├── .flake8 ├── .github └── workflows │ ├── python-publish.yml │ └── python-tests.yml ├── .pre-commit-config.yaml ├── .pylintrc ├── LICENSE ├── MANIFEST.in ├── MultiMedEvalAdditionalDatasets ├── exampleDatasetQA │ └── dataset.json └── exampleDatasetVQA │ ├── dataset.json │ ├── image1.png │ └── image2.png ├── README.md ├── figures ├── image_classification.png ├── modalities.png ├── sankey.png └── tasks.png ├── multimedeval ├── __init__.py ├── chestxray14.py ├── chexbert │ ├── __init__.py │ ├── bert_tokenizer.py │ ├── constants.py │ ├── datasets │ │ ├── __init__.py │ │ └── unlabeled_dataset.py │ ├── label.py │ ├── models │ │ ├── __init__.py │ │ └── bert_encoder.py │ └── utils.py ├── ct_rate.py ├── dynamic_datasets.py ├── engine.py ├── image_classification.py ├── mednli.py ├── mimic.py ├── mimic_iii.py ├── mnist.py ├── overrides_ │ ├── __init__.py │ ├── enforce.py │ ├── final.py │ └── overrides.py ├── qa.py ├── radcliq-v1.dill ├── radgraph │ ├── __init__.py │ ├── allennlp │ │ ├── __init__.py │ │ ├── __main__.py │ │ ├── commands │ │ │ ├── __init__.py │ │ │ ├── evaluate.py │ │ │ ├── find_learning_rate.py │ │ │ ├── predict.py │ │ │ ├── print_results.py │ │ │ ├── subcommand.py │ │ │ ├── test_install.py │ │ │ └── train.py │ │ ├── common │ │ │ ├── __init__.py │ │ │ ├── cached_transformers.py │ │ │ ├── checks.py │ │ │ ├── file_utils.py │ │ │ ├── from_params.py │ │ │ ├── lazy.py │ │ │ ├── logging.py │ │ │ ├── params.py │ │ │ ├── plugins.py │ │ │ ├── registrable.py │ │ │ ├── testing │ │ │ │ ├── __init__.py │ │ │ │ ├── distributed_test.py │ │ │ │ ├── model_test_case.py │ │ │ │ └── test_case.py │ │ │ ├── tqdm.py │ │ │ └── util.py │ │ ├── data │ │ │ ├── __init__.py │ │ │ ├── batch.py │ │ │ ├── dataloader.py │ │ │ ├── dataset_readers │ │ │ │ ├── __init__.py │ │ │ │ ├── babi.py │ │ │ │ ├── conll2003.py │ │ │ │ ├── dataset_reader.py │ │ │ │ ├── dataset_utils │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── span_utils.py │ │ │ │ ├── interleaving_dataset_reader.py │ │ │ │ ├── sequence_tagging.py │ │ │ │ ├── sharded_dataset_reader.py │ │ │ │ └── text_classification_json.py │ │ │ ├── fields │ │ │ │ ├── __init__.py │ │ │ │ ├── adjacency_field.py │ │ │ │ ├── array_field.py │ │ │ │ ├── field.py │ │ │ │ ├── flag_field.py │ │ │ │ ├── index_field.py │ │ │ │ ├── label_field.py │ │ │ │ ├── list_field.py │ │ │ │ ├── metadata_field.py │ │ │ │ ├── multilabel_field.py │ │ │ │ ├── namespace_swapping_field.py │ │ │ │ ├── sequence_field.py │ │ │ │ ├── sequence_label_field.py │ │ │ │ ├── span_field.py │ │ │ │ └── text_field.py │ │ │ ├── instance.py │ │ │ ├── samplers │ │ │ │ ├── __init__.py │ │ │ │ ├── bucket_batch_sampler.py │ │ │ │ ├── max_tokens_batch_sampler.py │ │ │ │ └── samplers.py │ │ │ ├── token_indexers │ │ │ │ ├── __init__.py │ │ │ │ ├── elmo_indexer.py │ │ │ │ ├── pretrained_transformer_indexer.py │ │ │ │ ├── pretrained_transformer_mismatched_indexer.py │ │ │ │ ├── single_id_token_indexer.py │ │ │ │ ├── spacy_indexer.py │ │ │ │ ├── token_characters_indexer.py │ │ │ │ └── token_indexer.py │ │ │ ├── tokenizers │ │ │ │ ├── __init__.py │ │ │ │ ├── character_tokenizer.py │ │ │ │ ├── letters_digits_tokenizer.py │ │ │ │ ├── pretrained_transformer_tokenizer.py │ │ │ │ ├── sentence_splitter.py │ │ │ │ ├── spacy_tokenizer.py │ │ │ │ ├── token.py │ │ │ │ ├── tokenizer.py │ │ │ │ └── whitespace_tokenizer.py │ │ │ └── vocabulary.py │ │ ├── interpret │ │ │ ├── __init__.py │ │ │ ├── attackers │ │ │ │ ├── __init__.py │ │ │ │ ├── attacker.py │ │ │ │ ├── hotflip.py │ │ │ │ ├── input_reduction.py │ │ │ │ └── utils.py │ │ │ └── saliency_interpreters │ │ │ │ ├── __init__.py │ │ │ │ ├── integrated_gradient.py │ │ │ │ ├── saliency_interpreter.py │ │ │ │ ├── simple_gradient.py │ │ │ │ └── smooth_gradient.py │ │ ├── models │ │ │ ├── __init__.py │ │ │ ├── archival.py │ │ │ ├── basic_classifier.py │ │ │ ├── model.py │ │ │ └── simple_tagger.py │ │ ├── modules │ │ │ ├── __init__.py │ │ │ ├── attention │ │ │ │ ├── __init__.py │ │ │ │ ├── additive_attention.py │ │ │ │ ├── attention.py │ │ │ │ ├── bilinear_attention.py │ │ │ │ ├── cosine_attention.py │ │ │ │ ├── dot_product_attention.py │ │ │ │ └── linear_attention.py │ │ │ ├── augmented_lstm.py │ │ │ ├── bimpm_matching.py │ │ │ ├── conditional_random_field.py │ │ │ ├── elmo.py │ │ │ ├── elmo_lstm.py │ │ │ ├── encoder_base.py │ │ │ ├── feedforward.py │ │ │ ├── gated_sum.py │ │ │ ├── highway.py │ │ │ ├── input_variational_dropout.py │ │ │ ├── layer_norm.py │ │ │ ├── lstm_cell_with_projection.py │ │ │ ├── masked_layer_norm.py │ │ │ ├── matrix_attention │ │ │ │ ├── __init__.py │ │ │ │ ├── bilinear_matrix_attention.py │ │ │ │ ├── cosine_matrix_attention.py │ │ │ │ ├── dot_product_matrix_attention.py │ │ │ │ ├── linear_matrix_attention.py │ │ │ │ └── matrix_attention.py │ │ │ ├── maxout.py │ │ │ ├── residual_with_layer_dropout.py │ │ │ ├── sampled_softmax_loss.py │ │ │ ├── scalar_mix.py │ │ │ ├── seq2seq_encoders │ │ │ │ ├── __init__.py │ │ │ │ ├── compose_encoder.py │ │ │ │ ├── feedforward_encoder.py │ │ │ │ ├── gated_cnn_encoder.py │ │ │ │ ├── pass_through_encoder.py │ │ │ │ ├── pytorch_seq2seq_wrapper.py │ │ │ │ ├── pytorch_transformer_wrapper.py │ │ │ │ └── seq2seq_encoder.py │ │ │ ├── seq2vec_encoders │ │ │ │ ├── __init__.py │ │ │ │ ├── bert_pooler.py │ │ │ │ ├── boe_encoder.py │ │ │ │ ├── cls_pooler.py │ │ │ │ ├── cnn_encoder.py │ │ │ │ ├── cnn_highway_encoder.py │ │ │ │ ├── pytorch_seq2vec_wrapper.py │ │ │ │ └── seq2vec_encoder.py │ │ │ ├── softmax_loss.py │ │ │ ├── span_extractors │ │ │ │ ├── __init__.py │ │ │ │ ├── bidirectional_endpoint_span_extractor.py │ │ │ │ ├── endpoint_span_extractor.py │ │ │ │ ├── self_attentive_span_extractor.py │ │ │ │ └── span_extractor.py │ │ │ ├── stacked_alternating_lstm.py │ │ │ ├── stacked_bidirectional_lstm.py │ │ │ ├── text_field_embedders │ │ │ │ ├── __init__.py │ │ │ │ ├── basic_text_field_embedder.py │ │ │ │ └── text_field_embedder.py │ │ │ ├── time_distributed.py │ │ │ └── token_embedders │ │ │ │ ├── __init__.py │ │ │ │ ├── bag_of_word_counts_token_embedder.py │ │ │ │ ├── elmo_token_embedder.py │ │ │ │ ├── embedding.py │ │ │ │ ├── empty_embedder.py │ │ │ │ ├── pass_through_token_embedder.py │ │ │ │ ├── pretrained_transformer_embedder.py │ │ │ │ ├── pretrained_transformer_mismatched_embedder.py │ │ │ │ ├── token_characters_encoder.py │ │ │ │ └── token_embedder.py │ │ ├── nn │ │ │ ├── __init__.py │ │ │ ├── activations.py │ │ │ ├── beam_search.py │ │ │ ├── chu_liu_edmonds.py │ │ │ ├── initializers.py │ │ │ ├── regularizers │ │ │ │ ├── __init__.py │ │ │ │ ├── regularizer.py │ │ │ │ ├── regularizer_applicator.py │ │ │ │ └── regularizers.py │ │ │ └── util.py │ │ ├── predictors │ │ │ ├── __init__.py │ │ │ ├── predictor.py │ │ │ ├── sentence_tagger.py │ │ │ └── text_classifier.py │ │ ├── tools │ │ │ ├── __init__.py │ │ │ ├── archive_surgery.py │ │ │ ├── create_elmo_embeddings_from_vocab.py │ │ │ └── inspect_cache.py │ │ ├── training │ │ │ ├── __init__.py │ │ │ ├── checkpointer.py │ │ │ ├── learning_rate_schedulers │ │ │ │ ├── __init__.py │ │ │ │ ├── cosine.py │ │ │ │ ├── learning_rate_scheduler.py │ │ │ │ ├── linear_with_warmup.py │ │ │ │ ├── noam.py │ │ │ │ ├── polynomial_decay.py │ │ │ │ └── slanted_triangular.py │ │ │ ├── metric_tracker.py │ │ │ ├── metrics │ │ │ │ ├── __init__.py │ │ │ │ ├── attachment_scores.py │ │ │ │ ├── auc.py │ │ │ │ ├── average.py │ │ │ │ ├── bleu.py │ │ │ │ ├── boolean_accuracy.py │ │ │ │ ├── categorical_accuracy.py │ │ │ │ ├── covariance.py │ │ │ │ ├── entropy.py │ │ │ │ ├── evalb_bracketing_scorer.py │ │ │ │ ├── f1_measure.py │ │ │ │ ├── fbeta_measure.py │ │ │ │ ├── mean_absolute_error.py │ │ │ │ ├── metric.py │ │ │ │ ├── pearson_correlation.py │ │ │ │ ├── perplexity.py │ │ │ │ ├── rouge.py │ │ │ │ ├── sequence_accuracy.py │ │ │ │ ├── span_based_f1_measure.py │ │ │ │ ├── spearman_correlation.py │ │ │ │ └── unigram_recall.py │ │ │ ├── momentum_schedulers │ │ │ │ ├── __init__.py │ │ │ │ ├── inverted_triangular.py │ │ │ │ └── momentum_scheduler.py │ │ │ ├── moving_average.py │ │ │ ├── no_op_trainer.py │ │ │ ├── optimizers.py │ │ │ ├── scheduler.py │ │ │ ├── tensorboard_writer.py │ │ │ ├── trainer.py │ │ │ └── util.py │ │ └── version.py │ ├── allennlp_models │ │ ├── __init__.py │ │ ├── classification │ │ │ ├── __init__.py │ │ │ ├── dataset_readers │ │ │ │ ├── __init__.py │ │ │ │ └── stanford_sentiment_tree_bank.py │ │ │ └── models │ │ │ │ ├── __init__.py │ │ │ │ └── biattentive_classification_network.py │ │ ├── common │ │ │ ├── __init__.py │ │ │ ├── model_card.py │ │ │ └── ontonotes.py │ │ ├── coref │ │ │ ├── __init__.py │ │ │ ├── dataset_readers │ │ │ │ ├── __init__.py │ │ │ │ ├── conll.py │ │ │ │ ├── preco.py │ │ │ │ └── winobias.py │ │ │ ├── metrics │ │ │ │ ├── __init__.py │ │ │ │ ├── conll_coref_scores.py │ │ │ │ └── mention_recall.py │ │ │ ├── models │ │ │ │ ├── __init__.py │ │ │ │ └── coref.py │ │ │ ├── predictors │ │ │ │ ├── __init__.py │ │ │ │ └── coref.py │ │ │ └── util.py │ │ ├── generation │ │ │ ├── __init__.py │ │ │ ├── dataset_readers │ │ │ │ ├── __init__.py │ │ │ │ ├── cnn_dm.py │ │ │ │ ├── copynet_seq2seq.py │ │ │ │ └── seq2seq.py │ │ │ ├── models │ │ │ │ ├── __init__.py │ │ │ │ ├── bart.py │ │ │ │ ├── composed_seq2seq.py │ │ │ │ ├── copynet_seq2seq.py │ │ │ │ └── simple_seq2seq.py │ │ │ ├── modules │ │ │ │ ├── __init__.py │ │ │ │ ├── decoder_nets │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── decoder_net.py │ │ │ │ │ ├── lstm_cell.py │ │ │ │ │ └── stacked_self_attention.py │ │ │ │ └── seq_decoders │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── auto_regressive.py │ │ │ │ │ └── seq_decoder.py │ │ │ └── predictors │ │ │ │ ├── __init__.py │ │ │ │ └── seq2seq.py │ │ ├── lm │ │ │ ├── __init__.py │ │ │ ├── dataset_readers │ │ │ │ ├── __init__.py │ │ │ │ ├── masked_language_model.py │ │ │ │ ├── next_token_lm.py │ │ │ │ └── simple_language_modeling.py │ │ │ ├── models │ │ │ │ ├── __init__.py │ │ │ │ ├── bidirectional_lm.py │ │ │ │ ├── language_model.py │ │ │ │ ├── masked_language_model.py │ │ │ │ └── next_token_lm.py │ │ │ ├── modules │ │ │ │ ├── __init__.py │ │ │ │ ├── language_model_heads │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── bert.py │ │ │ │ │ ├── gpt2.py │ │ │ │ │ ├── language_model_head.py │ │ │ │ │ └── linear.py │ │ │ │ ├── seq2seq_encoders │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── bidirectional_lm_transformer.py │ │ │ │ └── token_embedders │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── bidirectional_lm.py │ │ │ │ │ └── language_model.py │ │ │ └── predictors │ │ │ │ ├── __init__.py │ │ │ │ ├── masked_language_model.py │ │ │ │ └── next_token_lm.py │ │ ├── mc │ │ │ ├── __init__.py │ │ │ ├── dataset_readers │ │ │ │ ├── __init__.py │ │ │ │ ├── commonsenseqa.py │ │ │ │ ├── fake.py │ │ │ │ ├── piqa.py │ │ │ │ ├── swag.py │ │ │ │ └── transformer_mc.py │ │ │ ├── models │ │ │ │ ├── __init__.py │ │ │ │ └── transformer_mc.py │ │ │ └── predictors │ │ │ │ ├── __init__.py │ │ │ │ └── transformer_mc.py │ │ ├── pair_classification │ │ │ ├── __init__.py │ │ │ ├── dataset_readers │ │ │ │ ├── __init__.py │ │ │ │ ├── quora_paraphrase.py │ │ │ │ └── snli.py │ │ │ ├── models │ │ │ │ ├── __init__.py │ │ │ │ ├── bimpm.py │ │ │ │ ├── decomposable_attention.py │ │ │ │ └── esim.py │ │ │ └── predictors │ │ │ │ ├── __init__.py │ │ │ │ └── textual_entailment.py │ │ ├── pretrained.py │ │ ├── rc │ │ │ ├── __init__.py │ │ │ ├── dataset_readers │ │ │ │ ├── __init__.py │ │ │ │ ├── drop.py │ │ │ │ ├── qangaroo.py │ │ │ │ ├── quac.py │ │ │ │ ├── squad.py │ │ │ │ ├── transformer_squad.py │ │ │ │ ├── triviaqa.py │ │ │ │ └── utils.py │ │ │ ├── metrics │ │ │ │ ├── __init__.py │ │ │ │ ├── drop_em_and_f1.py │ │ │ │ └── squad_em_and_f1.py │ │ │ ├── models │ │ │ │ ├── __init__.py │ │ │ │ ├── bidaf.py │ │ │ │ ├── bidaf_ensemble.py │ │ │ │ ├── dialog_qa.py │ │ │ │ ├── naqanet.py │ │ │ │ ├── qanet.py │ │ │ │ ├── transformer_qa.py │ │ │ │ └── utils.py │ │ │ ├── modules │ │ │ │ ├── __init__.py │ │ │ │ └── seq2seq_encoders │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── multi_head_self_attention.py │ │ │ │ │ ├── qanet_encoder.py │ │ │ │ │ └── stacked_self_attention.py │ │ │ ├── predictors │ │ │ │ ├── __init__.py │ │ │ │ ├── bidaf.py │ │ │ │ ├── dialog_qa.py │ │ │ │ └── transformer_qa.py │ │ │ └── tools │ │ │ │ ├── __init__.py │ │ │ │ ├── drop.py │ │ │ │ ├── narrativeqa.py │ │ │ │ ├── orb.py │ │ │ │ ├── orb_utils.py │ │ │ │ ├── quoref.py │ │ │ │ ├── squad.py │ │ │ │ ├── squad2.py │ │ │ │ └── transformer_qa.py │ │ ├── structured_prediction │ │ │ ├── __init__.py │ │ │ ├── dataset_readers │ │ │ │ ├── __init__.py │ │ │ │ ├── penn_tree_bank.py │ │ │ │ ├── semantic_dependencies.py │ │ │ │ ├── srl.py │ │ │ │ └── universal_dependencies.py │ │ │ ├── metrics │ │ │ │ ├── __init__.py │ │ │ │ └── srl_eval_scorer.py │ │ │ ├── models │ │ │ │ ├── __init__.py │ │ │ │ ├── biaffine_dependency_parser.py │ │ │ │ ├── constituency_parser.py │ │ │ │ ├── graph_parser.py │ │ │ │ ├── srl.py │ │ │ │ └── srl_bert.py │ │ │ ├── predictors │ │ │ │ ├── __init__.py │ │ │ │ ├── biaffine_dependency_parser.py │ │ │ │ ├── constituency_parser.py │ │ │ │ ├── openie.py │ │ │ │ └── srl.py │ │ │ └── tools │ │ │ │ ├── __init__.py │ │ │ │ ├── convert_openie_to_conll.py │ │ │ │ └── write_srl_predictions_to_conll_format.py │ │ ├── tagging │ │ │ ├── __init__.py │ │ │ ├── dataset_readers │ │ │ │ ├── __init__.py │ │ │ │ ├── ccgbank.py │ │ │ │ ├── conll2000.py │ │ │ │ ├── conll2003.py │ │ │ │ └── ontonotes_ner.py │ │ │ ├── models │ │ │ │ ├── __init__.py │ │ │ │ └── crf_tagger.py │ │ │ └── predictors │ │ │ │ ├── __init__.py │ │ │ │ └── sentence_tagger.py │ │ └── version.py │ ├── dygie │ │ ├── __init__.py │ │ ├── data │ │ │ ├── __init__.py │ │ │ ├── dataset_readers │ │ │ │ ├── __init__.py │ │ │ │ ├── document.py │ │ │ │ └── dygie.py │ │ │ └── fields │ │ │ │ ├── __init__.py │ │ │ │ └── adjacency_field_assym.py │ │ ├── models │ │ │ ├── __init__.py │ │ │ ├── coref.py │ │ │ ├── dygie.py │ │ │ ├── entity_beam_pruner.py │ │ │ ├── events.py │ │ │ ├── ner.py │ │ │ ├── relation.py │ │ │ └── shared.py │ │ ├── predictors │ │ │ ├── __init__.py │ │ │ └── dygie.py │ │ └── training │ │ │ ├── __init__.py │ │ │ ├── event_metrics.py │ │ │ ├── f1.py │ │ │ ├── ner_metrics.py │ │ │ └── relation_metrics.py │ ├── radgpt.py │ ├── radgraph.py │ ├── rewards.py │ └── utils.py ├── refuge.py ├── report_comparison_utils.py ├── task_families.py ├── tqdm_loggable.py ├── utils.py ├── visualization.py └── vqa.py ├── poetry.lock ├── pyproject.toml ├── results ├── LLMs │ ├── batcher.py │ └── requirements.txt ├── __init__.py ├── ct_clip │ ├── attention.py │ ├── ct_clip.py │ ├── cvit.py │ ├── mlm.py │ ├── thresholds_CT-CLIP.json │ ├── thresholds_CT-LiPro.json │ ├── thresholds_CT-VocabFine.json │ └── visual_ssl.py ├── llava_med │ ├── README.md │ ├── batcher.py │ └── requirements.txt ├── main.py ├── pmc_llama │ ├── MedMCQA.csv │ ├── MedQA.csv │ ├── PubMedQA.csv │ ├── metrics_MedMCQA.json │ ├── metrics_MedQA.json │ └── metrics_PubMedQA.json ├── rad_fm │ ├── Model │ │ ├── __init__.py │ │ ├── blocks.py │ │ ├── helpers.py │ │ ├── multimodality_model.py │ │ ├── my_embedding_layer.py │ │ ├── position_encoding.py │ │ ├── transformer_decoder.py │ │ ├── utils.py │ │ └── vit_3d.py │ ├── README.md │ ├── __init__.py │ ├── batcher.py │ └── requirements.txt └── readme.md └── tests ├── __init__.py ├── test_config.json ├── test_config_chestxray14.json ├── test_dataclasses.py ├── test_image_classification.py ├── test_loading_all.py ├── test_nli.py ├── test_report_comparison.py ├── test_segmentation.py └── test_vqa_preprocessing.py /.flake8: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/corentin-ryr/MultiMedEval/HEAD/.flake8 -------------------------------------------------------------------------------- /.github/workflows/python-publish.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/corentin-ryr/MultiMedEval/HEAD/.github/workflows/python-publish.yml 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