Author
Brett K. Beaulieu-Jones
Other affiliations: Brigham and Women's Hospital, Beth Israel Deaconess Medical Center, University of Pennsylvania
Bio: Brett K. Beaulieu-Jones is an academic researcher from Harvard University. The author has contributed to research in topics: Medicine & Deep learning. The author has an hindex of 16, co-authored 47 publications receiving 2147 citations. Previous affiliations of Brett K. Beaulieu-Jones include Brigham and Women's Hospital & Beth Israel Deaconess Medical Center.
Topics: Medicine, Deep learning, Retrospective cohort study, Cohort, Source code
Papers
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University of Hawaii at Manoa1, University of Pennsylvania2, University of Michigan3, Harvard University4, GlaxoSmithKline5, Imperial College London6, University of Toronto7, Princess Margaret Cancer Centre8, Vanderbilt University9, Drexel University10, Carnegie Mellon University11, Stanford University12, University of Virginia13, Broad Institute14, Toyota Technological Institute at Chicago15, Trinity University16, Princeton University17, National Institutes of Health18, Howard Hughes Medical Institute19, University of Florida20, University of Colorado Denver21, University of Münster22, Georgetown University Medical Center23, Washington University in St. Louis24, Brown University25, Morgridge Institute for Research26, University of Wisconsin-Madison27
TL;DR: It is found that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art.
Abstract: Deep learning describes a class of machine learning algorithms that are capable of combining raw inputs into layers of intermediate features. These algorithms have recently shown impressive results across a variety of domains. Biology and medicine are data-rich disciplines, but the data are complex and often ill-understood. Hence, deep learning techniques may be particularly well suited to solve problems of these fields. We examine applications of deep learning to a variety of biomedical problems-patient classification, fundamental biological processes and treatment of patients-and discuss whether deep learning will be able to transform these tasks or if the biomedical sphere poses unique challenges. Following from an extensive literature review, we find that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art. Even though improvements over previous baselines have been modest in general, the recent progress indicates that deep learning methods will provide valuable means for speeding up or aiding human investigation. Though progress has been made linking a specific neural network's prediction to input features, understanding how users should interpret these models to make testable hypotheses about the system under study remains an open challenge. Furthermore, the limited amount of labelled data for training presents problems in some domains, as do legal and privacy constraints on work with sensitive health records. Nonetheless, we foresee deep learning enabling changes at both bench and bedside with the potential to transform several areas of biology and medicine.
1,491 citations
TL;DR: This research presents a novel probabilistic approach that allows us to assess the importance of knowing the carrier and removal status of canine coronavirus, as a source of infection for other animals.
Abstract: Background: Data sharing accelerates scientific progress but sharing individual-level data while preserving patient privacy presents a barrier. Methods and Results: Using pairs of deep neural netwo...
224 citations
TL;DR: The MI-CLAIM checklist is presented, a tool intended to improve transparent reporting of AI algorithms in medicine and to improve transparency in the evaluation of algorithms used in medicine.
Abstract: Here we present the MI-CLAIM checklist, a tool intended to improve transparent reporting of AI algorithms in medicine.
202 citations
TL;DR: Deep neural networks are trained that generate synthetic subjects closely resembling study participants and incorporate differential privacy, which offers strong guarantees on the likelihood that a subject could be identified as a member of the trial while preserving the privacy of study participants.
Abstract: Though it is widely recognized that data sharing enables faster scientific progress, the sensible need to protect participant privacy hampers this practice in medicine. We train deep neural networks that generate synthetic subjects closely resembling study participants. Using the SPRINT trial as an example, we show that machine-learning models built from simulated participants generalize to the original dataset. We incorporate differential privacy, which offers strong guarantees on the likelihood that a subject could be identified as a member of the trial. Investigators who have compiled a dataset can use our method to provide a freely accessible public version that enables other scientists to perform discovery-oriented analyses. Generated data can be released alongside analytical code to enable fully reproducible workflows, even when privacy is a concern. By addressing data sharing challenges, deep neural networks can facilitate the rigorous and reproducible investigation of clinical datasets.
158 citations
TL;DR: A semi-supervised learning method for EHR phenotype extraction using denoising autoencoders for phenotype stratification and a promising approach to clarify disease subtypes and improve genotype-phenotype association studies that leverage EHRs are developed.
155 citations
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TL;DR: Salmon is the first transcriptome-wide quantifier to correct for fragment GC-content bias, which substantially improves the accuracy of abundance estimates and the sensitivity of subsequent differential expression analysis.
