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X
A
abstract_record_to_string() (in module agatha.ml.gpt2_finetune.gpt2_finetune)
AbstractGeneratorTokenizer (class in agatha.ml.abstract_generator.tokenizer)
add() (agatha.ml.abstract_generator.misc_util.HashedIndex method)
(agatha.ml.abstract_generator.misc_util.OrderedIndex method)
add_bow_to_analyzed_sentence() (in module agatha.construct.text_util)
add_global_preloader() (in module agatha.construct.dask_process_global)
add_points_to_index() (in module agatha.construct.knn_util)
add_topical_network() (in module agatha.topic_query.aux_result_data)
agatha
module
agatha.construct
module
agatha.construct.checkpoint
module
agatha.construct.dask_process_global
module
agatha.construct.document_parsers
module
agatha.construct.document_parsers.document_record
module
agatha.construct.document_parsers.parse_covid_json
module
agatha.construct.document_parsers.parse_pubmed_xml
module
agatha.construct.document_parsers.test_parse_covid_json
module
agatha.construct.document_pipeline
module
agatha.construct.embedding_util
module
agatha.construct.file_util
module
agatha.construct.ftp_util
module
agatha.construct.graph_util
module
agatha.construct.knn_util
module
agatha.construct.ngram_util
module
agatha.construct.semrep_util
module
agatha.construct.test_checkpoint
module
agatha.construct.test_file_util
module
agatha.construct.test_semrep_util
module
agatha.construct.text_util
module
agatha.ml
module
agatha.ml.abstract_generator
module
agatha.ml.abstract_generator.abstract_generator
module
agatha.ml.abstract_generator.datasets
module
agatha.ml.abstract_generator.misc_util
module
agatha.ml.abstract_generator.tokenizer
module
agatha.ml.gpt2_finetune
module
agatha.ml.gpt2_finetune.gpt2_finetune
module
agatha.ml.hypothesis_predictor
module
agatha.ml.hypothesis_predictor.hypothesis_predictor
module
agatha.ml.hypothesis_predictor.predicate_util
module
agatha.ml.hypothesis_predictor.test_predicate_util
module
agatha.ml.model_summary
module
agatha.ml.module
module
agatha.ml.util
module
agatha.ml.util.embedding_lookup
module
agatha.ml.util.hparam_util
module
agatha.ml.util.kv_store_dataset
module
agatha.ml.util.lamb_optimizer
module
agatha.ml.util.sqlite3_dataset
module
agatha.ml.util.test_embedding_lookup
module
agatha.ml.util.test_sqlite3_dataset
module
agatha.topic_query
module
agatha.topic_query.aux_result_data
module
agatha.topic_query.bow_util
module
agatha.topic_query.path_util
module
agatha.topic_query.test_bow_util
module
agatha.topic_query.test_path_util
module
agatha.util
module
agatha.util.entity_types
module
agatha.util.misc_util
module
agatha.util.proto_util
module
agatha.util.semmeddb_util
module
agatha.util.sqlite3_lookup
module
agatha.util.test_proto_util
module
agatha.util.test_sqlite3_lookup
module
agatha.util.test_umls_util
module
agatha.util.umls_util
module
analyze_sentences() (in module agatha.construct.text_util)
assert_datestr() (in module agatha.util.semmeddb_util)
assert_table_contains_embeddings() (in module agatha.ml.util.test_embedding_lookup)
assert_valid_document_record() (in module agatha.construct.document_parsers.document_record)
assert_writable() (in module agatha.ml.util.test_embedding_lookup)
async_touch_after() (in module agatha.construct.test_file_util)
atom_contains_all_fields() (in module agatha.util.umls_util)
C
checkpoint() (in module agatha.construct.checkpoint)
ckpt() (in module agatha.construct.checkpoint)
