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2020 – today
- 2024
[j30]Van-The Le, Muhammad-Shahid Malik
, Yi-Hsuan Tseng, Yu-Cheng Lee, Cheng-I Huang, Yu-Yen Ou:
DeepPLM_mCNN: An approach for enhancing ion channel and ion transporter recognition by multi-window CNN based on features from pre-trained language models. Comput. Biol. Chem. 110: 108055 (2024)- [j29]Jui-Hsuan Lee, Eric Hsiao-Kuang Wu, Yu-Yen Ou, Yueh-Che Lee, Cheng-Hsun Lee, Chia-Ru Chung:
Anti-Drugs Chatbot: Chinese BERT-Based Cognitive Intent Analysis. IEEE Trans. Comput. Soc. Syst. 11(1): 514-521 (2024) - 2022
- [j28]Quang-Thai Ho, Nguyen-Quoc-Khanh Le, Yu-Yen Ou:
mCNN-ETC: identifying electron transporters and their functional families by using multiple windows scanning techniques in convolutional neural networks with evolutionary information of protein sequences. Briefings Bioinform. 23(1) (2022) - [j27]Trinh-Trung-Duong Nguyen, The-Anh Tran, Nguyen-Quoc-Khanh Le, Dinh-Minh Pham, Yu-Yen Ou:
An Extensive Examination of Discovering 5-Methylcytosine Sites in Genome-Wide DNA Promoters Using Machine Learning Based Approaches. IEEE ACM Trans. Comput. Biol. Bioinform. 19(1): 87-94 (2022) - [j26]Trinh-Trung-Duong Nguyen, Quang-Thai Ho, Nguyen-Quoc-Khanh Le, Van-Dinh Phan, Yu-Yen Ou:
Use Chou's 5-Steps Rule With Different Word Embedding Types to Boost Performance of Electron Transport Protein Prediction Model. IEEE ACM Trans. Comput. Biol. Bioinform. 19(2): 1235-1244 (2022) - 2021
- [j25]Nguyen-Quoc-Khanh Le, Quang-Thai Ho, Trinh-Trung-Duong Nguyen, Yu-Yen Ou:
A transformer architecture based on BERT and 2D convolutional neural network to identify DNA enhancers from sequence information. Briefings Bioinform. 22(5) (2021) - [j24]Trinh-Trung-Duong Nguyen, Duc-Khanh Nguyen, Yu-Yen Ou:
Addressing data imbalance problems in ligand-binding site prediction using a variational autoencoder and a convolutional neural network. Briefings Bioinform. 22(6) (2021) - [j23]Syed Muazzam Ali Shah, Semmy Wellem Taju, Bongani Brian Dlamini, Yu-Yen Ou:
DeepSIRT: A deep neural network for identification of sirtuin targets and their subcellular localizations. Comput. Biol. Chem. 93: 107514 (2021) - [j22]Semmy Wellem Taju, Syed Muazzam Ali Shah, Yu-Yen Ou:
ActTRANS: Functional classification in active transport proteins based on transfer learning and contextual representations. Comput. Biol. Chem. 93: 107537 (2021) - [j21]Trinh-Trung-Duong Nguyen, Nguyen-Quoc-Khanh Le, The-Anh Tran, Dinh-Minh Pham, Yu-Yen Ou:
Incorporating a transfer learning technique with amino acid embeddings to efficiently predict N-linked glycosylation sites in ion channels. Comput. Biol. Medicine 130: 104212 (2021) - [j20]Quang-Thai Ho, Trinh-Trung-Duong Nguyen, Nguyen-Quoc-Khanh Le, Yu-Yen Ou:
FAD-BERT: Improved prediction of FAD binding sites using pre-training of deep bidirectional transformers. Comput. Biol. Medicine 131: 104258 (2021) - [j19]Syed Muazzam Ali Shah, Semmy Wellem Taju, Quang-Thai Ho, Trinh-Trung-Duong Nguyen, Yu-Yen Ou:
