ISeeU: Visually interpretable deep learning for mortality prediction inside the ICU.

Abstract:

:To improve the performance of Intensive Care Units (ICUs), the field of bio-statistics has developed scores which try to predict the likelihood of negative outcomes. These help evaluate the effectiveness of treatments and clinical practice, and also help to identify patients with unexpected outcomes. However, they have been shown by several studies to offer sub-optimal performance. Alternatively, Deep Learning offers state of the art capabilities in certain prediction tasks and research suggests deep neural networks are able to outperform traditional techniques. Nevertheless, a main impediment for the adoption of Deep Learning in healthcare is its reduced interpretability, for in this field it is crucial to gain insight into the why of predictions, to assure that models are actually learning relevant features instead of spurious correlations. To address this, we propose a deep multi-scale convolutional architecture trained on the Medical Information Mart for Intensive Care III (MIMIC-III) for mortality prediction, and the use of concepts from coalitional game theory to construct visual explanations aimed to show how important these inputs are deemed by the network. Results show our model attains a ROC AUC of 0.8735 (± 0.0025) which is competitive with the state of the art of Deep Learning mortality models trained on MIMIC-III data, while remaining interpretable. Supporting code can be found at https://github.com/williamcaicedo/ISeeU.

journal_name

J Biomed Inform

authors

Caicedo-Torres W,Gutierrez J

doi

10.1016/j.jbi.2019.103269

subject

Has Abstract

pub_date

2019-10-01 00:00:00

pages

103269

eissn

1532-0464

issn

1532-0480

pii

S1532-0464(19)30188-1

journal_volume

98

pub_type

杂志文章
  • A knowledge-based system to find over-the-counter medicines for self-medication.

    abstract::This study developed a medicine query system based on Semantic Web and open data especially for self-medication users to search over-the-counter (OTC) medicines. Most existing medicine query systems are based on keyword searches. If users are uncertain about the exact search words, these query systems do not offer eff...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2020.103504

    authors: Sung HY,Chi YL

    更新日期:2020-08-01 00:00:00

  • Classification models for the prediction of clinicians' information needs.

    abstract:OBJECTIVE:Clinicians face numerous information needs during patient care activities and most of these needs are not met. Infobuttons are information retrieval tools that help clinicians to fulfill their information needs by providing links to on-line health information resources from within an electronic medical record...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2008.07.001

    authors: Del Fiol G,Haug PJ

    更新日期:2009-02-01 00:00:00

  • Vaidurya: a multiple-ontology, concept-based, context-sensitive clinical-guideline search engine.

    abstract::We designed and implemented a generic search engine (Vaidurya), as part of our Digital clinical-Guideline Library (DeGeL) framework. Two search methods were implemented in addition to full-text search: (1) concept-based search, which relies on pre-indexing the guidelines in a clinically meaningful fashion, and (2) con...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2008.07.003

    authors: Moskovitch R,Shahar Y

    更新日期:2009-02-01 00:00:00

  • Predicting biomedical metadata in CEDAR: A study of Gene Expression Omnibus (GEO).

    abstract::A crucial and limiting factor in data reuse is the lack of accurate, structured, and complete descriptions of data, known as metadata. Towards improving the quantity and quality of metadata, we propose a novel metadata prediction framework to learn associations from existing metadata that can be used to predict metada...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2017.06.017

    authors: Panahiazar M,Dumontier M,Gevaert O

    更新日期:2017-08-01 00:00:00

  • A comprehensive review of feature based methods for drug target interaction prediction.

    abstract::Drug target interaction is a prominent research area in the field of drug discovery. It refers to the recognition of interactions between chemical compounds and the protein targets in the human body. Wet lab experiments to identify these interactions are expensive as well as time consuming. The computational methods o...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章,评审

    doi:10.1016/j.jbi.2019.103159

    authors: Sachdev K,Gupta MK

    更新日期:2019-05-01 00:00:00

  • Specifying computer-based counseling systems in health care: a new approach to user-interface and interaction design.

