def main(): parser = argparse.ArgumentParser() parser.add_argument("model") args = parser.parse_args() model_dir = ModelDir(args.model) checkpoint = model_dir.get_best_weights() reader = tf.train.NewCheckpointReader(checkpoint) if reader.has_tensor("weight_embed_context_lm/layer_0/w"): x = "w" else: x = "ELMo_W_0" for i in reader.get_variable_to_shape_map().items(): print(i) input_w = reader.get_tensor( "weight_embed_lm/layer_0/%s/ExponentialMovingAverage" % x) output_w = reader.get_tensor( "weight_lm/layer_0/%s/ExponentialMovingAverage" % x) print("Input") print(input_w) print("(Softmax): " + str(softmax(input_w))) print("Output") print(output_w) print("(Softmax): " + str(softmax(output_w)))
def main(): parser = argparse.ArgumentParser(description='') parser.add_argument("model") args = parser.parse_args() model_dir = ModelDir(args.model) checkpoint = model_dir.get_best_weights() print(checkpoint) if checkpoint is None: print("Show latest checkpoint") checkpoint = model_dir.get_latest_checkpoint() else: print("Show best weights") reader = tf.train.NewCheckpointReader(checkpoint) param_map = reader.get_variable_to_shape_map() total = 0 for k in sorted(param_map): v = param_map[k] print('%s: %s' % (k, str(v))) total += np.prod(v) print("%d total" % total)
def main(): parser = argparse.ArgumentParser(description='Evaluate a model on TriviaQA data') parser.add_argument('model', help='model directory') parser.add_argument('-p', '--paragraph_output', type=str, help="Save fine grained results for each paragraph in csv format") parser.add_argument('-o', '--official_output', type=str, help="Build an offical output file with the model's" " most confident span for each (question, doc) pair") parser.add_argument('--no_ema', action="store_true", help="Don't use EMA weights even if they exist") parser.add_argument('--n_processes', type=int, default=None, help="Number of processes to do the preprocessing (selecting paragraphs+loading context) with") parser.add_argument('-i', '--step', type=int, default=None, help="checkpoint to load, default to latest") parser.add_argument('-n', '--n_sample', type=int, default=None, help="Number of questions to evaluate on") parser.add_argument('-a', '--async', type=int, default=10) parser.add_argument('-t', '--tokens', type=int, default=400, help="Max tokens per a paragraph") parser.add_argument('-g', '--n_paragraphs', type=int, default=15, help="Number of paragraphs to run the model on") parser.add_argument('-f', '--filter', type=str, default=None, choices=["tfidf", "truncate", "linear"], help="How to select paragraphs") parser.add_argument('-b', '--batch_size', type=int, default=200, help="Batch size, larger sizes might be faster but wll take more memory") parser.add_argument('--max_answer_len', type=int, default=8, help="Max answer span to select") parser.add_argument('-c', '--corpus', choices=["web-dev", "web-test", "web-verified-dev", "web-train", "open-dev", "open-train"], default="web-verified-dev") args = parser.parse_args() model_dir = ModelDir(args.model) model = model_dir.get_model() if args.corpus.startswith('web'): dataset = TriviaQaWebDataset() corpus = dataset.evidence if args.corpus == "web-dev": test_questions = dataset.get_dev() elif args.corpus == "web-test": test_questions = dataset.get_test() elif args.corpus == "web-verified-dev": test_questions = dataset.get_verified() elif args.corpus == "web-train": test_questions = dataset.get_train() else: raise RuntimeError() else: dataset = TriviaQaOpenDataset() corpus = dataset.evidence if args.corpus == "open-dev": test_questions = dataset.get_dev() elif args.corpus == "open-train": test_questions = dataset.get_train() else: raise RuntimeError() splitter = MergeParagraphs(args.tokens) per_document = not args.corpus.startswith("open") filter_name = args.filter if filter_name is None: if args.corpus.startswith("open"): filter_name = "linear" else: filter_name = "tfidf" print("Selecting %d paragraphs using %s method per %s" % (args.n_paragraphs, filter_name, ("question-document pair" if per_document else "question"))) if filter_name == "tfidf": para_filter = TopTfIdf(NltkPlusStopWords(punctuation=True), args.n_paragraphs) elif filter_name == "truncate": para_filter = FirstN(args.n_paragraphs) elif filter_name == "linear": para_filter = ShallowOpenWebRanker(args.n_paragraphs) else: raise ValueError() n_questions = args.n_sample if n_questions is not None: test_questions.sort(key=lambda x:x.question_id) np.random.RandomState(0).shuffle(test_questions) test_questions = test_questions[:n_questions] print("Building question/paragraph pairs...") # Loads the relevant questions/documents, selects the right paragraphs, and runs the model's preprocessor if per_document: prep = ExtractMultiParagraphs(splitter, para_filter, model.preprocessor, require_an_answer=False) else: prep = ExtractMultiParagraphsPerQuestion(splitter, para_filter, model.preprocessor, require_an_answer=False) prepped_data = preprocess_par(test_questions, corpus, prep, args.n_processes, 1000) data = [] for q in prepped_data.data: for i, p in enumerate(q.paragraphs): if q.answer_text is None: ans = None else: ans = TokenSpans(q.answer_text, p.answer_spans) data.append(DocumentParagraphQuestion(q.question_id, p.doc_id, (p.start, p.end), q.question, p.text, ans, i)) # Reverse so our first batch will be the largest (so OOMs happen early) questions = sorted(data, key=lambda x: (x.n_context_words, len(x.question)), reverse=True) print("Done, starting eval") if args.step is not None: if args.step == "latest": checkpoint = model_dir.get_latest_checkpoint() else: checkpoint = model_dir.get_checkpoint(int(args.step)) else: checkpoint = model_dir.get_best_weights() if checkpoint is not None: print("Using best weights") else: print("Using latest checkpoint") checkpoint = model_dir.get_latest_checkpoint() test_questions = ParagraphAndQuestionDataset(questions, FixedOrderBatcher(args.batch_size, True)) evaluation = trainer.test(model, [RecordParagraphSpanPrediction(args.max_answer_len, True)], {args.corpus:test_questions}, ResourceLoader(), checkpoint, not args.no_ema, args.async)[args.corpus] if not all(len(x) == len(data) for x in evaluation.per_sample.values()): raise RuntimeError() df = pd.DataFrame(evaluation.per_sample) if args.official_output is not None: print("Saving question result") # I didn't store the unormalized filenames exactly, so unfortunately we have to reload # the source data to get exact filename to output an official test script fns = {} print("Loading proper filenames") if args.corpus == 'web-test': source = join(TRIVIA_QA, "qa", "web-test-without-answers.json") elif args.corpus == "web-dev": source = join(TRIVIA_QA, "qa", "web-dev.json") else: raise NotImplementedError() with open(join(source)) as f: data = json.load(f)["Data"] for point in data: for doc in point["EntityPages"]: filename = doc["Filename"] fn = join("wikipedia", filename[:filename.rfind(".")]) fn = normalize_wiki_filename(fn) fns[(point["QuestionId"], fn)] = filename answers = {} scores = {} for q_id, doc_id, start, end, txt, score in df[["question_id", "doc_id", "para_start", "para_end", "text_answer", "predicted_score"]].itertuples(index=False): filename = dataset.evidence.file_id_map[doc_id] if filename.startswith("web"): true_name = filename[4:] + ".txt" else: true_name = fns[(q_id, filename)] key = q_id + "--" + true_name prev_score = scores.get(key) if prev_score is None or prev_score < score: scores[key] = score answers[key] = txt with open(args.official_output, "w") as f: json.dump(answers, f) if per_document: group_by = ["question_id", "doc_id"] else: group_by = ["question_id"] # Print a table of scores as more paragraphs are used df.sort_values(group_by + ["rank"], inplace=True) f1 = compute_model_scores(df, "predicted_score", "text_f1", group_by) em = compute_model_scores(df, "predicted_score", "text_em", group_by) table = [["N Paragraphs", "EM", "F1"]] table += list([str(i+1), "%.4f" % e, "%.4f" % f] for i, (e, f) in enumerate(zip(em, f1))) print_table(table) output_file = args.paragraph_output if output_file is not None: print("Saving paragraph result") if output_file.endswith("json"): with open(output_file, "w") as f: json.dump(evaluation.per_sample, f) elif output_file.endswith("pkl"): with open(output_file, "wb") as f: pickle.dump(evaluation.per_sample, f) elif output_file.endswith("csv"): df.to_csv(output_file, index=False) else: raise ValueError("Unrecognized file format")
def main(): parser = argparse.ArgumentParser(description='Evaluate a model on SQuAD') parser.add_argument('model', help='model directory to evaluate') parser.add_argument("-o", "--official_output", type=str, help="where to output an official result file") parser.add_argument('-n', '--sample_questions', type=int, default=None, help="(for testing) run on a subset of questions") parser.add_argument('--answer_bounds', nargs='+', type=int, default=[17], help="Max size of answer") parser.add_argument('-b', '--batch_size', type=int, default=200, help="Batch size, larger sizes can be faster but uses more memory") parser.add_argument('-s', '--step', default=None, help="Weights to load, can be a checkpoint step or 'latest'") # Add ja_test choice to test Multilingual QA dataset. parser.add_argument( '-c', '--corpus', choices=["dev", "train", "ja_test", "pred"], default="dev") parser.add_argument('--no_ema', action="store_true", help="Don't use EMA weights even if they exist") # Add ja_test choice to test Multilingual QA pipeline. parser.add_argument('-p', '--pred_filepath', default=None, help="The csv file path if you try pred mode") args = parser.parse_args() model_dir = ModelDir(args.model) corpus = SquadCorpus() if args.corpus == "dev": questions = corpus.get_dev() # Add ja_test choice to test Multilingual QA pipeline. elif args.corpus == "ja_test": questions = corpus.get_ja_test() # This is for prediction mode for MLQA pipeline. elif args.corpus == "pred": questions = create_pred_dataset(args.pred_filepath) else: questions = corpus.get_train() questions = split_docs(questions) if args.sample_questions: np.random.RandomState(0).shuffle( sorted(questions, key=lambda x: x.question_id)) questions = questions[:args.sample_questions] questions.sort(key=lambda x: x.n_context_words, reverse=True) dataset = ParagraphAndQuestionDataset( questions, FixedOrderBatcher(args.batch_size, True)) evaluators = [SpanEvaluator(args.answer_bounds, text_eval="squad")] if args.official_output is not None: evaluators.append(RecordSpanPrediction(args.answer_bounds[0])) if args.step is not None: if args.step == "latest": checkpoint = model_dir.get_latest_checkpoint() else: checkpoint = model_dir.get_checkpoint(int(args.step)) else: checkpoint = model_dir.get_best_weights() if checkpoint is not None: print("Using best weights") else: print("Using latest checkpoint") checkpoint = model_dir.get_latest_checkpoint() model = model_dir.get_model() evaluation = trainer.test(model, evaluators, {args.corpus: dataset}, corpus.get_resource_loader(), checkpoint, not args.no_ema)[args.corpus] # Print the scalar results in a two column table scalars = evaluation.scalars cols = list(sorted(scalars.keys())) table = [cols] header = ["Metric", ""] table.append([("%s" % scalars[x] if x in scalars else "-") for x in cols]) print_table([header] + transpose_lists(table)) # Save the official output if args.official_output is not None: quid_to_para = {} for x in questions: quid_to_para[x.question_id] = x.paragraph q_id_to_answers = {} q_ids = evaluation.per_sample["question_id"] spans = evaluation.per_sample["predicted_span"] for q_id, (start, end) in zip(q_ids, spans): text = quid_to_para[q_id].get_original_text(start, end) q_id_to_answers[q_id] = text with open(args.official_output, "w") as f: json.dump(q_id_to_answers, f)
