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Computer Vision, Deep Learning and Machine Learning with Applications in Genomics and Genetics

A special issue of Entropy (ISSN 1099-4300). This special issue belongs to the section "Entropy and Biology".

Deadline for manuscript submissions: closed (15 January 2021)

Special Issue Editors


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Guest Editor
Data Science and Informatics, Corteva AgriScience R&D, Indianapolis, IN, USA

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Guest Editor
Evolution & Ecology Research Centre, School of Biological Earth and Environmental Science, UNSW Sydney, Sydney NSW 2052, Australia
Interests: molecular ecology; evolutionary genetics; biodiversity; genomics, transciptomics; mathematics of forecasting and measuring biodiversity; conservation genetics and demography; endangered harvested and invasive species; evolutionary ecology of parentage, relatedness and group formation, especially in dolphins
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Special Issue Information

Dear Colleagues,

Machine learning and artificial intelligence is an interdisciplinary field of research focused on developing algorithms and statistical models for intelligent systems that can function without explicit instructions. One of the founding pillars of Artificial Intelligence and modern machine learning is information theory from Claude Shannon’s seminal work over 70 years ago that has its roots in communication systems and deals with data compression and coding theorems for transmission of information from one source to another over-noisy channels. More recently, deep learning has emerged as a front-runner within Artificial Intelligence inspired by neural information processing and functioning of the brain and powered by the availability of modern powerful GPUs. Over the last decade, deep learning has made impressive advances in applications ranging from computer vision and robotics to natural language processing and speech recognition. In this context, an emerging area of research has been the application of deep learning methodologies for several applications in genomics, genetics, and medical imaging (such as genomic prediction, genetic analysis of complex traits related to multifactorial diseases, and imaging genomics exploring relationships between genotypes, phenotypes and clinical outcomes). Although applications are growing at a very fast pace, many theoretical and practical challenges exist. The motivation behind this issue is to bring together researchers and practitioners from artificial intelligence, information theory, genomics, and genetics and provide a platform for sharing their research in addressing how information theory can help to advance theoretical understanding of machine learning and deep learning models (such as optimization, transfer learning, model interpretation, etc.), and at the same time demonstrating novel applications of deep learning and information theory in addressing problems in genomics, genetics, and computer vision for biological applications. Review articles exploring these areas are also welcome.

Dr. Chanda Pritam
Prof. William B. Sherwin
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Entropy is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (1 paper)

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19 pages, 7905 KiB  
Article
An Interpretation Architecture for Deep Learning Models with the Application of COVID-19 Diagnosis
by Yuchai Wan, Hongen Zhou and Xun Zhang
Entropy 2021, 23(2), 204; https://doi.org/10.3390/e23020204 - 7 Feb 2021
Cited by 14 | Viewed by 2914
Abstract
The Coronavirus disease 2019 (COVID-19) has become one of the threats to the world. Computed tomography (CT) is an informative tool for the diagnosis of COVID-19 patients. Many deep learning approaches on CT images have been proposed and brought promising performance. However, due [...] Read more.
The Coronavirus disease 2019 (COVID-19) has become one of the threats to the world. Computed tomography (CT) is an informative tool for the diagnosis of COVID-19 patients. Many deep learning approaches on CT images have been proposed and brought promising performance. However, due to the high complexity and non-transparency of deep models, the explanation of the diagnosis process is challenging, making it hard to evaluate whether such approaches are reliable. In this paper, we propose a visual interpretation architecture for the explanation of the deep learning models and apply the architecture in COVID-19 diagnosis. Our architecture designs a comprehensive interpretation about the deep model from different perspectives, including the training trends, diagnostic performance, learned features, feature extractors, the hidden layers, the support regions for diagnostic decision, and etc. With the interpretation architecture, researchers can make a comparison and explanation about the classification performance, gain insight into what the deep model learned from images, and obtain the supports for diagnostic decisions. Our deep model achieves the diagnostic result of 94.75%, 93.22%, 96.69%, 97.27%, and 91.88% in the criteria of accuracy, sensitivity, specificity, positive predictive value, and negative predictive value, which are 8.30%, 4.32%, 13.33%, 10.25%, and 6.19% higher than that of the compared traditional methods. The visualized features in 2-D and 3-D spaces provide the reasons for the superiority of our deep model. Our interpretation architecture would allow researchers to understand more about how and why deep models work, and can be used as interpretation solutions for any deep learning models based on convolutional neural network. It can also help deep learning methods to take a step forward in the clinical COVID-19 diagnosis field. Full article
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