Abstract: We introduce Salmon, a lightweight method for quantifying transcript abundance from RNA-seq reads. Salmon combines a new dual-phase parallel inference algorithm and feature-rich bias models with an ultra-fast read mapping procedure. It is the first transcriptome-wide quantifier to correct for fragment GC-content bias, which, as we demonstrate here, substantially improves the accuracy of abundance estimates and the sensitivity of subsequent differential expression analysis.
6,095 citations
TL;DR: A generative adversarial networks algorithm designed to solve the generative modeling problem and its applications in medicine, education and robotics are studied.
Abstract: Generative adversarial networks are a kind of artificial intelligence algorithm designed to solve the generative modeling problem. The goal of a generative model is to study a collection of training examples and learn the probability distribution that generated them. Generative Adversarial Networks (GANs) are then able to generate more examples from the estimated probability distribution. Generative models based on deep learning are common, but GANs are among the most successful generative models (especially in terms of their ability to generate realistic high-resolution images). GANs have been successfully applied to a wide variety of tasks (mostly in research settings) but continue to present unique challenges and research opportunities because they are based on game theory while most other approaches to generative modeling are based on optimization.
2,447 citations
TL;DR: How these computational techniques can impact a few key areas of medicine and explore how to build end-to-end systems are described.
Abstract: Here we present deep-learning techniques for healthcare, centering our discussion on deep learning in computer vision, natural language processing, reinforcement learning, and generalized methods. We describe how these computational techniques can impact a few key areas of medicine and explore how to build end-to-end systems. Our discussion of computer vision focuses largely on medical imaging, and we describe the application of natural language processing to domains such as electronic health record data. Similarly, reinforcement learning is discussed in the context of robotic-assisted surgery, and generalized deep-learning methods for genomics are reviewed.
1,843 citations
University of Hawaii at Manoa1, University of Pennsylvania2, University of Michigan3, Harvard University4, GlaxoSmithKline5, Imperial College London6, Princess Margaret Cancer Centre7, University of Toronto8, Vanderbilt University9, Drexel University10, Carnegie Mellon University11, Stanford University12, University of Virginia13, Broad Institute14, Toyota Technological Institute at Chicago15, Trinity University16, Princeton University17, National Institutes of Health18, Howard Hughes Medical Institute19, University of Florida20, University of Colorado Denver21, University of Münster22, Georgetown University Medical Center23, Washington University in St. Louis24, Brown University25, University of Wisconsin-Madison26, Morgridge Institute for Research27
TL;DR: It is found that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art.
Abstract: Deep learning describes a class of machine learning algorithms that are capable of combining raw inputs into layers of intermediate features. These algorithms have recently shown impressive results across a variety of domains. Biology and medicine are data-rich disciplines, but the data are complex and often ill-understood. Hence, deep learning techniques may be particularly well suited to solve problems of these fields. We examine applications of deep learning to a variety of biomedical problems-patient classification, fundamental biological processes and treatment of patients-and discuss whether deep learning will be able to transform these tasks or if the biomedical sphere poses unique challenges. Following from an extensive literature review, we find that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art. Even though improvements over previous baselines have been modest in general, the recent progress indicates that deep learning methods will provide valuable means for speeding up or aiding human investigation. Though progress has been made linking a specific neural network's prediction to input features, understanding how users should interpret these models to make testable hypotheses about the system under study remains an open challenge. Furthermore, the limited amount of labelled data for training presents problems in some domains, as do legal and privacy constraints on work with sensitive health records. Nonetheless, we foresee deep learning enabling changes at both bench and bedside with the potential to transform several areas of biology and medicine.
1,491 citations
TL;DR: CellProfiler 3.0 is described, a new version of the software supporting both whole-volume and plane-wise analysis of three-dimensional image stacks, increasingly common in biomedical research.
Abstract: CellProfiler has enabled the scientific research community to create flexible, modular image analysis pipelines since its release in 2005. Here, we describe CellProfiler 3.0, a new version of the software supporting both whole-volume and plane-wise analysis of three-dimensional (3D) image stacks, increasingly common in biomedical research. CellProfiler's infrastructure is greatly improved, and we provide a protocol for cloud-based, large-scale image processing. New plugins enable running pretrained deep learning models on images. Designed by and for biologists, CellProfiler equips researchers with powerful computational tools via a well-documented user interface, empowering biologists in all fields to create quantitative, reproducible image analysis workflows.
1,466 citations