def run(): parser = argparse.ArgumentParser() parser.add_argument("squad_path", help="path to squad dev data file") parser.add_argument("output_path", help="path where evaluation json file will be written") parser.add_argument("--model-path", default="model", help="path to model directory") parser.add_argument("--n", type=int, default=None) parser.add_argument("-b", "--batch_size", type=int, default=100) parser.add_argument("--ema", action="store_true") args = parser.parse_args() squad_path = args.squad_path output_path = args.output_path model_dir = ModelDir(args.model_path) nltk.data.path.append("nltk_data") print("Loading data") docs = parse_squad_data(squad_path, "", NltkAndPunctTokenizer(), False) pairs = split_docs(docs) dataset = ParagraphAndQuestionDataset( pairs, ClusteredBatcher(args.batch_size, ContextLenKey(), False, True)) print("Done, init model") model = model_dir.get_model() loader = ResourceLoader(lambda a, b: load_word_vector_file( join(VEC_DIR, "glove.840B.300d.txt"), b)) lm_model = model.lm_model basedir = join(LM_DIR, "squad-context-concat-skip") lm_model.lm_vocab_file = join(basedir, "squad_train_dev_all_unique_tokens.txt") lm_model.options_file = join( basedir, "options_squad_lm_2x4096_512_2048cnn_2xhighway_skip.json") lm_model.weight_file = join( basedir, "squad_context_concat_lm_2x4096_512_2048cnn_2xhighway_skip.hdf5") lm_model.embed_weights_file = None model.set_inputs([dataset], loader) print("Done, building graph") sess = tf.Session() with sess.as_default(): pred = model.get_prediction() best_span = pred.get_best_span(17)[0] all_vars = tf.global_variables() + tf.get_collection( tf.GraphKeys.SAVEABLE_OBJECTS) dont_restore_names = { x.name for x in all_vars if x.name.startswith("bilm") } print(sorted(dont_restore_names)) vars = [x for x in all_vars if x.name not in dont_restore_names] print("Done, loading weights") checkpoint = model_dir.get_best_weights() if checkpoint is None: print("Loading most recent checkpoint") checkpoint = model_dir.get_latest_checkpoint() else: print("Loading best weights") saver = tf.train.Saver(vars) saver.restore(sess, checkpoint) if args.ema: ema = tf.train.ExponentialMovingAverage(0) saver = tf.train.Saver( {ema.average_name(x): x for x in tf.trainable_variables()}) saver.restore(sess, checkpoint) sess.run( tf.variables_initializer( [x for x in all_vars if x.name in dont_restore_names])) print("Done, starting evaluation") out = {} for i, batch in enumerate(dataset.get_epoch()): if args.n is not None and i == args.n: break print("On batch: %d" % (i + 1)) enc = model.encode(batch, False) spans = sess.run(best_span, feed_dict=enc) for (s, e), point in zip(spans, batch): out[point.question_id] = point.get_original_text(s, e) sess.close() print("Done, saving") with open(output_path, "w") as f: json.dump(out, f) print("Mission accomplished!")
def main(): parser = argparse.ArgumentParser(description='Evaluate a model on SQuAD') parser.add_argument('model', help='model directory to evaluate') parser.add_argument("-o", "--official_output", type=str, help="where to output an official result file") parser.add_argument('-n', '--sample_questions', type=int, default=None, help="(for testing) run on a subset of questions") parser.add_argument('--answer_bounds', nargs='+', type=int, default=[17], help="Max size of answer") parser.add_argument('-b', '--batch_size', type=int, default=200, help="Batch size, larger sizes can be faster but uses more memory") parser.add_argument('-s', '--step', default=None, help="Weights to load, can be a checkpoint step or 'latest'") parser.add_argument('-c', '--corpus', choices=["dev", "train"], default="dev") parser.add_argument('--no_ema', action="store_true", help="Don't use EMA weights even if they exist") parser.add_argument('--none_prob', action="store_true", help="Output none probability for samples") parser.add_argument('--elmo', action="store_true", help="Use elmo model") parser.add_argument('--per_question_loss_file', type=str, default=None, help="Run question by question and output a question_id -> loss output to this file") args = parser.parse_known_args()[0] model_dir = ModelDir(args.model) corpus = SquadCorpus() if args.corpus == "dev": questions = corpus.get_dev() else: questions = corpus.get_train() questions = split_docs(questions) if args.sample_questions: np.random.RandomState(0).shuffle(sorted(questions, key=lambda x: x.question_id)) questions = questions[:args.sample_questions] questions.sort(key=lambda x:x.n_context_words, reverse=True) dataset = ParagraphAndQuestionDataset(questions, FixedOrderBatcher(args.batch_size, True)) evaluators = [SpanEvaluator(args.answer_bounds, text_eval="squad")] if args.official_output is not None: evaluators.append(RecordSpanPrediction(args.answer_bounds[0])) if args.per_question_loss_file is not None: evaluators.append(RecordSpanPredictionScore(args.answer_bounds[0], args.batch_size, args.none_prob)) if args.step is not None: if args.step == "latest": checkpoint = model_dir.get_latest_checkpoint() else: checkpoint = model_dir.get_checkpoint(int(args.step)) else: checkpoint = model_dir.get_best_weights() if checkpoint is not None: print("Using best weights") else: print("Using latest checkpoint") checkpoint = model_dir.get_latest_checkpoint() model = model_dir.get_model() if args.elmo: model.lm_model.lm_vocab_file = './elmo-params/squad_train_dev_all_unique_tokens.txt' model.lm_model.options_file = './elmo-params/options_squad_lm_2x4096_512_2048cnn_2xhighway_skip.json' model.lm_model.weight_file = './elmo-params/squad_context_concat_lm_2x4096_512_2048cnn_2xhighway_skip.hdf5' model.lm_model.embed_weights_file = None evaluation = trainer.test(model, evaluators, {args.corpus: dataset}, corpus.get_resource_loader(), checkpoint, not args.no_ema)[args.corpus] # Print the scalar results in a two column table scalars = evaluation.scalars cols = list(sorted(scalars.keys())) table = [cols] header = ["Metric", ""] table.append([("%s" % scalars[x] if x in scalars else "-") for x in cols]) print_table([header] + transpose_lists(table)) # Save the official output if args.official_output is not None: quid_to_para = {} for x in questions: quid_to_para[x.question_id] = x.paragraph q_id_to_answers = {} q_ids = evaluation.per_sample["question_id"] spans = evaluation.per_sample["predicted_span"] for q_id, (start, end) in zip(q_ids, spans): text = quid_to_para[q_id].get_original_text(start, end) q_id_to_answers[q_id] = text with open(args.official_output, "w") as f: json.dump(q_id_to_answers, f) if args.per_question_loss_file is not None: print("Saving result") output_file = args.per_question_loss_file ids = evaluation.per_sample["question_ids"] f1s = evaluation.per_sample["text_f1"] ems = evaluation.per_sample["text_em"] losses = evaluation.per_sample["loss"] if args.none_prob: none_probs = evaluation.per_sample["none_probs"] """ results = {question_id: {'f1': float(f1), 'em': float(em), 'loss': float(loss), 'none_prob': float(none_prob)} for question_id, f1, em, loss, none_prob in zip(ids, f1s, ems, losses, none_probs)} """ results = {question_id: float(none_prob) for question_id, none_prob in zip(ids, none_probs)} else: results = {question_id: {'f1': float(f1), 'em': float(em), 'loss': float(loss)} for question_id, f1, em, loss in zip(ids, f1s, ems, losses)} with open(output_file, 'w') as f: json.dump(results, f)
def main(): parser = argparse.ArgumentParser( description='Evaluate a model on document-level SQuAD') parser.add_argument('model', help='model to use') parser.add_argument( 'output', type=str, help="Store the per-paragraph results in csv format in this file") parser.add_argument('-n', '--n_sample', type=int, default=None, help="(for testing) sample documents") parser.add_argument( '-s', '--async', type=int, default=10, help="Encoding batch asynchronously, queueing up to this many") parser.add_argument('-a', '--answer_bound', type=int, default=17, help="Max answer span length") parser.add_argument('-p', '--n_paragraphs', type=int, default=None, help="Max number of paragraphs to use") parser.add_argument( '-b', '--batch_size', type=int, default=200, help="Batch size, larger sizes can be faster but uses more memory") parser.add_argument('-c', '--corpus', choices=["dev", "train", "doc-rd-dev"], default="dev") parser.add_argument('--no_ema', action="store_true", help="Don't use EMA weights even if they exist") args = parser.parse_args() model_dir = ModelDir(args.model) print("Loading data") questions = [] ranker = SquadTfIdfRanker(NltkPlusStopWords(True), args.n_paragraphs, force_answer=False) if args.corpus == "doc-rd-dev": docs = SquadCorpus().get_dev() if args.n_sample is not None: docs.sort(key=lambda x: x.doc_id) np.random.RandomState(0).shuffle(docs) docs = docs[:args.n_sample] print("Fetching document reader docs...") doc_rd_versions = get_doc_rd_doc(docs) print("Ranking and matching with questions...") for doc in tqdm(docs): doc_questions = flatten_iterable(x.questions for x in doc.paragraphs) paragraphs = doc_rd_versions[doc.title] ranks = ranker.rank([x.words for x in doc_questions], [x.text for x in paragraphs]) for i, question in enumerate(doc_questions): para_ranks = np.argsort(ranks[i]) for para_rank, para_num in enumerate( para_ranks[:args.n_paragraphs]): # Just use dummy answers spans for these pairs questions.append( RankedParagraphQuestion( question.words, TokenSpans(question.answer.answer_text, np.zeros((0, 2), dtype=np.int32)), question.question_id, paragraphs[para_num], para_rank, para_num)) rl = ResourceLoader() else: if args.corpus == "dev": docs = SquadCorpus().get_dev() else: docs = SquadCorpus().get_train() rl = SquadCorpus().get_resource_loader() if args.n_sample is not None: docs.sort(key=lambda x: x.doc_id) np.random.RandomState(0).shuffle(docs) docs = docs[:args.n_sample] for q in ranker.ranked_questions(docs): for i, p in enumerate(q.paragraphs): questions.append( RankedParagraphQuestion( q.question, TokenSpans(q.answer_text, p.answer_spans), q.question_id, ParagraphWithInverse([p.text], p.original_text, p.spans), i, p.paragraph_num)) print("Split %d docs into %d paragraphs" % (len(docs), len(questions))) questions = sorted(questions, key=lambda x: (x.n_context_words, len(x.question)), reverse=True) for q in questions: if len(q.answer.answer_spans.shape) != 2: raise ValueError() checkpoint = model_dir.get_best_weights() if checkpoint is not None: print("Using best weights") else: print("Using latest checkpoint") checkpoint = model_dir.get_latest_checkpoint() if checkpoint is None: raise ValueError("No checkpoints found") data = ParagraphAndQuestionDataset( questions, FixedOrderBatcher(args.batch_size, True)) model = model_dir.get_model() evaluation = trainer.test( model, [RecordParagraphSpanPrediction(args.answer_bound, True)], {args.corpus: data}, rl, checkpoint, not args.no_ema, args. async)[args.corpus] print("Saving result") output_file = args.output df = pd.DataFrame(evaluation.per_sample) df.sort_values(["question_id", "rank"], inplace=True, ascending=True) group_by = ["question_id"] f1 = compute_ranked_scores(df, "predicted_score", "text_f1", group_by) em = compute_ranked_scores(df, "predicted_score", "text_em", group_by) table = [["N Paragraphs", "EM", "F1"]] table += list([str(i + 1), "%.4f" % e, "%.4f" % f] for i, (e, f) in enumerate(zip(em, f1))) print_table(table) df.to_csv(output_file, index=False)