clean_coded_term() (in module agatha.ml.hypothesis_predictor.predicate_util)
clean_text_for_metamap() (agatha.construct.semrep_util.UnicodeToAsciiRunner method)
clear() (agatha.construct.dask_process_global.WorkerPreloader method)
(in module agatha.construct.dask_process_global)
clear_all_ckpt() (in module agatha.construct.checkpoint)
clear_cache() (agatha.ml.util.embedding_lookup.EmbeddingLookupTable method)
(agatha.util.sqlite3_lookup.Sqlite3LookupTable method)
clear_ckpt() (in module agatha.construct.checkpoint)
clear_halt_point() (in module agatha.construct.checkpoint)
clear_node_attribute() (in module agatha.topic_query.path_util)
codes() (agatha.util.umls_util.UmlsIndex method)
collate_encoded_abstracts() (in module agatha.ml.abstract_generator.datasets)
collate_predicate_embeddings() (in module agatha.ml.hypothesis_predictor.predicate_util)
collate_predicate_training_examples() (in module agatha.ml.hypothesis_predictor.predicate_util)
collate_token_batch() (in module agatha.ml.gpt2_finetune.gpt2_finetune)
compile_kv_json_dir_to_sqlite3() (in module agatha.util.sqlite3_lookup)
connected() (agatha.util.sqlite3_lookup.Sqlite3LookupTable method)
contains_code() (agatha.util.umls_util.UmlsIndex method)
contains_pref_text_for_code() (agatha.util.umls_util.UmlsIndex method)
copy_to_local_scratch() (in module agatha.construct.file_util)
create_lookup_table() (in module agatha.util.sqlite3_lookup)
D
decode_dep() (agatha.ml.abstract_generator.tokenizer.AbstractGeneratorTokenizer method)
decode_entity_label() (agatha.ml.abstract_generator.tokenizer.AbstractGeneratorTokenizer method)
decode_mesh() (agatha.ml.abstract_generator.tokenizer.AbstractGeneratorTokenizer method)
decode_pos() (agatha.ml.abstract_generator.tokenizer.AbstractGeneratorTokenizer method)
decode_text() (agatha.ml.abstract_generator.tokenizer.AbstractGeneratorTokenizer method)
decode_year() (agatha.ml.abstract_generator.tokenizer.AbstractGeneratorTokenizer method)
disable() (in module agatha.construct.checkpoint)
disable_cache() (agatha.ml.util.embedding_lookup.EmbeddingLookupTable method)
(agatha.util.sqlite3_lookup.Sqlite3LookupTable method)
E
earliest_occurances() (in module agatha.util.semmeddb_util)
embed_records() (in module agatha.construct.embedding_util)
EmbeddingLookupTable (class in agatha.ml.util.embedding_lookup)
enable() (in module agatha.construct.checkpoint)
enable_cache() (agatha.ml.util.embedding_lookup.EmbeddingLookupTable method)
(agatha.util.sqlite3_lookup.Sqlite3LookupTable method)
encode_dep() (agatha.ml.abstract_generator.tokenizer.AbstractGeneratorTokenizer method)
encode_entity_label() (agatha.ml.abstract_generator.tokenizer.AbstractGeneratorTokenizer method)
encode_for_generation() (agatha.ml.abstract_generator.tokenizer.AbstractGeneratorTokenizer method)
encode_mesh() (agatha.ml.abstract_generator.tokenizer.AbstractGeneratorTokenizer method)
encode_pos() (agatha.ml.abstract_generator.tokenizer.AbstractGeneratorTokenizer method)
encode_sentence() (agatha.ml.abstract_generator.tokenizer.AbstractGeneratorTokenizer method)
encode_year() (agatha.ml.abstract_generator.tokenizer.AbstractGeneratorTokenizer method)
entity_to_id() (in module agatha.construct.text_util)
estimate_plaintext_from_graph_key() (in module agatha.topic_query.aux_result_data)
export_key_value_records() (in module agatha.util.sqlite3_lookup)
extract_entities_and_predicates_from_sentences() (in module agatha.construct.semrep_util)
F
filter_atoms() (in module agatha.util.umls_util)