GT-Finder: Classify the family of glucose transporters with pre-trained BERT language models. Comput. Biol. Medicine 131: 104259 (2021) - [j18]Syed Muazzam Ali Shah, Yu-Yen Ou:
TRP-BERT: Discrimination of transient receptor potential (TRP) channels using contextual representations from deep bidirectional transformer based on BERT. Comput. Biol. Medicine 137: 104821 (2021) - 2020
- [j17]Eric Hsiao-Kuang Wu, Chun-Han Lin, Yu-Yen Ou, Chen-Zhong Liu, Wei-Kai Wang, Chi-Yun Chao:
Advantages and Constraints of a Hybrid Model K-12 E-Learning Assistant Chatbot. IEEE Access 8: 77788-77801 (2020) - [j16]Eric Hsiao-Kuang Wu, Sung-En Chen, Jhao-Jhong Liu, Yu-Yen Ou, Min-Te Sun:
A Self-Relevant CNN-SVM Model for Problem Classification in K-12 Question-Driven Learning. IEEE Access 8: 225822-225830 (2020) - [j15]Nguyen-Quoc-Khanh Le, Quang-Thai Ho, Edward Kien Yee Yapp, Yu-Yen Ou, Hui-Yuan Yeh:
DeepETC: A deep convolutional neural network architecture for investigating and classifying electron transport chain's complexes. Neurocomputing 375: 71-79 (2020)
2010 – 2019
- 2019
- [j14]Nguyen-Quoc-Khanh Le, Quang-Thai Ho, Yu-Yen Ou:
Using two-dimensional convolutional neural networks for identifying GTP binding sites in Rab proteins. J. Bioinform. Comput. Biol. 17(1): 1950005:1-1950005:19 (2019) - [j13]Semmy Wellem Taju, Yu-Yen Ou:
DeepIon: Deep learning approach for classifying ion transporters and ion channels from membrane proteins. J. Comput. Chem. 40(15): 1521-1529 (2019) - [i1]Rosdyana Mangir Irawan Kusuma, Trang-Thi Ho, Wei-Chun Kao, Yu-Yen Ou, Kai-Lung Hua:
Using Deep Learning Neural Networks and Candlestick Chart Representation to Predict Stock Market. CoRR abs/1903.12258 (2019) - 2018
- [j12]Semmy Wellem Taju, Trinh-Trung-Duong Nguyen, Nguyen-Quoc-Khanh Le, Rosdyana Mangir Irawan Kusuma, Yu-Yen Ou:
DeepEfflux: a 2D convolutional neural network model for identifying families of efflux proteins in transporters. Bioinform. 34(18): 3111-3117 (2018) - [j11]Nguyen-Quoc-Khanh Le, Green Arther Sandag, Yu-Yen Ou:
Incorporating post translational modification information for enhancing the predictive performance of membrane transport proteins. Comput. Biol. Chem. 77: 251-260 (2018) - 2017
- [j10]Nguyen-Quoc-Khanh Le, Quang-Thai Ho, Yu-Yen Ou:
Incorporating deep learning with convolutional neural networks and position specific scoring matrices for identifying electron transport proteins. J. Comput. Chem. 38(23): 2000-2006 (2017) - 2016
- [j9]Nguyen-Quoc-Khanh Le, Yu-Yen Ou:
Incorporating efficient radial basis function networks and significant amino acid pairs for predicting GTP binding sites in transport proteins. BMC Bioinform. 17(S-19): 183-192 (2016) - [j8]Nguyen-Quoc-Khanh Le, Yu-Yen Ou:
Prediction of FAD binding sites in electron transport proteins according to efficient radial basis function networks and significant amino acid pairs. BMC Bioinform. 17: 298 (2016) - [c9]Semmy Wellem Taju, Nguyen-Quoc-Khanh Le, Yu-Yen Ou:
