def main(args): # Initialize Emmental config = parse_args_to_config(args) emmental.init(log_dir=config["meta_config"]["log_path"], config=config) # Log configuration into files cmd_msg = " ".join(sys.argv) logger.info(f"COMMAND: {cmd_msg}") write_to_file(f"{emmental.Meta.log_path}/cmd.txt", cmd_msg) logger.info(f"Config: {emmental.Meta.config}") write_to_file(f"{emmental.Meta.log_path}/config.txt", emmental.Meta.config) # Create dataloaders dataloaders = get_dataloaders(args) # Assign transforms to dataloaders aug_dataloaders = [] if args.augment_policy: for idx in range(len(dataloaders)): if dataloaders[idx].split in args.train_split: dataloaders[idx].dataset.transform_cls = Augmentation( args=args) config["learner_config"]["task_scheduler_config"][ "task_scheduler"] = AugScheduler(augment_k=args.augment_k, enlarge=args.augment_enlarge) emmental.Meta.config["learner_config"]["task_scheduler_config"][ "task_scheduler"] = config["learner_config"]["task_scheduler_config"][ "task_scheduler"] # Create tasks model = EmmentalModel(name=f"{args.task}_task") model.add_task(create_task(args)) # Set cudnn benchmark cudnn.benchmark = True # Load the best model from the pretrained model if config["model_config"]["model_path"] is not None: model.load(config["model_config"]["model_path"]) if args.train: emmental_learner = EmmentalLearner() emmental_learner.learn(model, dataloaders + aug_dataloaders) # Remove all extra augmentation policy for idx in range(len(dataloaders)): dataloaders[idx].dataset.transform_cls = None scores = model.score(dataloaders) # Save metrics and models logger.info(f"Metrics: {scores}") scores["log_path"] = emmental.Meta.log_path write_to_json_file(f"{emmental.Meta.log_path}/metrics.txt", scores) model.save(f"{emmental.Meta.log_path}/last_model.pth")
def main(args): # Initialize Emmental config = parse_args_to_config(args) emmental.init(log_dir=config["meta_config"]["log_path"], config=config) # Log configuration into files cmd_msg = " ".join(sys.argv) logger.info(f"COMMAND: {cmd_msg}") write_to_file(f"{emmental.Meta.log_path}/cmd.txt", cmd_msg) logger.info(f"Config: {emmental.Meta.config}") write_to_file(f"{emmental.Meta.log_path}/config.txt", emmental.Meta.config) # Create dataloaders dataloaders = get_dataloaders(args) config["learner_config"]["task_scheduler_config"][ "task_scheduler"] = AugScheduler(augment_k=args.augment_k, enlarge=args.augment_enlarge) emmental.Meta.config["learner_config"]["task_scheduler_config"][ "task_scheduler"] = config["learner_config"]["task_scheduler_config"][ "task_scheduler"] # Specify parameter group for Adam BERT def grouped_parameters(model): no_decay = ["bias", "LayerNorm.weight"] return [ { "params": [ p for n, p in model.named_parameters() if not any(nd in n for nd in no_decay) ], "weight_decay": emmental.Meta.config["learner_config"]["optimizer_config"] ["l2"], }, { "params": [ p for n, p in model.named_parameters() if any(nd in n for nd in no_decay) ], "weight_decay": 0.0, }, ] emmental.Meta.config["learner_config"]["optimizer_config"][ "parameters"] = grouped_parameters # Create tasks model = EmmentalModel(name=f"{args.task}_task") model.add_task(create_task(args)) # Load the best model from the pretrained model if config["model_config"]["model_path"] is not None: model.load(config["model_config"]["model_path"]) if args.train: emmental_learner = EmmentalLearner() emmental_learner.learn(model, dataloaders) # Remove all extra augmentation policy for idx in range(len(dataloaders)): dataloaders[idx].dataset.transform_cls = None dataloaders[idx].dataset.k = 1 scores = model.score(dataloaders) # Save metrics and models logger.info(f"Metrics: {scores}") scores["log_path"] = emmental.Meta.log_path write_to_json_file(f"{emmental.Meta.log_path}/metrics.txt", scores) model.save(f"{emmental.Meta.log_path}/last_model.pth")
def test_e2e(): """Run an end-to-end test on documents of the hardware domain.""" # GitHub Actions gives 2 cores # help.github.com/en/actions/reference/virtual-environments-for-github-hosted-runners PARALLEL = 2 max_docs = 12 fonduer.init_logging( format="[%(asctime)s][%(levelname)s] %(name)s:%(lineno)s - %(message)s", level=logging.INFO, ) session = fonduer.Meta.init(CONN_STRING).Session() docs_path = "tests/data/html/" pdf_path = "tests/data/pdf/" doc_preprocessor = HTMLDocPreprocessor(docs_path, max_docs=max_docs) corpus_parser = Parser( session, parallelism=PARALLEL, structural=True, lingual=True, visual=True, pdf_path=pdf_path, ) corpus_parser.apply(doc_preprocessor) assert session.query(Document).count() == max_docs num_docs = session.query(Document).count() logger.info(f"Docs: {num_docs}") assert num_docs == max_docs num_sentences = session.query(Sentence).count() logger.info(f"Sentences: {num_sentences}") # Divide into test and train docs = sorted(corpus_parser.get_documents()) last_docs = sorted(corpus_parser.get_last_documents()) ld = len(docs) assert ld == len(last_docs) assert len(docs[0].sentences) == len(last_docs[0].sentences) assert len(docs[0].sentences) == 799 assert len(docs[1].sentences) == 663 assert len(docs[2].sentences) == 784 assert len(docs[3].sentences) == 661 assert len(docs[4].sentences) == 513 assert len(docs[5].sentences) == 700 assert len(docs[6].sentences) == 528 assert len(docs[7].sentences) == 161 assert len(docs[8].sentences) == 228 assert len(docs[9].sentences) == 511 assert len(docs[10].sentences) == 331 assert len(docs[11].sentences) == 528 # Check table numbers assert len(docs[0].tables) == 9 assert len(docs[1].tables) == 9 assert len(docs[2].tables) == 14 assert len(docs[3].tables) == 11 assert len(docs[4].tables) == 11 assert len(docs[5].tables) == 10 assert len(docs[6].tables) == 10 assert len(docs[7].tables) == 2 assert len(docs[8].tables) == 7 assert len(docs[9].tables) == 10 assert len(docs[10].tables) == 6 assert len(docs[11].tables) == 9 # Check figure numbers assert len(docs[0].figures) == 32 assert len(docs[1].figures) == 11 assert len(docs[2].figures) == 38 assert len(docs[3].figures) == 31 assert len(docs[4].figures) == 7 assert len(docs[5].figures) == 38 assert len(docs[6].figures) == 10 assert len(docs[7].figures) == 31 assert len(docs[8].figures) == 4 assert len(docs[9].figures) == 27 assert len(docs[10].figures) == 5 assert len(docs[11].figures) == 27 # Check caption numbers assert len(docs[0].captions) == 0 assert len(docs[1].captions) == 0 assert len(docs[2].captions) == 0 assert len(docs[3].captions) == 0 assert len(docs[4].captions) == 0 assert len(docs[5].captions) == 0 assert len(docs[6].captions) == 0 assert len(docs[7].captions) == 0 assert len(docs[8].captions) == 0 assert len(docs[9].captions) == 0 assert len(docs[10].captions) == 0 assert len(docs[11].captions) == 0 train_docs = set() dev_docs = set() test_docs = set() splits = (0.5, 0.75) data = [(doc.name, doc) for doc in docs] data.sort(key=lambda x: x[0]) for i, (doc_name, doc) in enumerate(data): if i < splits[0] * ld: train_docs.add(doc) elif i < splits[1] * ld: dev_docs.add(doc) else: test_docs.add(doc) logger.info([x.name for x in train_docs]) # NOTE: With multi-relation support, return values of getting candidates, # mentions, or sparse matrices are formatted as a list of lists. This means # that with a single relation, we need to index into the list of lists to # get the candidates/mentions/sparse matrix for a particular relation or # mention. # Mention Extraction part_ngrams = MentionNgramsPart(parts_by_doc=None, n_max=3) temp_ngrams = MentionNgramsTemp(n_max=2) volt_ngrams = MentionNgramsVolt(n_max=1) Part = mention_subclass("Part") Temp = mention_subclass("Temp") Volt = mention_subclass("Volt") mention_extractor = MentionExtractor( session, [Part, Temp, Volt], [part_ngrams, temp_ngrams, volt_ngrams], [part_matcher, temp_matcher, volt_matcher], ) mention_extractor.apply(docs, parallelism=PARALLEL) assert session.query(Part).count() == 299 assert session.query(Temp).count() == 138 assert session.query(Volt).count() == 140 assert len(mention_extractor.get_mentions()) == 3 assert len(mention_extractor.get_mentions()[0]) == 299 assert (len( mention_extractor.get_mentions(docs=[ session.query(Document).filter(Document.name == "112823").first() ])[0]) == 70) # Candidate Extraction PartTemp = candidate_subclass("PartTemp", [Part, Temp]) PartVolt = candidate_subclass("PartVolt", [Part, Volt]) candidate_extractor = CandidateExtractor( session, [PartTemp, PartVolt], throttlers=[temp_throttler, volt_throttler]) for i, docs in enumerate([train_docs, dev_docs, test_docs]): candidate_extractor.apply(docs, split=i, parallelism=PARALLEL) assert session.query(PartTemp).filter(PartTemp.split == 0).count() == 3493 assert session.query(PartTemp).filter(PartTemp.split == 1).count() == 61 assert session.query(PartTemp).filter(PartTemp.split == 2).count() == 416 assert session.query(PartVolt).count() == 4282 # Grab candidate lists train_cands = candidate_extractor.get_candidates(split=0, sort=True) dev_cands = candidate_extractor.get_candidates(split=1, sort=True) test_cands = candidate_extractor.get_candidates(split=2, sort=True) assert len(train_cands) == 2 assert len(train_cands[0]) == 3493 assert (len( candidate_extractor.get_candidates(docs=[ session.query(Document).filter(Document.name == "112823").first() ])[0]) == 1432) # Featurization featurizer = Featurizer(session, [PartTemp, PartVolt]) # Test that FeatureKey is properly reset featurizer.apply(split=1, train=True, parallelism=PARALLEL) assert session.query(Feature).count() == 214 assert session.query(FeatureKey).count() == 1260 # Test Dropping FeatureKey # Should force a row deletion featurizer.drop_keys(["DDL_e1_W_LEFT_POS_3_[NNP NN IN]"]) assert session.query(FeatureKey).count() == 1259 # Should only remove the part_volt as a relation and leave part_temp assert set( session.query(FeatureKey).filter( FeatureKey.name == "DDL_e1_LEMMA_SEQ_[bc182]").one().candidate_classes) == { "part_temp", "part_volt" } featurizer.drop_keys(["DDL_e1_LEMMA_SEQ_[bc182]"], candidate_classes=[PartVolt]) assert session.query(FeatureKey).filter( FeatureKey.name == "DDL_e1_LEMMA_SEQ_[bc182]").one().candidate_classes == ["part_temp"] assert session.query(FeatureKey).count() == 1259 # Inserting the removed key featurizer.upsert_keys(["DDL_e1_LEMMA_SEQ_[bc182]"], candidate_classes=[PartTemp, PartVolt]) assert set( session.query(FeatureKey).filter( FeatureKey.name == "DDL_e1_LEMMA_SEQ_[bc182]").one().candidate_classes) == { "part_temp", "part_volt" } assert session.query(FeatureKey).count() == 1259 # Removing the key again featurizer.drop_keys(["DDL_e1_LEMMA_SEQ_[bc182]"], candidate_classes=[PartVolt]) # Removing the last relation from a key should delete the row featurizer.drop_keys(["DDL_e1_LEMMA_SEQ_[bc182]"], candidate_classes=[PartTemp]) assert session.query(FeatureKey).count() == 1258 session.query(Feature).delete(synchronize_session="fetch") session.query(FeatureKey).delete(synchronize_session="fetch") featurizer.apply(split=0, train=True, parallelism=PARALLEL) assert session.query(Feature).count() == 6478 assert session.query(FeatureKey).count() == 4538 F_train = featurizer.get_feature_matrices(train_cands) assert F_train[0].shape == (3493, 4538) assert F_train[1].shape == (2985, 4538) assert len(featurizer.get_keys()) == 4538 featurizer.apply(split=1, parallelism=PARALLEL) assert session.query(Feature).count() == 6692 assert session.query(FeatureKey).count() == 4538 F_dev = featurizer.get_feature_matrices(dev_cands) assert F_dev[0].shape == (61, 4538) assert F_dev[1].shape == (153, 4538) featurizer.apply(split=2, parallelism=PARALLEL) assert session.query(Feature).count() == 8252 assert session.query(FeatureKey).count() == 4538 F_test = featurizer.get_feature_matrices(test_cands) assert F_test[0].shape == (416, 4538) assert F_test[1].shape == (1144, 4538) gold_file = "tests/data/hardware_tutorial_gold.csv" labeler = Labeler(session, [PartTemp, PartVolt]) labeler.apply( docs=last_docs, lfs=[[gold], [gold]], table=GoldLabel, train=True, parallelism=PARALLEL, ) assert session.query(GoldLabel).count() == 8252 stg_temp_lfs = [ LF_storage_row, LF_operating_row, LF_temperature_row, LF_tstg_row, LF_to_left, LF_negative_number_left, ] ce_v_max_lfs = [ LF_bad_keywords_in_row, LF_current_in_row, LF_non_ce_voltages_in_row, ] with pytest.raises(ValueError): labeler.apply(split=0, lfs=stg_temp_lfs, train=True, parallelism=PARALLEL) labeler.apply( docs=train_docs, lfs=[stg_temp_lfs, ce_v_max_lfs], train=True, parallelism=PARALLEL, ) assert session.query(Label).count() == 6478 assert session.query(LabelKey).count() == 9 L_train = labeler.get_label_matrices(train_cands) assert L_train[0].shape == (3493, 9) assert L_train[1].shape == (2985, 9) assert len(labeler.get_keys()) == 9 # Test Dropping LabelerKey labeler.drop_keys(["LF_storage_row"]) assert len(labeler.get_keys()) == 8 # Test Upserting LabelerKey labeler.upsert_keys(["LF_storage_row"]) assert "LF_storage_row" in [label.name for label in labeler.get_keys()] L_train_gold = labeler.get_gold_labels(train_cands) assert L_train_gold[0].shape == (3493, 1) L_train_gold = labeler.get_gold_labels(train_cands, annotator="gold") assert L_train_gold[0].shape == (3493, 1) label_model = LabelModel() label_model.fit(L_train=L_train[0], n_epochs=500, log_freq=100) train_marginals = label_model.predict_proba(L_train[0]) # Collect word counter word_counter = collect_word_counter(train_cands) emmental.init(fonduer.Meta.log_path) # Training config config = { "meta_config": { "verbose": False }, "model_config": { "model_path": None, "device": 0, "dataparallel": False }, "learner_config": { "n_epochs": 5, "optimizer_config": { "lr": 0.001, "l2": 0.0 }, "task_scheduler": "round_robin", }, "logging_config": { "evaluation_freq": 1, "counter_unit": "epoch", "checkpointing": False, "checkpointer_config": { "checkpoint_metric": { f"{ATTRIBUTE}/{ATTRIBUTE}/train/loss": "min" }, "checkpoint_freq": 1, "checkpoint_runway": 2, "clear_intermediate_checkpoints": True, "clear_all_checkpoints": True, }, }, } emmental.Meta.update_config(config=config) # Generate word embedding module arity = 2 # Geneate special tokens specials = [] for i in range(arity): specials += [f"~~[[{i}", f"{i}]]~~"] emb_layer = EmbeddingModule(word_counter=word_counter, word_dim=300, specials=specials) diffs = train_marginals.max(axis=1) - train_marginals.min(axis=1) train_idxs = np.where(diffs > 1e-6)[0] train_dataloader = EmmentalDataLoader( task_to_label_dict={ATTRIBUTE: "labels"}, dataset=FonduerDataset( ATTRIBUTE, train_cands[0], F_train[0], emb_layer.word2id, train_marginals, train_idxs, ), split="train", batch_size=100, shuffle=True, ) tasks = create_task(ATTRIBUTE, 2, F_train[0].shape[1], 2, emb_layer, model="LogisticRegression") model = EmmentalModel(name=f"{ATTRIBUTE}_task") for task in tasks: model.add_task(task) emmental_learner = EmmentalLearner() emmental_learner.learn(model, [train_dataloader]) test_dataloader = EmmentalDataLoader( task_to_label_dict={ATTRIBUTE: "labels"}, dataset=FonduerDataset(ATTRIBUTE, test_cands[0], F_test[0], emb_layer.word2id, 2), split="test", batch_size=100, shuffle=False, ) test_preds = model.predict(test_dataloader, return_preds=True) positive = np.where( np.array(test_preds["probs"][ATTRIBUTE])[:, TRUE] > 0.6) true_pred = [test_cands[0][_] for _ in positive[0]] pickle_file = "tests/data/parts_by_doc_dict.pkl" with open(pickle_file, "rb") as f: parts_by_doc = pickle.load(f) (TP, FP, FN) = entity_level_f1(true_pred, gold_file, ATTRIBUTE, test_docs, parts_by_doc=parts_by_doc) tp_len = len(TP) fp_len = len(FP) fn_len = len(FN) prec = tp_len / (tp_len + fp_len) if tp_len + fp_len > 0 else float("nan") rec = tp_len / (tp_len + fn_len) if tp_len + fn_len > 0 else float("nan") f1 = 2 * (prec * rec) / (prec + rec) if prec + rec > 0 else float("nan") logger.info(f"prec: {prec}") logger.info(f"rec: {rec}") logger.info(f"f1: {f1}") assert f1 < 0.7 and f1 > 0.3 stg_temp_lfs_2 = [ LF_to_left, LF_test_condition_aligned, LF_collector_aligned, LF_current_aligned, LF_voltage_row_temp, LF_voltage_row_part, LF_typ_row, LF_complement_left_row, LF_too_many_numbers_row, LF_temp_on_high_page_num, LF_temp_outside_table, LF_not_temp_relevant, ] labeler.update(split=0, lfs=[stg_temp_lfs_2, ce_v_max_lfs], parallelism=PARALLEL) assert session.query(Label).count() == 6478 assert session.query(LabelKey).count() == 16 L_train = labeler.get_label_matrices(train_cands) assert L_train[0].shape == (3493, 16) label_model = LabelModel() label_model.fit(L_train=L_train[0], n_epochs=500, log_freq=100) train_marginals = label_model.predict_proba(L_train[0]) diffs = train_marginals.max(axis=1) - train_marginals.min(axis=1) train_idxs = np.where(diffs > 1e-6)[0] train_dataloader = EmmentalDataLoader( task_to_label_dict={ATTRIBUTE: "labels"}, dataset=FonduerDataset( ATTRIBUTE, train_cands[0], F_train[0], emb_layer.word2id, train_marginals, train_idxs, ), split="train", batch_size=100, shuffle=True, ) valid_dataloader = EmmentalDataLoader( task_to_label_dict={ATTRIBUTE: "labels"}, dataset=FonduerDataset( ATTRIBUTE, train_cands[0], F_train[0], emb_layer.word2id, np.argmax(train_marginals, axis=1), train_idxs, ), split="valid", batch_size=100, shuffle=False, ) emmental.Meta.reset() emmental.init(fonduer.Meta.log_path) emmental.Meta.update_config(config=config) tasks = create_task(ATTRIBUTE, 2, F_train[0].shape[1], 2, emb_layer, model="LogisticRegression") model = EmmentalModel(name=f"{ATTRIBUTE}_task") for task in tasks: model.add_task(task) emmental_learner = EmmentalLearner() emmental_learner.learn(model, [train_dataloader, valid_dataloader]) test_preds = model.predict(test_dataloader, return_preds=True) positive = np.where( np.array(test_preds["probs"][ATTRIBUTE])[:, TRUE] > 0.7) true_pred = [test_cands[0][_] for _ in positive[0]] (TP, FP, FN) = entity_level_f1(true_pred, gold_file, ATTRIBUTE, test_docs, parts_by_doc=parts_by_doc) tp_len = len(TP) fp_len = len(FP) fn_len = len(FN) prec = tp_len / (tp_len + fp_len) if tp_len + fp_len > 0 else float("nan") rec = tp_len / (tp_len + fn_len) if tp_len + fn_len > 0 else float("nan") f1 = 2 * (prec * rec) / (prec + rec) if prec + rec > 0 else float("nan") logger.info(f"prec: {prec}") logger.info(f"rec: {rec}") logger.info(f"f1: {f1}") assert f1 > 0.7 # Testing LSTM emmental.Meta.reset() emmental.init(fonduer.Meta.log_path) emmental.Meta.update_config(config=config) tasks = create_task(ATTRIBUTE, 2, F_train[0].shape[1], 2, emb_layer, model="LSTM") model = EmmentalModel(name=f"{ATTRIBUTE}_task") for task in tasks: model.add_task(task) emmental_learner = EmmentalLearner() emmental_learner.learn(model, [train_dataloader]) test_preds = model.predict(test_dataloader, return_preds=True) positive = np.where( np.array(test_preds["probs"][ATTRIBUTE])[:, TRUE] > 0.7) true_pred = [test_cands[0][_] for _ in positive[0]] (TP, FP, FN) = entity_level_f1(true_pred, gold_file, ATTRIBUTE, test_docs, parts_by_doc=parts_by_doc) tp_len = len(TP) fp_len = len(FP) fn_len = len(FN) prec = tp_len / (tp_len + fp_len) if tp_len + fp_len > 0 else float("nan") rec = tp_len / (tp_len + fn_len) if tp_len + fn_len > 0 else float("nan") f1 = 2 * (prec * rec) / (prec + rec) if prec + rec > 0 else float("nan") logger.info(f"prec: {prec}") logger.info(f"rec: {rec}") logger.info(f"f1: {f1}") assert f1 > 0.7
) tasks = { task_name: create_task( task_name, args, datasets[task_name]["nclasses"], emb_layer ) for task_name in args.task } model = EmmentalModel(name="TC_task") if Meta.config["model_config"]["model_path"]: model.load(Meta.config["model_config"]["model_path"]) else: for task_name, task in tasks.items(): model.add_task(task) emmental_learner = EmmentalLearner() emmental_learner.learn(model, dataloaders) scores = model.score(dataloaders) logger.info(f"Metrics: {scores}") write_to_json_file(f"{Meta.log_path}/metrics.txt", scores) if args.checkpointing: logger.info( f"Best metrics: " f"{emmental_learner.logging_manager.checkpointer.best_metric_dict}" ) write_to_file( f"{Meta.log_path}/best_metrics.txt",