    abstract::Computer-based counseling systems in health care play an important role in the toolset available for medical doctors to inform, motivate and challenge their patients according to a well-defined therapeutic goal. The design, development and implementation of such systems require close collaboration between users, i.e. ...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2008.10.005

    authors: Herzberg D,Marsden N,Kübler P,Leonhardt C,Thomanek S,Jung H,Becker A

    更新日期:2009-04-01 00:00:00

  • Understanding infusion administration in the ICU through Distributed Cognition.

    abstract::To understand how healthcare technologies are used in practice and evaluate them, researchers have argued for adopting the theoretical framework of Distributed Cognition (DC). This paper describes the methods and results of a study in which a DC methodology, Distributed Cognition for Teamwork (DiCoT), was applied to s...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2012.02.003

    authors: Rajkomar A,Blandford A

    更新日期:2012-06-01 00:00:00

  • Unsupervised low-dimensional vector representations for words, phrases and text that are transparent, scalable, and produce similarity metrics that are not redundant with neural embeddings.

    abstract::Neural embeddings are a popular set of methods for representing words, phrases or text as a low dimensional vector (typically 50-500 dimensions). However, it is difficult to interpret these dimensions in a meaningful manner, and creating neural embeddings requires extensive training and tuning of multiple parameters a...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2019.103096

    authors: Smalheiser NR,Cohen AM,Bonifield G

    更新日期:2019-02-01 00:00:00

  • Desiderata for domain reference ontologies in biomedicine.

    abstract::Domain reference ontologies represent knowledge about a particular part of the world in a way that is independent from specific objectives, through a theory of the domain. An example of reference ontology in biomedical informatics is the Foundational Model of Anatomy (FMA), an ontology of anatomy that covers the entir...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2005.09.002

    authors: Burgun A

    更新日期:2006-06-01 00:00:00

  • A model-driven methodology for exploring complex disease comorbidities applied to autism spectrum disorder and inflammatory bowel disease.

    abstract::We propose a model-driven methodology aimed to shed light on complex disorders. Our approach enables exploring shared etiologies of comorbid diseases at the molecular pathway level. The method, Comparative Comorbidities Simulation (CCS), uses stochastic Petri net simulation for examining the phenotypic effects of pert...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2016.08.008

    authors: Somekh J,Peleg M,Eran A,Koren I,Feiglin A,Demishtein A,Shiloh R,Heiner M,Kong SW,Elazar Z,Kohane I

    更新日期:2016-10-01 00:00:00

  • Intradialytic blood pressure pattern recognition based on density peak clustering.

    abstract::End-stage renal disease (ESRD) is the final stage of chronic kidney disease (CKD) and requires hemodialysis (HD) for survival. Intradialytic blood pressure (IBP) measurements are necessary to ensure patient safety during HD treatments and have critical clinical and prognostic significance. Studies on IBP measurements,...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2018.05.013

    authors: Wang F,Zhou JY,Tian Y,Wang Y,Zhang P,Chen JH,Li JS

    更新日期:2018-07-01 00:00:00

  • On the reproducibility of results of pathway analysis in genome-wide expression studies of colorectal cancers.

    abstract::One of the major problems in genomics and medicine is the identification of gene networks and pathways deregulated in complex and polygenic diseases, like cancer. In this paper, we address the problem of assessing the variability of results of pathways analysis identified in different and independent genome wide expre...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2009.09.005

    authors: Maglietta R,Distaso A,Piepoli A,Palumbo O,Carella M,D'Addabbo A,Mukherjee S,Ancona N

    更新日期:2010-06-01 00:00:00

  • Development of a clinician reputation metric to identify appropriate problem-medication pairs in a crowdsourced knowledge base.

    abstract:BACKGROUND:Correlation of data within electronic health records is necessary for implementation of various clinical decision support functions, including patient summarization. A key type of correlation is linking medications to clinical problems; while some databases of problem-medication links are available, they are...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2013.11.010

    authors: McCoy AB,Wright A,Rogith D,Fathiamini S,Ottenbacher AJ,Sittig DF

    更新日期:2014-04-01 00:00:00

  • The development and validation of a simulation tool for health policy decision making.