def main(): parser = argparse.ArgumentParser( description='Train a model on document-level SQuAD') parser.add_argument( 'mode', choices=["paragraph", "confidence", "shared-norm", "merge", "sigmoid"]) parser.add_argument("name", help="Output directory") args = parser.parse_args() mode = args.mode out = args.name + "-" + datetime.now().strftime("%m%d-%H%M%S") corpus = SquadCorpus() if mode == "merge": # Adds paragraph start tokens, since we will be concatenating paragraphs together pre = WithIndicators(True, para_tokens=False, doc_start_token=False) else: pre = None # model = get_model(50, 100, args.mode, pre) tmp = ModelDir("models/squad-shared-norm") model = tmp.get_model() if mode == "paragraph": # Run in the "standard" known-paragraph setting if model.preprocessor is not None: raise NotImplementedError() n_epochs = 26 train_batching = ClusteredBatcher(45, ContextLenBucketedKey(3), True, False) eval_batching = ClusteredBatcher(45, ContextLenKey(), False, False) data = DocumentQaTrainingData(corpus, None, train_batching, eval_batching) eval = [LossEvaluator(), SpanEvaluator(bound=[17], text_eval="squad")] else: eval_set_mode = { "confidence": "flatten", "sigmoid": "flatten", "shared-norm": "group", "merge": "merge" }[mode] eval_dataset = RandomParagraphSetDatasetBuilder( 100, eval_set_mode, True, 0) if mode == "confidence" or mode == "sigmoid": if mode == "sigmoid": # needs to be trained for a really long time for reasons unknown, even this might be too small n_epochs = 100 else: n_epochs = 50 # more epochs since we only "see" the label very other epoch-osh train_batching = ClusteredBatcher(45, ContextLenBucketedKey(3), True, False) data = PreprocessedData( SquadCorpus(), SquadTfIdfRanker(NltkPlusStopWords(True), 4, True, model.preprocessor), StratifyParagraphsBuilder(train_batching, 1), eval_dataset, eval_on_verified=False, ) else: n_epochs = 26 data = PreprocessedData( SquadCorpus(), SquadTfIdfRanker(NltkPlusStopWords(True), 4, True, model.preprocessor), StratifyParagraphSetsBuilder(25, args.mode == "merge", True, 1), eval_dataset, eval_on_verified=False, ) eval = [LossEvaluator(), MultiParagraphSpanEvaluator(17, "squad")] data.preprocess(1) with open(__file__, "r") as f: notes = f.read() notes = args.mode + "\n" + notes params = train_params(n_epochs) if mode == "paragraph": params.best_weights = ("dev", "b17/text-f1") trainer.start_training(data, model, params, eval, model_dir.ModelDir(out), notes, initialize_from=tmp.get_best_weights())
def main(): parser = argparse.ArgumentParser( description='Evaluate a model on TriviaQA data') parser.add_argument('model', help='model directory') parser.add_argument( '-p', '--paragraph_output', type=str, help="Save fine grained results for each paragraph in csv format") parser.add_argument('-o', '--official_output', type=str, help="Build an offical output file with the model's" " most confident span for each (question, doc) pair") parser.add_argument('--no_ema', action="store_true", help="Don't use EMA weights even if they exist") parser.add_argument( '--n_processes', type=int, default=None, help= "Number of processes to do the preprocessing (selecting paragraphs+loading context) with" ) parser.add_argument('-i', '--step', type=int, default=None, help="checkpoint to load, default to latest") parser.add_argument('-n', '--n_sample', type=int, default=None, help="Number of questions to evaluate on") parser.add_argument('-a', '--async', type=int, default=10) parser.add_argument('-t', '--tokens', type=int, default=400, help="Max tokens per a paragraph") parser.add_argument('-g', '--n_paragraphs', type=int, default=15, help="Number of paragraphs to run the model on") parser.add_argument('-f', '--filter', type=str, default=None, choices=["tfidf", "truncate", "linear"], help="How to select paragraphs") parser.add_argument( '-b', '--batch_size', type=int, default=200, help="Batch size, larger sizes might be faster but wll take more memory" ) parser.add_argument('--max_answer_len', type=int, default=8, help="Max answer span to select") parser.add_argument('-c', '--corpus', choices=[ "web-dev", "web-test", "web-verified-dev", "web-train", "open-dev", "open-train", "wiki-dev", "wiki-test" ], default="web-verified-dev") parser.add_argument("-s", "--source_dir", type=str, default=None, help="where to take input files") parser.add_argument("--n_span_per_q", type=int, default=1, help="where to take input files") args = parser.parse_args() dataset_name = args.source_dir.split('/')[-1] model_name = args.model.split('/')[-1] ElasticLogger().write_log('INFO', 'Start Evaluation', context_dict={ 'model': model_name, 'dataset': dataset_name }) model_dir = ModelDir(args.model) model = model_dir.get_model() if args.corpus.startswith('web'): dataset = TriviaQaWebDataset() if args.corpus == "web-dev": test_questions = dataset.get_dev() elif args.corpus == "web-test": test_questions = dataset.get_test() elif args.corpus == "web-verified-dev": test_questions = dataset.get_verified() elif args.corpus == "web-train": test_questions = dataset.get_train() else: raise AssertionError() elif args.corpus.startswith("wiki"): dataset = TriviaQaWikiDataset() if args.corpus == "wiki-dev": test_questions = dataset.get_dev() elif args.corpus == "wiki-test": test_questions = dataset.get_test() else: raise AssertionError() else: dataset = TriviaQaOpenDataset(args.source_dir) if args.corpus == "open-dev": # just loading the pkl that was saved in build_span_corpus test_questions = dataset.get_dev() elif args.corpus == "open-train": test_questions = dataset.get_train() else: raise AssertionError() ### ALON debuging #test_questions = test_questions[0:5] corpus = dataset.evidence splitter = MergeParagraphs(args.tokens) per_document = args.corpus.startswith( "web") # wiki and web are both multi-document #per_document = True filter_name = args.filter if filter_name is None: # Pick default depending on the kind of data we are using if per_document: filter_name = "tfidf" else: filter_name = "linear" print("Selecting %d paragraphs using method \"%s\" per %s" % (args.n_paragraphs, filter_name, ("question-document pair" if per_document else "question"))) if filter_name == "tfidf": para_filter = TopTfIdf(NltkPlusStopWords(punctuation=True), args.n_paragraphs) elif filter_name == "truncate": para_filter = FirstN(args.n_paragraphs) elif filter_name == "linear": para_filter = ShallowOpenWebRanker(args.n_paragraphs) else: raise ValueError() n_questions = args.n_sample docqa.config.SPANS_PER_QUESTION = args.n_span_per_q #n_questions = 1 if n_questions is not None: test_questions.sort(key=lambda x: x.question_id) np.random.RandomState(0).shuffle(test_questions) test_questions = test_questions[:n_questions] print("Building question/paragraph pairs...") # Loads the relevant questions/documents, selects the right paragraphs, and runs the model's preprocessor if per_document: prep = ExtractMultiParagraphs(splitter, para_filter, model.preprocessor, require_an_answer=False) else: prep = ExtractMultiParagraphsPerQuestion(splitter, para_filter, model.preprocessor, require_an_answer=False) prepped_data = preprocess_par(test_questions, corpus, prep, args.n_processes, 1000) data = [] for q in prepped_data.data: for i, p in enumerate(q.paragraphs): if q.answer_text is None: ans = None else: ans = TokenSpans(q.answer_text, p.answer_spans) data.append( DocumentParagraphQuestion(q.question_id, p.doc_id, (p.start, p.end), q.question, p.text, ans, i)) # Reverse so our first batch will be the largest (so OOMs happen early) questions = sorted(data, key=lambda x: (x.n_context_words, len(x.question)), reverse=True) print("Done, starting eval") if args.step is not None: if args.step == "latest": checkpoint = model_dir.get_latest_checkpoint() else: checkpoint = model_dir.get_checkpoint(int(args.step)) else: checkpoint = model_dir.get_best_weights() if checkpoint is not None: print("Using best weights") else: print("Using latest checkpoint") checkpoint = model_dir.get_latest_checkpoint() test_questions = ParagraphAndQuestionDataset( questions, FixedOrderBatcher(args.batch_size, True)) evaluation = trainer.test( model, [RecordParagraphSpanPrediction(args.max_answer_len, True)], {args.corpus: test_questions}, ResourceLoader(), checkpoint, not args.no_ema, args. async)[args.corpus] if not all(len(x) == len(data) for x in evaluation.per_sample.values()): raise RuntimeError() df = pd.DataFrame(evaluation.per_sample) if args.official_output is not None: print("Saving question result") fns = {} if per_document: # I didn't store the unormalized filenames exactly, so unfortunately we have to reload # the source data to get exact filename to output an official test script print("Loading proper filenames") if args.corpus == 'web-test': source = join(TRIVIA_QA, "qa", "web-test-without-answers.json") elif args.corpus == "web-dev": source = join(TRIVIA_QA, "qa", "web-dev.json") else: raise AssertionError() with open(join(source)) as f: data = json.load(f)["Data"] for point in data: for doc in point["EntityPages"]: filename = doc["Filename"] fn = join("wikipedia", filename[:filename.rfind(".")]) fn = normalize_wiki_filename(fn) fns[(point["QuestionId"], fn)] = filename answers = {} scores = {} for q_id, doc_id, start, end, txt, score in df[[ "question_id", "doc_id", "para_start", "para_end", "text_answer", "predicted_score" ]].itertuples(index=False): filename = dataset.evidence.file_id_map[doc_id] if per_document: if filename.startswith("web"): true_name = filename[4:] + ".txt" else: true_name = fns[(q_id, filename)] # Alon Patch for triviaqa test results true_name = true_name.replace('TriviaQA_Org/', '') key = q_id + "--" + true_name else: key = q_id prev_score = scores.get(key) if prev_score is None or prev_score < score: scores[key] = score answers[key] = txt with open(args.official_output, "w") as f: json.dump(answers, f) output_file = args.paragraph_output if output_file is not None: print("Saving paragraph result") df.to_csv(output_file, index=False) print("Computing scores") if per_document: group_by = ["question_id", "doc_id"] else: group_by = ["question_id"] # Print a table of scores as more paragraphs are used df.sort_values(group_by + ["rank"], inplace=True) df_scores = df.copy(deep=True) df_scores['predicted_score'] = df_scores['predicted_score'].apply( lambda x: pd.Series(x).max()) em = compute_ranked_scores(df_scores, "predicted_score", "text_em", group_by) f1 = compute_ranked_scores(df_scores, "predicted_score", "text_f1", group_by) table = [["N Paragraphs", "EM", "F1"]] table += list([str(i + 1), "%.4f" % e, "%.4f" % f] for i, (e, f) in enumerate(zip(em, f1))) table_df = pd.DataFrame(table[1:], columns=table[0]).drop(['N Paragraphs'], axis=1) ElasticLogger().write_log('INFO', 'Results', context_dict={'model': model_name, 'dataset': dataset_name, \ 'max_EM':table_df.max().ix['EM'], \ 'max_F1':table_df.max().ix['F1'], \ 'result_table': str(table_df)}) df_flat = [] for id, question in df.iterrows(): for text_answer, predicted_span, predicted_score in zip( question['text_answer'], question['predicted_span'], question['predicted_score']): new_question = dict(question.copy()) new_question.update({ 'text_answer': text_answer, 'predicted_span': predicted_span, 'predicted_score': predicted_score }) df_flat.append(new_question) results_df = pd.DataFrame(df_flat) #Alon: outputing the estimates for all the #results_df = results_df.groupby(['question_id', 'text_answer']).apply(lambda df: df.ix[df['predicted_score'].argmax()]).reset_index(drop=True) results_df.sort_values(by=['question_id', 'predicted_score'], ascending=False).set_index([ 'question_id', 'text_answer' ])[['question', 'predicted_score', 'text_em']].to_csv('results.csv') print_table(table)