filter_by_date() (in module agatha.util.semmeddb_util)
filter_words() (in module agatha.topic_query.bow_util)
find_codes_with_close_text() (agatha.util.umls_util.UmlsIndex method)
find_codes_with_pattern() (agatha.util.umls_util.UmlsIndex method)
flatten_list() (in module agatha.util.misc_util)
ftp_connect() (in module agatha.construct.ftp_util)
ftp_download() (in module agatha.construct.ftp_util)
ftp_download_if_missing() (in module agatha.construct.ftp_util)
ftp_list_files() (in module agatha.construct.ftp_util)
ftp_retreive_all() (in module agatha.construct.ftp_util)
G
generate() (agatha.ml.hypothesis_predictor.predicate_util.NegativePredicateGenerator method)
generator_to_list() (in module agatha.util.misc_util)
get() (agatha.construct.dask_process_global.WorkerPreloader method)
(in module agatha.construct.dask_process_global)
get_adjacent_sentences() (in module agatha.construct.text_util)
get_allow_partial() (in module agatha.construct.checkpoint)
get_bert_initializer() (in module agatha.construct.embedding_util)
get_checkpoints_like() (in module agatha.construct.checkpoint)
get_covid_documents() (in module agatha.construct.document_pipeline)
get_current_year() (in module agatha.ml.abstract_generator.tokenizer)
get_document_frequencies() (in module agatha.topic_query.bow_util)
get_done_file_path() (in module agatha.construct.checkpoint)
get_element_with_min_criteria() (in module agatha.topic_query.path_util)
get_elements() (agatha.ml.abstract_generator.misc_util.HashedIndex method)
(agatha.ml.abstract_generator.misc_util.OrderedIndex method)
get_entity_keys() (in module agatha.construct.text_util)
get_entity_text() (in module agatha.construct.text_util)
get_expected_texts() (in module agatha.construct.document_parsers.test_parse_covid_json)
get_faiss_index_initializer() (in module agatha.construct.knn_util)
get_field() (in module agatha.util.proto_util)
get_frequent_ngrams() (in module agatha.construct.ngram_util)
get_full_field_names() (in module agatha.util.proto_util)
get_global_preloader() (in module agatha.construct.dask_process_global)
get_index() (agatha.ml.abstract_generator.misc_util.HashedIndex method)
(agatha.ml.abstract_generator.misc_util.OrderedIndex method)
get_interesting_token_keys() (in module agatha.construct.text_util)
get_medline_documents() (in module agatha.construct.document_pipeline)
get_mesh_keys() (in module agatha.construct.text_util)
get_metamap_server_initializer() (in module agatha.construct.semrep_util)
get_nearby_nodes() (in module agatha.topic_query.path_util)
get_ngram_keys() (in module agatha.construct.text_util)
get_or_make_ckpt_dir() (in module agatha.construct.checkpoint)
get_part_files() (in module agatha.construct.file_util)
get_paths() (in module agatha.construct.semrep_util)
get_pref_text() (agatha.util.umls_util.UmlsIndex method)
get_pretrained_model_initializer() (in module agatha.construct.embedding_util)
get_pytorch_device_initalizer() (in module agatha.construct.embedding_util)
get_random_ascii_str() (in module agatha.construct.file_util)
get_root() (in module agatha.construct.checkpoint)
get_scispacy_initalizer() (in module agatha.construct.text_util)
get_sentence_id() (in module agatha.construct.text_util)
get_shortest_path() (in module agatha.topic_query.path_util)
get_sqlite_files() (in module agatha.ml.util.kv_store_dataset)
get_stopwordlist_initializer() (in module agatha.construct.text_util)
get_texts() (agatha.util.umls_util.UmlsIndex method)