    abstract::Computer simulations have been used to model infectious diseases to examine the outcomes of alternative strategies for managing their spread. Methicillin resistant Staphylococcus aureus (MRSA) skin and soft tissue infections have become prominent in many communities and efforts are underway to reduce the spread of thi...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2010.03.013

    authors: Panchanathan SS,Petitti DB,Fridsma DB

    更新日期:2010-08-01 00:00:00

  • A comparison of two methods for retrieving ICD-9-CM data: the effect of using an ontology-based method for handling terminology changes.

    abstract:OBJECTIVE:Most existing controlled terminologies can be characterized as collections of terms, wherein the terms are arranged in a simple list or organized in a hierarchy. These kinds of terminologies are considered useful for standardizing terms and encoding data and are currently used in many existing information sys...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2011.01.005

    authors: Yu AC,Cimino JJ

    更新日期:2011-04-01 00:00:00

  • A deep learning approach for predicting the quality of online health expert question-answering services.

    abstract::Recently, online health expert question-answering (HQA) services (systems) have attracted more and more health consumers to ask health-related questions everywhere at any time due to the convenience and effectiveness. However, the quality of answers in existing HQA systems varies in different situations. It is signifi...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2017.06.012

    authors: Hu Z,Zhang Z,Yang H,Chen Q,Zuo D

    更新日期:2017-07-01 00:00:00

  • Predicting the function of transplanted kidney in long-term care processes: Application of a hybrid model.

    abstract:BACKGROUND:A tool that can predict the estimated glomerular filtration rate (eGFR) in routine daily care can help clinicians to make better decisions for kidney transplant patients and to improve transplantation outcome. In this paper, we proposed a hybrid prediction model for predicting a future value for eGFR during ...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2019.103116

    authors: Rashidi Khazaee P,Bagherzadeh M J,Niazkhani Z,Pirnejad H

    更新日期:2019-03-01 00:00:00

  • The Counterfactual χ-GAN: Finding comparable cohorts in observational health data.

    abstract::Causal inference often relies on the counterfactual framework, which requires that treatment assignment is independent of the outcome, known as strong ignorability. Approaches to enforcing strong ignorability in causal analyses of observational data include weighting and matching methods. Effect estimates, such as the...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2020.103515

    authors: Averitt AJ,Vanitchanant N,Ranganath R,Perotte AJ

    更新日期:2020-09-01 00:00:00

  • Algorithms for rapid outbreak detection: a research synthesis.

    abstract::The threat of bioterrorism has stimulated interest in enhancing public health surveillance to detect disease outbreaks more rapidly than is currently possible. To advance research on improving the timeliness of outbreak detection, the Defense Advanced Research Project Agency sponsored the Bio-event Advanced Leading In...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2004.11.007

    authors: Buckeridge DL,Burkom H,Campbell M,Hogan WR,Moore AW

    更新日期:2005-04-01 00:00:00

  • Multi-step ahead meningitis case forecasting based on decomposition and multi-objective optimization methods.

    abstract::Epidemiological time series forecasting plays an important role in health public systems, due to its ability to allow managers to develop strategic planning to avoid possible epidemics. In this paper, a hybrid learning framework is developed to forecast multi-step-ahead (one, two, and three-month-ahead) meningitis cas...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2020.103575

    authors: Ribeiro MHDM,Mariani VC,Coelho LDS

    更新日期:2020-11-01 00:00:00

  • Collaborative text-annotation resource for disease-centered relation extraction from biomedical text.

    abstract::Agglomerating results from studies of individual biological components has shown the potential to produce biomedical discovery and the promise of therapeutic development. Such knowledge integration could be tremendously facilitated by automated text mining for relation extraction in the biomedical literature. Relation...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2009.02.001

    authors: Cano C,Monaghan T,Blanco A,Wall DP,Peshkin L

    更新日期:2009-10-01 00:00:00

  • Monitoring Obstructive Sleep Apnea by means of a real-time mobile system based on the automatic extraction of sets of rules through Differential Evolution.

