Visualizing Convolutional Networks for MRI-based Diagnosis of Alzheimer's Disease

Visualizing and interpreting convolutional neural networks (CNNs) is an important task to increase trust in automatic medical decision making systems. In this study, we train a 3D CNN to detect Alzheimer's disease based on structural MRI scans of the brain. Then, we apply four different gradient-based and occlusion-based visualization methods that explain the network's classification decisions by highlighting relevant areas in the input image. We compare the methods qualitatively and quantitatively. We find that all four methods focus on brain regions known to be involved in Alzheimer's disease, such as inferior and middle temporal gyrus. While the occlusion-based methods focus more on specific regions, the gradient-based methods pick up distributed relevance patterns. Additionally, we find that the distribution of relevance varies across patients, with some having a stronger focus on the temporal lobe, whereas for others more cortical areas are relevant. In summary, we show that applying different visualization methods is important to understand the decisions of a CNN, a step that is crucial to increase clinical impact and trust in computer-based decision support systems.Comment: MLCN 201

PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model.

MotivationElectronic health records (EHRs) are quickly becoming omnipresent in healthcare, but interoperability issues and technical demands limit their use for biomedical and clinical research. Interactive and flexible software that interfaces directly with EHR data structured around a common data model (CDM) could accelerate more EHR-based research by making the data more accessible to researchers who lack computational expertise and/or domain knowledge.ResultsWe present PatientExploreR, an extensible application built on the R/Shiny framework that interfaces with a relational database of EHR data in the Observational Medical Outcomes Partnership CDM format. PatientExploreR produces patient-level interactive and dynamic reports and facilitates visualization of clinical data without any programming required. It allows researchers to easily construct and export patient cohorts from the EHR for analysis with other software. This application could enable easier exploration of patient-level data for physicians and researchers. PatientExploreR can incorporate EHR data from any institution that employs the CDM for users with approved access. The software code is free and open source under the MIT license, enabling institutions to install and users to expand and modify the application for their own purposes.Availability and implementationPatientExploreR can be freely obtained from GitHub: https://github.com/BenGlicksberg/PatientExploreR. We provide instructions for how researchers with approved access to their institutional EHR can use this package. We also release an open sandbox server of synthesized patient data for users without EHR access to explore: http://patientexplorer.ucsf.edu.Supplementary informationSupplementary data are available at Bioinformatics online

Imaging Informatics and the Human Brain Project: the Role of Structure, Review

(no abstract

MedTruth: A Semi-supervised Approach to Discovering Knowledge Condition Information from Multi-Source Medical Data

Knowledge Graph (KG) contains entities and the relations between entities. Due to its representation ability, KG has been successfully applied to support many medical/healthcare tasks. However, in the medical domain, knowledge holds under certain conditions. For example, symptom \emph{runny nose} highly indicates the existence of disease \emph{whooping cough} when the patient is a baby rather than the people at other ages. Such conditions for medical knowledge are crucial for decision-making in various medical applications, which is missing in existing medical KGs. In this paper, we aim to discovery medical knowledge conditions from texts to enrich KGs. Electronic Medical Records (EMRs) are systematized collection of clinical data and contain detailed information about patients, thus EMRs can be a good resource to discover medical knowledge conditions. Unfortunately, the amount of available EMRs is limited due to reasons such as regularization. Meanwhile, a large amount of medical question answering (QA) data is available, which can greatly help the studied task. However, the quality of medical QA data is quite diverse, which may degrade the quality of the discovered medical knowledge conditions. In the light of these challenges, we propose a new truth discovery method, MedTruth, for medical knowledge condition discovery, which incorporates prior source quality information into the source reliability estimation procedure, and also utilizes the knowledge triple information for trustworthy information computation. We conduct series of experiments on real-world medical datasets to demonstrate that the proposed method can discover meaningful and accurate conditions for medical knowledge by leveraging both EMR and QA data. Further, the proposed method is tested on synthetic datasets to validate its effectiveness under various scenarios.Comment: Accepted as CIKM2019 long pape

Visual Exploration and Cohort Identification of Acute Patient Histories Aggregated from Heterogeneous Sources

How can we use information visualization to support retrospective, exploratory analysis of collections of histories for patients admitted to acute care? This paper describes a novel design for visual cohort identification and exploration. We have developed a tool that integrates multiple, heterogeneous clinical data sources and allows alignment, querying and abstraction in a common workbench. This paper presents results from two projects and a review of related work in the field of information visualization including both presentation and interactive navigation of the information. We have developed an interactive prototype and present the visualization aspect of this prototype and a brief demonstration of its use in a research project with a large cohort of patients. The prototype represents and reasons with patient events in different OWL-formalizations according to the perspective and use: One for integration and alignment of patient records and observations; Another for visual presentation of individual or cohort trajectories. Health researchers have successfully analyzed large cohorts (over 100,000 individuals) using the tool. We have also used the tool to produce interactive personal health time-lines (for more than 10,000 individuals) on the web. Utility, usability and effect have been tested extensively and the results so far are promising. We envision that clinicians who want to learn more about groups of patients and their treatment processes will find the tool valuable. In addition, we believe that the visualization can be useful to researchers looking at data to be statistically evaluated, in order to discover new hypotheses or get ideas for the best analysis strategies. Our main conclusion is that the tool is usable, but it can be challenging to use for large data sets.Postprint version. © 2016 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other users, including reprinting/ republishing this material for advertising or promotional purposes, creating new collective works for resale or redistribution to servers or lists, or reuse of any copyrighted components of this work in other works

Mapping lung cancer epithelial-mesenchymal transition states and trajectories with single-cell resolution.

Elucidating the spectrum of epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET) states in clinical samples promises insights on cancer progression and drug resistance. Using mass cytometry time-course analysis, we resolve lung cancer EMT states through TGFβ-treatment and identify, through TGFβ-withdrawal, a distinct MET state. We demonstrate significant differences between EMT and MET trajectories using a computational tool (TRACER) for reconstructing trajectories between cell states. In addition, we construct a lung cancer reference map of EMT and MET states referred to as the EMT-MET PHENOtypic STAte MaP (PHENOSTAMP). Using a neural net algorithm, we project clinical samples onto the EMT-MET PHENOSTAMP to characterize their phenotypic profile with single-cell resolution in terms of our in vitro EMT-MET analysis. In summary, we provide a framework to phenotypically characterize clinical samples in the context of in vitro EMT-MET findings which could help assess clinical relevance of EMT in cancer in future studies