Guo-Wei Wei

ORCID

Publication Activity (10 Years)

Years Active: 2002-2024
Publications (10 Years): 86

Top Venues

J. Chem. Inf. Model.

CoRR

Comput. Biol. Medicine

J. Comput. Chem.

Publications

Nicole Hayes, Ekaterina Merkurjev, Guo-Wei Wei
Graph-Based Bidirectional Transformer Decision Threshold Adjustment Algorithm for Class-Imbalanced Molecular Data. CoRR (2024)
Sheik Ahmed Ullah, Xin Yang, Benjamin Jones, Shan Zhao, Weihua Geng, Guo-Wei Wei
Bridging Eulerian and Lagrangian Poisson-Boltzmann solvers by ESES. J. Comput. Chem. 45 (6) (2024)
Zhe Su, Yiying Tong, Guo-Wei Wei
Hodge Decomposition of Single-Cell RNA Velocity. J. Chem. Inf. Model. 64 (8) (2024)
Sean Cottrell, Rui Wang, Guo-Wei Wei
PLPCA: Persistent Laplacian-Enhanced PCA for Microarray Data Analysis. J. Chem. Inf. Model. 64 (7) (2024)
Yuta Hozumi, Kiyoto Aramis Tanemura, Guo-Wei Wei
Preprocessing of Single Cell RNA Sequencing Data Using Correlated Clustering and Projection. J. Chem. Inf. Model. 64 (7) (2024)
Junjie Wee, Jiahui Chen, Kelin Xia, Guo-Wei Wei
Integration of persistent Laplacian and pre-trained transformer for protein solubility changes upon mutation. Comput. Biol. Medicine 169 (2024)
Kenneth M. Merz Jr., Yee-Siew Choong, Zoe Cournia, Olexandr Isayev, Thereza A. Soares, Guo-Wei Wei, Feng Zhu
Editorial: Machine Learning in Materials Science. J. Chem. Inf. Model. 64 (10) (2024)
Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu
Editorial: Machine Learning in Bio-cheminformatics. J. Chem. Inf. Model. 64 (7) (2024)
Hongsong Feng, Sean Cottrell, Yuta Hozumi, Guo-Wei Wei
Multiscale differential geometry learning of networks with applications to single-cell RNA sequencing data. Comput. Biol. Medicine 171 (2024)
Yuta Hozumi, Guo-Wei Wei
Analyzing single cell RNA sequencing with topological nonnegative matrix factorization. J. Comput. Appl. Math. 445 (2024)
Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu
Editorial: Cutting-Edge Methodologies in Omics Data Analysis. J. Chem. Inf. Model. 64 (13) (2024)
Emily Ribando-Gros, Rui Wang, Jiahui Chen, Yiying Tong, Guo-Wei Wei
Combinatorial and Hodge Laplacians: Similarities and Differences. SIAM Rev. 66 (3) (2024)
Sean Cottrell, Yuta Hozumi, Guo-Wei Wei
K-nearest-neighbors induced topological PCA for single cell RNA-sequence data analysis. Comput. Biol. Medicine 175 (2024)
Rui Wang, Hongsong Feng, Guo-Wei Wei
ChatGPT in Drug Discovery: A Case Study on Anticocaine Addiction Drug Development with Chatbots. J. Chem. Inf. Model. 63 (22) (2023)
Rui Wang, Hongsong Feng, Guo-Wei Wei
Chatbots in Drug Discovery: A Case Study on Anti-Cocaine Addiction Drug Development with ChatGPT. CoRR (2023)
Guo-Wei Wei
Topological data analysis hearing the shapes of drums and bells. CoRR (2023)
Kevin J. Naidoo, Kenneth M. Merz Jr., Guo-Wei Wei
Modeling Reactions from Chemical Theories to Machine Learning. J. Chem. Inf. Model. 63 (23) (2023)
Jiahui Chen, Rui Wang, Yuta Hozumi, Gengzhuo Liu, Yuchi Qiu, Xiaoqi Wei, Guo-Wei Wei
Emerging Dominant SARS-CoV-2 Variants. J. Chem. Inf. Model. 63 (1) (2023)
Jiahui Chen, Daniel R. Woldring, Faqing Huang, Xuefei Huang, Guo-Wei Wei