split=split, batch_size=args.batch_size, shuffle=True if split == "train" else False, ) ) logger.info(f"Built dataloader for {task_name} {split} set.") tasks = get_gule_task(args.task, args.bert_model) mtl_model = EmmentalModel(name="GLUE_multi_task") if Meta.config["model_config"]["model_path"]: mtl_model.load(Meta.config["model_config"]["model_path"]) else: for task_name, task in tasks.items(): mtl_model.add_task(task) emmental_learner = EmmentalLearner() emmental_learner.learn(mtl_model, dataloaders) scores = mtl_model.score(dataloaders) logger.info(f"Metrics: {scores}") write_to_file("metrics.txt", scores) logger.info( f"Best metrics: " f"{emmental_learner.logging_manager.checkpointer.best_metric_dict}" ) write_to_file( "best_metrics.txt", emmental_learner.logging_manager.checkpointer.best_metric_dict,
def test_model(caplog): """Unit test of model.""" caplog.set_level(logging.INFO) dirpath = "temp_test_model" Meta.reset() emmental.init(dirpath) def ce_loss(module_name, immediate_output_dict, Y, active): return F.cross_entropy(immediate_output_dict[module_name][0][active], (Y.view(-1))[active]) def output(module_name, immediate_output_dict): return F.softmax(immediate_output_dict[module_name][0], dim=1) task1 = EmmentalTask( name="task_1", module_pool=nn.ModuleDict({ "m1": nn.Linear(10, 10, bias=False), "m2": nn.Linear(10, 2, bias=False) }), task_flow=[ { "name": "m1", "module": "m1", "inputs": [("_input_", "data")] }, { "name": "m2", "module": "m2", "inputs": [("m1", 0)] }, ], loss_func=partial(ce_loss, "m2"), output_func=partial(output, "m2"), scorer=Scorer(metrics=["accuracy"]), ) new_task1 = EmmentalTask( name="task_1", module_pool=nn.ModuleDict({ "m1": nn.Linear(10, 5, bias=False), "m2": nn.Linear(5, 2, bias=False) }), task_flow=[ { "name": "m1", "module": "m1", "inputs": [("_input_", "data")] }, { "name": "m2", "module": "m2", "inputs": [("m1", 0)] }, ], loss_func=partial(ce_loss, "m2"), output_func=partial(output, "m2"), scorer=Scorer(metrics=["accuracy"]), ) task2 = EmmentalTask( name="task_2", module_pool=nn.ModuleDict({ "m1": nn.Linear(10, 5, bias=False), "m2": nn.Linear(5, 2, bias=False) }), task_flow=[ { "name": "m1", "module": "m1", "inputs": [("_input_", "data")] }, { "name": "m2", "module": "m2", "inputs": [("m1", 0)] }, ], loss_func=partial(ce_loss, "m2"), output_func=partial(output, "m2"), scorer=Scorer(metrics=["accuracy"]), ) config = {"model_config": {"dataparallel": False}} emmental.Meta.update_config(config) model = EmmentalModel(name="test", tasks=task1) assert repr(model) == "EmmentalModel(name=test)" assert model.name == "test" assert model.task_names == set(["task_1"]) assert model.module_pool["m1"].weight.data.size() == (10, 10) assert model.module_pool["m2"].weight.data.size() == (2, 10) model.update_task(new_task1) assert model.module_pool["m1"].weight.data.size() == (5, 10) assert model.module_pool["m2"].weight.data.size() == (2, 5) model.update_task(task2) assert model.task_names == set(["task_1"]) model.add_task(task2) assert model.task_names == set(["task_1", "task_2"]) model.remove_task("task_1") assert model.task_names == set(["task_2"]) model.remove_task("task_1") assert model.task_names == set(["task_2"]) model.save(f"{dirpath}/saved_model.pth") model.load(f"{dirpath}/saved_model.pth") # Test add_tasks model = EmmentalModel(name="test") model.add_tasks([task1, task2]) assert model.task_names == set(["task_1", "task_2"]) shutil.rmtree(dirpath)
def train_model(cands, F, align_type, model_type="LogisticRegression"): # Extract candidates and features based on the align type (row/column) align_val = 0 if align_type == "row" else 1 train_cands = cands[align_val][0] F_train = F[align_val][0] train_marginals = np.array([[0, 1] if gold[align_val](x) else [1, 0] for x in train_cands[0]]) # 1.) Setup training config config = { "meta_config": { "verbose": True }, "model_config": { "model_path": None, "device": 0, "dataparallel": False }, "learner_config": { "n_epochs": 50, "optimizer_config": { "lr": 0.001, "l2": 0.0 }, "task_scheduler": "round_robin", }, "logging_config": { "evaluation_freq": 1, "counter_unit": "epoch", "checkpointing": False, "checkpointer_config": { "checkpoint_metric": { f"{ATTRIBUTE}/{ATTRIBUTE}/train/loss": "min" }, "checkpoint_freq": 1, "checkpoint_runway": 2, "clear_intermediate_checkpoints": True, "clear_all_checkpoints": True, }, }, } emmental.init(Meta.log_path) emmental.Meta.update_config(config=config) # 2.) Collect word counter from training data word_counter = collect_word_counter(train_cands) # 3.) Generate word embedding module for LSTM model # (in Logistic Regression, we generate it since Fonduer dataset requires word2id dict) # Geneate special tokens arity = 2 specials = [] for i in range(arity): specials += [f"~~[[{i}", f"{i}]]~~"] emb_layer = EmbeddingModule(word_counter=word_counter, word_dim=300, specials=specials) # 4.) Generate dataloader for training set # No noise in Gold labels train_dataloader = EmmentalDataLoader( task_to_label_dict={ATTRIBUTE: "labels"}, dataset=FonduerDataset( ATTRIBUTE, train_cands[0], F_train[0], emb_layer.word2id, train_marginals, ), split="train", batch_size=100, shuffle=True, ) # 5.) Training tasks = create_task( ATTRIBUTE, 2, F_train[0].shape[1], 2, emb_layer, model=model_type # "LSTM" ) model = EmmentalModel(name=f"{ATTRIBUTE}_task") for task in tasks: model.add_task(task) emmental_learner = EmmentalLearner() emmental_learner.learn(model, [train_dataloader]) return (model, emb_layer)
def main( conn_string, gain=False, current=False, max_docs=float("inf"), parse=False, first_time=False, re_label=False, parallel=8, log_dir="logs", verbose=False, ): # Setup initial configuration if not log_dir: log_dir = "logs" if verbose: level = logging.INFO else: level = logging.WARNING dirname = os.path.dirname(os.path.abspath(__file__)) init_logging(log_dir=os.path.join(dirname, log_dir), level=level) rel_list = [] if gain: rel_list.append("gain") if current: rel_list.append("current") logger.info(f"=" * 30) logger.info(f"Running with parallel: {parallel}, max_docs: {max_docs}") session = Meta.init(conn_string).Session() # Parsing start = timer() logger.info(f"Starting parsing...") docs, train_docs, dev_docs, test_docs = parse_dataset(session, dirname, first_time=parse, parallel=parallel, max_docs=max_docs) logger.debug(f"Done") end = timer() logger.warning(f"Parse Time (min): {((end - start) / 60.0):.1f}") logger.info(f"# of Documents: {len(docs)}") logger.info(f"# of train Documents: {len(train_docs)}") logger.info(f"# of dev Documents: {len(dev_docs)}") logger.info(f"# of test Documents: {len(test_docs)}") logger.info(f"Documents: {session.query(Document).count()}") logger.info(f"Sections: {session.query(Section).count()}") logger.info(f"Paragraphs: {session.query(Paragraph).count()}") logger.info(f"Sentences: {session.query(Sentence).count()}") logger.info(f"Figures: {session.query(Figure).count()}") # Mention Extraction start = timer() mentions = [] ngrams = [] matchers = [] # Only do those that are enabled if gain: Gain = mention_subclass("Gain") gain_matcher = get_gain_matcher() gain_ngrams = MentionNgrams(n_max=2) mentions.append(Gain) ngrams.append(gain_ngrams) matchers.append(gain_matcher) if current: Current = mention_subclass("SupplyCurrent") current_matcher = get_supply_current_matcher() current_ngrams = MentionNgramsCurrent(n_max=3) mentions.append(Current) ngrams.append(current_ngrams) matchers.append(current_matcher) mention_extractor = MentionExtractor(session, mentions, ngrams, matchers) if first_time: mention_extractor.apply(docs, parallelism=parallel) logger.info(f"Total Mentions: {session.query(Mention).count()}") if gain: logger.info(f"Total Gain: {session.query(Gain).count()}") if current: logger.info(f"Total Current: {session.query(Current).count()}") cand_classes = [] if gain: GainCand = candidate_subclass("GainCand", [Gain]) cand_classes.append(GainCand) if current: CurrentCand = candidate_subclass("CurrentCand", [Current]) cand_classes.append(CurrentCand) candidate_extractor = CandidateExtractor(session, cand_classes) if first_time: for i, docs in enumerate([train_docs, dev_docs, test_docs]): candidate_extractor.apply(docs, split=i, parallelism=parallel) # These must be sorted for deterministic behavior. train_cands = candidate_extractor.get_candidates(split=0, sort=True) dev_cands = candidate_extractor.get_candidates(split=1, sort=True) test_cands = candidate_extractor.get_candidates(split=2, sort=True) logger.info( f"Total train candidate: {len(train_cands[0]) + len(train_cands[1])}") logger.info( f"Total dev candidate: {len(dev_cands[0]) + len(dev_cands[1])}") logger.info( f"Total test candidate: {len(test_cands[0]) + len(test_cands[1])}") logger.info("Done w/ candidate extraction.") end = timer() logger.warning(f"CE Time (min): {((end - start) / 60.0):.1f}") # First, check total recall # result = entity_level_scores( # candidates_to_entities(dev_cands[0], is_gain=True), # corpus=dev_docs, # is_gain=True, # ) # logger.info(f"Gain Total Dev Recall: {result.rec:.3f}") # logger.info(f"\n{pformat(result.FN)}") # result = entity_level_scores( # candidates_to_entities(test_cands[0], is_gain=True), # corpus=test_docs, # is_gain=True, # ) # logger.info(f"Gain Total Test Recall: {result.rec:.3f}") # logger.info(f"\n{pformat(result.FN)}") # # result = entity_level_scores( # candidates_to_entities(dev_cands[1], is_gain=False), # corpus=dev_docs, # is_gain=False, # ) # logger.info(f"Current Total Dev Recall: {result.rec:.3f}") # logger.info(f"\n{pformat(result.FN)}") # result = entity_level_scores( # candidates_to_entities(test_cands[1], is_gain=False), # corpus=test_docs, # is_gain=False, # ) # logger.info(f"Current Test Recall: {result.rec:.3f}") # logger.info(f"\n{pformat(result.FN)}") start = timer() # Using parallelism = 1 for deterministic behavior. featurizer = Featurizer(session, cand_classes, parallelism=1) if first_time: logger.info("Starting featurizer...") # Set feature space based on dev set, which we use for training rather # than the large train set. featurizer.apply(split=1, train=True) featurizer.apply(split=0) featurizer.apply(split=2) logger.info("Done") logger.info("Getting feature matrices...") # Serialize feature matrices on first run if first_time: F_train = featurizer.get_feature_matrices(train_cands) F_dev = featurizer.get_feature_matrices(dev_cands) F_test = featurizer.get_feature_matrices(test_cands) end = timer() logger.warning( f"Featurization Time (min): {((end - start) / 60.0):.1f}") F_train_dict = {} F_dev_dict = {} F_test_dict = {} for idx, relation in enumerate(rel_list): F_train_dict[relation] = F_train[idx] F_dev_dict[relation] = F_dev[idx] F_test_dict[relation] = F_test[idx] pickle.dump(F_train_dict, open(os.path.join(dirname, "F_train_dict.pkl"), "wb")) pickle.dump(F_dev_dict, open(os.path.join(dirname, "F_dev_dict.pkl"), "wb")) pickle.dump(F_test_dict, open(os.path.join(dirname, "F_test_dict.pkl"), "wb")) else: F_train_dict = pickle.load( open(os.path.join(dirname, "F_train_dict.pkl"), "rb")) F_dev_dict = pickle.load( open(os.path.join(dirname, "F_dev_dict.pkl"), "rb")) F_test_dict = pickle.load( open(os.path.join(dirname, "F_test_dict.pkl"), "rb")) F_train = [] F_dev = [] F_test = [] for relation in rel_list: F_train.append(F_train_dict[relation]) F_dev.append(F_dev_dict[relation]) F_test.append(F_test_dict[relation]) logger.info("Done.") start = timer() logger.info("Labeling training data...") # labeler = Labeler(session, cand_classes) # lfs = [] # if gain: # lfs.append(gain_lfs) # # if current: # lfs.append(current_lfs) # # if first_time: # logger.info("Applying LFs...") # labeler.apply(split=0, lfs=lfs, train=True, parallelism=parallel) # elif re_label: # logger.info("Re-applying LFs...") # labeler.update(split=0, lfs=lfs, parallelism=parallel) # # logger.info("Done...") # logger.info("Getting label matrices...") # L_train = labeler.get_label_matrices(train_cands) # logger.info("Done...") if first_time: marginals_dict = {} for idx, relation in enumerate(rel_list): # Manually create marginals from human annotations marginal = [] dev_gold_entities = get_gold_set(is_gain=(relation == "gain")) for c in dev_cands[idx]: flag = False for entity in cand_to_entity(c, is_gain=(relation == "gain")): if entity in dev_gold_entities: flag = True if flag: marginal.append([0.0, 1.0]) else: marginal.append([1.0, 0.0]) marginals_dict[relation] = np.array(marginal) pickle.dump(marginals_dict, open(os.path.join(dirname, "marginals_dict.pkl"), "wb")) else: marginals_dict = pickle.load( open(os.path.join(dirname, "marginals_dict.pkl"), "rb")) marginals = [] for relation in rel_list: marginals.append(marginals_dict[relation]) end = timer() logger.warning( f"Weak Supervision Time (min): {((end - start) / 60.0):.1f}") start = timer() word_counter = collect_word_counter(train_cands) # Training config config = { "meta_config": { "verbose": True, "seed": 30 }, "model_config": { "model_path": None, "device": 0, "dataparallel": False }, "learner_config": { "n_epochs": 500, "optimizer_config": { "lr": 0.001, "l2": 0.005 }, "task_scheduler": "round_robin", }, "logging_config": { "evaluation_freq": 1, "counter_unit": "epoch", "checkpointing": False, "checkpointer_config": { "checkpoint_metric": { "model/all/train/loss": "min" }, "checkpoint_freq": 1, "checkpoint_runway": 2, "clear_intermediate_checkpoints": True, "clear_all_checkpoints": True, }, }, } emmental.init(log_dir=Meta.log_path, config=config) # Generate word embedding module arity = 2 # Geneate special tokens specials = [] for i in range(arity): specials += [f"~~[[{i}", f"{i}]]~~"] emb_layer = EmbeddingModule(word_counter=word_counter, word_dim=300, specials=specials) train_idxs = [] train_dataloader = [] for idx, relation in enumerate(rel_list): diffs = marginals[idx].max(axis=1) - marginals[idx].min(axis=1) train_idxs.append(np.where(diffs > 1e-6)[0]) # only uses dev set as training data, with human annotations train_dataloader.append( EmmentalDataLoader( task_to_label_dict={relation: "labels"}, dataset=FonduerDataset( relation, dev_cands[idx], F_dev[idx], emb_layer.word2id, marginals[idx], train_idxs[idx], ), split="train", batch_size=256, shuffle=True, )) num_feature_keys = len(featurizer.get_keys()) model = EmmentalModel(name=f"opamp_tasks") # List relation names, arities, list of classes tasks = create_task( rel_list, [2] * len(rel_list), num_feature_keys, [2] * len(rel_list), emb_layer, model="LogisticRegression", ) for task in tasks: model.add_task(task) emmental_learner = EmmentalLearner() # If given a list of multi, will train on multiple emmental_learner.learn(model, train_dataloader) # List of dataloader for each relation for idx, relation in enumerate(rel_list): test_dataloader = EmmentalDataLoader( task_to_label_dict={relation: "labels"}, dataset=FonduerDataset(relation, test_cands[idx], F_test[idx], emb_layer.word2id, 2), split="test", batch_size=256, shuffle=False, ) test_preds = model.predict(test_dataloader, return_preds=True) best_result, best_b = scoring( test_preds, test_cands[idx], test_docs, is_gain=(relation == "gain"), num=100, ) # Dump CSV files for analysis if relation == "gain": train_dataloader = EmmentalDataLoader( task_to_label_dict={relation: "labels"}, dataset=FonduerDataset(relation, train_cands[idx], F_train[idx], emb_layer.word2id, 2), split="train", batch_size=256, shuffle=False, ) train_preds = model.predict(train_dataloader, return_preds=True) Y_prob = np.array(train_preds["probs"][relation])[:, TRUE] output_csv(train_cands[idx], Y_prob, is_gain=True) Y_prob = np.array(test_preds["probs"][relation])[:, TRUE] output_csv(test_cands[idx], Y_prob, is_gain=True, append=True) dump_candidates(test_cands[idx], Y_prob, "gain_test_probs.csv", is_gain=True) dev_dataloader = EmmentalDataLoader( task_to_label_dict={relation: "labels"}, dataset=FonduerDataset(relation, dev_cands[idx], F_dev[idx], emb_layer.word2id, 2), split="dev", batch_size=256, shuffle=False, ) dev_preds = model.predict(dev_dataloader, return_preds=True) Y_prob = np.array(dev_preds["probs"][relation])[:, TRUE] output_csv(dev_cands[idx], Y_prob, is_gain=True, append=True) dump_candidates(dev_cands[idx], Y_prob, "gain_dev_probs.csv", is_gain=True) if relation == "current": train_dataloader = EmmentalDataLoader( task_to_label_dict={relation: "labels"}, dataset=FonduerDataset(relation, train_cands[idx], F_train[idx], emb_layer.word2id, 2), split="train", batch_size=256, shuffle=False, ) train_preds = model.predict(train_dataloader, return_preds=True) Y_prob = np.array(train_preds["probs"][relation])[:, TRUE] output_csv(train_cands[idx], Y_prob, is_gain=False) Y_prob = np.array(test_preds["probs"][relation])[:, TRUE] output_csv(test_cands[idx], Y_prob, is_gain=False, append=True) dump_candidates(test_cands[idx], Y_prob, "current_test_probs.csv", is_gain=False) dev_dataloader = EmmentalDataLoader( task_to_label_dict={relation: "labels"}, dataset=FonduerDataset(relation, dev_cands[idx], F_dev[idx], emb_layer.word2id, 2), split="dev", batch_size=256, shuffle=False, ) dev_preds = model.predict(dev_dataloader, return_preds=True) Y_prob = np.array(dev_preds["probs"][relation])[:, TRUE] output_csv(dev_cands[idx], Y_prob, is_gain=False, append=True) dump_candidates(dev_cands[idx], Y_prob, "current_dev_probs.csv", is_gain=False) end = timer() logger.warning( f"Classification AND dump data Time (min): {((end - start) / 60.0):.1f}" )
{ "params": [ p for n, p in model.named_parameters() if any(nd in n for nd in no_decay) ], "weight_decay": 0.0, }, ] emmental.Meta.config["learner_config"]["optimizer_config"][ "parameters"] = grouped_parameters # Create tasks model = EmmentalModel(name="TACRED_task") model.add_task(create_task(args)) # Load the best model from the pretrained model if config["model_config"]["model_path"] is not None: model.load(config["model_config"]["model_path"]) if args.train: emmental_learner = EmmentalLearner() emmental_learner.learn(model, dataloaders) # Remove all extra augmentation policy for idx in range(len(dataloaders)): dataloaders[idx].dataset.transform_cls = None scores = model.score(dataloaders)
class BootlegAnnotator(object): """BootlegAnnotator class: convenient wrapper of preprocessing and model eval to allow for annotating single sentences at a time for quick experimentation, e.g. in notebooks. Args: config: model config (default None) device: model device, -1 for CPU (default None) max_alias_len: maximum alias length (default 6) cand_map: alias candidate map (default None) threshold: probability threshold (default 0.0) cache_dir: cache directory (default None) model_name: model name (default None) verbose: verbose boolean (default False) """ def __init__( self, config=None, device=None, max_alias_len=6, cand_map=None, threshold=0.0, cache_dir=None, model_name=None, verbose=False, ): self.max_alias_len = ( max_alias_len # minimum probability of prediction to return mention ) self.verbose = verbose self.threshold = threshold if not cache_dir: self.cache_dir = get_default_cache() self.model_path = self.cache_dir / "models" self.data_path = self.cache_dir / "data" else: self.cache_dir = Path(cache_dir) self.model_path = self.cache_dir / "models" self.data_path = self.cache_dir / "data" if not model_name: model_name = "bootleg_uncased" assert model_name in { "bootleg_cased", "bootleg_cased_mini", "bootleg_uncased", "bootleg_uncased_mini", }, (f"model_name must be one of [bootleg_cased, bootleg_cased_mini, " f"bootleg_uncased_mini, bootleg_uncased]. You have {model_name}.") if not config: self.cache_dir.mkdir(parents=True, exist_ok=True) self.model_path.mkdir(parents=True, exist_ok=True) self.data_path.mkdir(parents=True, exist_ok=True) create_sources(self.model_path, self.data_path, model_name) self.config = create_config(self.model_path, self.data_path, model_name) else: if "emmental" in config: config = parse_boot_and_emm_args(config) self.config = config # Ensure some of the critical annotator args are the correct type self.config.data_config.max_aliases = int( self.config.data_config.max_aliases) self.config.run_config.eval_batch_size = int( self.config.run_config.eval_batch_size) self.config.data_config.max_seq_len = int( self.config.data_config.max_seq_len) self.config.data_config.train_in_candidates = bool( self.config.data_config.train_in_candidates) if not device: device = 0 if torch.cuda.is_available() else -1 if self.verbose: self.config.run_config.log_level = "DEBUG" else: self.config.run_config.log_level = "INFO" self.torch_device = (torch.device(device) if device != -1 else torch.device("cpu")) self.config.model_config.device = device log_level = logging.getLevelName( self.config["run_config"]["log_level"].upper()) emmental.init( log_dir=self.config["meta_config"]["log_path"], config=self.config, use_exact_log_path=self.config["meta_config"] ["use_exact_log_path"], level=log_level, ) logger.debug("Reading entity database") self.entity_db = EntitySymbols.load_from_cache( os.path.join( self.config.data_config.entity_dir, self.config.data_config.entity_map_dir, ), alias_cand_map_file=self.config.data_config.alias_cand_map, alias_idx_file=self.config.data_config.alias_idx_map, ) logger.debug("Reading word tokenizers") self.tokenizer = BertTokenizer.from_pretrained( self.config.data_config.word_embedding.bert_model, do_lower_case=True if "uncased" in self.config.data_config.word_embedding.bert_model else False, cache_dir=self.config.data_config.word_embedding.cache_dir, ) # Create tasks tasks = [NED_TASK] if self.config.data_config.type_prediction.use_type_pred is True: tasks.append(TYPE_PRED_TASK) self.task_to_label_dict = {t: NED_TASK_TO_LABEL[t] for t in tasks} # Create tasks self.model = EmmentalModel(name="Bootleg") self.model.add_task(ned_task.create_task(self.config, self.entity_db)) if TYPE_PRED_TASK in tasks: self.model.add_task( type_pred_task.create_task(self.config, self.entity_db)) # Add the mention type embedding to the embedding payload type_pred_task.update_ned_task(self.model) logger.debug("Loading model") # Load the best model from the pretrained model assert ( self.config["model_config"]["model_path"] is not None ), f"Must have a model to load in the model_path for the BootlegAnnotator" self.model.load(self.config["model_config"]["model_path"]) self.model.eval() if cand_map is None: alias_map = self.entity_db.get_alias2qids() else: logger.debug(f"Loading candidate map") alias_map = ujson.load(open(cand_map)) self.all_aliases_trie = get_all_aliases(alias_map, verbose) logger.debug("Reading in alias table") self.alias2cands = AliasEntityTable( data_config=self.config.data_config, entity_symbols=self.entity_db) # get batch_on_the_fly embeddings self.batch_on_the_fly_embs = get_dataloader_embeddings( self.config, self.entity_db) def extract_mentions(self, text, label_func): """Wrapper function for mention extraction. Args: text: text to extract mentions from label_func: function that performs extraction (input is (text, alias trie, max alias length) -> output is list of found aliases and found spans Returns: JSON object of sentence to be used in eval """ found_aliases, found_spans = label_func(text, self.all_aliases_trie, self.max_alias_len) return { "sentence": text, "aliases": found_aliases, "spans": found_spans, # we don't know the true QID "qids": ["Q-1" for i in range(len(found_aliases))], "gold": [True for i in range(len(found_aliases))], } def set_threshold(self, value): """Sets threshold. Args: value: threshold value Returns: """ self.threshold = value def label_mentions(self, text_list, label_func=find_aliases_in_sentence_tag): """Extracts mentions and runs disambiguation. Args: text_list: list of text to disambiguate (or single sentence) label_func: mention extraction funciton (optional) Returns: Dict of * ``qids``: final predicted QIDs, * ``probs``: final predicted probs, * ``titles``: final predicted titles, * ``cands``: all entity canddiates, * ``cand_probs``: probabilities of all candidates, * ``spans``: final extracted word spans, * ``aliases``: final extracted aliases, """ if type(text_list) is str: text_list = [text_list] else: assert (type(text_list) is list and len(text_list) > 0 and type(text_list[0]) is str ), f"We only accept inputs of strings and lists of strings" ebs = int(self.config.run_config.eval_batch_size) self.config.data_config.max_aliases = int( self.config.data_config.max_aliases) total_start_exs = 0 total_final_exs = 0 dropped_by_thresh = 0 final_char_spans = [] batch_example_aliases = [] batch_example_aliases_locs_start = [] batch_example_aliases_locs_end = [] batch_example_alias_list_pos = [] batch_example_true_entities = [] batch_word_indices = [] batch_spans_arr = [] batch_aliases_arr = [] batch_idx_unq = [] batch_subsplit_idx = [] for idx_unq, text in tqdm( enumerate(text_list), desc="Prepping data", total=len(text_list), disable=not self.verbose, ): sample = self.extract_mentions(text, label_func) total_start_exs += len(sample["aliases"]) char_spans = self.get_char_spans(sample["spans"], text) final_char_spans.append(char_spans) ( idxs_arr, aliases_to_predict_per_split, spans_arr, phrase_tokens_arr, pos_idxs, ) = sentence_utils.split_sentence( max_aliases=self.config.data_config.max_aliases, phrase=sample["sentence"], spans=sample["spans"], aliases=sample["aliases"], aliases_seen_by_model=list(range(len(sample["aliases"]))), seq_len=self.config.data_config.max_seq_len, is_bert=True, tokenizer=self.tokenizer, ) aliases_arr = [[sample["aliases"][idx] for idx in idxs] for idxs in idxs_arr] old_spans_arr = [[sample["spans"][idx] for idx in idxs] for idxs in idxs_arr] qids_arr = [[sample["qids"][idx] for idx in idxs] for idxs in idxs_arr] word_indices_arr = [ self.tokenizer.convert_tokens_to_ids(pt) for pt in phrase_tokens_arr ] # iterate over each sample in the split for sub_idx in range(len(idxs_arr)): # ==================================================== # GENERATE MODEL INPUTS # ==================================================== aliases_to_predict_arr = aliases_to_predict_per_split[sub_idx] assert ( len(aliases_to_predict_arr) >= 0 ), f"There are no aliases to predict for an example. This should not happen at this point." assert ( len(aliases_arr[sub_idx]) <= self.config.data_config.max_aliases ), f"{sample} should have no more than {self.config.data_config.max_aliases} aliases." example_aliases = np.ones( self.config.data_config.max_aliases) * PAD_ID example_aliases_locs_start = ( np.ones(self.config.data_config.max_aliases) * PAD_ID) example_aliases_locs_end = ( np.ones(self.config.data_config.max_aliases) * PAD_ID) example_alias_list_pos = ( np.ones(self.config.data_config.max_aliases) * PAD_ID) example_true_entities = ( np.ones(self.config.data_config.max_aliases) * PAD_ID) for mention_idx, alias in enumerate(aliases_arr[sub_idx]): span_start_idx, span_end_idx = spans_arr[sub_idx][ mention_idx] # generate indexes into alias table. alias_trie_idx = self.entity_db.get_alias_idx(alias) alias_qids = np.array(self.entity_db.get_qid_cands(alias)) if not qids_arr[sub_idx][mention_idx] in alias_qids: # assert not data_args.train_in_candidates if not self.config.data_config.train_in_candidates: # set class label to be "not in candidate set" true_entity_idx = 0 else: true_entity_idx = -2 else: # Here we are getting the correct class label for training. # Our training is "which of the max_entities entity candidates is the right one # (class labels 1 to max_entities) or is it none of these (class label 0)". # + (not discard_noncandidate_entities) is to ensure label 0 is # reserved for "not in candidate set" class true_entity_idx = np.nonzero( alias_qids == qids_arr[sub_idx][mention_idx] )[0][0] + ( not self.config.data_config.train_in_candidates) example_aliases[mention_idx] = alias_trie_idx example_aliases_locs_start[mention_idx] = span_start_idx # The span_idxs are [start, end). We want [start, end]. So subtract 1 from end idx. example_aliases_locs_end[mention_idx] = span_end_idx - 1 example_alias_list_pos[mention_idx] = idxs_arr[sub_idx][ mention_idx] # leave as -1 if it's not an alias we want to predict; we get these if we split a sentence # and need to only predict subsets if mention_idx in aliases_to_predict_arr: example_true_entities[mention_idx] = true_entity_idx # get word indices word_indices = word_indices_arr[sub_idx] batch_example_aliases.append(example_aliases) batch_example_aliases_locs_start.append( example_aliases_locs_start) batch_example_aliases_locs_end.append(example_aliases_locs_end) batch_example_alias_list_pos.append(example_alias_list_pos) batch_example_true_entities.append(example_true_entities) batch_word_indices.append(word_indices) batch_aliases_arr.append(aliases_arr[sub_idx]) # Add the orginal sample spans because spans_arr is w.r.t BERT subword token batch_spans_arr.append(old_spans_arr[sub_idx]) batch_idx_unq.append(idx_unq) batch_subsplit_idx.append(sub_idx) batch_example_aliases = torch.tensor(batch_example_aliases).long() batch_example_aliases_locs_start = torch.tensor( batch_example_aliases_locs_start, device=self.torch_device) batch_example_aliases_locs_end = torch.tensor( batch_example_aliases_locs_end, device=self.torch_device) batch_example_true_entities = torch.tensor(batch_example_true_entities, device=self.torch_device) batch_word_indices = torch.tensor(batch_word_indices, device=self.torch_device) final_pred_cands = [[] for _ in range(len(text_list))] final_all_cands = [[] for _ in range(len(text_list))] final_cand_probs = [[] for _ in range(len(text_list))] final_pred_probs = [[] for _ in range(len(text_list))] final_titles = [[] for _ in range(len(text_list))] final_spans = [[] for _ in range(len(text_list))] final_aliases = [[] for _ in range(len(text_list))] for b_i in tqdm( range(0, batch_example_aliases.shape[0], ebs), desc="Evaluating model", disable=not self.verbose, ): start_span_idx = batch_example_aliases_locs_start[b_i:b_i + ebs] end_span_idx = batch_example_aliases_locs_end[b_i:b_i + ebs] word_indices = batch_word_indices[b_i:b_i + ebs] alias_indices = batch_example_aliases[b_i:b_i + ebs] x_dict = self.get_forward_batch(start_span_idx, end_span_idx, word_indices, alias_indices) x_dict["guid"] = torch.arange(b_i, b_i + ebs, device=self.torch_device) (uid_bdict, _, prob_bdict, _) = self.model( # type: ignore uids=x_dict["guid"], X_dict=x_dict, Y_dict=None, task_to_label_dict=self.task_to_label_dict, return_action_outputs=False, ) # ==================================================== # EVALUATE MODEL OUTPUTS # ==================================================== # recover predictions probs = prob_bdict[NED_TASK] max_probs = probs.max(2) max_probs_indices = probs.argmax(2) for ex_i in range(probs.shape[0]): idx_unq = batch_idx_unq[b_i + ex_i] entity_cands = eval_utils.map_aliases_to_candidates( self.config.data_config.train_in_candidates, self.config.data_config.max_aliases, self.entity_db.get_alias2qids(), batch_aliases_arr[b_i + ex_i], ) # batch size is 1 so we can reshape probs_ex = probs[ex_i].reshape( self.config.data_config.max_aliases, probs.shape[2]) for alias_idx, true_entity_pos_idx in enumerate( batch_example_true_entities[b_i + ex_i]): if true_entity_pos_idx != PAD_ID: pred_idx = max_probs_indices[ex_i][alias_idx] pred_prob = max_probs[ex_i][alias_idx].item() all_cands = entity_cands[alias_idx] pred_qid = all_cands[pred_idx] if pred_prob > self.threshold: final_all_cands[idx_unq].append(all_cands) final_cand_probs[idx_unq].append( probs_ex[alias_idx]) final_pred_cands[idx_unq].append(pred_qid) final_pred_probs[idx_unq].append(pred_prob) final_aliases[idx_unq].append( batch_aliases_arr[b_i + ex_i][alias_idx]) final_spans[idx_unq].append( batch_spans_arr[b_i + ex_i][alias_idx]) final_titles[idx_unq].append( self.entity_db.get_title(pred_qid) if pred_qid != "NC" else "NC") total_final_exs += 1 else: dropped_by_thresh += 1 assert total_final_exs + dropped_by_thresh == total_start_exs, ( f"Something went wrong and we have predicted fewer mentions than extracted. " f"Start {total_start_exs}, Out {total_final_exs}, No cand {dropped_by_thresh}" ) res_dict = { "qids": final_pred_cands, "probs": final_pred_probs, "titles": final_titles, "cands": final_all_cands, "cand_probs": final_cand_probs, "spans": final_spans, "aliases": final_aliases, } return res_dict def get_forward_batch(self, start_span_idx, end_span_idx, token_ids, alias_idx): """Preps the forward batch for disambiguation. Args: start_span_idx: start span tensor end_span_idx: end span tensor token_ids: word token tensor alias_idx: alias index used for extracting candidate eids Returns: X_dict used in Emmental """ entity_cand_eid = self.alias2cands(alias_idx).long() entity_cand_eid_mask = entity_cand_eid == -1 entity_cand_eid_noneg = torch.where( entity_cand_eid >= 0, entity_cand_eid, (torch.ones_like(entity_cand_eid, dtype=torch.long) * (self.entity_db.num_entities_with_pad_and_nocand - 1)), ) kg_prepped_embs = {} for emb_key in self.batch_on_the_fly_embs: kg_adj = self.batch_on_the_fly_embs[emb_key]["kg_adj"] prep_func = self.batch_on_the_fly_embs[emb_key][ "kg_adj_process_func"] batch_prep = [] for j in range(entity_cand_eid_noneg.shape[0]): batch_prep.append( prep_func(entity_cand_eid_noneg[j].cpu(), kg_adj).reshape(1, -1)) kg_prepped_embs[emb_key] = torch.tensor(batch_prep, device=self.torch_device) X_dict = { "guids": [], "start_span_idx": start_span_idx, "end_span_idx": end_span_idx, "token_ids": token_ids, "entity_cand_eid": entity_cand_eid_noneg, "entity_cand_eid_mask": entity_cand_eid_mask, "batch_on_the_fly_kg_adj": kg_prepped_embs, } return X_dict def get_char_spans(self, spans, text): """Helper function to get character spans instead of default word spans. Args: spans: word spans text: text Returns: character spans """ query_toks = text.split() char_spans = [] for span in spans: space_btwn_toks = (len(" ".join(query_toks[0:span[0] + 1])) - len(" ".join(query_toks[0:span[0]])) - len(query_toks[span[0]])) char_b = len(" ".join(query_toks[0:span[0]])) + space_btwn_toks char_e = char_b + len(" ".join(query_toks[span[0]:span[1]])) char_spans.append([char_b, char_e]) return char_spans
def main( conn_string, stg_temp_min=False, stg_temp_max=False, polarity=False, ce_v_max=False, max_docs=float("inf"), parse=False, first_time=False, re_label=False, parallel=4, log_dir=None, verbose=False, ): if not log_dir: log_dir = "logs" if verbose: level = logging.INFO else: level = logging.WARNING dirname = os.path.dirname(os.path.abspath(__file__)) init_logging(log_dir=os.path.join(dirname, log_dir), level=level) rel_list = [] if stg_temp_min: rel_list.append("stg_temp_min") if stg_temp_max: rel_list.append("stg_temp_max") if polarity: rel_list.append("polarity") if ce_v_max: rel_list.append("ce_v_max") session = Meta.init(conn_string).Session() # Parsing logger.info(f"Starting parsing...") start = timer() docs, train_docs, dev_docs, test_docs = parse_dataset(session, dirname, first_time=parse, parallel=parallel, max_docs=max_docs) end = timer() logger.warning(f"Parse Time (min): {((end - start) / 60.0):.1f}") logger.info(f"# of train Documents: {len(train_docs)}") logger.info(f"# of dev Documents: {len(dev_docs)}") logger.info(f"# of test Documents: {len(test_docs)}") logger.info(f"Documents: {session.query(Document).count()}") logger.info(f"Sections: {session.query(Section).count()}") logger.info(f"Paragraphs: {session.query(Paragraph).count()}") logger.info(f"Sentences: {session.query(Sentence).count()}") logger.info(f"Figures: {session.query(Figure).count()}") # Mention Extraction start = timer() mentions = [] ngrams = [] matchers = [] # Only do those that are enabled Part = mention_subclass("Part") part_matcher = get_matcher("part") part_ngrams = MentionNgramsPart(parts_by_doc=None, n_max=3) mentions.append(Part) ngrams.append(part_ngrams) matchers.append(part_matcher) if stg_temp_min: StgTempMin = mention_subclass("StgTempMin") stg_temp_min_matcher = get_matcher("stg_temp_min") stg_temp_min_ngrams = MentionNgramsTemp(n_max=2) mentions.append(StgTempMin) ngrams.append(stg_temp_min_ngrams) matchers.append(stg_temp_min_matcher) if stg_temp_max: StgTempMax = mention_subclass("StgTempMax") stg_temp_max_matcher = get_matcher("stg_temp_max") stg_temp_max_ngrams = MentionNgramsTemp(n_max=2) mentions.append(StgTempMax) ngrams.append(stg_temp_max_ngrams) matchers.append(stg_temp_max_matcher) if polarity: Polarity = mention_subclass("Polarity") polarity_matcher = get_matcher("polarity") polarity_ngrams = MentionNgrams(n_max=1) mentions.append(Polarity) ngrams.append(polarity_ngrams) matchers.append(polarity_matcher) if ce_v_max: CeVMax = mention_subclass("CeVMax") ce_v_max_matcher = get_matcher("ce_v_max") ce_v_max_ngrams = MentionNgramsVolt(n_max=1) mentions.append(CeVMax) ngrams.append(ce_v_max_ngrams) matchers.append(ce_v_max_matcher) mention_extractor = MentionExtractor(session, mentions, ngrams, matchers) if first_time: mention_extractor.apply(docs, parallelism=parallel) logger.info(f"Total Mentions: {session.query(Mention).count()}") logger.info(f"Total Part: {session.query(Part).count()}") if stg_temp_min: logger.info(f"Total StgTempMin: {session.query(StgTempMin).count()}") if stg_temp_max: logger.info(f"Total StgTempMax: {session.query(StgTempMax).count()}") if polarity: logger.info(f"Total Polarity: {session.query(Polarity).count()}") if ce_v_max: logger.info(f"Total CeVMax: {session.query(CeVMax).count()}") # Candidate Extraction cands = [] throttlers = [] if stg_temp_min: PartStgTempMin = candidate_subclass("PartStgTempMin", [Part, StgTempMin]) stg_temp_min_throttler = stg_temp_filter cands.append(PartStgTempMin) throttlers.append(stg_temp_min_throttler) if stg_temp_max: PartStgTempMax = candidate_subclass("PartStgTempMax", [Part, StgTempMax]) stg_temp_max_throttler = stg_temp_filter cands.append(PartStgTempMax) throttlers.append(stg_temp_max_throttler) if polarity: PartPolarity = candidate_subclass("PartPolarity", [Part, Polarity]) polarity_throttler = polarity_filter cands.append(PartPolarity) throttlers.append(polarity_throttler) if ce_v_max: PartCeVMax = candidate_subclass("PartCeVMax", [Part, CeVMax]) ce_v_max_throttler = ce_v_max_filter cands.append(PartCeVMax) throttlers.append(ce_v_max_throttler) candidate_extractor = CandidateExtractor(session, cands, throttlers=throttlers) if first_time: for i, docs in enumerate([train_docs, dev_docs, test_docs]): candidate_extractor.apply(docs, split=i, parallelism=parallel) num_cands = session.query(Candidate).filter( Candidate.split == i).count() logger.info(f"Candidates in split={i}: {num_cands}") # These must be sorted for deterministic behavior. train_cands = candidate_extractor.get_candidates(split=0, sort=True) dev_cands = candidate_extractor.get_candidates(split=1, sort=True) test_cands = candidate_extractor.get_candidates(split=2, sort=True) end = timer() logger.warning( f"Candidate Extraction Time (min): {((end - start) / 60.0):.1f}") logger.info(f"Total train candidate: {sum(len(_) for _ in train_cands)}") logger.info(f"Total dev candidate: {sum(len(_) for _ in dev_cands)}") logger.info(f"Total test candidate: {sum(len(_) for _ in test_cands)}") pickle_file = os.path.join(dirname, "data/parts_by_doc_new.pkl") with open(pickle_file, "rb") as f: parts_by_doc = pickle.load(f) # Check total recall for i, name in enumerate(rel_list): logger.info(name) result = entity_level_scores( candidates_to_entities(dev_cands[i], parts_by_doc=parts_by_doc), attribute=name, corpus=dev_docs, ) logger.info(f"{name} Total Dev Recall: {result.rec:.3f}") result = entity_level_scores( candidates_to_entities(test_cands[i], parts_by_doc=parts_by_doc), attribute=name, corpus=test_docs, ) logger.info(f"{name} Total Test Recall: {result.rec:.3f}") # Featurization start = timer() cands = [] if stg_temp_min: cands.append(PartStgTempMin) if stg_temp_max: cands.append(PartStgTempMax) if polarity: cands.append(PartPolarity) if ce_v_max: cands.append(PartCeVMax) # Using parallelism = 1 for deterministic behavior. featurizer = Featurizer(session, cands, parallelism=1) if first_time: logger.info("Starting featurizer...") featurizer.apply(split=0, train=True) featurizer.apply(split=1) featurizer.apply(split=2) logger.info("Done") logger.info("Getting feature matrices...") if first_time: F_train = featurizer.get_feature_matrices(train_cands) F_dev = featurizer.get_feature_matrices(dev_cands) F_test = featurizer.get_feature_matrices(test_cands) end = timer() logger.warning( f"Featurization Time (min): {((end - start) / 60.0):.1f}") F_train_dict = {} F_dev_dict = {} F_test_dict = {} for idx, relation in