al-BERT: a semi-supervised denoising technique for disease prediction

Abstract

Abstract Background Medical records are a valuable source for understanding patient health conditions. Doctors often use these records to assess health without solely depending on time-consuming and complex examinations. However, these records may not always be directly relevant to a patient’s current health issue. For instance, information about common colds may not be relevant to a more specific health condition. While experienced doctors can effectively navigate through unnecessary details in medical records, this excess information presents a challenge for machine learning models in predicting diseases electronically. To address this, we have developed ‘al-BERT’, a new disease prediction model that leverages the BERT framework. This model is designed to identify crucial information from medical records and use it to predict diseases. ‘al-BERT’ operates on the principle that the structure of sentences in diagnostic records is similar to regular linguistic patterns. However, just as stuttering in speech can introduce ‘noise’ or irrelevant information, similar issues can arise in written records, complicating model training. To overcome this, ‘al-BERT’ incorporates a semi-supervised layer that filters out irrelevant data from patient visitation records. This process aims to refine the data, resulting in more reliable indicators for disease correlations and enhancing the model’s predictive accuracy and utility in medical diagnostics. Method To discern noise diseases within patient records, especially those resembling influenza-like illnesses, our approach employs a customized semi-supervised learning algorithm equipped with a focused attention mechanism. This mechanism is specifically calibrated to enhance the model’s sensitivity to chronic conditions while concurrently distilling salient features from patient records, thereby augmenting the predictive accuracy and utility of the model in clinical settings. We evaluate the performance of al-BERT using real-world health insurance data provided by Taiwan’s National Health Insurance. Result In our study, we evaluated our model against two others: one based on BERT that uses complete disease records, and another variant that includes extra filtering techniques. Our findings show that models incorporating filtering mechanisms typically perform better than those using the entire, unfiltered dataset. Our approach resulted in improved outcomes across several key measures: AUC-ROC (an indicator of a model’s ability to distinguish between classes), precision (the accuracy of positive predictions), recall (the model’s ability to find all relevant cases), and overall accuracy. Most notably, our model showed a 15% improvement in recall compared to the current best-performing method in the field of disease prediction. Conclusion The conducted ablation study affirms the advantages of our attention mechanism and underscores the crucial role of the selection module within al-BERT.

Keywords

• Disease prediction
• Semi-supervised learning
• Attention
• Health insurance data
• Electronic medical records
• EMR