Topological deep learning based deep mutational scanning. Comput. Biol. Medicine 164 (2023)
Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu
Editorial: Machine Learning in Bio-cheminformatics. J. Chem. Inf. Model. 63 (1) (2023)
Hongsong Feng, Rana Elladki, Jian Jiang, Guo-Wei Wei
Machine-learning analysis of opioid use disorder informed by MOR, DOR, KOR, NOR and ZOR-based interactome networks. Comput. Biol. Medicine 157 (2023)
Yuchi Qiu, Guo-Wei Wei
Persistent spectral theory-guided protein engineering. Nat. Comput. Sci. 3 (2) (2023)
Yuchi Qiu, Guo-Wei Wei
Mathematics-assisted directed evolution and protein engineering. CoRR (2023)
Yuchi Qiu, Guo-Wei Wei
Artificial intelligence-aided protein engineering: from topological data analysis to deep protein language models. Briefings Bioinform. 24 (5) (2023)
Hongsong Feng, Guo-Wei Wei
Virtual screening of DrugBank database for hERG blockers using topological Laplacian-assisted AI models. Comput. Biol. Medicine 153 (2023)
Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu
Editorial: Harnessing the Power of Large Language Model-Based Chatbots for Scientific Discovery. J. Chem. Inf. Model. 63 (17) (2023)
Nicole Hayes, Ekaterina Merkurjev, Guo-Wei Wei
Integrating transformer and autoencoder techniques with spectral graph algorithms for the prediction of scarcely labeled molecular data. Comput. Biol. Medicine 153 (2023)
Jian Liu, Li Shen, Guo-Wei Wei
ChatGPT for Computational Topology. CoRR (2023)
Sean Cottrell, Yuta Hozumi, Guo-Wei Wei
K-Nearest-Neighbors Induced Topological PCA for scRNA Sequence Data Analysis. CoRR (2023)
Yuta Hozumi, Guo-Wei Wei
Analyzing Single Cell RNA Sequencing with Topological Nonnegative Matrix Factorization. CoRR (2023)
Hongsong Feng, Jian Jiang, Guo-Wei Wei
Machine-learning repurposing of DrugBank compounds for opioid use disorder. Comput. Biol. Medicine 160 (2023)
Hongsong Feng, Rui Wang, Chang-Guo Zhan, Guo-Wei Wei
Multi-objective Molecular Optimization for Opioid Use Disorder Treatment Using Generative Network Complex. CoRR (2023)
Zailiang Zhu, Bozheng Dou, Yukang Cao, Jian Jiang, Yueying Zhu, Dong Chen, Hongsong Feng, Jie Liu, Ben-gong Zhang, Tianshou Zhou, Guo-Wei Wei
TIDAL: Topology-Inferred Drug Addiction Learning. J. Chem. Inf. Model. 63 (5) (2023)
Long Chen, Jian Jiang, Bozheng Dou, Hongsong Feng, Jie Liu, Yueying Zhu, Ben-gong Zhang, Tianshou Zhou, Guo-Wei Wei
Machine Learning Study of the Extended Drug-target Interaction Network informed by Pain Related Voltage-Gated Sodium Channels. CoRR (2023)
Gokul Bhusal, Ekaterina Merkurjev, Guo-Wei Wei
Persistent Laplacian-enhanced Algorithm for Scarcely Labeled Data Classification. CoRR (2023)
Guo-Wei Wei, Feng Zhu, Kenneth M. Merz Jr.
Editorial on Machine Learning. J. Chem. Inf. Model. 62 (17) (2022)
Thereza A. Soares, Ariane Nunes-Alves, Angelica Mazzolari, Fiorella Ruggiu, Guo-Wei Wei, Kenneth M. Merz Jr.
The (Re)-Evolution of Quantitative Structure-Activity Relationship (QSAR) Studies Propelled by the Surge of Machine Learning Methods. J. Chem. Inf. Model. 62 (22) (2022)
Guo-Wei Wei, Thereza A. Soares, Habibah A. Wahab, Feng Zhu
