├── .gitignore ├── LICENSE ├── README.md ├── analysis_framework ├── README.md ├── analysis.ipynb ├── compile_results.py ├── compile_results.sh ├── zeno_upload.py └── zeno_upload.sh ├── download_data.py ├── file_utils.py ├── reader ├── README.md ├── bash_scripts │ └── example_generation_script.sh ├── evaluate_top_k.py ├── generate_top_k.py ├── reader_model.py └── utils.py ├── requirements.txt ├── retriever ├── BM25 │ ├── BM25_connector.py │ ├── base_retriever.py │ ├── bm25.sh │ ├── bm25_utils.py │ ├── dataset_config.json │ ├── default_bm25.json │ ├── execute_retrieval.py │ ├── get_indices.sh │ └── retrieval.py ├── ColBERT │ ├── colbert.sh │ └── get_colbert_predictions.py ├── README.md ├── data_processing │ ├── categorize_questions.py │ ├── compile_bioasq_questions.py │ ├── create_corpus_tsv.py │ ├── create_pubmed_jsonl.py │ ├── create_query_tsv.py │ ├── create_wikipedia_jsonl.py │ ├── download_pubmed_corpus.py │ ├── get_gold_compilation.py │ └── get_gold_contexts.py ├── evaluate_retriever.ipynb ├── evaluate_retriever.py └── evaluate_retriever.sh └── utils.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/README.md -------------------------------------------------------------------------------- /analysis_framework/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/analysis_framework/README.md -------------------------------------------------------------------------------- /analysis_framework/analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/analysis_framework/analysis.ipynb -------------------------------------------------------------------------------- /analysis_framework/compile_results.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/analysis_framework/compile_results.py -------------------------------------------------------------------------------- /analysis_framework/compile_results.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/analysis_framework/compile_results.sh -------------------------------------------------------------------------------- /analysis_framework/zeno_upload.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/analysis_framework/zeno_upload.py -------------------------------------------------------------------------------- /analysis_framework/zeno_upload.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/analysis_framework/zeno_upload.sh -------------------------------------------------------------------------------- /download_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/download_data.py -------------------------------------------------------------------------------- /file_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/file_utils.py -------------------------------------------------------------------------------- /reader/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/reader/README.md -------------------------------------------------------------------------------- /reader/bash_scripts/example_generation_script.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/reader/bash_scripts/example_generation_script.sh -------------------------------------------------------------------------------- /reader/evaluate_top_k.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/reader/evaluate_top_k.py -------------------------------------------------------------------------------- /reader/generate_top_k.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/reader/generate_top_k.py -------------------------------------------------------------------------------- /reader/reader_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/reader/reader_model.py -------------------------------------------------------------------------------- /reader/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/reader/utils.py -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/requirements.txt -------------------------------------------------------------------------------- /retriever/BM25/BM25_connector.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/retriever/BM25/BM25_connector.py -------------------------------------------------------------------------------- /retriever/BM25/base_retriever.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/retriever/BM25/base_retriever.py -------------------------------------------------------------------------------- /retriever/BM25/bm25.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/retriever/BM25/bm25.sh -------------------------------------------------------------------------------- /retriever/BM25/bm25_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/retriever/BM25/bm25_utils.py -------------------------------------------------------------------------------- /retriever/BM25/dataset_config.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/retriever/BM25/dataset_config.json -------------------------------------------------------------------------------- /retriever/BM25/default_bm25.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/retriever/BM25/default_bm25.json -------------------------------------------------------------------------------- /retriever/BM25/execute_retrieval.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/retriever/BM25/execute_retrieval.py -------------------------------------------------------------------------------- /retriever/BM25/get_indices.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/retriever/BM25/get_indices.sh -------------------------------------------------------------------------------- /retriever/BM25/retrieval.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/retriever/BM25/retrieval.py -------------------------------------------------------------------------------- /retriever/ColBERT/colbert.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/retriever/ColBERT/colbert.sh -------------------------------------------------------------------------------- /retriever/ColBERT/get_colbert_predictions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/retriever/ColBERT/get_colbert_predictions.py -------------------------------------------------------------------------------- /retriever/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/retriever/README.md -------------------------------------------------------------------------------- /retriever/data_processing/categorize_questions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/retriever/data_processing/categorize_questions.py -------------------------------------------------------------------------------- /retriever/data_processing/compile_bioasq_questions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/retriever/data_processing/compile_bioasq_questions.py -------------------------------------------------------------------------------- /retriever/data_processing/create_corpus_tsv.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/retriever/data_processing/create_corpus_tsv.py -------------------------------------------------------------------------------- /retriever/data_processing/create_pubmed_jsonl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/retriever/data_processing/create_pubmed_jsonl.py -------------------------------------------------------------------------------- /retriever/data_processing/create_query_tsv.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/retriever/data_processing/create_query_tsv.py -------------------------------------------------------------------------------- /retriever/data_processing/create_wikipedia_jsonl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/retriever/data_processing/create_wikipedia_jsonl.py -------------------------------------------------------------------------------- /retriever/data_processing/download_pubmed_corpus.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/retriever/data_processing/download_pubmed_corpus.py -------------------------------------------------------------------------------- /retriever/data_processing/get_gold_compilation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/retriever/data_processing/get_gold_compilation.py -------------------------------------------------------------------------------- /retriever/data_processing/get_gold_contexts.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/retriever/data_processing/get_gold_contexts.py -------------------------------------------------------------------------------- /retriever/evaluate_retriever.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/retriever/evaluate_retriever.ipynb -------------------------------------------------------------------------------- /retriever/evaluate_retriever.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/retriever/evaluate_retriever.py -------------------------------------------------------------------------------- /retriever/evaluate_retriever.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/retriever/evaluate_retriever.sh -------------------------------------------------------------------------------- /utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neulab/ragged/HEAD/utils.py --------------------------------------------------------------------------------