get_verbose() (in module agatha.construct.checkpoint)
get_worker_lock() (in module agatha.construct.dask_process_global)
H
has_element() (agatha.ml.abstract_generator.misc_util.HashedIndex method)
(agatha.ml.abstract_generator.misc_util.OrderedIndex method)
has_index() (agatha.ml.abstract_generator.misc_util.HashedIndex method)
(agatha.ml.abstract_generator.misc_util.OrderedIndex method)
hash_str_to_int() (in module agatha.util.misc_util)
hash_str_to_int32() (in module agatha.util.misc_util)
hash_str_to_int64() (in module agatha.util.misc_util)
HashedIndex (class in agatha.ml.abstract_generator.misc_util)
I
is_ckpt_done() (in module agatha.construct.checkpoint)
is_data_bank_type() (in module agatha.util.entity_types)
is_entity_type() (in module agatha.util.entity_types)
is_gene_type() (in module agatha.util.entity_types)
is_graph_key() (in module agatha.util.entity_types)
is_lemma_type() (in module agatha.util.entity_types)
is_mesh_term_type() (in module agatha.util.entity_types)
is_ngram_type() (in module agatha.util.entity_types)
is_predicate_type() (in module agatha.util.entity_types)
is_preloaded() (agatha.ml.util.embedding_lookup.EmbeddingLookupTable method)
(agatha.util.sqlite3_lookup.Sqlite3LookupTable method)
is_result_saved() (in module agatha.construct.file_util)
is_sentence_type() (in module agatha.util.entity_types)
is_type() (in module agatha.util.entity_types)
is_umls_term_type() (in module agatha.util.entity_types)
is_valid_predicate_name() (in module agatha.ml.hypothesis_predictor.predicate_util)
items_to_hashed_index() (in module agatha.ml.abstract_generator.misc_util)
items_to_ordered_index() (in module agatha.ml.abstract_generator.misc_util)
iter_to_batches() (in module agatha.util.misc_util)
iterate() (agatha.util.sqlite3_lookup.Sqlite3LookupTable method)
J
json_path_to_record() (in module agatha.construct.document_parsers.parse_covid_json)
K
keys() (agatha.ml.util.embedding_lookup.EmbeddingLookupTable method)
(agatha.util.sqlite3_lookup.Sqlite3LookupTable method)
L
len_dep() (agatha.ml.abstract_generator.tokenizer.AbstractGeneratorTokenizer method)
len_entity_label() (agatha.ml.abstract_generator.tokenizer.AbstractGeneratorTokenizer method)
len_mesh() (agatha.ml.abstract_generator.tokenizer.AbstractGeneratorTokenizer method)
len_pos() (agatha.ml.abstract_generator.tokenizer.AbstractGeneratorTokenizer method)
len_text() (agatha.ml.abstract_generator.tokenizer.AbstractGeneratorTokenizer method)
len_year() (agatha.ml.abstract_generator.tokenizer.AbstractGeneratorTokenizer method)
load() (in module agatha.construct.file_util)
load_json() (in module agatha.construct.document_parsers.test_parse_covid_json)
load_json_as_proto() (in module agatha.util.proto_util)
load_part() (in module agatha.construct.file_util)
load_proto() (in module agatha.util.proto_util)
load_random_sample_to_memory() (in module agatha.construct.file_util)
load_serialized_pb_as_proto() (in module agatha.util.proto_util)
load_text_as_proto() (in module agatha.util.proto_util)
load_to_memory() (in module agatha.construct.file_util)
load_value() (in module agatha.construct.file_util)
LocalMockWorker (class in agatha.construct.dask_process_global)
M
make_embedding_hdf5s() (in module agatha.ml.util.test_embedding_lookup)
make_entity_lookup_table() (in module agatha.ml.util.test_embedding_lookup)
make_sqlite3_db() (in module agatha.util.test_sqlite3_lookup)
merge_counts() (in module agatha.util.misc_util)
merge_index() (in module agatha.construct.knn_util)
