SYMBOL INDEX (272 symbols across 25 files) FILE: baseline_utils.py function _get_sequence_name_from_sequence_header (line 60) | def _get_sequence_name_from_sequence_header(s): function _get_labels_from_sequence_header (line 70) | def _get_labels_from_sequence_header(s): class BlastResult (line 86) | class BlastResult( method from_string (line 98) | def from_string(s, ground_truth_lookup): class InterproScanResult (line 119) | class InterproScanResult( method from_string (line 125) | def from_string(s): function load_ground_truth (line 137) | def load_ground_truth(filename): function _set_predicted_labels_missing (line 169) | def _set_predicted_labels_missing(row): function _fillna (line 177) | def _fillna(df, column_name, value): function _blast_row_to_confidence_array (line 192) | def _blast_row_to_confidence_array( function load_blast_output (line 205) | def load_blast_output(filename, label_vocab, function _pad_ec_label_with_hyphens (line 278) | def _pad_ec_label_with_hyphens(label): function limit_set_of_labels (line 286) | def limit_set_of_labels(df, acceptable_labels, function limit_labels_for_label_normalizer (line 296) | def limit_labels_for_label_normalizer( function load_interproscan_output (line 309) | def load_interproscan_output( FILE: baseline_utils_test.py function _write_to_file (line 35) | def _write_to_file(contents): class BaselineUtilsTest (line 42) | class BaselineUtilsTest(parameterized.TestCase): method test_get_sequence_name_from_sequence_header (line 56) | def test_get_sequence_name_from_sequence_header(self, header, expected): method test_get_labels_from_sequence_header (line 72) | def test_get_labels_from_sequence_header(self, header, expected): method test_load_ground_truth (line 76) | def test_load_ground_truth(self): method test_blast_row_to_confidence_array (line 130) | def test_blast_row_to_confidence_array(self, input_row, input_label_vo... method test_load_blast_output (line 138) | def test_load_blast_output(self): method test_limit_set_of_labels (line 186) | def test_limit_set_of_labels(self): method test_limit_labels_for_label_normalizer (line 207) | def test_limit_labels_for_label_normalizer(self): method test_load_interproscan_output (line 295) | def test_load_interproscan_output(self, interproscan_output, FILE: colab_evaluation.py function read_blast_table (line 32) | def read_blast_table(filename): function stats_by_group (line 55) | def stats_by_group(df): function get_stats (line 73) | def get_stats(df): function apply_threshold_and_return_stats (line 81) | def apply_threshold_and_return_stats(predictions_df, function batch_inferences (line 95) | def batch_inferences(iterator, batch_size): function batched_inferences_from_files (line 117) | def batched_inferences_from_files(shard_names, batch_size=100): function batched_inferences_from_dir (line 129) | def batched_inferences_from_dir(shard_dir_path, batch_size=100): function _make_tidy_df_from_seq_names_and_prediction_array (line 135) | def _make_tidy_df_from_seq_names_and_prediction_array( function get_normalized_inference_results (line 155) | def get_normalized_inference_results(shard_dir_path, function make_tidy_df_from_ground_truth (line 189) | def make_tidy_df_from_ground_truth(ground_truth): function merge_predictions_and_ground_truth (line 202) | def merge_predictions_and_ground_truth(predictions_df, ground_truth_df): function get_pr_curve_df (line 213) | def get_pr_curve_df(predictions_df, function filter_pr_curve (line 259) | def filter_pr_curve(precisions, recalls, thresholds, resolution=1e-4): function assign_tp_fp_fn (line 278) | def assign_tp_fp_fn(predictions_df, ground_truth_df, threshold): FILE: colab_evaluation_test.py class ColabEvaluationTest (line 34) | class ColabEvaluationTest(parameterized.TestCase): method _generate_random_inferences (line 35) | def _generate_random_inferences(self, n): method test_batched_inferences_from_dir (line 51) | def test_batched_inferences_from_dir(self, batch_size, num_examples=100): method test_make_tidy_df_from_seq_names_and_prediction_array (line 93) | def test_make_tidy_df_from_seq_names_and_prediction_array(self): method test_make_tidy_df_from_ground_truth (line 