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Construction of extra-large scale screening tools for risks of severe mental illnesses using real world healthcare data
Dec 20, 2022
Importance: The prevalence of severe mental illnesses (SMIs) in the United States is approximately 3% of the whole population. The ability to conduct risk screening of SMIs at large scale could inform early prevention and treatment. Objective: A scalable machine learning based tool was developed to conduct population-level risk screening for SMIs, including schizophrenia, schizoaffective disorders, psychosis, and bipolar disorders,using 1) healthcare insurance claims and 2) electronic health records (EHRs). Design, setting and participants: Data from beneficiaries from a nationwide commercial healthcare insurer with 77.4 million members and data from patients from EHRs from eight academic hospitals based in the U.S. were used. First, the predictive models were constructed and tested using data in case-control cohorts from insurance claims or EHR data. Second, performance of the predictive models across data sources were analyzed. Third, as an illustrative application, the models were further trained to predict risks of SMIs among 18-year old young adults and individuals with substance associated conditions. Main outcomes and measures: Machine learning-based predictive models for SMIs in the general population were built based on insurance claims and EHR.
Ten Quick Tips for Deep Learning in Biology
May 29, 2021
Machine learning is a modern approach to problem-solving and task automation. In particular, machine learning is concerned with the development and applications of algorithms that can recognize patterns in data and use them for predictive modeling. Artificial neural networks are a particular class of machine learning algorithms and models that evolved into what is now described as deep learning. Given the computational advances made in the last decade, deep learning can now be applied to massive data sets and in innumerable contexts. Therefore, deep learning has become its own subfield of machine learning. In the context of biological research, it has been increasingly used to derive novel insights from high-dimensional biological data. To make the biological applications of deep learning more accessible to scientists who have some experience with machine learning, we solicited input from a community of researchers with varied biological and deep learning interests. These individuals collaboratively contributed to this manuscript's writing using the GitHub version control platform and the Manubot manuscript generation toolset. The goal was to articulate a practical, accessible, and concise set of guidelines and suggestions to follow when using deep learning. In the course of our discussions, several themes became clear: the importance of understanding and applying machine learning fundamentals as a baseline for utilizing deep learning, the necessity for extensive model comparisons with careful evaluation, and the need for critical thought in interpreting results generated by deep learning, among others.