mesh_to_id() (in module agatha.construct.text_util)
MetaMapServer (class in agatha.construct.semrep_util)
module
agatha
agatha.construct
agatha.construct.checkpoint
agatha.construct.dask_process_global
agatha.construct.document_parsers
agatha.construct.document_parsers.document_record
agatha.construct.document_parsers.parse_covid_json
agatha.construct.document_parsers.parse_pubmed_xml
agatha.construct.document_parsers.test_parse_covid_json
agatha.construct.document_pipeline
agatha.construct.embedding_util
agatha.construct.file_util
agatha.construct.ftp_util
agatha.construct.graph_util
agatha.construct.knn_util
agatha.construct.ngram_util
agatha.construct.semrep_util
agatha.construct.test_checkpoint
agatha.construct.test_file_util
agatha.construct.test_semrep_util
agatha.construct.text_util
agatha.ml
agatha.ml.abstract_generator
agatha.ml.abstract_generator.abstract_generator
agatha.ml.abstract_generator.datasets
agatha.ml.abstract_generator.misc_util
agatha.ml.abstract_generator.tokenizer
agatha.ml.gpt2_finetune
agatha.ml.gpt2_finetune.gpt2_finetune
agatha.ml.hypothesis_predictor
agatha.ml.hypothesis_predictor.hypothesis_predictor
agatha.ml.hypothesis_predictor.predicate_util
agatha.ml.hypothesis_predictor.test_predicate_util
agatha.ml.model_summary
agatha.ml.module
agatha.ml.util
agatha.ml.util.embedding_lookup
agatha.ml.util.hparam_util
agatha.ml.util.kv_store_dataset
agatha.ml.util.lamb_optimizer
agatha.ml.util.sqlite3_dataset
agatha.ml.util.test_embedding_lookup
agatha.ml.util.test_sqlite3_dataset
agatha.topic_query
agatha.topic_query.aux_result_data
agatha.topic_query.bow_util
agatha.topic_query.path_util
agatha.topic_query.test_bow_util
agatha.topic_query.test_path_util
agatha.util
agatha.util.entity_types
agatha.util.misc_util
agatha.util.proto_util
agatha.util.semmeddb_util
agatha.util.sqlite3_lookup
agatha.util.test_proto_util
agatha.util.test_sqlite3_lookup
agatha.util.test_umls_util
agatha.util.umls_util
N
nearest_neighbors_network_from_index() (in module agatha.construct.knn_util)
NegativePredicateGenerator (class in agatha.ml.hypothesis_predictor.predicate_util)
new_document_record() (in module agatha.construct.document_parsers.document_record)
ngram_to_id() (in module agatha.construct.text_util)
node_sets_equal() (in module agatha.topic_query.test_path_util)
num_codes() (agatha.util.umls_util.UmlsIndex method)
O
obj (agatha.ml.hypothesis_predictor.predicate_util.PredicateEmbeddings attribute)
obj_neigh (agatha.ml.hypothesis_predictor.predicate_util.PredicateEmbeddings attribute)
OrderedIndex (class in agatha.ml.abstract_generator.misc_util)
P
parse() (in module agatha.util.semmeddb_util)
parse_args_to_config_proto() (in module agatha.util.proto_util)
parse_embedding_path() (in module agatha.ml.util.embedding_lookup)
parse_mrconso() (in module agatha.util.umls_util)
parse_predicate_name() (in module agatha.ml.hypothesis_predictor.predicate_util)
parse_zipped_pubmed_xml() (in module agatha.construct.document_parsers.parse_pubmed_xml)
perform_document_independent_tasks() (in module agatha.construct.document_pipeline)
predicate_to_key() (in module agatha.util.semmeddb_util)
PredicateEmbeddings (class in agatha.ml.hypothesis_predictor.predicate_util)
PredicateObservationGenerator (class in agatha.ml.hypothesis_predictor.predicate_util)
PredicateScrambleObservationGenerator (class in agatha.ml.hypothesis_predictor.predicate_util)
preload() (agatha.ml.util.embedding_lookup.EmbeddingLookupTable method)