110) | def test_make_tidy_df_from_ground_truth(self): method test_merge_predictions_and_ground_truth (line 123) | def test_merge_predictions_and_ground_truth(self): method test_get_pr_curve_df (line 145) | def test_get_pr_curve_df(self): method test_assign_tp_fp_fn (line 165) | def test_assign_tp_fp_fn(self): method test_apply_threshold_and_return_stats (line 187) | def test_apply_threshold_and_return_stats(self): method test_read_blast_table (line 215) | def test_read_blast_table(self): FILE: evaluation.py function normalize_confidences (line 40) | def normalize_confidences( function get_ground_truth_multihots (line 76) | def get_ground_truth_multihots(label_sets, function get_pr_f1_df_from_arrays (line 89) | def get_pr_f1_df_from_arrays( function get_pr_f1_df (line 130) | def get_pr_f1_df( function true_false_positive_negative_df (line 175) | def true_false_positive_negative_df(df): function multilabel_precision_per_example_label_pair (line 220) | def multilabel_precision_per_example_label_pair( function multilabel_recall_per_example_label_pair (line 239) | def multilabel_recall_per_example_label_pair( function multilabel_f1_per_example_label_pair (line 258) | def multilabel_f1_per_example_label_pair( function normalize_predictions (line 278) | def normalize_predictions( function precision_recall_f1 (line 285) | def precision_recall_f1( function filter_predictions_to_above_threshold (line 314) | def filter_predictions_to_above_threshold( function get_predictions_above_threshold (line 341) | def get_predictions_above_threshold( function _family_and_clan_to_just_clan (line 379) | def _family_and_clan_to_just_clan( function pfam_label_normalizer_to_lifted_clan (line 408) | def pfam_label_normalizer_to_lifted_clan( function convert_pfam_ground_truth_to_lifted_clans (line 416) | def convert_pfam_ground_truth_to_lifted_clans( function _ec_label_at_level (line 441) | def _ec_label_at_level(label, level): function ec_agreement_for_level (line 452) | def ec_agreement_for_level(df, FILE: evaluation_test.py class _InferrerFixture (line 32) | class _InferrerFixture(object): method __init__ (line 35) | def __init__(self, vocab_size): method get_activations (line 38) | def get_activations(self, l): method get_variable (line 42) | def get_variable(self, _): class TestEvaluation (line 46) | class TestEvaluation(parameterized.TestCase): method test_normalize_confidences_edge (line 70) | def test_normalize_confidences_edge(self, confidences, vocab, normalized, method test_normalize_confidences (line 76) | def test_normalize_confidences(self): method test_get_ground_truth_multihots (line 96) | def test_get_ground_truth_multihots(self): method test_get_pr_f1_df (line 120) | def test_get_pr_f1_df(self, method test_get_pr_f1_df_precision_truncation (line 144) | def test_get_pr_f1_df_precision_truncation(self): method test_multilabel_recall_per_example_label_pair (line 239) | def test_multilabel_recall_per_example_label_pair(self, df, expected): method test_multilabel_precision_per_example_label_pair (line 318) | def test_multilabel_precision_per_example_label_pair(self, df, expected): method test_multilabel_f1_per_example_label_pair (line 323) | def test_multilabel_f1_per_example_label_pair(self): method test_precision_recall_f1_integration_test (line 334) | def test_precision_recall_f1_integration_test(self): method test_filter_predictions_to_above_threshold (line 398) | def test_filter_predictions_to_above_threshold(self, input_predictions, method test_get_predictions_above_threshold (line 428) | def test_get_predictions_above_threshold(self, input_seqs, decision_th... method test_pfam_label_normalizer_to_lifted_clan (line 474) | def test_pfam_label_normalizer_to_lifted_clan(self, input_normalizer, method test_pfam_label_normalizer_to_lifted_clan_raises_when_wrong_num (line 485) | def test_pfam_label_normalizer_to_lifted_clan_raises_when_wrong_num(se... method test_pfam_label_normalizer_to_lifted_clan_raises_when_no_clan (line 491) | def test_pfam_label_normalizer_to_lifted_clan_raises_when_no_clan(self): method test_convert_pfam_ground_truth_to_lifted_clans (line 498) | def test_convert_pfam_ground_truth_to_lifted_clans(self): method