Deep learning (DL) models for disease classification or segmentation from medical images are increasingly trained using transfer learning (TL) from unrelated natural world images. However, shortcomings and utility of TL for specialized tasks in the medical imaging domain remain unknown and are based on assumptions that increasing training data will improve performance. We report detailed comparisons, rigorous statistical analysis and comparisons of widely used DL architecture for binary segmentation after TL with ImageNet initialization (TII-models) with supervised learning with only medical images(LMI-models) of macroscopic optical skin cancer, microscopic prostate core biopsy and Computed Tomography (CT) DICOM images. Through visual inspection of TII and LMI model outputs and their Grad-CAM counterparts, our results identify several counter intuitive scenarios where automated segmentation of one tumor by both models or the use of individual segmentation output masks in various combinations from individual models leads to 10% increase in performance. We also report sophisticated ensemble DL strategies for achieving clinical grade medical image segmentation and model explanations under low data regimes. For example; estimating performance, explanations and replicability of LMI and TII models described by us can be used for situations in which sparsity promotes better learning. A free GitHub repository of TII and LMI models, code and more than 10,000 medical images and their Grad-CAM output from this study can be used as starting points for advanced computational medicine and DL research for biomedical discovery and applications.
University of Oklahoma（俄克拉荷马大学）；Lamar University（拉马尔大学）；Islamic University（伊斯兰大学）；Government College of Applied Human Science（政府应用人文科学学院）；Arizona State University（亚利桑那州立大学）；Clark Atlanta University（克拉克亚特兰大大学）
The recent development of Monkeypox disease among various nations poses a global pandemic threat when the world is still fighting Coronavirus Disease-2019 (COVID-19). At its dawn, the slow and steady transmission of Monkeypox disease among individuals needs to be addressed seriously. Over the years, Deep learning (DL) based disease prediction has demonstrated true potential by providing early, cheap, and affordable diagnosis facilities. Considering this opportunity, we have conducted two studies where we modified and tested six distinct deep learning models-VGG16, InceptionResNetV2, ResNet50, …
Drug repositioning is an attractive cost-efficient strategy for the development of treatments for human diseases. Here, we propose an interpretable model that learns disease self-representations for drug repositioning. Our self-representation model represents each disease as a linear combination of a few other diseases. We enforce proximity in the learnt representations in a way to preserve the geometric structure of the human phenome network - a domain-specific knowledge that naturally adds relational inductive bias to the disease self-representations. We prove that our method is globally opt…
Disease progression models are instrumental in predicting individual-level health trajectories and understanding disease dynamics. Existing models are capable of providing either accurate predictions of patients prognoses or clinically interpretable representations of disease pathophysiology, but not both. In this paper, we develop the phased attentive state space (PASS) model of disease progression, a deep probabilistic model that captures complex representations for disease progression while maintaining clinical interpretability. Unlike Markovian state space models which assume memoryless dy…
Deep neural network models have been proven to be very successful in image classification tasks, also for medical diagnosis, but their main concern is its lack of interpretability. They use to work as intuition machines with high statistical confidence but unable to give interpretable explanations about the reported results. The vast amount of parameters of these models make difficult to infer a rationale interpretation from them. In this paper we present a diabetic retinopathy interpretable classifier able to classify retine images into the different levels of disease severity and of explaini…
King’s College London（伦敦国王学院）；University College London（伦敦大学学院）；King’s College Hospital（国王学院医院）
Deep learning is attracting significant interest in the neuroimaging community as a means to diagnose psychiatric and neurological disorders from structural magnetic resonance images. However, there is a tendency amongst researchers to adopt architectures optimized for traditional computer vision tasks, rather than design networks customized for neuroimaging data. We address this by introducing NEURO-DRAM, a 3D recurrent visual attention model tailored for neuroimaging classification. The model comprises an agent which, trained by reinforcement learning, learns to navigate through volumetric i…
