:46
↓ 1 callersFunctionmerge_results
(data, sent_data, predicDict, logitsDict, rep_ent, is_raw_text=False)
biobert_ner/ops.py:169
↓ 1 callersFunctionmodel_fn_builder
(bert_config, num_labels, init_checkpoint, learning_rate, num_train_steps, num_warmup_ste
biobert_ner/run_ner.py:315
↓ 1 callersMethodnormalize
(self, miRNA)
normalizers/miRNA_normalizer.py:64
↓ 1 callersMethodpredict
Runs a prediction on a set of features. Calling multiple times does *not* regenerate the graph which makes predict much faster.
biobert_ner/fast_predict2.py:40
↓ 1 callersMethodpreprocess_input
(self, text, cur_thread_name)
server.py:338
↓ 1 callersFunctionpubtator2dict_list
(pubtator_file_path, is_raw_text)
convert.py:9
↓ 1 callersFunctionpubtator2pubannotation
(pubtator)
convert.py:351
↓ 1 callersFunctionpubtatorstr2dict_list
(pubtator, is_raw_text)
convert.py:103
↓ 1 callersFunctionquery_pubtator2biocxml
(pmids)
download.py:581
↓ 1 callersFunctionquery_raw
(text, url='https://bern.korea.ac.kr/plain')
utils.py:11
↓ 1 callersFunctionquery_raw_bern
(input_str, bern_post_url='https://bern.korea.ac.kr/plain')
download.py:636
↓ 1 callersFunctionquery_tmtool
(pmids, entity_type='Mutation', out_format='JSON')
download.py:545
↓ 1 callersMethodrun_normalizer
(self, ent_type, base_name, names, saved_items, cur_thread_name, is_raw_text)
normalize.py:298
↓ 1 callersFunctionrun_server
(logic_func, port)
normalizers/mutation_normalizer.py:9
↓ 1 callersFunctionrun_server
(logic_func, port)
normalizers/chemical_normalizer.py:10
↓ 1 callersFunctionrun_server
(logic_func, port)
normalizers/species_normalizer.py:9
↓ 1 callersFunctionsend_mail
(from_addr, to, subject, content, gmail_id, password)
utils.py:138
↓ 1 callersFunctionshow_prof_data
()
biobert_ner/utils.py:30
↓ 1 callersMethodtag
(self, text)
normalizers/pathway_normalizer.py:40
↓ 1 callersMethodtag_entities
(self, text, cur_thread_name, is_raw_text, reuse=False)
server.py:372
↓ 1 callersFunctiontest_bern_get
(num_thread, period_delay_seconds, tries, url='https://bern.korea.ac.kr/pubmed')
utils.py:37
↓ 1 callersFunctiontest_bern_post
(base_text, num_thread, period_delay_seconds, tries, url='https://bern.korea.ac.kr/plain')
utils.py:59
↓ 1 callersMethodto_dict
Serializes this instance to a Python dictionary.
biobert_ner/modeling.py:96
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