In JAMIA open
OBJECTIVE : The aim of this study was to test the feasibility of PICO (participants, interventions, comparators, outcomes) entity extraction using weak supervision and natural language processing.
METHODOLOGY : We re-purpose more than 127 medical and nonmedical ontologies and expert-generated rules to obtain multiple noisy labels for PICO entities in the evidence-based medicine (EBM)-PICO corpus. These noisy labels are aggregated using simple majority voting and generative modeling to get consensus labels. The resulting probabilistic labels are used as weak signals to train a weakly supervised (WS) discriminative model and observe performance changes. We explore mistakes in the EBM-PICO that could have led to inaccurate evaluation of previous automation methods.
RESULTS : In total, 4081 randomized clinical trials were weakly labeled to train the WS models and compared against full supervision. The models were separately trained for PICO entities and evaluated on the EBM-PICO test set. A WS approach combining ontologies and expert-generated rules outperformed full supervision for the participant entity by 1.71% macro-F1. Error analysis on the EBM-PICO subset revealed 18-23% erroneous token classifications.
DISCUSSION : Automatic PICO entity extraction accelerates the writing of clinical systematic reviews that commonly use PICO information to filter health evidence. However, PICO extends to more entities-PICOS (S-study type and design), PICOC (C-context), and PICOT (T-timeframe) for which labelled datasets are unavailable. In such cases, the ability to use weak supervision overcomes the expensive annotation bottleneck.
CONCLUSIONS : We show the feasibility of WS PICO entity extraction using freely available ontologies and heuristics without manually annotated data. Weak supervision has encouraging performance compared to full supervision but requires careful design to outperform it.
Dhrangadhariya Anjani, Müller Henning
2023-Apr
evidence-based medicine, information extraction, machine learning, weak supervision