Computational Chemistry in Asia. J. Chem. Inf. Model. 62 (21) (2022)
Nicole Hayes, Ekaterina Merkurjev, Guo-Wei Wei
Integrating Transformer and Autoencoder Techniques with Spectral Graph Algorithms for the Prediction of Scarcely Labeled Molecular Data. CoRR (2022)
Yuchi Qiu, Guo-Wei Wei
CLADE 2.0: Evolution-Driven Cluster Learning-Assisted Directed Evolution. J. Chem. Inf. Model. 62 (19) (2022)
Jiahui Chen, Yuchi Qiu, Rui Wang, Guo-Wei Wei
Persistent Laplacian projected Omicron BA.4 and BA.5 to become new dominating variants. Comput. Biol. Medicine 151 (Part) (2022)
Jiahui Chen, Rui Wang, Nancy Benovich Gilby, Guo-Wei Wei
Omicron Variant (B.1.1.529): Infectivity, Vaccine Breakthrough, and Antibody Resistance. J. Chem. Inf. Model. 62 (2) (2022)
Yuta Hozumi, Rui Wang, Guo-Wei Wei
CCP: Correlated Clustering and Projection for Dimensionality Reduction. CoRR (2022)
Ekaterina Merkurjev, Duc Duy Nguyen, Guo-Wei Wei
Multiscale Laplacian Learning. CoRR (2021)
Jiahui Chen, Rui Wang, Guo-Wei Wei
SARS-CoV-2 becoming more infectious as revealed by algebraic topology and deep learning. Commun. Inf. Syst. 21 (1) (2021)
Guo-Wei Wei, Thereza A. Soares, Habibah A. Wahab, Renxiao Wang
Computational Chemistry in Asia. J. Chem. Inf. Model. 61 (2) (2021)
Jian Jiang, Rui Wang, Guo-Wei Wei
GGL-Tox: Geometric Graph Learning for Toxicity Prediction. J. Chem. Inf. Model. 61 (4) (2021)
Timothy Szocinski, Duc Duy Nguyen, Guo-Wei Wei
AweGNN: Auto-parametrized weighted element-specific graph neural networks for molecules. Comput. Biol. Medicine 134 (2021)
Azzam Alfarraj, Guo-Wei Wei
Geometric algebra generation of molecular surfaces. CoRR (2021)
Jiahui Chen, Weihua Geng, Guo-Wei Wei
MLIMC: Machine learning-based implicit-solvent Monte Carlo. CoRR (2021)
Yuta Hozumi, Rui Wang, Changchuan Yin, Guo-Wei Wei
-means clustering of large-scale SARS-CoV-2 mutation datasets. Comput. Biol. Medicine 131 (2021)
Kaifu Gao, Dong Chen, Alfred J. Robison, Guo-Wei Wei
Proteome-informed machine learning studies of cocaine addiction. CoRR (2021)
Yuchi Qiu, Jian Hu, Guo-Wei Wei
Cluster learning-assisted directed evolution. Nat. Comput. Sci. 1 (12) (2021)
Jian Jiang, Rui Wang, Menglun Wang, Kaifu Gao, Duc Duy Nguyen, Guo-Wei Wei
Boosting Tree-Assisted Multitask Deep Learning for Small Scientific Datasets. J. Chem. Inf. Model. 60 (3) (2020)
Zixuan Cang, Guo-Wei Wei
Persistent Cohomology for Data With Multicomponent Heterogeneous Information. SIAM J. Math. Data Sci. 2 (2) (2020)
Rui Wang, Yuta Hozumi, Changchuan Yin, Guo-Wei Wei
Decoding SARS-CoV-2 Transmission and Evolution and Ramifications for COVID-19 Diagnosis, Vaccine, and Medicine. J. Chem. Inf. Model. 60 (12) (2020)
Kenneth M. Merz Jr., Gianni De Fabritiis, Guo-Wei Wei
Generative Models for Molecular Design. J. Chem. Inf. Model. 60 (12) (2020)
Menglun Wang, Zixuan Cang, Guo-Wei Wei
A topology-based network tree for the prediction of protein-protein binding affinity changes following mutation. Nat. Mach. Intell. 2 (2) (2020)
Kaifu Gao, Duc Duy Nguyen, Meihua Tu, Guo-Wei Wei
Generative Network Complex for the Automated Generation of Drug-like Molecules. J. Chem. Inf. Model. 60 (12) (2020)
