metadata
license: mit
CTMatch Information Retrieval Dataset
This is a dataset of processed clinical trials documents, somehwat of a duplication of that found in datasets/ir_datasets
except that these have been preprocessed with ctproc to clean and extract useful fields from the clinical trial documents.
Each of the has exactly 374648 lines of corresponding data:
doc_texts.csv
- texts extracted from processed documents using several fields including eligbility min and max age, and eligbility criteria, structured as this example from NCT00000102: "Inclusion Criteria: diagnosed with Congenital Adrenal Hyperplasia (CAH) normal ECG during baseline evaluation, Exclusion Criteria: history of liver disease, or elevated liver function tests history of cardiovascular disease"
doc_categories.csv:
- 1 x 15 vectors of somewhat arbitrarily chosen topic probabilities (softmax output) generated by zero-shot classification model, CTMatch.category_model(doc['condition']) lexically ordered as such: cancer,cardiac,endocrine,gastrointestinal,genetic,healthy,infection,neurological,other,pediatric,psychological,pulmonary,renal,reproductive
doc_embeddings.csv:
- 1 x 384 vectors of embeddings taken from last hidden state of CTMatch.embedding_model.encode(doc_text) using SentenceTransformers
index2docid.csv:
- simple mapping of index to NCTID's for filtering/reference throughout IR program, corresponding to vector, texts representation order