(agatha.util.sqlite3_lookup.Sqlite3LookupTable method)
prep_scratches() (in module agatha.construct.file_util)
print_model_summary() (in module agatha.ml.model_summary)
pubmed_xml_to_record() (in module agatha.construct.document_parsers.parse_pubmed_xml)
R
record_to_bipartite_edges() (in module agatha.construct.graph_util)
recover_shortest_path_from_tight_edges() (in module agatha.topic_query.path_util)
register() (agatha.construct.dask_process_global.WorkerPreloader method)
remove_paths_from_namespace() (in module agatha.ml.util.hparam_util)
run() (agatha.construct.semrep_util.SemRepRunner method)
running() (agatha.construct.semrep_util.MetaMapServer method)
S
safe_get_worker() (in module agatha.construct.dask_process_global)
save() (in module agatha.construct.file_util)
save_part() (in module agatha.construct.file_util)
save_value() (in module agatha.construct.file_util)
semrep_xml_to_records() (in module agatha.construct.semrep_util)
SemRepRunner (class in agatha.construct.semrep_util)
sentence_to_id() (in module agatha.construct.text_util)
sentences_to_semrep_input() (in module agatha.construct.semrep_util)
set_allow_partial() (in module agatha.construct.checkpoint)
set_field() (in module agatha.util.proto_util)
set_halt_point() (in module agatha.construct.checkpoint)
set_root() (in module agatha.construct.checkpoint)
set_verbose() (in module agatha.construct.checkpoint)
setup() (agatha.construct.dask_process_global.WorkerPreloader method)
setup_done_checkpoints() (in module agatha.construct.test_checkpoint)
setup_embedding_lookup_data() (in module agatha.ml.util.test_embedding_lookup)
setup_parser_with_proto() (in module agatha.util.proto_util)
shift_text_features_for_training() (in module agatha.ml.abstract_generator.datasets)
simple_encode_text() (agatha.ml.abstract_generator.tokenizer.AbstractGeneratorTokenizer method)
split_multi_term_predicate() (in module agatha.util.semmeddb_util)
split_sentences() (in module agatha.construct.text_util)
Sqlite3Bow (class in agatha.util.sqlite3_lookup)
Sqlite3Graph (class in agatha.util.sqlite3_lookup)
Sqlite3LookupTable (class in agatha.util.sqlite3_lookup)
start() (agatha.construct.semrep_util.MetaMapServer method)
stop() (agatha.construct.semrep_util.MetaMapServer method)
subj (agatha.ml.hypothesis_predictor.predicate_util.PredicateEmbeddings attribute)
subj_neigh (agatha.ml.hypothesis_predictor.predicate_util.PredicateEmbeddings attribute)
T
teardown() (agatha.construct.dask_process_global.WorkerPreloader method)
test_async_touch_after() (in module agatha.construct.test_file_util)
test_backward_compatable_fallback() (in module agatha.util.test_sqlite3_lookup)
test_clean_coded_term() (in module agatha.ml.hypothesis_predictor.test_predicate_util)
test_clean_coded_term_lower() (in module agatha.ml.hypothesis_predictor.test_predicate_util)
test_clean_coded_term_passthrough() (in module agatha.ml.hypothesis_predictor.test_predicate_util)
test_clean_coded_term_passthrough_lower() (in module agatha.ml.hypothesis_predictor.test_predicate_util)
test_clear_ckpt() (in module agatha.construct.test_checkpoint)
test_codes_with_minimum_edit_distance() (in module agatha.util.test_umls_util)
test_create_umls_index() (in module agatha.util.test_umls_util)
test_create_umls_index_filter() (in module agatha.util.test_umls_util)
test_custom_key_column_name() (in module agatha.util.test_sqlite3_lookup)
test_custom_table_name() (in module agatha.util.test_sqlite3_lookup)