Zixuan Cang, Elizabeth Munch, Guo-Wei Wei
Evolutionary homology on coupled dynamical systems with applications to protein flexibility analysis. J. Appl. Comput. Topol. 4 (4) (2020)
Kenneth M. Merz Jr., Gianni De Fabritiis, Guo-Wei Wei
JCIM Special Issue on Generative Models for Molecular Design. J. Chem. Inf. Model. 60 (3) (2020)
Duc Duy Nguyen, Kaifu Gao, Menglun Wang, Guo-Wei Wei
MathDL: mathematical deep learning for D3R Grand Challenge 4. J. Comput. Aided Mol. Des. 34 (2) (2020)
Rundong Zhao, Mathieu Desbrun, Guo-Wei Wei, Yiying Tong
3D hodge decompositions of edge- and face-based vector fields. ACM Trans. Graph. 38 (6) (2019)
Duc Duy Nguyen, Zixuan Cang, Kedi Wu, Menglun Wang, Yin Cao, Guo-Wei Wei
Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges. J. Comput. Aided Mol. Des. 33 (1) (2019)
Limei Cheng, Guo-Wei Wei, Tarek Leil
Review of quantitative systems pharmacological modeling in thrombosis. Commun. Inf. Syst. 19 (3) (2019)
Christopher Grow, Kaifu Gao, Duc Duy Nguyen, Guo-Wei Wei
Generative network complex (GNC) for drug discovery. Commun. Inf. Syst. 19 (3) (2019)
Guo-Wei Wei
Protein structure prediction beyond AlphaFold. Nat. Mach. Intell. 1 (8) (2019)
Duc Duy Nguyen, Guo-Wei Wei
AGL-Score: Algebraic Graph Learning Score for Protein-Ligand Binding Scoring, Ranking, Docking, and Screening. J. Chem. Inf. Model. 59 (7) (2019)
Zixuan Cang, Lin Mu, Guo-Wei Wei
Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening. PLoS Comput. Biol. 14 (1) (2018)
Kedi Wu, Zhixiong Zhao, Renxiao Wang, Guo-Wei Wei
TopP-S: Persistent homology-based multi-task deep neural networks for simultaneous predictions of partition coefficient and aqueous solubility. J. Comput. Chem. 39 (20) (2018)
Bao Wang, Chengzhang Wang, Kedi Wu, Guo-Wei Wei
Breaking the polar-nonpolar division in solvation free energy prediction. J. Comput. Chem. 39 (4) (2018)
Rundong Zhao, Zixuan Cang, Yiying Tong, Guo-Wei Wei
Protein pocket detection via convex hull surface evolution and associated Reeb graph. Bioinform. 34 (17) (2018)
Kedi Wu, Guo-Wei Wei
Quantitative Toxicity Prediction Using Topology Based Multitask Deep Neural Networks. J. Chem. Inf. Model. 58 (2) (2018)
Rundong Zhao, Menglun Wang, Yiying Tong, Guo-Wei Wei
Divide-and-conquer strategy for large-scale Eulerian solvent excluded surface. Commun. Inf. Syst. 18 (4) (2018)
Zixuan Cang, Guo-Wei Wei
Analysis and prediction of protein folding energy changes upon mutation by element specific persistent homology. Bioinform. 33 (22) (2017)
Zixuan Cang, Guo-Wei Wei
TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions. PLoS Comput. Biol. 13 (7) (2017)
Yin Cao, Bao Wang, Kelin Xia, Guo-Wei Wei
Finite volume formulation of the MIB method for elliptic interface problems. J. Comput. Appl. Math. 321 (2017)
Kedi Wu, Guo-Wei Wei
Comparison of multi-task convolutional neural network (MT-CNN) and a few other methods for toxicity prediction. CoRR (2017)
Duc Duy Nguyen, Tian Xiao, Menglun Wang, Guo-Wei Wei
Rigidity Strengthening: A Mechanism for Protein-Ligand Binding. J. Chem. Inf. Model. 57 (7) (2017)
