György Simon

Sicheng Zhou, Rui Zhang, Anne Blaes et al.

Cardiotoxicity induced by the breast cancer treatments (i.e., chemotherapy, targeted therapy and radiation therapy) is a significant problem for breast cancer patients. The cardiotoxicity risk for breast cancer patients receiving different treatments remains unclear. We developed and evaluated risk predictive models for cardiotoxicity in breast cancer patients using EHR data. The AUC scores to predict the CHF, CAD, CM and MI are 0.846, 0.857, 0.858 and 0.804 respectively. After adjusting for baseline differences in cardiovascular health, patients who received chemotherapy or targeted therapy appeared to have higher risk of cardiotoxicity than patients who received radiation therapy. Due to differences in baseline cardiac health across the different breast cancer treatment groups, caution is recommended in interpreting the cardiotoxic effect of these treatments.

Xinpeng Shen, Sisi Ma, Prashanthi Vemuri et al.

Introduction: The discovery of causal mechanisms underlying diseases enables better diagnosis, prognosis and treatment selection. Clinical trials have been the gold standard for determining causality, but they are resource intensive, sometimes infeasible or unethical. Electronic Health Records (EHR) contain a wealth of real-world data that holds promise for the discovery of disease mechanisms, yet the existing causal structure discovery (CSD) methods fall short on leveraging them due to the special characteristics of the EHR data. We propose a new data transformation method and a novel CSD algorithm to overcome the challenges posed by these characteristics. Materials and methods: We demonstrated the proposed methods on an application to type-2 diabetes mellitus. We used a large EHR data set from Mayo Clinic to internally evaluate the proposed transformation and CSD methods and used another large data set from an independent health system, Fairview Health Services, as external validation. We compared the performance of our proposed method to Fast Greedy Equivalence Search (FGES), a state-of-the-art CSD method in terms of correctness, stability and completeness. We tested the generalizability of the proposed algorithm through external validation. Results and conclusions: The proposed method improved over the existing methods by successfully incorporating study design considerations, was robust in face of unreliable EHR timestamps and inferred causal effect directions more correctly and reliably. The proposed data transformation successfully improved the clinical correctness of the discovered graph and the consistency of edge orientation across bootstrap samples. It resulted in superior accuracy, stability, and completeness.

Jia Li, Haoyu Yang, Xiaowei Jia et al.

Electronic Health Records (EHR) data analysis plays a crucial role in healthcare system quality. Because of its highly complex underlying causality and limited observable nature, causal inference on EHR is quite challenging. Deep Learning (DL) achieved great success among the advanced machine learning methodologies. Nevertheless, it is still obstructed by the inappropriately assumed causal conditions. This work proposed a novel method to quantify clinically well-defined causal effects as a generalized estimation vector that is simply utilizable for causal models. We incorporated it into DL models to achieve better predictive performance and result interpretation. Furthermore, we also proved the existence of causal information blink spots that regular DL models cannot reach.

Pranjul Yadav, Michael Steinbach, Vipin Kumar et al.

The continuously increasing cost of the US healthcare system has received significant attention. Central to the ideas aimed at curbing this trend is the use of technology, in the form of the mandate to implement electronic health records (EHRs). EHRs consist of patient information such as demographics, medications, laboratory test results, diagnosis codes and procedures. Mining EHRs could lead to improvement in patient health management as EHRs contain detailed information related to disease prognosis for large patient populations. In this manuscript, we provide a structured and comprehensive overview of data mining techniques for modeling EHR data. We first provide a detailed understanding of the major application areas to which EHR mining has been applied and then discuss the nature of EHR data and its accompanying challenges. Next, we describe major approaches used for EHR mining, the metrics associated with EHRs, and the various study designs. With this foundation, we then provide a systematic and methodological organization of existing data mining techniques used to model EHRs and discuss ideas for future research. We conclude this survey with a comprehensive summary of clinical data mining applications of EHR data, as illustrated in the online supplement.

Pranjul Yadav, Lisiane Prunelli, Alexander Hoff et al.

Our aging population increasingly suffers from multiple chronic diseases simultaneously, necessitating the comprehensive treatment of these conditions. Finding the optimal set of drugs for a combinatorial set of diseases is a combinatorial pattern exploration problem. Association rule mining is a popular tool for such problems, but the requirement of health care for finding causal, rather than associative, patterns renders association rule mining unsuitable. To address this issue, we propose a novel framework based on the Rubin-Neyman causal model for extracting causal rules from observational data, correcting for a number of common biases. Specifically, given a set of interventions and a set of items that define subpopulations (e.g., diseases), we wish to find all subpopulations in which effective intervention combinations exist and in each such subpopulation, we wish to find all intervention combinations such that dropping any intervention from this combination will reduce the efficacy of the treatment. A key aspect of our framework is the concept of closed intervention sets which extend the concept of quantifying the effect of a single intervention to a set of concurrent interventions. We also evaluated our causal rule mining framework on the Electronic Health Records (EHR) data of a large cohort of patients from Mayo Clinic and showed that the patterns we extracted are sufficiently rich to explain the controversial findings in the medical literature regarding the effect of a class of cholesterol drugs on Type-II Diabetes Mellitus (T2DM).