├── .github └── workflows │ └── static.yml ├── .gitignore ├── CODE_OF_CONDUCT.md ├── CTO.png ├── LICENSE ├── README.md ├── arrange_labels.py ├── baselines ├── README.md ├── baselines.py ├── biobert_trial_outcome.py ├── hint_test.ipynb ├── run_bert.sh └── run_spot.py ├── clinical_trial_linkage ├── FDA_approvals │ └── EOBZIP_2024_04 │ │ ├── exclusivity.txt │ │ ├── patent.txt │ │ └── products.txt ├── README.md ├── create_drug_mapping.py ├── create_trial_linkage.py ├── download_data.py ├── drug_mapping.json ├── evaluate_top.py ├── extract_outcome_from_trial_linkage.py ├── extract_trial_info.py ├── get_embedding_for_trial_linkage.py ├── match_fda_approvals.py ├── process_drugbank.py ├── support_functions.py ├── trial_linkage_algorithm.png └── trial_linkage_utils.py ├── download_ctti.py ├── index.html ├── labeling ├── README.md ├── create_labels.ipynb ├── hint_test.ipynb └── lfs.py ├── llm_prediction_on_pubmed ├── LLM_prediction_method.png ├── README.md ├── clean_and_extract_final_outcomes.py ├── extract_pubmed_abstracts.py ├── extract_pubmed_abstracts_through_search.py ├── get_llm_predictions.py ├── retrieve_top2_abstracts.py ├── support_functions.py └── utils.py ├── news_headlines ├── README.md ├── get_news.py └── get_news2.py ├── pipeline.sh ├── requirements.txt ├── stock_price ├── README.md ├── get_stocks.py ├── scrape_amendments.py ├── slope_calculation.ipynb └── tickers.csv ├── tutorials ├── example_collab.ipynb ├── full_experiments.ipynb ├── getting_started_cto_vs_top.ipynb ├── predictions_on_current_trials.ipynb ├── readme.md ├── resources │ ├── CTO_intro.mp4 │ └── CTO_slides.pdf └── vis_utils.py ├── update_labels.sh └── update_news.sh /.github/workflows/static.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chufangao/CTOD/HEAD/.github/workflows/static.yml -------------------------------------------------------------------------------- /.gitignore: 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