├── .gitignore ├── LICENSE ├── README.md ├── img ├── Flowchart.png └── screenshot.png ├── neo4j_primekg ├── Dockerfile ├── README.md ├── graph_preprocessing_scripts │ ├── __init__.py │ ├── allowed_preferred_name_mapping_categories.py │ ├── apply_preferred_term_mapping.py │ ├── drugbank_id_mapper.py │ ├── id_based_mapper.py │ ├── mapper.py │ ├── mondo_id_mapper.py │ ├── preferred_term_category_finder.py │ └── preferred_term_mapper.py ├── import_primekg.sh └── primekg_to_neo4j_csv.py ├── pyproject.toml ├── src ├── fact_finder │ ├── __init__.py │ ├── app.py │ ├── chains │ │ ├── __init__.py │ │ ├── answer_generation_chain.py │ │ ├── combined_graph_rag_qa_chain.py │ │ ├── cypher_query_generation_chain.py │ │ ├── cypher_query_preprocessors_chain.py │ │ ├── entity_detection_question_preprocessing_chain.py │ │ ├── filtered_primekg_question_preprocessing_chain.py │ │ ├── graph_chain.py │ │ ├── graph_qa_chain │ │ │ ├── __init__.py │ │ │ ├── config.py │ │ │ ├── early_stopping_chain.py │ │ │ ├── graph_qa_chain.py │ │ │ ├── output.py │ │ │ └── output_chain.py │ │ ├── graph_summary_chain.py │ │ ├── rag │ │ │ ├── __init__.py │ │ │ ├── semantic_scholar_chain.py │ │ │ └── text_search_qa_chain.py │ │ └── subgraph_extractor_chain.py │ ├── config │ │ ├── __init__.py │ │ ├── primekg_config.py │ │ ├── primekg_predicate_descriptions.py │ │ └── simple_config.py │ ├── evaluator │ │ ├── __init__.py │ │ ├── adv_result_gpt4_o.json │ │ ├── adv_result_gpt4_turbo.json │ │ ├── adversarial_attack_evaluation.py │ │ ├── evaluation.py │ │ ├── evaluation_sample.py │ │ ├── evaluation_samples.py │ │ ├── llm_judge │ │ │ └── llm_judge_evaluator.py │ │ ├── score │ │ │ ├── __init__.py │ │ │ ├── bleu_score.py │ │ │ ├── difflib_score.py │ │ │ ├── embedding_score.py │ │ │ ├── levenshtein_score.py │ │ │ └── score.py │ │ ├── set_evaluator │ │ │ ├── __init__.py │ │ │ └── set_evaluator.py │ │ └── util.py │ ├── prompt_templates.py │ ├── py.typed │ ├── tools │ │ ├── __init__.py │ │ ├── cypher_preprocessors │ │ │ ├── __init__.py │ │ │ ├── always_distinct_preprocessor.py │ │ │ ├── child_to_parent_preprocessor.py │ │ │ ├── cypher_query_preprocessor.py │ │ │ ├── format_preprocessor.py │ │ │ ├── lower_case_properties_cypher_query_preprocessor.py │ │ │ ├── property_string_preprocessor.py │ │ │ ├── size_to_count_preprocessor.py │ │ │ └── synonym_cypher_query_preprocessor.py │ │ ├── entity_detector.py │ │ ├── semantic_scholar_search_api_wrapper.py │ │ ├── sub_graph_extractor.py │ │ ├── subgraph_extension.py │ │ └── synonym_finder │ │ │ ├── __init__.py │ │ │ ├── aggregate_state_synonym_finder.py │ │ │ ├── preferred_term_finder.py │ │ │ ├── synonym_finder.py │ │ │ ├── wiki_data_synonym_finder.py │ │ │ └── word_net_synonym_finder.py │ ├── ui │ │ ├── __init__.py │ │ ├── graph_conversion.py │ │ └── util.py │ └── utils.py └── img │ └── logo.png └── tests ├── __init__.py ├── chains ├── __init__.py ├── graph_qa_chain │ ├── __init__.py │ ├── test_graph_qa_chain.py │ └── test_graph_qa_chain_e2e.py ├── helpers.py ├── test_answer_generation_chain.py ├── test_cypher_query_generation_chain.py ├── test_entity_detection_question_preprocessing_chain.py ├── test_filtered_primekg_question_preprocessing_chain.py ├── test_graph_chain.py ├── test_graph_summary_chain.py ├── test_preprocessors_chain.py ├── test_subgraph_extractor_chain.py └── test_text_search_qa_chain.py ├── evaluator ├── __init__.py ├── score │ ├── __init__.py │ ├── test_bleu_score.py │ ├── test_difflib_score.py │ └── test_embedding_score.py └── set_evaluator │ └── test_set_evaluator.py └── tools ├── __init__.py ├── cypher_preprocessors ├── test_always_distinct_preprocessor.py ├── test_child_to_parent_preprocessor.py ├── test_format_preprocessor.py ├── test_lower_case_property_names.py ├── test_size_to_count_preprocessor.py └── test_synonym_query_preprocessor.py ├── semantic_scholar_search_api_wrapper_test.py ├── synonym_finder └── test_word_net_synonym_finder.py ├── test_entity_detector.py ├── test_llm_subgraph_extractor.py ├── 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