Beibei Liu, Bao Wang, Rundong Zhao, Yiying Tong, Guo-Wei Wei
ESES: Software for Eulerian solvent excluded surface. J. Comput. Chem. 38 (7) (2017)
Duc Duy Nguyen, Guo-Wei Wei
The impact of surface area, volume, curvature, and Lennard-Jones potential to solvation modeling. J. Comput. Chem. 38 (1) (2017)
Lin Mu, Kelin Xia, Guo-Wei Wei
Geometric and electrostatic modeling using molecular rigidity functions. J. Comput. Appl. Math. 313 (2017)
Duc Duy Nguyen, Bao Wang, Guo-Wei Wei
Accurate, robust, and reliable calculations of Poisson-Boltzmann binding energies. J. Comput. Chem. 38 (13) (2017)
Bao Wang, Zhixiong Zhao, Duc Duy Nguyen, Guo-Wei Wei
Feature functional theory - binding predictor (FFT-BP) for the blind prediction of binding free energies. CoRR (2017)
Bao Wang, Guo-Wei Wei
Object-oriented persistent homology. J. Comput. Phys. 305 (2016)
Kristopher Opron, Kelin Xia, Zach Burton, Guo-Wei Wei
Flexibility-rigidity index for protein-nucleic acid flexibility and fluctuation analysis. J. Comput. Chem. 37 (14) (2016)
Langhua Hu, Duan Chen, Guo-Wei Wei
Impact of geometric, thermal and tunneling effects on nano-transistors. J. Comput. Phys. 290 (2015)
Kelin Xia, Zhixiong Zhao, Guo-Wei Wei
Multiresolution Topological Simplification. J. Comput. Biol. 22 (9) (2015)
Kelin Xia, Guo-Wei Wei
Multidimensional persistence in biomolecular data. J. Comput. Chem. 36 (20) (2015)
Bao Wang, Kelin Xia, Guo-Wei Wei
Second order method for solving 3D elasticity equations with complex interfaces. J. Comput. Phys. 294 (2015)
Kelin Xia, Xin Feng, Yiying Tong, Guo-Wei Wei
Persistent homology for the quantitative prediction of fullerene stability. J. Comput. Chem. 36 (6) (2015)
Bao Wang, Kelin Xia, Guo-Wei Wei
Matched interface and boundary method for elasticity interface problems. J. Comput. Appl. Math. 285 (2015)
Kelin Xia, Guo-Wei Wei
A Galerkin formulation of the MIB method for three dimensional elliptic interface problems. Comput. Math. Appl. 68 (7) (2014)
Kelin Xia, Meng Zhan, Guo-Wei Wei
MIB Galerkin method for elliptic interface problems. J. Comput. Appl. Math. 272 (2014)
Kelin Xia, Xin Feng, Zhan Chen, Yiying Tong, Guo-Wei Wei
Multiscale geometric modeling of macromolecules I: Cartesian representation. J. Comput. Phys. 257 (2014)
Xin Feng, Kelin Xia, Zhan Chen, Yiying Tong, Guo-Wei Wei
Multiscale geometric modeling of macromolecules II: Lagrangian representation. J. Comput. Chem. 34 (24) (2013)
Jinkyoung Park, Guo-Wei Wei
A molecular level prototype for mechanoelectrical transducer in mammalian hair cells. J. Comput. Neurosci. 35 (2) (2013)
Kelin Xia, Meng Zhan, Decheng Wan, Guo-Wei Wei
Adaptively deformed mesh based interface method for elliptic equations with discontinuous coefficients. J. Comput. Phys. 231 (4) (2012)
Guo-Wei Wei, Qiong Zheng, Zhan Chen, Kelin Xia
Variational Multiscale Models for Charge Transport. SIAM Rev. 54 (4) (2012)
Yang Wang, Guo-Wei Wei, Siyang Yang
Iterative Filtering Decomposition Based on Local Spectral Evolution Kernel. J. Sci. Comput. 50 (3) (2012)

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Publication Activity (10 Years)

Top Topics

Top Venues

Guo-Wei Wei