enumerate(rel_list): F_train_dict[relation] = F_train[idx] F_dev_dict[relation] = F_dev[idx] F_test_dict[relation] = F_test[idx] pickle.dump(F_train_dict, open(os.path.join(dirname, "F_train_dict.pkl"), "wb")) pickle.dump(F_dev_dict, open(os.path.join(dirname, "F_dev_dict.pkl"), "wb")) pickle.dump(F_test_dict, open(os.path.join(dirname, "F_test_dict.pkl"), "wb")) else: F_train_dict = pickle.load( open(os.path.join(dirname, "F_train_dict.pkl"), "rb")) F_dev_dict = pickle.load( open(os.path.join(dirname, "F_dev_dict.pkl"), "rb")) F_test_dict = pickle.load( open(os.path.join(dirname, "F_test_dict.pkl"), "rb")) F_train = [] F_dev = [] F_test = [] for relation in rel_list: F_train.append(F_train_dict[relation]) F_dev.append(F_dev_dict[relation]) F_test.append(F_test_dict[relation]) logger.info("Done.") for i, cand in enumerate(cands): logger.info(f"{cand} Train shape: {F_train[i].shape}") logger.info(f"{cand} Test shape: {F_test[i].shape}") logger.info(f"{cand} Dev shape: {F_dev[i].shape}") logger.info("Labeling training data...") # Labeling start = timer() lfs = [] if stg_temp_min: lfs.append(stg_temp_min_lfs) if stg_temp_max: lfs.append(stg_temp_max_lfs) if polarity: lfs.append(polarity_lfs) if ce_v_max: lfs.append(ce_v_max_lfs) # Using parallelism = 1 for deterministic behavior. labeler = Labeler(session, cands, parallelism=1) if first_time: logger.info("Applying LFs...") labeler.apply(split=0, lfs=lfs, train=True) logger.info("Done...") # Uncomment if debugging LFs # load_transistor_labels(session, cands, ["ce_v_max"]) # labeler.apply(split=1, lfs=lfs, train=False, parallelism=parallel) # labeler.apply(split=2, lfs=lfs, train=False, parallelism=parallel) elif re_label: logger.info("Updating LFs...") labeler.update(split=0, lfs=lfs) logger.info("Done...") # Uncomment if debugging LFs # labeler.apply(split=1, lfs=lfs, train=False, parallelism=parallel) # labeler.apply(split=2, lfs=lfs, train=False, parallelism=parallel) logger.info("Getting label matrices...") L_train = labeler.get_label_matrices(train_cands) # Uncomment if debugging LFs # L_dev = labeler.get_label_matrices(dev_cands) # L_dev_gold = labeler.get_gold_labels(dev_cands, annotator="gold") # # L_test = labeler.get_label_matrices(test_cands) # L_test_gold = labeler.get_gold_labels(test_cands, annotator="gold") logger.info("Done.") if first_time: marginals_dict = {} for idx, relation in enumerate(rel_list): marginals_dict[relation] = generative_model(L_train[idx]) pickle.dump(marginals_dict, open(os.path.join(dirname, "marginals_dict.pkl"), "wb")) else: marginals_dict = pickle.load( open(os.path.join(dirname, "marginals_dict.pkl"), "rb")) marginals = [] for relation in rel_list: marginals.append(marginals_dict[relation]) end = timer() logger.warning(f"Supervision Time (min): {((end - start) / 60.0):.1f}") start = timer() word_counter = collect_word_counter(train_cands) # Training config config = { "meta_config": { "verbose": True, "seed": 17 }, "model_config": { "model_path": None, "device": 0, "dataparallel": False }, "learner_config": { "n_epochs": 5, "optimizer_config": { "lr": 0.001, "l2": 0.0 }, "task_scheduler": "round_robin", }, "logging_config": { "evaluation_freq": 1, "counter_unit": "epoch", "checkpointing": False, "checkpointer_config": { "checkpoint_metric": { "model/all/train/loss": "min" }, "checkpoint_freq": 1, "checkpoint_runway": 2, "clear_intermediate_checkpoints": True, "clear_all_checkpoints": True, }, }, } emmental.init(log_dir=Meta.log_path, config=config) # Generate word embedding module arity = 2 # Geneate special tokens specials = [] for i in range(arity): specials += [f"~~[[{i}", f"{i}]]~~"] emb_layer = EmbeddingModule(word_counter=word_counter, word_dim=300, specials=specials) train_idxs = [] train_dataloader = [] for idx, relation in enumerate(rel_list): diffs = marginals[idx].max(axis=1) - marginals[idx].min(axis=1) train_idxs.append(np.where(diffs > 1e-6)[0]) train_dataloader.append( EmmentalDataLoader( task_to_label_dict={relation: "labels"}, dataset=FonduerDataset( relation, train_cands[idx], F_train[idx], emb_layer.word2id, marginals[idx], train_idxs[idx], ), split="train", batch_size=100, shuffle=True, )) num_feature_keys = len(featurizer.get_keys()) model = EmmentalModel(name=f"transistor_tasks") # List relation names, arities, list of classes tasks = create_task( rel_list, [2] * len(rel_list), num_feature_keys, [2] * len(rel_list), emb_layer, model="LogisticRegression", ) for task in tasks: model.add_task(task) emmental_learner = EmmentalLearner() # If given a list of multi, will train on multiple emmental_learner.learn(model, train_dataloader) # List of dataloader for each rlation for idx, relation in enumerate(rel_list): test_dataloader = EmmentalDataLoader( task_to_label_dict={relation: "labels"}, dataset=FonduerDataset(relation, test_cands[idx], F_test[idx], emb_layer.word2id, 2), split="test", batch_size=100, shuffle=False, ) test_preds = model.predict(test_dataloader, return_preds=True) best_result, best_b = scoring( relation, test_preds, test_cands[idx], test_docs, F_test[idx], parts_by_doc, num=100, ) # Dump CSV files for CE_V_MAX for digi-key analysis if relation == "ce_v_max": dev_dataloader = EmmentalDataLoader( task_to_label_dict={relation: "labels"}, dataset=FonduerDataset(relation, dev_cands[idx], F_dev[idx], emb_layer.word2id, 2), split="dev", batch_size=100, shuffle=False, ) dev_preds = model.predict(dev_dataloader, return_preds=True) Y_prob = np.array(test_preds["probs"][relation])[:, TRUE] dump_candidates(test_cands[idx], Y_prob, "ce_v_max_test_probs.csv") Y_prob = np.array(dev_preds["probs"][relation])[:, TRUE] dump_candidates(dev_cands[idx], Y_prob, "ce_v_max_dev_probs.csv") # Dump CSV files for POLARITY for digi-key analysis if relation == "polarity": dev_dataloader = EmmentalDataLoader( task_to_label_dict={relation: "labels"}, dataset=FonduerDataset(relation, dev_cands[idx], F_dev[idx], emb_layer.word2id, 2), split="dev", batch_size=100, shuffle=False, ) dev_preds = model.predict(dev_dataloader, return_preds=True) Y_prob = np.array(test_preds["probs"][relation])[:, TRUE] dump_candidates(test_cands[idx], Y_prob, "polarity_test_probs.csv") Y_prob = np.array(dev_preds["probs"][relation])[:, TRUE] dump_candidates(dev_cands[idx], Y_prob, "polarity_dev_probs.csv") end = timer() logger.warning(f"Classification Time (min): {((end - start) / 60.0):.1f}")
def main( conn_string, max_docs=float("inf"), parse=False, first_time=False, gpu=None, parallel=4, log_dir=None, verbose=False, ): if not log_dir: log_dir = "logs" if verbose: level = logging.INFO else: level = logging.WARNING dirname = os.path.dirname(os.path.abspath(__file__)) init_logging(log_dir=os.path.join(dirname, log_dir), level=level) session = Meta.init(conn_string).Session() # Parsing logger.info(f"Starting parsing...") start = timer() docs, train_docs, dev_docs, test_docs = parse_dataset( session, dirname, first_time=first_time, parallel=parallel, max_docs=max_docs ) end = timer() logger.warning(f"Parse Time (min): {((end - start) / 60.0):.1f}") logger.info(f"# of train Documents: {len(train_docs)}") logger.info(f"# of dev Documents: {len(dev_docs)}") logger.info(f"# of test Documents: {len(test_docs)}") logger.info(f"Documents: {session.query(Document).count()}") logger.info(f"Sections: {session.query(Section).count()}") logger.info(f"Paragraphs: {session.query(Paragraph).count()}") logger.info(f"Sentences: {session.query(Sentence).count()}") logger.info(f"Figures: {session.query(Figure).count()}") start = timer() Thumbnails = mention_subclass("Thumbnails") thumbnails_img = MentionFigures() class HasFigures(_Matcher): def _f(self, m): file_path = "" for prefix in [ f"{dirname}/data/train/html/", f"{dirname}/data/dev/html/", f"{dirname}/data/test/html/", ]: if os.path.exists(prefix + m.figure.url): file_path = prefix + m.figure.url if file_path == "": return False img = Image.open(file_path) width, height = img.size min_value = min(width, height) return min_value > 50 mention_extractor = MentionExtractor( session, [Thumbnails], [thumbnails_img], [HasFigures()], parallelism=parallel ) if first_time: mention_extractor.apply(docs) logger.info("Total Mentions: {}".format(session.query(Mention).count())) ThumbnailLabel = candidate_subclass("ThumbnailLabel", [Thumbnails]) candidate_extractor = CandidateExtractor( session, [ThumbnailLabel], throttlers=[None], parallelism=parallel ) if first_time: candidate_extractor.apply(train_docs, split=0) candidate_extractor.apply(dev_docs, split=1) candidate_extractor.apply(test_docs, split=2) train_cands = candidate_extractor.get_candidates(split=0) # Sort the dev_cands, which are used for training, for deterministic behavior dev_cands = candidate_extractor.get_candidates(split=1, sort=True) test_cands = candidate_extractor.get_candidates(split=2) end = timer() logger.warning(f"Candidate Extraction Time (min): {((end - start) / 60.0):.1f}") logger.info("Total train candidate:\t{}".format(len(train_cands[0]))) logger.info("Total dev candidate:\t{}".format(len(dev_cands[0]))) logger.info("Total test candidate:\t{}".format(len(test_cands[0]))) fin = open(f"{dirname}/data/ground_truth.txt", "r") gt = set() for line in fin: gt.add("::".join(line.lower().split())) fin.close() # Labeling start = timer() def LF_gt_label(c): doc_file_id = ( f"{c[0].context.figure.document.name.lower()}.pdf::" f"{os.path.basename(c[0].context.figure.url.lower())}" ) return TRUE if doc_file_id in gt else FALSE gt_dev = [LF_gt_label(cand) for cand in dev_cands[0]] gt_test = [LF_gt_label(cand) for cand in test_cands[0]] end = timer() logger.warning(f"Supervision Time (min): {((end - start) / 60.0):.1f}") batch_size = 64 input_size = 224 K = 2 emmental.init(log_dir=Meta.log_path, config=emmental_config) emmental.Meta.config["learner_config"]["task_scheduler_config"][ "task_scheduler" ] = DauphinScheduler(augment_k=K, enlarge=1) train_dataset = ThumbnailDataset( "Thumbnail", dev_cands[0], gt_dev, "train", prob_label=True, prefix=f"{dirname}/data/dev/html/", input_size=input_size, transform_cls=Augmentation(2), k=K, ) val_dataset = ThumbnailDataset( "Thumbnail", dev_cands[0], gt_dev, "valid", prob_label=False, prefix=f"{dirname}/data/dev/html/", input_size=input_size, k=1, ) test_dataset = ThumbnailDataset( "Thumbnail", test_cands[0], gt_test, "test", prob_label=False, prefix=f"{dirname}/data/test/html/", input_size=input_size, k=1, ) dataloaders = [] dataloaders.append( EmmentalDataLoader( task_to_label_dict={"Thumbnail": "labels"}, dataset=train_dataset, split="train", shuffle=True, batch_size=batch_size, num_workers=1, ) ) dataloaders.append( EmmentalDataLoader( task_to_label_dict={"Thumbnail": "labels"}, dataset=val_dataset, split="valid", shuffle=False, batch_size=batch_size, num_workers=1, ) ) dataloaders.append( EmmentalDataLoader( task_to_label_dict={"Thumbnail": "labels"}, dataset=test_dataset, split="test", shuffle=False, batch_size=batch_size, num_workers=1, ) ) model = EmmentalModel(name=f"Thumbnail") model.add_task( create_task("Thumbnail", n_class=2, model="resnet18", pretrained=True) ) emmental_learner = EmmentalLearner() emmental_learner.learn(model, dataloaders) scores = model.score(dataloaders) logger.warning("Model Score:") logger.warning(f"precision: {scores['Thumbnail/Thumbnail/test/precision']:.3f}") logger.warning(f"recall: {scores['Thumbnail/Thumbnail/test/recall']:.3f}") logger.warning(f"f1: {scores['Thumbnail/Thumbnail/test/f1']:.3f}")