def convert(model_dir, output_dir, best_weights=False): print("Load model") md = ModelDir(model_dir) model = md.get_model() print("Setting up cudnn version") # global_step = tf.get_variable('global_step', shape=[], dtype='int32', trainable=False) sess = tf.Session() with sess.as_default(): model.set_input_spec(ParagraphAndQuestionSpec(1, None, None, 14), {"the"}, ResourceLoader(lambda a,b: {"the": np.zeros(300, np.float32)})) print("Buiding graph") pred = model.get_prediction() test_questions = ParagraphAndQuestion(["Harry", "Potter", "was", "written", "by", "JK"], ["Who", "wrote", "Harry", "Potter", "?"], None, "test_questions") print("Load vars") save = tf.train.Saver() if best_weights: checkpoint = md.get_best_weights() else: checkpoint = md.get_latest_checkpoint() print("Loading checkpoint: " + checkpoint) save.restore(sess, checkpoint) print("Restoring EMA variables") ema = tf.train.ExponentialMovingAverage(0) saver = tf.train.Saver({ema.average_name(x): x for x in tf.trainable_variables()}) saver.restore(sess, checkpoint) feed = model.encode([test_questions], False) cuddn_out = sess.run([pred.start_logits, pred.end_logits], feed_dict=feed) dim = 90 print("Done, copying files...") if not exists(output_dir): mkdir(output_dir) for file in listdir(model_dir): if isfile(file) and file != "model.npy": copyfile(join(model_dir, file), join(output_dir, file)) print("Done, mapping tensors...") to_save = [] to_init = [] for x in tf.trainable_variables(): if x.name.endswith("/gru_parameters:0"): key = x.name[:-len("/gru_parameters:0")] fw_params = x if "map_embed" in x.name: c = cudnn_rnn_ops.CudnnGRU(1, dim, 1424) elif "chained-out" in x.name: c = cudnn_rnn_ops.CudnnGRU(1, dim, dim * 4) else: c = cudnn_rnn_ops.CudnnGRU(1, dim, dim * 2) params_saveable = cudnn_rnn_ops.RNNParamsSaveable( c, c.params_to_canonical, c.canonical_to_params, [fw_params], key) for spec in params_saveable.specs: if spec.name.endswith("bias_cudnn 0") or \ spec.name.endswith("bias_cudnn 1"): # ??? What do these even do? continue name = spec.name.split("/") name.remove("cell_0") if "forward" in name: ix = name.index("forward") name.insert(ix+2, "fw") else: ix = name.index("backward") name.insert(ix + 2, "bw") del name[ix] ix = name.index("multi_rnn_cell") name[ix] = "bidirectional_rnn" name = "/".join(name) v = tf.Variable(sess.run(spec.tensor), name=name) to_init.append(v) to_save.append(v) else: to_save.append(x) other = [x for x in tf.get_collection(tf.GraphKeys.GLOBAL_VARIABLES) if x not in tf.trainable_variables()] print(other) sess.run(tf.initialize_variables(to_init)) saver = tf.train.Saver(to_save + other) save_dir = join(output_dir, "save") if not exists(save_dir): mkdir(save_dir) print("GLOBAL STEP HACK REMOVE ME") saver.save(sess, join(save_dir, "checkpoint"), 42000) sess.close() tf.reset_default_graph() print("Updating model...") model.embed_mapper.layers = [model.embed_mapper.layers[0], BiRecurrentMapper(CompatGruCellSpec(dim))] model.match_encoder.layers = list(model.match_encoder.layers) other = model.match_encoder.layers[1].other other.layers = list(other.layers) other.layers[1] = BiRecurrentMapper(CompatGruCellSpec(dim)) pred = model.predictor.predictor pred.first_layer = BiRecurrentMapper(CompatGruCellSpec(dim)) pred.second_layer = BiRecurrentMapper(CompatGruCellSpec(dim)) with open(join(output_dir, "model.pkl"), "wb") as f: pickle.dump(model, f) print("Testing...") with open(join(output_dir, "model.pkl"), "rb") as f: model = pickle.load(f) sess = tf.Session() model.set_input_spec(ParagraphAndQuestionSpec(1, None, None, 14), {"the"}, ResourceLoader(lambda a, b: {"the": np.zeros(300, np.float32)})) pred = model.get_prediction() print("Rebuilding") saver = tf.train.Saver() saver.restore(sess, tf.train.latest_checkpoint(save_dir)) feed = model.encode([test_questions], False) cpu_out = sess.run([pred.start_logits, pred.end_logits], feed_dict=feed) print("These should be close:") print([np.allclose(a, b) for a,b in zip(cpu_out, cuddn_out)]) print(cpu_out) print(cuddn_out)
def run(): parser = argparse.ArgumentParser() parser.add_argument("input_data") parser.add_argument("output_data") parser.add_argument("--plot_dir", type=str, default=None) parser.add_argument("--model_dir", type=str, default="/tmp/model/document-qa") parser.add_argument("--lm_dir", type=str, default="/home/castle/data/lm/squad-context-concat-skip") parser.add_argument("--glove_dir", type=str, default="/home/castle/data/glove") parser.add_argument("--n", type=int, default=None) parser.add_argument("-b", "--batch_size", type=int, default=30) parser.add_argument("--ema", action="store_true") args = parser.parse_args() input_data = args.input_data output_path = args.output_data model_dir = ModelDir(args.model_dir) nltk.data.path.append("nltk_data") print("Loading data") docs = parse_squad_data(input_data, "", NltkAndPunctTokenizer(), False) pairs = split_docs(docs) dataset = ParagraphAndQuestionDataset(pairs, ClusteredBatcher(args.batch_size, ContextLenKey(), False, True)) print("Done, init model") model = model_dir.get_model() # small hack, just load the vector file at its expected location rather then using the config location loader = ResourceLoader(lambda a, b: load_word_vector_file(join(args.glove_dir, "glove.840B.300d.txt"), b)) lm_model = model.lm_model basedir = args.lm_dir plotdir = args.plot_dir lm_model.lm_vocab_file = join(basedir, "squad_train_dev_all_unique_tokens.txt") lm_model.options_file = join(basedir, "options_squad_lm_2x4096_512_2048cnn_2xhighway_skip.json") lm_model.weight_file = join(basedir, "squad_context_concat_lm_2x4096_512_2048cnn_2xhighway_skip.hdf5") lm_model.embed_weights_file = None model.set_inputs([dataset], loader) print("Done, building graph") sess = tf.Session() with sess.as_default(): pred = model.get_prediction() best_span = pred.get_best_span(17)[0] if plotdir != None: start_logits_op, end_logits_op = pred.get_logits() all_vars = tf.global_variables() + tf.get_collection(tf.GraphKeys.SAVEABLE_OBJECTS) dont_restore_names = {x.name for x in all_vars if x.name.startswith("bilm")} print(sorted(dont_restore_names)) vars = [x for x in all_vars if x.name not in dont_restore_names] print("Done, loading weights") checkpoint = model_dir.get_best_weights() if checkpoint is None: print("Loading most recent checkpoint") checkpoint = model_dir.get_latest_checkpoint() else: print("Loading best weights") saver = tf.train.Saver(vars) saver.restore(sess, checkpoint) if args.ema: ema = tf.train.ExponentialMovingAverage(0) saver = tf.train.Saver({ema.average_name(x): x for x in tf.trainable_variables()}) saver.restore(sess, checkpoint) sess.run(tf.variables_initializer([x for x in all_vars if x.name in dont_restore_names])) print("Done, starting evaluation") out = {} for i, batch in enumerate(dataset.get_epoch()): if args.n is not None and i == args.n: break print("On batch size [%d], now in %d th batch" % (args.batch_size, i +1)) enc = model.encode(batch, False) if plotdir != None: spans, start_logits, end_logits = sess.run([best_span, start_logits_op, end_logits_op], feed_dict=enc) for bi, point in enumerate(batch): q = ' '.join(point.question) c = point.paragraph.get_context() gt = ' | '.join(point.answer.answer_text) s, e = spans[bi] pred = point.get_original_text(s, e) start_dist = start_logits[bi] end_dist = end_logits[bi] c_interval = np.arange(0.0, start_dist.shape[0], 1) c_label = c plt.figure(1) plt.subplot(211) plt.plot(c_interval, start_dist, color='r') plt.title("Q : " + q + " // A : " + gt, fontsize=9) plt.text(0, 0, r'Predict : %s [%d:%d]' % (pred, s, e), color='b') axes = plt.gca() axes.set_ylim([-20, 20]) plt.subplot(212) plt.plot(c_interval, end_dist, color='g') plt.xticks(c_interval, c_label, rotation=90, fontsize=5) axes = plt.gca() axes.set_ylim([-20, 20]) plt.show() break else: spans = sess.run(best_span, feed_dict=enc) for (s, e), point in zip(spans, batch): out[point.question_id] = point.get_original_text(s, e) sess.close() print("Done, saving") with open(output_path, "w") as f: json.dump(out, f) print("Mission accomplished!")
def main(): parser = argparse.ArgumentParser(description='Evaluate a model on SQuAD') parser.add_argument('model', help='model directory to evaluate') parser.add_argument("-o", "--official_output", type=str, help="where to output an official result file") parser.add_argument('-n', '--sample_questions', type=int, default=None, help="(for testing) run on a subset of questions") parser.add_argument('--answer_bounds', nargs='+', type=int, default=[17], help="Max size of answer") parser.add_argument('-b', '--batch_size', type=int, default=45, help="Batch size, larger sizes can be faster but uses more memory") parser.add_argument('-s', '--step', default=None, help="Weights to load, can be a checkpoint step or 'latest'") parser.add_argument('-c', '--corpus', choices=["dev", "train"], default="dev") parser.add_argument('--no_ema', action="store_true", help="Don't use EMA weights even if they exist") args = parser.parse_args() num_choices = 4 model_dir = ModelDir(args.model) corpus = SquadCorpus() if args.corpus == "dev": questions = corpus.get_dev() else: questions = corpus.get_train() questions = split_docs(questions) if args.sample_questions: np.random.RandomState(0).shuffle(sorted(questions, key=lambda x: x.question_id)) questions = questions[:args.sample_questions] questions.sort(key=lambda x:x.n_context_words, reverse=True) #pdb.set_trace() #print(args.batch_size) #dataset = ParagraphAndQuestionDataset(questions, FixedOrderBatcher(args.batch_size, False),None,num_choices) dataset = ParagraphAndQuestionDataset(questions, ClusteredBatcher(45, ContextLenKey(), False, False),None,num_choices) #ClusteredBatcher(45, ContextLenKey(), False, False) evaluators = [MultiChoiceEvaluator(num_choices)] #if args.official_output is not None: #evaluators.append(RecordSpanPrediction(args.answer_bounds[0])) #pdb.set_trace() if args.step is not None: if args.step == "latest": checkpoint = model_dir.get_latest_checkpoint() else: checkpoint = model_dir.get_checkpoint(int(args.step)) else: checkpoint = model_dir.get_best_weights() if checkpoint is not None: print("Using best weights") else: print("Using latest checkpoint") checkpoint = model_dir.get_latest_checkpoint() model = model_dir.get_model() #pdb.set_trace() evaluation = trainer.test(model, evaluators, {args.corpus: dataset}, corpus.get_resource_loader(), checkpoint, not args.no_ema)[args.corpus] #pdb.set_trace() # Print the scalar results in a two column table scalars = evaluation.scalars cols = list(sorted(scalars.keys())) table = [cols] header = ["Metric", ""] table.append([("%s" % scalars[x] if x in scalars else "-") for x in cols]) print_table([header] + transpose_lists(table)) # Save the official output if args.official_output is not None: data_to_dump = {} list_of_choices = ['A','B','C','D'] q_ids = evaluation.per_sample["question_id"] correct_ans = evaluation.per_sample["correct answer"] correct_ids = evaluation.per_sample["correct index"] pred_ids = evaluation.per_sample["predictied index"] pred_ans = evaluation.per_sample["predictied answer"] is_correct = evaluation.per_sample["is correct"] #pdb.set_trace() for ix, q_ids in enumerate(q_ids): if(is_correct[ix]): data_to_dump[q_ids] = {'Is Correct' : 'True', 'predictied' : [' '.join(pred_ans[ix]),list_of_choices[pred_ids[ix]]], 'correct' : [' '.join(correct_ans[ix]),list_of_choices[correct_ids[ix]]] } else: data_to_dump[q_ids] = {'Is Correct' : 'False', 'predictied' : [' '.join(pred_ans[ix]),list_of_choices[pred_ids[ix]]], 'correct' : [' '.join(correct_ans[ix]),list_of_choices[correct_ids[ix]]] } #pdb.set_trace() with open(args.official_output, "w") as f: json.dump(data_to_dump , f)