Yu-Yen Ou - RankMe

51 papers B 5C 1Journal 40Unranked 5

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Enhancing the classification of metal-binding residue in proteins with retrieval-augmented generation, protein language models, and deep learning. Eng. Appl. Artif. Intell. Muhammad-Shahid Malik, Van-The Le, Yu-Yen Ou
2026	J	`jnl`	IFNg_DeepKG: A Novel Model for Identifying Interferon-Gamma-Inducing Epitopes Using Knowledge Graph RAG in Biomedical Applications. J. Chem. Inf. Model. Van-The Le, Juan Peter Timothy Yuune, Yu-Yen Ou
2026	J	`jnl`	RAG-msCNN: predicting protein-DNA binding sites by integration of retrieval-augmented generation (RAG) with protein language models and the multi-scale separable convolutional neural network. Biomed. Signal Process. Control. Muhammad-Shahid Malik, Muhammad Hussain, Quang-Thai Ho, Van-The Le, Yu-Yen Ou
2025	J	`jnl`	ATP_mCNN: Predicting ATP binding sites through pretrained language models and multi-window neural networks. Comput. Biol. Medicine Van-The Le, Muhammad-Shahid Malik, Yi-Jing Lin, Yu-Chen Liu, Yan-Yun Chang, Yu-Yen Ou
2025	J	`jnl`	CaBind_MCNN: Identifying Potential Calcium Channel Blocker Targets by Predicting Calcium-Binding Sites in Ion Channels and Ion Transporters Using Protein Language Models and Multiscale Feature Extraction. J. Chem. Inf. Model. Yan-Yun Chang, Yu-Chen Liu, Wei-En Jhang, Sin-Siang Wei, Yu-Yen Ou
2025	J	`jnl`	RAG_MCNNIL6: A Retrieval-Augmented Multi-Window Convolutional Network for Accurate Prediction of IL-6 Inducing Epitopes. J. Chem. Inf. Model. Cheng-Che Chuang, Yu-Chen Liu, Wei-En Jhang, Sin-Siang Wei, Yu-Yen Ou
2025	J	`jnl`	RTK_RAG: Leveraging Retrieval Augmented Generation with Multi-Window Convolutional Neural Networks for Superior ATP Binding Site Prediction in Receptor Tyrosine Kinases. J. Chem. Inf. Model. Sin-Siang Wei, Wei-En Jhang, Yu-Chen Liu, Cheng-Che Chuang, Yu-Yen Ou
2025	J	`jnl`	mCNN-GenEfflux: enhanced predicting Efflux protein and their super families by using generative proteins combined with multiple windows convolution neural networks. Comput. Biol. Chem. Muhammad Hussain, Yu-Yen Ou, Quang-Thai Ho
2024	J	`jnl`	Anti-Drugs Chatbot: Chinese BERT-Based Cognitive Intent Analysis. IEEE Trans. Comput. Soc. Syst. Jui-Hsuan Lee, Eric Hsiao-Kuang Wu, Yu-Yen Ou, Yueh-Che Lee, Cheng-Hsun Lee, Chia-Ru Chung
2024	J	`jnl`	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. Van-The Le, Muhammad-Shahid Malik, Yi-Hsuan Tseng, Yu-Cheng Lee, Cheng-I Huang, Yu-Yen Ou
2024	J	`jnl`	MCNN_MC: Computational Prediction of Mitochondrial Carriers and Investigation of Bongkrekic Acid Toxicity Using Protein Language Models and Convolutional Neural Networks. J. Chem. Inf. Model. Muhammad-Shahid Malik, Yan-Yun Chang, Yu-Chen Liu, Van-The Le, Yu-Yen Ou
2022	J	`jnl`	An Extensive Examination of Discovering 5-Methylcytosine Sites in Genome-Wide DNA Promoters Using Machine Learning Based Approaches. IEEE ACM Trans. Comput. Biol. Bioinform. Trinh-Trung-Duong Nguyen, The-Anh Tran, Nguyen-Quoc-Khanh Le, Dinh-Minh Pham, Yu-Yen Ou
2022	J	`jnl`	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. Trinh-Trung-Duong Nguyen, Quang-Thai Ho, Nguyen-Quoc-Khanh Le, Van-Dinh Phan, Yu-Yen Ou
2022	J	`jnl`	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. Quang-Thai Ho, Nguyen-Quoc-Khanh Le, Yu-Yen Ou
2021	J	`jnl`	A transformer architecture based on BERT and 2D convolutional neural network to identify DNA enhancers from sequence information. Briefings Bioinform. Nguyen-Quoc-Khanh Le, Quang-Thai Ho, Trinh-Trung-Duong Nguyen, Yu-Yen Ou
