data

The processed data are based on ClinicalTrials.gov database on Feb 20, 2021.

data file

• data/raw_data.csv: all the data samples in benchmark.
• data/phase_I_train.csv: phase I training data.
• data/phase_I_valid.csv: phase I validation data.
• data/phase_I_test.csv: phase I test data.
• data/phase_II_train.csv: phase II training data.
• data/phase_II_valid.csv: phase II validation data.
• data/phase_II_test.csv: phase II test data.
• data/phase_III_train.csv: phase III training data.
• data/phase_III_valid.csv: phase III validation data.
• data/phase_III_test.csv: phase III test data.
• data/toy_train.csv: training data used for toy model (tutorial).
• data/toy_valid.csv: validation data used for toy model (tutorial).
• data/toy_test.csv: test data used for toy model (tutorial).
• data/ADMET: processed ADMET data.
• data/drugbank_mini.csv: a demo of drugbank data
• data/sentence2embedding.pkl: a mapping from sentence in eligibility criteria to BERT embedding.

column of csv file

All the data files are in format of csv with the same header. We show the meaning of the columns of csv file.

• nctid: identifiers of a clinical trial
• status: the status of the clinical trial, it can be completed, net yet recruiting, active, recruiting, suspended, terminated, unknown status, withdrawn.
• why_stop: the reasons why the trial stops. It can be empty.
• label: binary outcome label, 0 means trial fails while 1 means success.
• phase: the phase of the trial. phase I, or phase II, or phase III.
• diseases: list of disease names.
• icdcodes: list of icd-10 codes of diseases.
• drugs: list of drug names.
• smiless: list of SMILES of the drugs.
• criteria: eligibility criteria.

Benchmark Usage Agreement

The benchmark dataset and code (including data collection and preprocessing, model construction, learning process, evaluation), referred as the Works, are publicly available for Non-Commercial Use only at https://github.com/futianfan/clinical-trial-outcome-prediction. Non-Commercial Use is defined as for academic research or other non-profit educational use which is: (1) not-for-profit; (2) not conducted or funded (unless such funding confers no commercial rights to the funding entity) by an entity engaged in the commercial use, application or exploitation of works similar to the Works; and (3) not intended to produce works for commercial use.