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| Title: | 深度學習應用在偵測拓撲結構域
Topology Association Domain Identification using Deep Learning |
| Authors: | 楊鎮遠
Yang, Jhen-Yuan |
| Contributors: | 張家銘
Chang, Jia-Ming
楊鎮遠
Yang, Jhen-Yuan |
| Keywords: | 拓撲關聯域
TAD
Hi-C
染色體組織
深度學習
Topology Association Domain
TAD
Hi-C
Chromosome organization
Deep learning |
| Date: | 2019 |
| Issue Date: | 2019-09-05 16:15:31 (UTC+8) |
| Abstract: | 摘要
● 背景：近年來，越來越多的證據表明三維染色體結構在基因組功能中起著重要作用。拓撲關聯域（TAD）是一種自相互作用區域，已被證明是染色體的結構單元。然而，在高通量染色體構象捕獲圖中鑑定TAD 是一項計算挑戰。
● 結果：我們提出了一個新問題，即TAD 分類，而不是原始的TAD 識別。具體地，我們將Hi-C 圖考慮為圖像，使得TAD 分類是使用兩個深度學習模型，卷積神經網絡和殘差神經網絡來解決的圖像分類問題。此外，我們設計了一種合乎邏輯的方法來生成非TAD 數據，用於二元分類問題。通過跨物種和細胞類型驗證，深度學習模型的表現
良好，AUC> 0.80。
● 結論：TAD 在進化過程中被證明是保守的。有趣的是，我們的結果證實TAD 分類模型是實用的跨物種。從圖像分類的角度來看，它表明人與鼠之間的TAD 顯示了共同的模式。我們的方法可以成為測試Hi-C 圖中TAD 變化或保存的新方法。例如，如果兩個分類模型是可交換的，則保留兩個Hi-C 圖的TAD
Abstract
● Background: In the last years, increasing evidence indicates that three-dimensional
chromosome structure plays important rule in genomic function. A Topologically
Associating Domain (TAD), a self-interacting region, has been shown
as a structure unit of chromosome. However, it is a computational challenge to
identify TADs in high-throughput chromosome conformation capture map.
● Results: We proposed a novel problem, TAD classification, instead of original
TAD identification. Specifically, we consider Hi-C map as image such that TAD
classification is an image classification problem which is solved using two deep
learning models, convolutional neural network and residual neural network. Besides,
we designed an elegant way to generate non-TAD data for binary classification
problem. The performance of deep learning models is quite promising,
AUC > 0.80, through cross species and cell types validation.
● Conclusions: TAD has been shown conserved during evolution. Interestingly,
our results confirm TAD classification model is practical cross species. It indicates
TADs between human and mouse show common pattern from point of
view of image classification. Our approach could be a new way to test variation
or conservation of TADs among Hi-C maps. For example, TADs of two Hi-C
maps are conserved if two classification models are exchangeable. |
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| Description: | 碩士
國立政治大學
資訊科學系
105753033 |
| Source URI: | http://thesis.lib.nccu.edu.tw/record/#G1057530331 |
| Data Type: | thesis |
| DOI: | 10.6814/NCCU201901133 |
| Appears in Collections: | [資訊科學系] 學位論文
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