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license: mit |
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**CTMatch Information Retrieval Dataset** |
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This is a dataset of processed clinical trials documents, somehwat of a duplication of that found in `datasets/ir_datasets` |
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except that these have been preprocessed with `ctproc` to clean and extract useful fields from the clinical trial documents. |
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Note: They are currently saved as text files because of the downstream task in ctmatch, though in the future they may be converted to .csv. |
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Each .txt file has exactly 374648 lines of corresponding data: |
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`doc_texts.txt` |
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- texts extracted from documents processed with `ctproc` using and eligbility criteria fields only, structured as this example from NCT00000102: |
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"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" |
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`doc_categories.txt`: |
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- 1 x 14 vectors of somewhat arbitrarily chosen topic probabilities (softmax output) generated by zero-shot classification model `facebook/bart-large-mnli`, CTMatch.category_model(doc['condition']) lexically ordered as such: |
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cancer,cardiac,endocrine,gastrointestinal,genetic,healthy,infection,neurological,other,pediatric,psychological,pulmonary,renal,reproductive |
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`doc_embeddings.txt`: |
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- 1 x 384 vectors of embeddings taken from last hidden state of model encoded doc_text using SentenceTransformers(`sentence-transformers/all-MiniLM-L6-v2`) |
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`index2docid.txt`: |
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- simple mapping of index to NCTID's for filtering/reference throughout IR program, corresponding to vector, texts representation order |
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