test_ec_agreement_for_level (line 662) | def test_ec_agreement_for_level(self, input_level, input_df, expected_... FILE: hparams_sets.py function _starting_hparams (line 26) | def _starting_hparams(): function tuned_for_ec (line 42) | def tuned_for_ec(): function small_test_model (line 65) | def small_test_model(): FILE: inference.py function call_module (line 41) | def call_module(module, one_hots, row_lengths, signature): function in_graph_inferrer (line 92) | def in_graph_inferrer(sequences, function memoized_inferrer (line 131) | def memoized_inferrer( class Inferrer (line 153) | class Inferrer(object): method __init__ (line 156) | def __init__( method __repr__ (line 220) | def __repr__(self): method _get_tensor_by_name (line 226) | def _get_tensor_by_name(self, name): method _get_activations_for_batch_unmemoized (line 230) | def _get_activations_for_batch_unmemoized(self, method _get_activations_for_batch_memoized (line 263) | def _get_activations_for_batch_memoized(self, method get_activations (line 269) | def get_activations(self, list_of_seqs, custom_tensor_to_retrieve=None): method get_variable (line 323) | def get_variable(self, variable_name): function latest_savedmodel_path_from_base_path (line 336) | def latest_savedmodel_path_from_base_path(base_path): function predictions_for_df (line 354) | def predictions_for_df(df, inferrer): function serialize_inference_result (line 372) | def serialize_inference_result(sequence_name, function deserialize_inference_result (line 403) | def deserialize_inference_result(results_b64): function parse_shard (line 441) | def parse_shard(shard_path): function parse_all_shards (line 459) | def parse_all_shards(shard_dir_path): function get_preds_at_or_above_threshold (line 479) | def get_preds_at_or_above_threshold(input_df, FILE: inference_test.py class _InferrerFixture (line 39) | class _InferrerFixture(object): method __init__ (line 46) | def __init__(self, activation_rank=1): method get_variable (line 55) | def get_variable(self, x): method get_activations (line 62) | def get_activations(self, input_seqs): class InGraphInferrerTest (line 81) | class InGraphInferrerTest(tf.test.TestCase, parameterized.TestCase): method testCanInfer (line 83) | def testCanInfer(self): class InferenceLibTest (line 101) | class InferenceLibTest(parameterized.TestCase, tf.test.TestCase): method testBatchedInference (line 103) | def testBatchedInference(self): method testSortUnsortInference (line 112) | def testSortUnsortInference(self): method testStringInput (line 122) | def testStringInput(self): method testMemoizedInferrerLoading (line 130) | def testMemoizedInferrerLoading(self): method testMemoizedInferenceResults (line 138) | def testMemoizedInferenceResults(self): method testGetVariable (line 146) | def testGetVariable(self): method test_predictions_for_df (line 151) | def test_predictions_for_df(self): method test_serialize_deserialize_inference_result (line 165) | def test_serialize_deserialize_inference_result(self): method test_parse_sharded_inference_results (line 178) | def test_parse_sharded_inference_results(self): method testGetPredsAboveThreshold (line 250) | def testGetPredsAboveThreshold(self, input_df, expected, threshold): method testGetPredsAboveThresholdRaisesOnZeroThreshold (line 258) | def testGetPredsAboveThresholdRaisesOnZeroThreshold(self): FILE: install_models.py function download_models (line 41) | def download_models(model_cache_path, function get_description_file (line 58) | def get_description_file(model_cache_path): function run (line 66) | def run(install_ensemble, model_cache_path): function main (line 83) | def main(_): FILE: parenthood_bin.py function _get_ec_transitive (line 47) | def _get_ec_transitive(): function _get_go_transitive (line 61) | def _get_go_transitive(): function get_output_dict (line 72) | def get_output_dict(): function write_output_dict (line 96) | def write_output_dict(output_dict, output_path): function main (line 113) | def main(_): FILE: parenthood_lib.py class GoTerm (line 143) | class GoTerm( method from_string (line 166) | def from_string(cls, s): function _is_go_attribute_line (line 216) | def _is_go_attribute_line(s): function _parse_go_attribute (line 220) | def _parse_go_attribute(s): function _get_go_term_from_text (line 225) | def _get_go_term_from_text(s): function _yield_terms_for_alt_ids (line 235) | def _yield_terms_for_alt_ids(term): function parse_full_go_file (line 263) | def parse_full_go_file(file_contents = None): function go_label_to_description (line 287) | def go_label_to_description( function _go_term_applicable_labels_should_include_themselves (line 294) | def _go_term_applicable_labels_should_include_themselves(term): function transitive_go_parenthood (line 313) | def transitive_go_parenthood(go_terms): function _transitive_parenthood (line 356) | def _transitive_parenthood(key, function _replace_one_level_up_with_dash_for_ec (line 384) | def _replace_one_level_up_with_dash_for_ec(s): function _all_ec_parents_for_label (line 408) | def _all_ec_parents_for_label(label): function _get_leaf_node_ec_labels_from_file_contents (line 433) | def _get_leaf_node_ec_labels_from_file_contents( function _get_non_leaf_node_ec_labels_from_file_contents (line 473) | def _get_non_leaf_node_ec_labels_from_file_contents( function ec_label_to_description (line 508) | def ec_label_to_description( function parse_full_ec_file_to_transitive_parenthood (line 539) | def parse_full_ec_file_to_transitive_parenthood( function get_applicable_label_dict (line 584) | def get_applicable_label_dict( function reverse_map (line 589) | def reverse_map( function is_implied_by_something_else (line 619) | def is_implied_by_something_else( function _filter_label_set_to_most_specific (line 650) | def _filter_label_set_to_most_specific( function filter_labels_to_most_specific (line 669) | def filter_labels_to_most_specific( FILE: parenthood_lib_test.py class ParenthoodLibTest (line 34) | class ParenthoodLibTest(parameterized.TestCase): method setUp (line 36) | def setUp(self): method test_go_term_from_string (line 125) | def test_go_term_from_string(self, input_text, expected): method test_go_term_parsing_integration_test (line 130) | def test_go_term_parsing_integration_test(self): method test_transitive_go_parenthood (line 148) | def test_transitive_go_parenthood(self): method test_transitive_go_parenthood_with_cycle (line 189) | def test_transitive_go_parenthood_with_cycle(self): method test_all_ec_parents_for_term (line 265) | def test_all_ec_parents_for_term(self, label, expected): method test_parse_full_ec_file_to_transitive_parenthood_integration_test (line 269) | def test_parse_full_ec_file_to_transitive_parenthood_integration_test(... method test_ec_label_to_description (line 315) | def test_ec_label_to_description(self): method test_yield_terms_for_alt_ids (line 442) | def test_yield_terms_for_alt_ids(self, input_go_term, expected): method test_reverse_map_filters_items (line 447) | def test_reverse_map_filters_items(self): method test_is_implied_by_something_else_positive_case (line 454) | def test_is_implied_by_something_else_positive_case(self): method test_is_implied_by_something_else_negative_case (line 466) | def test_is_implied_by_something_else_negative_case(self): method test_filter_labels_to_most_specific (line 477) | def test_filter_labels_to_most_specific(self): FILE: protein_dataset.py function _map_sequence_to_ints (line 57) | def _map_sequence_to_ints(example, amino_acid_table): function _map_labels_to_ints (line 77) | def _map_labels_to_ints(example, protein_class_table): function _to_one_hot_sequence (line 98) | def _to_one_hot_sequence(indexed_sequence_tensors): function _add_sequence_length (line 128) | def _add_sequence_length(example): function _is_sequence_short_enough_for_training (line 133) | def _is_sequence_short_enough_for_training(example): function non_batched_dataset (line 138) | def non_batched_dataset(train_dev_or_test, function batched_dataset (line 192) | def batched_dataset(input_dataset, batch_size, bucket_boundaries): function make_input_fn (line 236) | def make_input_fn(batch_size, data_file_pattern, train_dev_or_test, function yield_examples (line 279) | def yield_examples(tfrecord_path): FILE: protein_dataset_test.py function _numpy_one_hot (line 31) | def _numpy_one_hot(x, depth): function _dataset_iterator_to_list (line 44) | def _dataset_iterator_to_list(itr, session): class ProteinDatasetTest (line 63) | class ProteinDatasetTest(parameterized.TestCase): method test_non_padded_dataset (line 65) | def test_non_padded_dataset(self): method test_padded_dataset (line 125) | def test_padded_dataset(self): method test_yield_examples (line 171) | def test_yield_examples(self): FILE: protein_model.py function _f1_score (line 35) | def _f1_score(labels, predictions): function _mean_examplewise_f1_score (line 44) | def _mean_examplewise_f1_score(labels, predictions): function _custom_recall_at_k (line 79) | def _custom_recall_at_k(labels_as_multi_hot, predictions, k): function _make_evaluation_metrics (line 127) | def _make_evaluation_metrics(labels, predictions, num_output_classes, hp... function _set_padding_to_sentinel (line 174) | def _set_padding_to_sentinel(padded_representations, sequence_lengths, function _make_per_sequence_features (line 216) | def _make_per_sequence_features(per_location_representations, raw_features, function _convert_representation_to_prediction_ops (line 243) | def _convert_representation_to_prediction_ops(representation, raw_features, function _make_representation (line 275) | def _make_representation(features, hparams, mode): function _make_prediction_ops (line 311) | def _make_prediction_ops(features, hparams, mode, label_vocab): function _batch_norm (line 331) | def _batch_norm(features, is_training): function _conv_layer (line 335) | def _conv_layer(sequence_features, sequence_lengths, num_units, dilation... function _residual_block (line 354) | def _residual_block(sequence_features, sequence_lengths, hparams, layer_... function _indices_to_multihot (line 391) | def _indices_to_multihot(indices, vocab_size): function _make_loss (line 421) | def _make_loss(predictions_for_loss, labels, num_output_classes): function _make_train_op (line 435) | def _make_train_op(loss, hparams): function make_model_fn (line 459) | def make_model_fn(label_vocab, hparams): FILE: protein_model_test.py class ProteinModelTest (line 31) | class ProteinModelTest(parameterized.TestCase): method testF1Score (line 33) | def testF1Score(self): method testMeanExampleWiseF1Score (line 47) | def testMeanExampleWiseF1Score(self): method testRecallAtK (line 63) | def testRecallAtK(self): method testSetPaddingToSentinel (line 128) | def testSetPaddingToSentinel(self, padded_representations, sequence_le... method testIndicesToMultiHot (line 148) | def testIndicesToMultiHot(self, input_array, vocab_size, expected): FILE: proteinfer.py function _num_decimal_places (line 77) | def _num_decimal_places(f): function _gcs_path_to_relative_unzipped_path (line 83) | def _gcs_path_to_relative_unzipped_path(p): function _get_inferrer_paths (line 89) | def _get_inferrer_paths(model_urls, function load_models (line 98) | def load_models(model_cache_path, num_ensemble_elements): function _assert_fasta_parsable (line 162) | def _assert_fasta_parsable(input_text): function parse_input_to_text (line 177) | def parse_input_to_text(input_fasta_path): function input_text_to_df (line 197) | def input_text_to_df(input_text): function perform_inference (line 207) | def perform_inference(input_df, models, function _sort_df_multiple_columns (line 235) | def _sort_df_multiple_columns(df, key): function order_df_for_output (line 254) | def order_df_for_output(predictions_df): function _format_float_confidence_for_output (line 305) | def _format_float_confidence_for_output(input_float, function format_df_for_output (line 311) | def format_df_for_output(predictions_df, function write_output (line 338) | def write_output(predictions_df, output_path): function run (line 345) | def run(input_text, models, reporting_threshold, function load_assets_and_run (line 376) | def load_assets_and_run(input_fasta_path, output_path, function main (line 405) | def main(_): FILE: proteinfer_test.py class ProteinferTest (line 26) | class ProteinferTest(parameterized.TestCase): method test_gcs_path_to_relative_unzipped_path (line 28) | def test_gcs_path_to_relative_unzipped_path(self): method test_parse_input (line 34) | def test_parse_input(self): method