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2. Overfit deep neural network for predicting drug-target interactions

Author

Xiao Xiaolin, Liu Xiaozhi, He Guoping, Liu Hongwei, Guo Jinkuo, Bian Xiyun, Tian Zhen, Ma Xiaofang, Li Yanxia, Xue Na, Zhang Chunyan, Gao Rui, Wang Kuan, Zhang Cheng, Wang Cuancuan, Liu Mingyong, and Du Xinping

Subjects
Biological sciences, Biochemistry, Structural biology, Mathematical biosciences, Science
Abstract

Summary: Drug-target interactions (DTIs) prediction is an important step in drug discovery. As traditional biological experiments or high-throughput screening are high cost and time-consuming, many deep learning models have been developed. Overfitting must be avoided when training deep learning models. We propose a simple framework, called OverfitDTI, for DTI prediction. In OverfitDTI, a deep neural network (DNN) model is overfit to sufficiently learn the features of the chemical space of drugs and the biological space of targets. The weights of trained DNN model form an implicit representation of the nonlinear relationship between drugs and targets. Performance of OverfitDTI on three public datasets showed that the overfit DNN models fit the nonlinear relationship with high accuracy. We identified fifteen compounds that interacted with TEK, a receptor tyrosine kinase contributing to vascular homeostasis, and the predicted AT9283 and dorsomorphin were experimentally demonstrated as inhibitors of TEK in human umbilical vein endothelial cells (HUVECs).

Published
2023
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12. Supplementary Figure 1 from Suppression of Cyclin D1 by Hypoxia-Inducible Factor-1 via Direct Mechanism Inhibits the Proliferation and 5-Fluorouracil–Induced Apoptosis of A549 Cells

Author

Wen, Wen, primary, Ding, Jin, primary, Sun, Wen, primary, Wu, Kun, primary, Ning, Beifang, primary, Gong, Wenfeng, primary, He, Guoping, primary, Huang, Shanna, primary, Ding, Xinyu, primary, Yin, Peipei, primary, Chen, Lei, primary, Liu, Qiong, primary, Xie, Weifen, primary, and Wang, Hongyang, primary

Published
2023
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13. Supplementary Figure Legends 1-4 from Suppression of Cyclin D1 by Hypoxia-Inducible Factor-1 via Direct Mechanism Inhibits the Proliferation and 5-Fluorouracil–Induced Apoptosis of A549 Cells

Author

Wen, Wen, primary, Ding, Jin, primary, Sun, Wen, primary, Wu, Kun, primary, Ning, Beifang, primary, Gong, Wenfeng, primary, He, Guoping, primary, Huang, Shanna, primary, Ding, Xinyu, primary, Yin, Peipei, primary, Chen, Lei, primary, Liu, Qiong, primary, Xie, Weifen, primary, and Wang, Hongyang, primary

Published
2023
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14. Supplementary Figure 4 from Suppression of Cyclin D1 by Hypoxia-Inducible Factor-1 via Direct Mechanism Inhibits the Proliferation and 5-Fluorouracil–Induced Apoptosis of A549 Cells

Author

Wen, Wen, primary, Ding, Jin, primary, Sun, Wen, primary, Wu, Kun, primary, Ning, Beifang, primary, Gong, Wenfeng, primary, He, Guoping, primary, Huang, Shanna, primary, Ding, Xinyu, primary, Yin, Peipei, primary, Chen, Lei, primary, Liu, Qiong, primary, Xie, Weifen, primary, and Wang, Hongyang, primary

Published
2023
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15. Supplementary Figure 2 from Suppression of Cyclin D1 by Hypoxia-Inducible Factor-1 via Direct Mechanism Inhibits the Proliferation and 5-Fluorouracil–Induced Apoptosis of A549 Cells

Author

Wen, Wen, primary, Ding, Jin, primary, Sun, Wen, primary, Wu, Kun, primary, Ning, Beifang, primary, Gong, Wenfeng, primary, He, Guoping, primary, Huang, Shanna, primary, Ding, Xinyu, primary, Yin, Peipei, primary, Chen, Lei, primary, Liu, Qiong, primary, Xie, Weifen, primary, and Wang, Hongyang, primary

Published
2023
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16. Supplementary Figure 3 from Suppression of Cyclin D1 by Hypoxia-Inducible Factor-1 via Direct Mechanism Inhibits the Proliferation and 5-Fluorouracil–Induced Apoptosis of A549 Cells

Author

Wen, Wen, primary, Ding, Jin, primary, Sun, Wen, primary, Wu, Kun, primary, Ning, Beifang, primary, Gong, Wenfeng, primary, He, Guoping, primary, Huang, Shanna, primary, Ding, Xinyu, primary, Yin, Peipei, primary, Chen, Lei, primary, Liu, Qiong, primary, Xie, Weifen, primary, and Wang, Hongyang, primary

Published
2023
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17. Data from Suppression of Cyclin D1 by Hypoxia-Inducible Factor-1 via Direct Mechanism Inhibits the Proliferation and 5-Fluorouracil–Induced Apoptosis of A549 Cells

Author

Wen, Wen, primary, Ding, Jin, primary, Sun, Wen, primary, Wu, Kun, primary, Ning, Beifang, primary, Gong, Wenfeng, primary, He, Guoping, primary, Huang, Shanna, primary, Ding, Xinyu, primary, Yin, Peipei, primary, Chen, Lei, primary, Liu, Qiong, primary, Xie, Weifen, primary, and Wang, Hongyang, primary

Published
2023
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23. A Large-Update Primal-Dual Interior-Point Method for Second-Order Cone Programming

Author

Fang, Liang, He, Guoping, Feng, Zengzhe, Wang, Yongli, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Zhang, Liqing, editor, Lu, Bao-Liang, editor, and Kwok, James, editor

Published
2010
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26. Predicting Time Series Using Incremental Langrangian Support Vector Regression

Author

Duan, Hua, Hou, Weizhen, He, Guoping, Zeng, Qingtian, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Rangan, C. Pandu, editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Liu, Derong, editor, Fei, Shumin, editor, Hou, Zengguang, editor, Zhang, Huaguang, editor, and Sun, Changyin, editor

Published
2007
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27. An Improved SVM Based on 1-Norm for Selection of Personal Credit Scoring Index System

Author

Xue, Xin, He, Guoping, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Rangan, C. Pandu, editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Liu, Derong, editor, Fei, Shumin, editor, Hou, Zengguang, editor, Zhang, Huaguang, editor, and Sun, Changyin, editor

Published
2007
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