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Functions176 in github.com/dmis-lab/bern

↓ 1 callersMethodtokenize
(self, text)
biobert_ner/tokenization.py:171
↓ 1 callersFunctiontransformer_model
Multi-headed, multi-layer Transformer from "Attention is All You Need". This is almost an exact implementation of the original Transformer encode
biobert_ner/modeling.py:763
↓ 1 callersMethodwrite_tokens
(tokens, mode, req_id)
biobert_ner/run_ner.py:850
Method__call__
(self, fn)
biobert_ner/utils.py:11
Method__init__
(self)
normalize.py:16
Method__init__
(self, params)
server.py:592
Method__init__
(self, vocab_file, do_lower_case=True)
biobert_ner/tokenization.py:165
Method__init__
Constructs a BasicTokenizer. Args: do_lower_case: Whether to lower case the input.
biobert_ner/tokenization.py:189
Method__init__
(self, vocab, unk_token="[UNK]", max_input_chars_per_word=200)
biobert_ner/tokenization.py:304
Method__init__
(self, prefix)
biobert_ner/utils.py:8
Method__init__
(self, estimator, input_fn)
biobert_ner/fast_predict2.py:22
Method__init__
Constructs BertConfig. Args: vocab_size: Vocabulary size of `inputs_ids` in `BertModel`. hidden_size: Size of the encoder
biobert_ner/modeling.py:33
Method__init__
Constructor for BertModel. Args: config: `BertConfig` instance. is_training: bool. true for training model, false for eva
biobert_ner/modeling.py:130
Method__init__
Constructs a InputExample. Args: guid: Unique id for the example. text: string. The untokenized text of the first sequenc
biobert_ner/run_ner.py:116
Method__init__
(self, input_ids, input_mask, segment_ids, label_ids,)
biobert_ner/run_ner.py:134
Method__init__
(self, _)
biobert_ner/run_ner.py:362
Method__init__
(self, dict_path)
normalizers/pathway_normalizer.py:5
Method__init__
(self, dict_path)
normalizers/miRNA_normalizer.py:5
Method_create_generator
(self)
biobert_ner/fast_predict2.py:31
Function_inner_input_fn
()
biobert_ner/fast_predict2.py:80
Functionbenchmark
(tries, batch_size=None, log_interval=100)
service_checker.py:49
Functionclear_prof_data
()
biobert_ner/utils.py:40
Methodclose
(self)
biobert_ner/fast_predict2.py:68
Functionconvert_ids_to_tokens
(inv_vocab, ids)
biobert_ner/tokenization.py:149
Methodconvert_ids_to_tokens
(self, ids)
biobert_ner/tokenization.py:182
Functionconvert_tokens_to_ids
(vocab, tokens)
biobert_ner/tokenization.py:145
Methodcreate_int_feature
(values)
biobert_ner/run_ner.py:672
Methoddo_GET
(self)
server.py:34
Methoddo_POST
(self)
server.py:262
Functionexample_input_fn
An example input function to pass to predict. It must take a generator as input
biobert_ner/fast_predict2.py:76
Methodfast_input_fn_builder_gen
(self, gen_predict_examples)
biobert_ner/run_ner.py:731
Methodfast_input_fn_builder_gen_batch
(self, gen_predict_examples)
biobert_ner/run_ner.py:754
Functionfile_based_input_fn_builder
(input_file, seq_length, drop_remainder)
biobert_ner/run_ner.py:238
Methodfiled_based_convert_examples_to_features
(self, examples, max_seq_length, output_file, req_id,
biobert_ner/run_ner.py:663
Functiongelu
Gaussian Error Linear Unit. This is a smoother version of the RELU. Original paper: https://arxiv.org/abs/1606.08415 Args: input_t
biobert_ner/modeling.py:269
Methodget_all_encoder_layers
(self)
biobert_ner/modeling.py:251
Functionget_bern_status
(ps_grep_res)
utils.py:105
Methodget_dev_examples
Gets a collection of `InputExample`s for the dev set.
biobert_ner/run_ner.py:149
Methodget_embedding_output
Gets output of the embedding lookup (i.e., input to the transformer). Returns: float Tensor of shape [batch_size, seq_length, hidde
biobert_ner/modeling.py:254
Methodget_embedding_table
(self)
biobert_ner/modeling.py:265
Methodget_input_generator
(self, predict_examples, req_id, mode='test')
biobert_ner/run_ner.py:702
Methodget_inputs
(self, predict_examples, req_id, mode='test')
biobert_ner/run_ner.py:715
Functionget_item_key1
(item)
convert.py:550
Functionget_item_key2
(item)
convert.py:553
Methodget_labels
Gets the list of labels for this data set.
biobert_ner/run_ner.py:153
Functionget_pmc_xml
(pmcid, output_path=None)
download.py:117
Methodget_pooled_output
(self)
biobert_ner/modeling.py:239
Functionget_pubmed
(pmid, out_format='json', encoding='unicode')
download.py:531
Functionget_pubmed_xml
(pmid, output_path=None)
download.py:15
Methodget_train_examples
Gets a collection of `InputExample`s for the train set.
biobert_ner/run_ner.py:145
Functioninput_fn
(params)
biobert_ner/run_ner.py:257
FunctionisFloat
(string)
biobert_ner/ops.py:74
FunctionisInt
(string)
biobert_ner/ops.py:66
Functionmain
(_)
biobert_ner/run_ner.py:864
Functionmodel_fn
(features, labels, mode, params)
biobert_ner/run_ner.py:318
Functionpmc_xml2pubtator
(pmcid, xml_path, output_path=None)
download.py:179
Functionprintable_text
Returns text encoded in a way suitable for print or `tf.logging`.
biobert_ner/tokenization.py:99
Functionps_grep
(q)
utils.py:96
Functionpubmed_xml2pubtator
(pmid, xml_path, output_path=None)
download.py:45
Functionquery_pubtator2
(pmids, out_format='pubtator', escape_html=True)
download.py:561
Functionquery_raw_tmtool
(input_str, trigger='tmVar')
download.py:602
Methodrecognize_etype
(self, etype, predict_example_list, tokens, tot_tokens, predict_dict, logits_dict, dat
biobert_ner/run_ner.py:592
Functionrun_command
(command, cwd)
utils.py:84
Functionrun_normalizer
(data, _)
normalizers/mutation_normalizer.py:24
Functionrun_normalizer
(data, _)
normalizers/chemical_normalizer.py:25
Functionrun_normalizer
(data, _)
normalizers/species_normalizer.py:24
Methodrun_normalizers_wrap
(self, ent_type, base_name, names, saved_items, cur_thread_name, is_raw_text, res
normalize.py:291
Functionstress_test
(num_threads, wait_seconds, num_try)
service_checker.py:185
Functiontmtooljson2bern
(tmtool_res)
convert.py:589
Methodto_json_string
Serializes this instance to a JSON string.
biobert_ner/modeling.py:101
Methodtokenize
Tokenizes a piece of text.
biobert_ner/tokenization.py:197
Methodtokenize
Tokenizes a piece of text into its word pieces. This uses a greedy longest-match-first algorithm to perform tokenization using the gi
biobert_ner/tokenization.py:309
Functiontpu_scaffold
()
biobert_ner/run_ner.py:336
Functionvalidate_case_matches_checkpoint
Checks whether the casing config is consistent with the checkpoint name.
biobert_ner/tokenization.py:28
Methodwith_profiling
(*args, **kwargs)
biobert_ner/utils.py:12
Functionworker
()
download.py:451
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