test_custom_value_column_name() (in module agatha.util.test_sqlite3_lookup)
test_default_none_ckpt_root() (in module agatha.construct.test_checkpoint)
test_delete_attribute() (in module agatha.topic_query.test_path_util)
test_embedding_keys() (in module agatha.ml.util.test_embedding_lookup)
test_extract_entitites_and_predicates_with_dask() (in module agatha.construct.test_semrep_util)
test_filter_atoms_code_subset() (in module agatha.util.test_umls_util)
test_filter_atoms_language_eng() (in module agatha.util.test_umls_util)
test_filter_atoms_suppress_content() (in module agatha.util.test_umls_util)
test_filter_words() (in module agatha.topic_query.test_bow_util)
test_find_codes() (in module agatha.util.test_umls_util)
test_get_all_paths() (in module agatha.construct.test_semrep_util)
test_get_checkpoints_like() (in module agatha.construct.test_checkpoint)
test_get_checkpoints_like_complete() (in module agatha.construct.test_checkpoint)
test_get_metamap_paths() (in module agatha.construct.test_semrep_util)
test_get_or_make_ckpt_dir() (in module agatha.construct.test_checkpoint)
test_get_semrep_paths_fails() (in module agatha.construct.test_semrep_util)
test_getitem() (in module agatha.ml.util.test_sqlite3_dataset)
test_has_code() (in module agatha.util.test_umls_util)
test_has_pref_text() (in module agatha.util.test_umls_util)
test_is_valid_predicate_name() (in module agatha.ml.hypothesis_predictor.test_predicate_util)
test_iter() (in module agatha.util.test_sqlite3_lookup)
test_iter_where() (in module agatha.util.test_sqlite3_lookup)
test_keys() (in module agatha.util.test_sqlite3_lookup)
test_len() (in module agatha.ml.util.test_sqlite3_dataset)
(in module agatha.util.test_sqlite3_lookup)
test_load_json_as_proto() (in module agatha.util.test_proto_util)
test_load_serialized_pb_as_proto() (in module agatha.util.test_proto_util)
test_load_text_as_proto() (in module agatha.util.test_proto_util)
test_make_sqlite3_db() (in module agatha.util.test_sqlite3_lookup)
test_metamap_server() (in module agatha.construct.test_semrep_util)
TEST_MRCONSO_PATH (in module agatha.util.test_umls_util)
test_new_sqlite3bow() (in module agatha.util.test_sqlite3_lookup)
test_new_sqlite3graph() (in module agatha.util.test_sqlite3_lookup)
test_old_sqlite3bow() (in module agatha.util.test_sqlite3_lookup)
test_old_sqlite3graph() (in module agatha.util.test_sqlite3_lookup)
test_parse_first_line() (in module agatha.util.test_umls_util)
test_parse_id_1() (in module agatha.construct.document_parsers.test_parse_covid_json)
test_parse_id_2() (in module agatha.construct.document_parsers.test_parse_covid_json)
test_parse_mrconso() (in module agatha.util.test_umls_util)
test_parse_proto_fields_build_config() (in module agatha.util.test_proto_util)
test_parse_proto_fields_ftp_source() (in module agatha.util.test_proto_util)
test_parse_semrep_end_to_end() (in module agatha.construct.test_semrep_util)
test_parse_semrep_end_to_end_difficult() (in module agatha.construct.test_semrep_util)
test_parse_semrep_xml_entity() (in module agatha.construct.test_semrep_util)
test_parse_semrep_xml_predication() (in module agatha.construct.test_semrep_util)
test_parse_success_1() (in module agatha.construct.document_parsers.test_parse_covid_json)
test_parse_success_2() (in module agatha.construct.document_parsers.test_parse_covid_json)
test_parse_text_1() (in module agatha.construct.document_parsers.test_parse_covid_json)
test_parse_text_2() (in module agatha.construct.document_parsers.test_parse_covid_json)
