Shirley W. I. Siu

27 papers B 2Journal 18Unranked 7

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	CrossToGene: A bidirectional cross-modality interaction framework for predicting spatial gene expression from histopathological images. Eng. Appl. Artif. Intell. Xiangyu Ma, Xinke Zhan, Yutao Hu, Shirley W. I. Siu
2026	J	`jnl`	Enzyformer: a two-stage pretrained model for enzymatic retrosynthesis. J. Cheminformatics Tiantao Liu, Jiangcheng Xu, Xinke Zhan, Shaolong Lin, Shirley W. I. Siu
2026	J	`jnl`	MambaTransDTA: A Hybrid Mamba-Transformer Architecture for Accurate Drug-Target Binding Affinity Prediction. J. Chem. Inf. Model. Xinpo Lou, Jianxiu Cai, Qidong Liu, Shirley W. I. Siu
2026	J	`jnl`	Multi-MoleScale: a multi-scale approach for molecular property prediction with graph contrastive and sequence learning. J. Cheminformatics Xinpo Lou, Jianxiu Cai, Shirley W. I. Siu
2025	J	`jnl`	BERT-AmPEP60: A BERT-Based Transfer Learning Approach to Predict the Minimum Inhibitory Concentrations of Antimicrobial Peptides for J. Chem. Inf. Model. Jianxiu Cai, Jielu Yan, Chonwai Un, Yapeng Wang, François-Xavier Campbell-Valois, Shirley W. I. Siu
2025	—	`conf`	CALM-AcPEP: Predicting Anticancer Peptides Using Cross-Attention and Pre-Trained Language Model. ICIC (26) Xinke Zhan, Tiantao Liu, Pratiti Bhadra, Yu-An Huang, Zhuhong You, Shirley W. I. Siu
2025	—	`conf`	xLSTM-AmPEP60: An xLSTM Model for the Minimum Inhibitory Concentrations Prediction of Antimicrobial Peptides. BIBM Jianxiu Cai, Xinpo Lou, Jielu Yan, Joel P. Arrais, Yapeng Wang, Shirley W. I. Siu
2024	J	`jnl`	Editorial: Machine learning approaches to antimicrobials: discovery and resistance. Frontiers Bioinform. Shira L. Broschat, Shirley W. I. Siu, Cesar de la Fuente-Nunez
2024	J	`jnl`	Enhancing Diagnostic Precision in Gastric Bleeding through Automated Lesion Segmentation: A Deep DuS-KFCM Approach. CoRR Xian-Xian Liu, Mingkun Xu, Yuanyuan Wei, Huafeng Qin, Qun Song, Simon Fong, Feng Tien, Wei Luo, Juntao Gao, Zhihua Zhang, Shirley W. I. Siu
2024	J	`jnl`	Identification of Anticancer Peptides from the Genome of J. Chem. Inf. Model. Hong-Hin Cheong, Weimin Zuo, Jiarui Chen, Chonwai Un, Yain-Whar Si, Koon Ho Wong, Hang Fai Kwok, Shirley W. I. Siu
2022	J	`jnl`	Multi-Branch-CNN: Classification of ion channel interacting peptides using multi-branch convolutional neural network. Comput. Biol. Medicine Jielu Yan, Bob Zhang, Mingliang Zhou, Hang Fai Kwok, Shirley W. I. Siu
2021	J	`jnl`	Chemical toxicity prediction based on semi-supervised learning and graph convolutional neural network. J. Cheminformatics Jiarui Chen, Yain-Whar Si, Chonwai Un, Shirley W. I. Siu
2021	J	`jnl`	LigTMap: ligand and structure-based target identification and activity prediction for small molecular compounds. J. Cheminformatics Faraz Shaikh, Hio Kuan Tai, Nirali Desai, Shirley W. I. Siu
2021	J	`jnl`	xDeep-AcPEP: Deep Learning Method for Anticancer Peptide Activity Prediction Based on Convolutional Neural Network and Multitask Learning. J. Chem. Inf. Model. Jiarui Chen, Hong-Hin Cheong, Shirley W. I. Siu
2020	—	`conf`	Evaluating Variants of Firefly Algorithm for Ligand Pose Prediction in Protein-ligand Docking Program. ICBBT Meng Chi Ao, Shirley W. I. Siu
2020	—	`conf`	Study of Data Imbalanced Problem in Protein-peptide Binding Prediction. ICBBT Lu Gao, Shirley W. I. Siu
2020	J	`jnl`	White learning methodology: A case study of cancer-related disease factors analysis in real-time PACS environment. Comput. Methods Programs Biomed. Tengyue Li, Simon Fong, Shirley W. I. Siu, Xin-She Yang, Liansheng Liu, Sabah Mohammed
2018	J	`jnl`	Adaptive Incremental Genetic Algorithm for Task Scheduling in Cloud Environments. Symmetry Kairong Duan, Simon Fong, Shirley W. I. Siu, Wei Song, Steven Sheng-Uei Guan
2018	J	`jnl`	Chaos-embedded particle swarm optimization approach for protein-ligand docking and virtual screening. J. Cheminformatics Hio Kuan Tai, Siti Azma Jusoh, Shirley W. I. Siu
2017	J	`jnl`	TMDIM: an improved algorithm for the structure prediction of transmembrane domains of bitopic dimers. J. Comput. Aided Mol. Des. Han Cao, Marcus C. K. Ng, Siti Azma Jusoh, Hio Kuan Tai, Shirley W. I. Siu
2016	B	`conf`	Improving the efficiency of PSOVina for protein-ligand docking by two-stage local search. CEC Hio Kuan Tai, Hang Lin, Shirley W. I. Siu
2016	J	`jnl`	ProtPOS: a python package for the prediction of protein preferred orientation on a surface. Bioinform. Jimmy C. F. Ngai, Pui-In Mak, Shirley W. I. Siu
2015	J	`jnl`	PSOVina: The hybrid particle swarm optimization algorithm for protein-ligand docking. J. Bioinform. Comput. Biol. Marcus C. K. Ng, Simon Fong, Shirley W. I. Siu
2015	B	`conf`	Predicting favorable protein docking poses on a solid surface by particle swarm optimization. CEC Jimmy C. F. Ngai, Pui-In Mak, Shirley W. I. Siu
2013	—	`conf`	Comparison of Cutoff Strategies for Geometrical Features in Machine Learning-Based Scoring Functions. ADMA (2) Shirley W. I. Siu, Thomas K. F. Wong, Simon Fong
2006	—	`conf`	DynaPred: A structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations. ISMB (Supplement of Bioinformatics) Iris Antes, Shirley W. I. Siu, Thomas Lengauer
2004	—	`conf`	Smart Card-Based Irregular Access Patterns Detection System. EEE António Leong, Simon Fong, Shirley W. I. Siu