2021	J	`jnl`	ActTRANS: Functional classification in active transport proteins based on transfer learning and contextual representations. Comput. Biol. Chem. Semmy Wellem Taju, Syed Muazzam Ali Shah, Yu-Yen Ou
2021	J	`jnl`	Addressing data imbalance problems in ligand-binding site prediction using a variational autoencoder and a convolutional neural network. Briefings Bioinform. Trinh-Trung-Duong Nguyen, Duc-Khanh Nguyen, Yu-Yen Ou
2021	J	`jnl`	DeepSIRT: A deep neural network for identification of sirtuin targets and their subcellular localizations. Comput. Biol. Chem. Syed Muazzam Ali Shah, Semmy Wellem Taju, Bongani Brian Dlamini, Yu-Yen Ou
2021	J	`jnl`	FAD-BERT: Improved prediction of FAD binding sites using pre-training of deep bidirectional transformers. Comput. Biol. Medicine Quang-Thai Ho, Trinh-Trung-Duong Nguyen, Nguyen-Quoc-Khanh Le, Yu-Yen Ou
2021	J	`jnl`	GT-Finder: Classify the family of glucose transporters with pre-trained BERT language models. Comput. Biol. Medicine Syed Muazzam Ali Shah, Semmy Wellem Taju, Quang-Thai Ho, Trinh-Trung-Duong Nguyen, Yu-Yen Ou
2021	J	`jnl`	Incorporating a transfer learning technique with amino acid embeddings to efficiently predict N-linked glycosylation sites in ion channels. Comput. Biol. Medicine Trinh-Trung-Duong Nguyen, Nguyen-Quoc-Khanh Le, The-Anh Tran, Dinh-Minh Pham, Yu-Yen Ou
2021	J	`jnl`	TRP-BERT: Discrimination of transient receptor potential (TRP) channels using contextual representations from deep bidirectional transformer based on BERT. Comput. Biol. Medicine Syed Muazzam Ali Shah, Yu-Yen Ou
2020	J	`jnl`	A Self-Relevant CNN-SVM Model for Problem Classification in K-12 Question-Driven Learning. IEEE Access Eric Hsiao-Kuang Wu, Sung-En Chen, Jhao-Jhong Liu, Yu-Yen Ou, Min-Te Sun
2020	J	`jnl`	Advantages and Constraints of a Hybrid Model K-12 E-Learning Assistant Chatbot. IEEE Access Eric Hsiao-Kuang Wu, Chun-Han Lin, Yu-Yen Ou, Chen-Zhong Liu, Wei-Kai Wang, Chi-Yun Chao
2020	J	`jnl`	DeepETC: A deep convolutional neural network architecture for investigating and classifying electron transport chain's complexes. Neurocomputing Nguyen-Quoc-Khanh Le, Quang-Thai Ho, Edward Kien Yee Yapp, Yu-Yen Ou, Hui-Yuan Yeh
2019	J	`jnl`	DeepIon: Deep learning approach for classifying ion transporters and ion channels from membrane proteins. J. Comput. Chem. Semmy Wellem Taju, Yu-Yen Ou
2019	J	`jnl`	Using Deep Learning Neural Networks and Candlestick Chart Representation to Predict Stock Market. CoRR Rosdyana Mangir Irawan Kusuma, Trang-Thi Ho, Wei-Chun Kao, Yu-Yen Ou, Kai-Lung Hua
2019	J	`jnl`	Using two-dimensional convolutional neural networks for identifying GTP binding sites in Rab proteins. J. Bioinform. Comput. Biol. Nguyen-Quoc-Khanh Le, Quang-Thai Ho, Yu-Yen Ou
2018	J	`jnl`	DeepEfflux: a 2D convolutional neural network model for identifying families of efflux proteins in transporters. Bioinform. Semmy Wellem Taju, Trinh-Trung-Duong Nguyen, Nguyen-Quoc-Khanh Le, Rosdyana Mangir Irawan Kusuma, Yu-Yen Ou
2018	J	`jnl`	Incorporating post translational modification information for enhancing the predictive performance of membrane transport proteins. Comput. Biol. Chem. Nguyen-Quoc-Khanh Le, Green Arther Sandag, Yu-Yen Ou
2017	J	`jnl`	Incorporating deep learning with convolutional neural networks and position specific scoring matrices for identifying electron transport proteins. J. Comput. Chem. Nguyen-Quoc-Khanh Le, Quang-Thai Ho, Yu-Yen Ou