test_parse_input_malformed_fasta (line 49) | def test_parse_input_malformed_fasta(self): method test_format_output_adds_description_and_formats_float_confidence (line 55) | def test_format_output_adds_description_and_formats_float_confidence(s... method test_format_float_confidence (line 83) | def test_format_float_confidence(self, input_confidence, num_decimal_p... method test_load_models_raises_on_model_missing_no_ensemble (line 89) | def test_load_models_raises_on_model_missing_no_ensemble(self): method test_load_models_raises_on_model_missing_with_ensemble (line 103) | def test_load_models_raises_on_model_missing_with_ensemble(self): method test_order_df_for_output (line 202) | def test_order_df_for_output(self, input_df, expected): FILE: test_util.py function model_testdata_path (line 31) | def model_testdata_path(): function savedmodel_path (line 36) | def savedmodel_path(): function assert_dataframes_equal (line 40) | def assert_dataframes_equal(abseil_testcase_instance, FILE: test_util_test.py class TestUtilTest (line 31) | class TestUtilTest(parameterized.TestCase): method test_assert_dataframes_equal_no_error (line 113) | def test_assert_dataframes_equal_no_error(self, method test_assert_dataframes_equal_error (line 176) | def test_assert_dataframes_equal_error(self, df1, df2, order_by_column... method test_assert_dataframes_equal_nan_equal_nan (line 180) | def test_assert_dataframes_equal_nan_equal_nan(self): method test_assert_dataframes_equal_nan_raises (line 185) | def test_assert_dataframes_equal_nan_raises(self): FILE: train.py function _make_estimator (line 70) | def _make_estimator(hparams, label_vocab, output_dir): function get_serving_input_fn (line 94) | def get_serving_input_fn(): function _make_estimator_and_inputs (line 126) | def _make_estimator_and_inputs(hparams, label_vocab, data_base_path, out... function get_hparams (line 178) | def get_hparams(hparams_set_name): function parse_label_vocab (line 191) | def parse_label_vocab(label_vocab_path): function train (line 216) | def train(data_base_path, output_dir, label_vocab_path, hparams_set_name, function main (line 250) | def main(_): FILE: train_test.py class TrainTest (line 35) | class TrainTest(parameterized.TestCase): method setUp (line 37) | def setUp(self): method test_parse_label_vocab (line 44) | def test_parse_label_vocab(self): method test_train_gives_non_nan_loss (line 55) | def test_train_gives_non_nan_loss(self): FILE: utils.py function residues_to_indices (line 117) | def residues_to_indices(amino_acid_residues): function normalize_sequence_to_blosum_characters (line 121) | def normalize_sequence_to_blosum_characters(seq): function _build_one_hot_encodings (line 138) | def _build_one_hot_encodings(): function residues_to_one_hot (line 169) | def residues_to_one_hot(amino_acid_residues): function fasta_indexer (line 197) | def fasta_indexer(): function fasta_encoder (line 208) | def fasta_encoder(): function in_graph_residues_to_onehot (line 220) | def in_graph_residues_to_onehot(residues): function calculate_bucket_batch_sizes (line 244) | def calculate_bucket_batch_sizes(bucket_boundaries, max_expected_sequenc... function batch_iterable (line 281) | def batch_iterable(iterable, batch_size): function pad_one_hot (line 314) | def pad_one_hot(one_hot, length): function make_padded_np_array (line 323) | def make_padded_np_array(ragged_arrays): function absolute_paths_of_files_in_dir (line 341) | def absolute_paths_of_files_in_dir(dir_path): function load_gz_json (line 346) | def load_gz_json(path): function fetch_oss_pretrained_models (line 352) | def fetch_oss_pretrained_models( FILE: utils_test.py class TestTensorUtils (line 32) | class TestTensorUtils(parameterized.TestCase): method testBucketSize (line 34) | def testBucketSize(self): method testBatchIterable (line 54) | def testBatchIterable(self, input_iterable, batch_size, expected): method testSparseToOneHot (line 59) | def testSparseToOneHot(self): method testPadOneHotSameLength (line 100) | def testPadOneHotSameLength(self, input_one_hot, pad_length, expected): method test_absolute_paths_of_files_in_dir (line 107) | def test_absolute_paths_of_files_in_dir(self):