test_parse_title_1() (in module agatha.construct.document_parsers.test_parse_covid_json)
test_parse_title_2() (in module agatha.construct.document_parsers.test_parse_covid_json)
test_replace_attribute() (in module agatha.topic_query.test_path_util)
test_run_semrep() (in module agatha.construct.test_semrep_util)
test_run_semrep_covid() (in module agatha.construct.test_semrep_util)
test_semrep_fails_with_bad_sentence() (in module agatha.construct.test_semrep_util)
test_semrep_id_to_agatha_sentence_id() (in module agatha.construct.test_semrep_util)
test_semrep_id_to_agatha_sentence_id_weird_id() (in module agatha.construct.test_semrep_util)
test_semrep_paths() (in module agatha.construct.test_semrep_util)
test_semrep_xml_to_records() (in module agatha.construct.test_semrep_util)
test_sentence_to_semrep_input() (in module agatha.construct.test_semrep_util)
test_sentence_to_semrep_input_filter_newline() (in module agatha.construct.test_semrep_util)
test_sentence_to_semrep_input_filter_single_quote() (in module agatha.construct.test_semrep_util)
test_sentence_to_semrep_input_filter_unicode() (in module agatha.construct.test_semrep_util)
test_set_field_nested() (in module agatha.util.test_proto_util)
test_set_field_unnested() (in module agatha.util.test_proto_util)
test_set_root() (in module agatha.construct.test_checkpoint)
test_setup_done_checkpoints() (in module agatha.construct.test_checkpoint)
test_setup_lookup_data() (in module agatha.ml.util.test_embedding_lookup)
test_setup_lookup_data_two_parts() (in module agatha.ml.util.test_embedding_lookup)
test_setup_parser_with_proto() (in module agatha.util.test_proto_util)
test_sqlite3_is_preloaded() (in module agatha.util.test_sqlite3_lookup)
test_sqlite3_lookup_contains() (in module agatha.util.test_sqlite3_lookup)
test_sqlite3_lookup_getitem() (in module agatha.util.test_sqlite3_lookup)
test_sqlite3_lookup_pickle() (in module agatha.util.test_sqlite3_lookup)
test_sqlite3_lookup_preload() (in module agatha.util.test_sqlite3_lookup)
test_subset() (in module agatha.ml.util.test_sqlite3_dataset)
test_transfer_args_to_proto() (in module agatha.util.test_proto_util)
test_typical_embedding_lookup() (in module agatha.ml.util.test_embedding_lookup)
test_unicode_to_ascii() (in module agatha.construct.test_semrep_util)
test_wait_for_file_to_appear_exists() (in module agatha.construct.test_file_util)
test_wait_for_file_to_appear_not_exists() (in module agatha.construct.test_file_util)
to_graph_key() (in module agatha.util.entity_types)
to_hash_and_embedding() (in module agatha.construct.knn_util)
to_predicate_name() (in module agatha.ml.hypothesis_predictor.predicate_util)
token_to_id() (in module agatha.construct.text_util)
touch_random_unused_file() (in module agatha.construct.file_util)
train_distributed_knn() (in module agatha.construct.knn_util)
train_initial_index() (in module agatha.construct.knn_util)
transfer_args_to_proto() (in module agatha.util.proto_util)
U
UmlsIndex (class in agatha.util.umls_util)
UnicodeToAsciiRunner (class in agatha.construct.semrep_util)
W
wait_for_file_to_appear() (in module agatha.construct.file_util)
weighted_index_sample() (in module agatha.ml.gpt2_finetune.gpt2_finetune)
WorkerPreloader (class in agatha.construct.dask_process_global)
write_done_file() (in module agatha.construct.file_util)
X
xml_obj_to_date() (in module agatha.construct.document_parsers.parse_pubmed_xml)
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