Deepr: A Convolutional Net for Medical Records

Feature engineering remains a major bottleneck when creating predictive systems from electronic medical records. At present, an important missing element is detecting predictive regular clinical motifs from irregular episodic records. We present Deepr (short for Deep record), a new end-to-end deep learning system that learns to extract features from medical records and predicts future risk automatically. Deepr transforms a record into a sequence of discrete elements separated by coded time gaps and hospital transfers. On top of the sequence is a convolutional neural net that detects and combines predictive local clinical motifs to stratify the risk. Deepr permits transparent inspection and visualization of its inner working. We validate Deepr on hospital data to predict unplanned readmission after discharge. Deepr achieves superior accuracy compared to traditional techniques, detects meaningful clinical motifs, and uncovers the underlying structure of the disease and intervention space

The Impact of Stigmatizing Language in EHR Notes on AI Performance and Fairness

Today, there is significant interest in using electronic health record data to generate new clinical insights for diagnosis and treatment decisions. However, there are concerns that such data may be biased and result in accentuating racial disparities. We study how clinician biases reflected in EHR notes affect the performance and fairness of artificial intelligence models in the context of mortality prediction for intensive care unit patients. We apply a Transformer-based deep learning model and explainable AI techniques to quantify negative impacts on performance and fairness. Our findings demonstrate that stigmatizing language written by clinicians adversely affects AI performance, particularly so for black patients, highlighting SL as a source of racial disparity in AI model development. As an effective mitigation approach, removing SL from EHR notes can significantly improve AI performance and fairness. This study provides actionable insights for responsible AI development and contributes to understanding clinician EHR note writing

People Talking and AI Listening: How Stigmatizing Language in EHR Notes Affect AI Performance

Electronic health records (EHRs) serve as an essential data source for the envisioned artificial intelligence (AI)-driven transformation in healthcare. However, clinician biases reflected in EHR notes can lead to AI models inheriting and amplifying these biases, perpetuating health disparities. This study investigates the impact of stigmatizing language (SL) in EHR notes on mortality prediction using a Transformer-based deep learning model and explainable AI (XAI) techniques. Our findings demonstrate that SL written by clinicians adversely affects AI performance, particularly so for black patients, highlighting SL as a source of racial disparity in AI model development. To explore an operationally efficient way to mitigate SL's impact, we investigate patterns in the generation of SL through a clinicians' collaborative network, identifying central clinicians as having a stronger impact on racial disparity in the AI model. We find that removing SL written by central clinicians is a more efficient bias reduction strategy than eliminating all SL in the entire corpus of data. This study provides actionable insights for responsible AI development and contributes to understanding clinician behavior and EHR note writing in healthcare.Comment: 54 pages, 9 figure

Enhance Representation Learning of Clinical Narrative with Neural Networks for Clinical Predictive Modeling

Medicine is undergoing a technological revolution. Understanding human health from clinical data has major challenges from technical and practical perspectives, thus prompting methods that understand large, complex, and noisy data. These methods are particularly necessary for natural language data from clinical narratives/notes, which contain some of the richest information on a patient. Meanwhile, deep neural networks have achieved superior performance in a wide variety of natural language processing (NLP) tasks because of their capacity to encode meaningful but abstract representations and learn the entire task end-to-end. In this thesis, I investigate representation learning of clinical narratives with deep neural networks through a number of tasks ranging from clinical concept extraction, clinical note modeling, and patient-level language representation. I present methods utilizing representation learning with neural networks to support understanding of clinical text documents. I first introduce the notion of representation learning from natural language processing and patient data modeling. Then, I investigate word-level representation learning to improve clinical concept extraction from clinical notes. I present two works on learning word representations and evaluate them to extract important concepts from clinical notes. The first study focuses on cancer-related information, and the second study evaluates shared-task data. The aims of these two studies are to automatically extract important entities from clinical notes. Next, I present a series of deep neural networks to encode hierarchical, longitudinal, and contextual information for modeling a series of clinical notes. I also evaluate the models by predicting clinical outcomes of interest, including mortality, length of stay, and phenotype predictions. Finally, I propose a novel representation learning architecture to develop a generalized and transferable language representation at the patient level. I also identify pre-training tasks appropriate for constructing a generalizable language representation. The main focus is to improve predictive performance of phenotypes with limited data, a challenging task due to a lack of data. Overall, this dissertation addresses issues in natural language processing for medicine, including clinical text classification and modeling. These studies show major barriers to understanding large-scale clinical notes. It is believed that developing deep representation learning methods for distilling enormous amounts of heterogeneous data into patient-level language representations will improve evidence-based clinical understanding. The approach to solving these issues by learning representations could be used across clinical applications despite noisy data. I conclude that considering different linguistic components in natural language and sequential information between clinical events is important. Such results have implications beyond the immediate context of predictions and further suggest future directions for clinical machine learning research to improve clinical outcomes. This could be a starting point for future phenotyping methods based on natural language processing that construct patient-level language representations to improve clinical predictions. While significant progress has been made, many open questions remain, so I will highlight a few works to demonstrate promising directions

Machine learning and electronic health records

In this work, we investigate the benefits and complications of using machine learning on EHR data. We survey some recent literature and conduct experiments on real data collected from hospital EHR systems.Masteroppgave i informatikkINF399MAMN-INFMAMN-PRO