2016	J	`jnl`	Incorporating efficient radial basis function networks and significant amino acid pairs for predicting GTP binding sites in transport proteins. BMC Bioinform. Nguyen-Quoc-Khanh Le, Yu-Yen Ou
2016	J	`jnl`	Prediction of FAD binding sites in electron transport proteins according to efficient radial basis function networks and significant amino acid pairs. BMC Bioinform. Nguyen-Quoc-Khanh Le, Yu-Yen Ou
2016	C	`conf`	Using Deep Learning with Position Specific Scoring Matrices to Identify Efflux Proteins in Membrane and Transport Proteins. BIBE Semmy Wellem Taju, Nguyen-Quoc-Khanh Le, Yu-Yen Ou
2014	J	`jnl`	Bioinformatics approaches for functional annotation of membrane proteins. Briefings Bioinform. M. Michael Gromiha, Yu-Yen Ou
2011	J	`jnl`	Prediction of transporter targets using efficient RBF networks with PSSM profiles and biochemical properties. Bioinform. Shu-An Chen, Yu-Yen Ou, Tzong-Yi Lee, M. Michael Gromiha
2010	J	`jnl`	Incorporating significant amino acid pairs to identify O-linked glycosylation sites on transmembrane proteins and non-transmembrane proteins. BMC Bioinform. Shu-An Chen, Tzong-Yi Lee, Yu-Yen Ou
2010	J	`jnl`	Prediction of membrane spanning segments and topology in beta-barrel membrane proteins at better accuracy. J. Comput. Chem. Yu-Yen Ou, Shu-An Chen, M. Michael Gromiha
2010	—	`conf`	Topology Prediction of ICIC (1) Shu-An Chen, Yu-Yen Ou, M. Michael Gromiha
2009	—	`conf`	Using Efficient RBF Networks to Classify Transport Proteins Based on PSSM Profiles and Biochemical Properties. IWANN (1) Yu-Yen Ou, Shu-An Chen
2008	J	`jnl`	TMBETADISC-RBF: Discrimination of beta-barrel membrane proteins using RBF networks and PSSM profiles. Comput. Biol. Chem. Yu-Yen Ou, M. Michael Gromiha, Shu-An Chen, Makiko Suwa
2007	—	`conf`	Enhancing Protein Disorder Detection by Refined Secondary Structure Prediction. BIRD Chung-Tsai Su, Tong-Ming Hsu, Chien-Yu Chen, Yu-Yen Ou, Yen-Jen Oyang
2007	—	`conf`	Prediction of Protein Secondary Structures with a Novel Kernel Density Estimator. MLMTA Yen-Jen Oyang, Darby Tien-Hao Chang, Yu-Yen Ou, Hao-Geng Hung, Chien-Yu Chen
2007	—	`conf`	Using Efficient RBF Network to Identify Interface Residues Based on PSSM Profiles and Biochemical Properties. PRIB Yu-Yen Ou, Shu-An Chen, Chung-Lu Shao, Hao-Geng Hung
2006	B	`conf`	A Study of Supervised Learning with Multivariate Analysis on Unbalanced Datasets. IJCNN Yu-Yen Ou, Hao-Geng Hung, Yen-Jen Oyang
2006	B	`conf`	Expediting Model Selection for Support Vector Machines Based on an Advanced Data Reduction Algorithm. PRICAI Yu-Yen Ou, Guan-Hau Chen, Yen-Jen Oyang
2006	J	`jnl`	Protein disorder prediction by condensed PSSM considering propensity for order or disorder. BMC Bioinform. Chung-Tsai Su, Chien-Yu Chen, Yu-Yen Ou
2005	B	`conf`	A novel radial basis function network classifier with centers set by hierarchical clustering. IJCNN Yu-Yen Ou, Yen-Jen Oyang, Chien-Yu Chen
2005	B	`conf`	Data classification with a relaxed model of variable kernel density estimation. IJCNN Yen-Jen Oyang, Yu-Yen Ou, Shien-Ching Hwang, Chien-Yu Chen, Darby Tien-Hao Chang
2005	J	`jnl`	Data classification with radial basis function networks based on a novel kernel density estimation algorithm. IEEE Trans. Neural Networks Yen-Jen Oyang, Shien-Ching Hwang, Yu-Yen Ou, Chien-Yu Chen, Zhi-Wei Chen
2003	B	`conf`	Expediting model selection for Support Vector Machines based on data reduction. SMC Yu-Yen Ou, Chien-Yu Chen, Shien-Ching Hwang, Yen-Jen Oyang