Using Deep Learning with Position Specific Scoring Matrices to Identify Efflux Proteins in Membrane and Transport Proteins. BIBE 2016: 101-108 - 2014
- [j7]M. Michael Gromiha, Yu-Yen Ou:
Bioinformatics approaches for functional annotation of membrane proteins. Briefings Bioinform. 15(2): 155-168 (2014) - 2011
- [j6]Shu-An Chen, Yu-Yen Ou, Tzong-Yi Lee, M. Michael Gromiha:
Prediction of transporter targets using efficient RBF networks with PSSM profiles and biochemical properties. Bioinform. 27(15): 2062-2067 (2011) - 2010
- [j5]Shu-An Chen, Tzong-Yi Lee, Yu-Yen Ou:
Incorporating significant amino acid pairs to identify O-linked glycosylation sites on transmembrane proteins and non-transmembrane proteins. BMC Bioinform. 11: 536 (2010) - [j4]Yu-Yen Ou, Shu-An Chen, M. Michael Gromiha:
Prediction of membrane spanning segments and topology in beta-barrel membrane proteins at better accuracy. J. Comput. Chem. 31(1): 217-223 (2010) - [c8]Shu-An Chen, Yu-Yen Ou, M. Michael Gromiha:
Topology Prediction of alpha-Helical and beta-Barrel Transmembrane Proteins Using RBF Networks. ICIC (1) 2010: 642-649
2000 – 2009
- 2009
- [c7]Yu-Yen Ou, Shu-An Chen:
Using Efficient RBF Networks to Classify Transport Proteins Based on PSSM Profiles and Biochemical Properties. IWANN (1) 2009: 869-876 - 2008
- [j3]Yu-Yen Ou, M. Michael Gromiha, Shu-An Chen, Makiko Suwa:
TMBETADISC-RBF: Discrimination of beta-barrel membrane proteins using RBF networks and PSSM profiles. Comput. Biol. Chem. 32(3): 227-231 (2008) - 2007
- [c6]Chung-Tsai Su, Tong-Ming Hsu, Chien-Yu Chen, Yu-Yen Ou, Yen-Jen Oyang:
Enhancing Protein Disorder Detection by Refined Secondary Structure Prediction. BIRD 2007: 395-409 - [c5]Yen-Jen Oyang, Darby Tien-Hao Chang, Yu-Yen Ou, Hao-Geng Hung, Chien-Yu Chen:
Prediction of Protein Secondary Structures with a Novel Kernel Density Estimator. MLMTA 2007: 79-84 - [c4]Yu-Yen Ou, Shu-An Chen, Chung-Lu Shao, Hao-Geng Hung:
Using Efficient RBF Network to Identify Interface Residues Based on PSSM Profiles and Biochemical Properties. PRIB 2007: 132-141 - 2006
- [j2]Chung-Tsai Su, Chien-Yu Chen, Yu-Yen Ou:
Protein disorder prediction by condensed PSSM considering propensity for order or disorder. BMC Bioinform. 7: 319 (2006) - [c3]Yu-Yen Ou, Hao-Geng Hung, Yen-Jen Oyang:
A Study of Supervised Learning with Multivariate Analysis on Unbalanced Datasets. IJCNN 2006: 2201-2205 - [c2]Yu-Yen Ou, Guan-Hau Chen, Yen-Jen Oyang:
Expediting Model Selection for Support Vector Machines Based on an Advanced Data Reduction Algorithm. PRICAI 2006: 1017-1021 - 2005
- [j1]Yen-Jen Oyang, Shien-Ching Hwang, Yu-Yen Ou, Chien-Yu Chen, Zhi-Wei Chen:
Data classification with radial basis function networks based on a novel kernel density estimation algorithm. IEEE Trans. Neural Networks 16(1): 225-236 (2005) - 2003
- [c1]Yu-Yen Ou, Chien-Yu Chen, Shien-Ching Hwang, Yen-Jen Oyang:
Expediting model selection for Support Vector Machines based on data reduction. SMC 2003: 786-791
Coauthor Index
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