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Semantic Segmentation by Using Down-Sampling and Subpixel Convolution: DSSC-UNet

Computers, Materials & Continua 2023年第4期75卷 683-696页

作者： Young-Man Kwon sunghoon bae Dong-Keun Chung Myung-Jae Lim Department of Medical IT Eulji University553Sanseong-daeroSujeong-guSeongnam-siGyeonggi-do13135Korea

Recently, semantic segmentation has been widely applied toimage processing, scene understanding, and many others. Especially, indeep learning-based semantic segmentation, the U-Net with convolutionalencoder-decoder architecture is a representative model which is proposed forimage segmentation in the biomedical field. It used max pooling operationfor reducing the size of image and making noise robust. However, instead ofreducing the complexity of the model, max pooling has the disadvantageof omitting some information about the image in reducing it. So, thispaper used two diagonal elements of down-sampling operation instead ofit. We think that the down-sampling feature maps have more informationintrinsically than max pooling feature maps because of keeping the Nyquisttheorem and extracting the latent information from them. In addition,this paper used two other diagonal elements for the skip connection. Indecoding, we used Subpixel Convolution rather than transposed convolutionto efficiently decode the encoded feature maps. Including all the ideas, thispaper proposed the new encoder-decoder model called Down-Sampling andSubpixel Convolution U-Net (DSSC-UNet). To prove the better performanceof the proposed model, this paper measured the performance of the UNetand DSSC-UNet on the Cityscapes. As a result, DSSC-UNet achieved89.6% Mean Intersection OverUnion (Mean-IoU) andU-Net achieved 85.6%Mean-IoU, confirming that DSSC-UNet achieved better performance.

关键词： Semantic segmentation encoder-decoder U-Net DSSC-UNet subpixel convolution down-sampling

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Noninvasive Prenatal Testing for Fetal Chromosomal Abnormalities Using Massively Parallel Sequencing: Clinical Experience from 7910 Korean Pregnancies

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Open Journal of Genetics 2018年第3期8卷 42-53页

作者： Seon Young Yun Hyuk Jung Kwon Amit Goyal Katiyar P. Shashank Heesu Im Joungsu Joo Jin-Sik bae Min Seob Lee sunghoon Lee EONE-DIAGNOMICS Genome Center (EDGC) Incheon South Korea

Objective: The purpose of this study is to review the clinical experience and performance of noninvasive prenatal testing (NIPT) method, using cell-free DNAto detect chromosomes 21, 18, 13, X, and Y abnormalities in over 7910 clinical samples from South Korean population. Method: Pregnant women between 1st of November 2015 to 18th of February 2018, with obstetric clinical findings participated in the study. NIPT was performed based on masivelly parallel sequencing with 0.3× low coverage paired-end sequencing using cell-free DNA in maternal plasma. Further invasive prenatal testing was recommended for pregnant women with positive NIPT results. Results: Of the total 7910 participants, 7890 (99.75%) were tested for NIPT and the remaining 20 (0.25%) were below the Quality Control (QC) standards. T13, T18, XXX, XXY and XYY had 100% of sensitivity, specificity, positive predictive values (PPV) and accuracy. The overall sensitivity was 100% and specificity, PPV and accuracy of all chromosomal abnormalities with further validation were 99.92%, 94.25%, and, 99.92% respectively. Conclusion: Our NIPT results showed high positive predictive value for the detection of autosomal trisomies and sex chromosome aneuploidies in our sample cohort.

关键词： Cell-Free DNA Trisomy Clinical Performance Mosaicism CPM Fetal Abnormality Noninvasive Prenatal Testing NIPT

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Multiple z-Score Based Method for Noninvasive Prenatal Test Using Cell-Free DNA in Maternal Plasma

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Open Journal of Genetics 2017年第1期7卷 1-8页

作者： Hyuk Jung Kwon Amit Goyal Heesu Im Kichan Lee Seon Young Yun Yoon Hee Kim Sungjong Lee Mi-Gyeong Lee Hyuna Lee Reena Garg Boram Park Soyoung Choi Joungsu Joo Jin-Sik bae Min-Jeong Kim Min Seob Lee sunghoon Lee EONE-DIAGNOMICS Genome Center Co. Ltd. Inchon Korea

Objective: To improve the detecting accuracy of chromosomal aneuploidy of fetus by non-invasive prenatal testing (NIPT) using next generation sequencing data of pregnant women’s cell-free DNA. Methods: We proposed the multi-Z method which uses 21 z-scores for each autosomal chromosome to detect aneuploidy of the chromosome, while the conventional NIPT method uses only one z-score. To do this, mapped read numbers of a certain chromosome were normalized by those of the other 21 chromosomes. Average and standard deviation (SD), which are used for calculating z-score of each sample, were obtained with normalized values between all autosomal chromosomes of control samples. In this way, multiple z-scores can be calculated for 21 autosomal chromosomes except oneself. Results: Multi-Z method showed 100% sensitivity and specificity for 187 samples sequenced to 3 M reads while the conventional NIPT method showed 95.1% specificity. Similarly, for 216 samples sequenced to 1 M reads, Multi-Z method showed 100% sensitivity and 95.6% specificity and the conventional NIPT method showed a result of 75.1% specificity. Conclusion: Multi-Z method showed higher accuracy and robust results than the conventional method even at low coverage reads.

关键词： Cell-Free DNA z-Score Multiple Thresholds Coefficient of Variance Noninvasive Prenatal Testing NIPT

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