    abstract::Real-time Obstructive Sleep Apnea (OSA) episode detection and monitoring are important for society in terms of an improvement in the health of the general population and of a reduction in mortality and healthcare costs. Currently, to diagnose OSA patients undergo PolySomnoGraphy (PSG), a complicated and invasive test ...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2014.02.015

    authors: Sannino G,De Falco I,De Pietro G

    更新日期:2014-06-01 00:00:00

  • Challenges in clinical natural language processing for automated disorder normalization.

    abstract:BACKGROUND:Identifying key variables such as disorders within the clinical narratives in electronic health records has wide-ranging applications within clinical practice and biomedical research. Previous research has demonstrated reduced performance of disorder named entity recognition (NER) and normalization (or groun...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2015.07.010

    authors: Leaman R,Khare R,Lu Z

    更新日期:2015-10-01 00:00:00

  • Word sense disambiguation across two domains: biomedical literature and clinical notes.

    abstract::The aim of this study is to explore the word sense disambiguation (WSD) problem across two biomedical domains-biomedical literature and clinical notes. A supervised machine learning technique was used for the WSD task. One of the challenges addressed is the creation of a suitable clinical corpus with manual sense anno...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2008.02.003

    authors: Savova GK,Coden AR,Sominsky IL,Johnson R,Ogren PV,de Groen PC,Chute CG

    更新日期:2008-12-01 00:00:00

  • Emerging medical informatics with case-based reasoning for aiding clinical decision in multi-agent system.

    abstract::This research aims to depict the methodological steps and tools about the combined operation of case-based reasoning (CBR) and multi-agent system (MAS) to expose the ontological application in the field of clinical decision support. The multi-agent architecture works for the consideration of the whole cycle of clinica...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2015.06.012

    authors: Shen Y,Colloc J,Jacquet-Andrieu A,Lei K

    更新日期:2015-08-01 00:00:00

  • Evaluation of an Enhanced Role-Based Access Control model to manage information access in collaborative processes for a statewide clinical education program.

    abstract:BACKGROUND:Managing information access in collaborative processes is a critical requirement to team-based biomedical research, clinical education, and patient care. We have previously developed a computation model, Enhanced Role-Based Access Control (EnhancedRBAC), and applied it to coordinate information access in the...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2013.11.007

    authors: Le XH,Doll T,Barbosu M,Luque A,Wang D

    更新日期:2014-08-01 00:00:00

  • Description of a method to support public health information management: organizational network analysis.

    abstract::In this case study, we describe a method that has potential to provide systematic support for public health information management. Public health agencies depend on specialized information that travels throughout an organization via communication networks among employees. Interactions that occur within these networks ...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2006.09.004

    authors: Merrill J,Bakken S,Rockoff M,Gebbie K,Carley KM

    更新日期:2007-08-01 00:00:00

  • Benchmarking relief-based feature selection methods for bioinformatics data mining.

    abstract::Modern biomedical data mining requires feature selection methods that can (1) be applied to large scale feature spaces (e.g. 'omics' data), (2) function in noisy problems, (3) detect complex patterns of association (e.g. gene-gene interactions), (4) be flexibly adapted to various problem domains and data types (e.g. g...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2018.07.015

    authors: Urbanowicz RJ,Olson RS,Schmitt P,Meeker M,Moore JH

    更新日期:2018-09-01 00:00:00

  • Modelling and analysing the dynamics of disease progression from cross-sectional studies.

    abstract::Clinical trials are typically conducted over a population within a defined time period in order to illuminate certain characteristics of a health issue or disease process. These cross-sectional studies give us a 'snapshot' of this disease process over a large number of people but do not allow us to model the temporal ...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2012.11.003

    authors: Li Y,Swift S,Tucker A

    更新日期:2013-04-01 00:00:00

  • Evaluation of a rule-based method for epidemiological document classification towards the automation of systematic reviews.

    abstract:INTRODUCTION:Most data extraction efforts in epidemiology are focused on obtaining targeted information from clinical trials. In contrast, limited research has been conducted on the identification of information from observational studies, a major source for human evidence in many fields, including environmental health...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章,评审

    doi:10.1016/j.jbi.2017.04.004

    authors: Karystianis G,Thayer K,Wolfe M,Tsafnat G

    更新日期:2017-06-01 00:00:00