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      Liver imaging features by convolutional neural network to predict the metachronous liver metastasis in stage I-III colorectal cancer patients based on preoperative abdominal CT scan

      research-article
      1 , 2 , 3 , 3 , 4 , 5 , 6 , 3 , 7 ,
      BMC Bioinformatics
      BioMed Central
      The 18th Asia Pacific Bioinformatics Conference (APBC 2020)
      18-20 August 2020
      Radiomics, Colorectal cancer, Convolutional neural network, Artificial intelligence

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          Abstract

          Background

          Introducing deep learning approach to medical images has rendered a large amount of un-decoded information into usage in clinical research. But mostly, it has been focusing on the performance of the prediction modeling for disease-related entity, but not on the clinical implication of the feature itself. Here we analyzed liver imaging features of abdominal CT images collected from 2019 patients with stage I – III colorectal cancer (CRC) using convolutional neural network (CNN) to elucidate its clinical implication in oncological perspectives.

          Results

          CNN generated imaging features from the liver parenchyma. Dimension reduction was done for the features by principal component analysis. We designed multiple prediction models for 5-year metachronous liver metastasis (5YLM) using combinations of clinical variables (age, sex, T stage, N stage) and top principal components (PCs), with logistic regression classification. The model using “1 st PC (PC1) + clinical information” had the highest performance (mean AUC = 0.747) to predict 5YLM, compared to the model with clinical features alone (mean AUC = 0.709). The PC1 was independently associated with 5YLM in multivariate analysis (beta = − 3.831, P < 0.001). For the 5-year mortality rate, PC1 did not contribute to an improvement to the model with clinical features alone. For the PC1, Kaplan-Meier plots showed a significant difference between PC1 low vs. high group. The 5YLM-free survival of low PC1 was 89.6% and the high PC1 was 95.9%. In addition, PC1 had a significant correlation with sex, body mass index, alcohol consumption, and fatty liver status.

          Conclusion

          The imaging features combined with clinical information improved the performance compared to the standardized prediction model using only clinical information. The liver imaging features generated by CNN may have the potential to predict liver metastasis. These results suggest that even though there were no liver metastasis during the primary colectomy, the features of liver imaging can impose characteristics that could be predictive for metachronous liver metastasis.

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          Most cited references29

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          Very Deep Convolutional Networks for Large-Scale Image Recognition

          In this work we investigate the effect of the convolutional network depth on its accuracy in the large-scale image recognition setting. Our main contribution is a thorough evaluation of networks of increasing depth using an architecture with very small (3x3) convolution filters, which shows that a significant improvement on the prior-art configurations can be achieved by pushing the depth to 16-19 weight layers. These findings were the basis of our ImageNet Challenge 2014 submission, where our team secured the first and the second places in the localisation and classification tracks respectively. We also show that our representations generalise well to other datasets, where they achieve state-of-the-art results. We have made our two best-performing ConvNet models publicly available to facilitate further research on the use of deep visual representations in computer vision.
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            A systematic review shows no performance benefit of machine learning over logistic regression for clinical prediction models

            The objective of this study was to compare performance of logistic regression (LR) with machine learning (ML) for clinical prediction modeling in the literature.
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              Methods of integrating data to uncover genotype-phenotype interactions.

              Recent technological advances have expanded the breadth of available omic data, from whole-genome sequencing data, to extensive transcriptomic, methylomic and metabolomic data. A key goal of analyses of these data is the identification of effective models that predict phenotypic traits and outcomes, elucidating important biomarkers and generating important insights into the genetic underpinnings of the heritability of complex traits. There is still a need for powerful and advanced analysis strategies to fully harness the utility of these comprehensive high-throughput data, identifying true associations and reducing the number of false associations. In this Review, we explore the emerging approaches for data integration - including meta-dimensional and multi-staged analyses - which aim to deepen our understanding of the role of genetics and genomics in complex outcomes. With the use and further development of these approaches, an improved understanding of the relationship between genomic variation and human phenotypes may be revealed.
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                Author and article information

                Contributors
                dokyoon.kim@pennmedicine.upenn.edu
                Conference
                BMC Bioinformatics
                BMC Bioinformatics
                BMC Bioinformatics
                BioMed Central (London )
                1471-2105
                17 September 2020
                17 September 2020
                2020
                : 21
                Issue : Suppl 13 Issue sponsor : Publication of this supplement has not been supported by sponsorship. Information about the source of funding for publication charges can be found in the individual articles. The articles have undergone the journal's standard peer review process for supplements. The Supplement Editors declare that they have no competing interests.
                : 382
                Affiliations
                [1 ]GRID grid.496108.2, Division of Future Convergent, , The Cyber University of Korea, ; Seoul, 03051 South Korea
                [2 ]GRID grid.412484.f, ISNI 0000 0001 0302 820X, Department of Surgery, , Seoul National University Hospital Healthcare System Gangnam Center, ; Seoul, 06236 South Korea
                [3 ]GRID grid.25879.31, ISNI 0000 0004 1936 8972, Department of Biostatistics, Epidemiology & Informatics, Perelman School of Medicine, , University of Pennsylvania, ; B304 Richards Building, 3700 Hamilton Walk, Philadelphia, PA 19104-6116 USA
                [4 ]GRID grid.251916.8, ISNI 0000 0004 0532 3933, Department of Software and Computer Engineering, , Ajou University, ; Suwon, 16499 South Korea
                [5 ]GRID grid.31501.36, ISNI 0000 0004 0470 5905, Department of Radiology, , Seoul National University College of Medicine, ; Seoul, 03080 South Korea
                [6 ]GRID grid.31501.36, ISNI 0000 0004 0470 5905, Department of Surgery, , Seoul National University College of Medicine, ; Seoul, 03080 South Korea
                [7 ]GRID grid.25879.31, ISNI 0000 0004 1936 8972, Institute for Biomedical Informatics, University of Pennsylvania, ; Philadelphia, PA 19104 USA
                Article
                3686
                10.1186/s12859-020-03686-0
                7495853
                32938394
                ab29585e-4e64-4c13-b9ed-de1034f8b5ff
                © The Author(s) 2020

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                The 18th Asia Pacific Bioinformatics Conference
                APBC 2020
                Seoul, Korea
                18-20 August 2020
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                Research
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                © The Author(s) 2020

                Bioinformatics & Computational biology
                radiomics,colorectal cancer,convolutional neural network,artificial intelligence

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