Kasetsart University（农业大学）；Mahidol University（玛希隆大学）；Vidyasirimedhi Institute of Science & Technology（维迪亚西里梅迪科学技术研究所）
In the past few years, there are several researches on Parkinson's disease (PD) recognition using single-photon emission computed tomography (SPECT) images with deep learning (DL) approach. However, the DL model's complexity usually results in difficult model interpretation when used in clinical. Even though there are multiple interpretation methods available for the DL model, there is no evidence of which method is suitable for PD recognition application. This tutorial aims to demonstrate the procedure to choose a suitable interpretation method for the PD recognition model. We exhibit four DC…
Longitudinal study designs are indispensable for studying disease progression. Inferring covariate effects from longitudinal data, however, requires interpretable methods that can model complicated covariance structures and detect nonlinear effects of both categorical and continuous covariates, as well as their interactions. Detecting disease effects is hindered by the fact that they often occur rapidly near the disease initiation time, and this time point cannot be exactly observed. An additional challenge is that the effect magnitude can be heterogeneous over the subjects. We present lgpr, a…
Detecting Structural Heart Disease from Electrocardiograms via a Generalized Additive Model of Interpretable Foundation-Model Predictors
Department of Information Center, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College（信息中心部门，阜外医院，中国医学科学院和北京协和医学院）；The Tsinghua Shenzhen International Graduate School, Tsinghua University（清华大学深圳国际研究生院）；National Clinical Research Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College（心血管疾病临床医学研究中心，阜外医院，中国医学科学院和北京协和医学院）
State University of New York at Buffalo（纽约州立大学布法罗分校）
Hospital readmissions have become one of the key measures of healthcare quality. Preventable readmissions have been identified as one of the primary targets for reducing costs and improving healthcare delivery. However, most data driven studies for understanding readmissions have produced black box classification and predictive models with moderate performance, which precludes them from being used effectively within the decision support systems in the hospitals. In this paper we present an application of structured sparsity-inducing norms for predicting readmission risk for patients based on t…
Modeling disease progression in healthcare administrative databases is complicated by the fact that patients are observed only at irregular intervals when they seek healthcare services. In a longitudinal cohort of 76,888 patients with chronic obstructive pulmonary disease (COPD), we used a continuous-time hidden Markov model with a generalized linear model to model healthcare utilization events. We found that the fitted model provides interpretable results suitable for summarization and hypothesis generation.
Massachusetts Institute of Technology（麻省理工学院）；University of Toronto（多伦多大学）；Microsoft Research New England（微软新英格兰研究院）
Unsupervised learning is often used to uncover clusters in data. However, different kinds of noise may impede the discovery of useful patterns from real-world time-series data. In this work, we focus on mitigating the interference of interval censoring in the task of clustering for disease phenotyping. We develop a deep generative, continuous-time model of time-series data that clusters time-series while correcting for censorship time. We provide conditions under which clusters and the amount of delayed entry may be identified from data under a noiseless model. On synthetic data, we demonstrat…
Disease phenotyping algorithms process observational clinical data to identify patients with specific diseases. Supervised phenotyping methods require significant quantities of expert-labeled data, while unsupervised methods may learn non-disease phenotypes. To address these limitations, we propose the Semi-Supervised Mixed Membership Model (SS3M) -- a probabilistic graphical model for learning disease phenotypes from clinical data with relatively few labels. We show SS3M can learn interpretable, disease-specific phenotypes which capture the clinical characteristics of the diseases specified b…
Unifying Physics- and Data-Driven Modeling via Novel Causal Spatiotemporal Graph Neural Network for Interpretable Epidemic Forecasting
Frankfurt Institute for Advanced Studies（法兰克福高等研究院）；Goethe Universität Frankfurt（法兰克福大学）；Xidian-FIAS International Joint Research Center（西电-法兰克福高等研究院国际联合研究中心）；School of Science and Engineering, The Chinese University of Hong Kong（香港中文大学（深圳）理工学院）；GSI Helmholtzzentrum für Schwerionenforschung GmbH（GSI亥姆霍兹重离子研究中心）