def run_model(mode, config, run_config_path=None): """ Main run method for Emmental Bootleg models. Args: mode: run mode (train, eval, dump_preds, dump_embs) config: parsed model config run_config_path: original config path (for saving) Returns: """ # Set up distributed backend and save configuration files setup(config, run_config_path) # Load entity symbols log_rank_0_info(logger, f"Loading entity symbols...") entity_symbols = EntitySymbols.load_from_cache( load_dir=os.path.join(config.data_config.entity_dir, config.data_config.entity_map_dir), alias_cand_map_file=config.data_config.alias_cand_map, alias_idx_file=config.data_config.alias_idx_map, ) # Create tasks tasks = [NED_TASK] if config.data_config.type_prediction.use_type_pred is True: tasks.append(TYPE_PRED_TASK) # Create splits for data loaders data_splits = [TRAIN_SPLIT, DEV_SPLIT, TEST_SPLIT] # Slices are for eval so we only split on test/dev slice_splits = [DEV_SPLIT, TEST_SPLIT] # If doing eval, only run on test data if mode in ["eval", "dump_preds", "dump_embs"]: data_splits = [TEST_SPLIT] slice_splits = [TEST_SPLIT] # We only do dumping if weak labels is True if mode in ["dump_preds", "dump_embs"]: if config.data_config[ f"{TEST_SPLIT}_dataset"].use_weak_label is False: raise ValueError( f"When calling dump_preds or dump_embs, we require use_weak_label to be True." ) # Gets embeddings that need to be prepped during data prep or in the __get_item__ method batch_on_the_fly_kg_adj = get_dataloader_embeddings(config, entity_symbols) # Gets dataloaders dataloaders = get_dataloaders( config, tasks, data_splits, entity_symbols, batch_on_the_fly_kg_adj, ) slice_datasets = get_slicedatasets(config, slice_splits, entity_symbols) configure_optimizer(config) # Create models and add tasks if config.model_config.attn_class == "BERTNED": log_rank_0_info(logger, f"Starting NED-Base Model") assert (config.data_config.type_prediction.use_type_pred is False), f"NED-Base does not support type prediction" assert ( config.data_config.word_embedding.use_sent_proj is False ), f"NED-Base requires word_embeddings.use_sent_proj to be False" model = EmmentalModel(name="NED-Base") model.add_tasks( ned_task.create_task(config, entity_symbols, slice_datasets)) else: log_rank_0_info(logger, f"Starting Bootleg Model") model = EmmentalModel(name="Bootleg") # TODO: make this more general for other tasks -- iterate through list of tasks # and add task for each model.add_task( ned_task.create_task(config, entity_symbols, slice_datasets)) if TYPE_PRED_TASK in tasks: model.add_task( type_pred_task.create_task(config, entity_symbols, slice_datasets)) # Add the mention type embedding to the embedding payload type_pred_task.update_ned_task(model) # Print param counts if mode == "train": log_rank_0_debug(logger, "PARAMS WITH GRAD\n" + "=" * 30) total_params = count_parameters(model, requires_grad=True, logger=logger) log_rank_0_info(logger, f"===> Total Params With Grad: {total_params}") log_rank_0_debug(logger, "PARAMS WITHOUT GRAD\n" + "=" * 30) total_params = count_parameters(model, requires_grad=False, logger=logger) log_rank_0_info(logger, f"===> Total Params Without Grad: {total_params}") # Load the best model from the pretrained model if config["model_config"]["model_path"] is not None: model.load(config["model_config"]["model_path"]) # Barrier if config["learner_config"]["local_rank"] == 0: torch.distributed.barrier() # Train model if mode == "train": emmental_learner = EmmentalLearner() emmental_learner._set_optimizer(model) emmental_learner.learn(model, dataloaders) if config.learner_config.local_rank in [0, -1]: model.save(f"{emmental.Meta.log_path}/last_model.pth") # Multi-gpu DataParallel eval (NOT distributed) if mode in ["eval", "dump_embs", "dump_preds"]: # This happens inside EmmentalLearner for training if (config["learner_config"]["local_rank"] == -1 and config["model_config"]["dataparallel"]): model._to_dataparallel() # If just finished training a model or in eval mode, run eval if mode in ["train", "eval"]: scores = model.score(dataloaders) # Save metrics and models log_rank_0_info(logger, f"Saving metrics to {emmental.Meta.log_path}") log_rank_0_info(logger, f"Metrics: {scores}") scores["log_path"] = emmental.Meta.log_path if config.learner_config.local_rank in [0, -1]: write_to_file(f"{emmental.Meta.log_path}/{mode}_metrics.txt", scores) eval_utils.write_disambig_metrics_to_csv( f"{emmental.Meta.log_path}/{mode}_disambig_metrics.csv", scores) return scores # If you want detailed dumps, save model outputs assert mode in [ "dump_preds", "dump_embs", ], 'Mode must be "dump_preds" or "dump_embs"' dump_embs = False if mode != "dump_embs" else True assert ( len(dataloaders) == 1 ), f"We should only have length 1 dataloaders for dump_embs and dump_preds!" final_result_file, final_out_emb_file = None, None if config.learner_config.local_rank in [0, -1]: # Setup files/folders filename = os.path.basename(dataloaders[0].dataset.raw_filename) log_rank_0_debug( logger, f"Collecting sentence to mention map {os.path.join(config.data_config.data_dir, filename)}", ) sentidx2num_mentions, sent_idx2row = eval_utils.get_sent_idx2num_mens( os.path.join(config.data_config.data_dir, filename)) log_rank_0_debug(logger, f"Done collecting sentence to mention map") eval_folder = eval_utils.get_eval_folder(filename) subeval_folder = os.path.join(eval_folder, "batch_results") utils.ensure_dir(subeval_folder) # Will keep track of sentences dumped already. These will only be ones with mentions all_dumped_sentences = set() number_dumped_batches = 0 total_mentions_seen = 0 all_result_files = [] all_out_emb_files = [] # Iterating over batches of predictions for res_i, res_dict in enumerate( eval_utils.batched_pred_iter( model, dataloaders[0], config.run_config.eval_accumulation_steps, sentidx2num_mentions, )): ( result_file, out_emb_file, final_sent_idxs, mentions_seen, ) = eval_utils.disambig_dump_preds( res_i, total_mentions_seen, config, res_dict, sentidx2num_mentions, sent_idx2row, subeval_folder, entity_symbols, dump_embs, NED_TASK, ) all_dumped_sentences.update(final_sent_idxs) all_result_files.append(result_file) all_out_emb_files.append(out_emb_file) total_mentions_seen += mentions_seen number_dumped_batches += 1 # Dump the sentences that had no mentions and were not already dumped # Assert all remaining sentences have no mentions assert all( v == 0 for k, v in sentidx2num_mentions.items() if k not in all_dumped_sentences ), (f"Sentences with mentions were not dumped: " f"{[k for k, v in sentidx2num_mentions.items() if k not in all_dumped_sentences]}" ) empty_sentidx2row = { k: v for k, v in sent_idx2row.items() if k not in all_dumped_sentences } empty_resultfile = eval_utils.get_result_file(number_dumped_batches, subeval_folder) all_result_files.append(empty_resultfile) # Dump the outputs eval_utils.write_data_labels_single( sentidx2row=empty_sentidx2row, output_file=empty_resultfile, filt_emb_data=None, sental2embid={}, alias_cand_map=entity_symbols.get_alias2qids(), qid2eid=entity_symbols.get_qid2eid(), result_alias_offset=total_mentions_seen, train_in_cands=config.data_config.train_in_candidates, max_cands=entity_symbols.max_candidates, dump_embs=dump_embs, ) log_rank_0_info( logger, f"Finished dumping. Merging results across accumulation steps.") # Final result files for labels and embeddings final_result_file = os.path.join(eval_folder, config.run_config.result_label_file) # Copy labels output = open(final_result_file, "wb") for file in all_result_files: shutil.copyfileobj(open(file, "rb"), output) output.close() log_rank_0_info(logger, f"Bootleg labels saved at {final_result_file}") # Try to copy embeddings if dump_embs: final_out_emb_file = os.path.join( eval_folder, config.run_config.result_emb_file) log_rank_0_info( logger, f"Trying to merge numpy embedding arrays. " f"If your machine is limited in memory, this may cause OOM errors. " f"Is that happens, result files should be saved in {subeval_folder}.", ) all_arrays = [] for i, npfile in enumerate(all_out_emb_files): all_arrays.append(np.load(npfile)) np.save(final_out_emb_file, np.concatenate(all_arrays)) log_rank_0_info( logger, f"Bootleg embeddings saved at {final_out_emb_file}") # Cleanup try_rmtree(subeval_folder) return final_result_file, final_out_emb_file
train_marginals, train_idxs, ), split="train", batch_size=100, shuffle=True, ) tasks = create_task( ATTRIBUTE, 2, F_train[0].shape[1], 2, emb_layer, model="LogisticRegression" ) emmental_model = EmmentalModel() for task in tasks: emmental_model.add_task(task) emmental_learner = EmmentalLearner() emmental_learner.learn(emmental_model, [train_dataloader]) from my_fonduer_model import MyFonduerModel model = MyFonduerModel() code_paths = [ "fonduer_subclasses.py", "fonduer_model.py", # will no longer needed once HazyResearch/fonduer#407 is merged. "my_fonduer_model.py", ] import fonduer_model # Discrinative model