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Wei, Guo-Wei

  1. Persistent spectral graph
    2019/12/09 by Rui Wang, Wang, Rui, Duc Duy Nguyen +3 · 17 citations
    Biochemistry, Genetics and Molecular Biology · Computer Science · Neuroscience · #Bioinformatics and Genomic Networks #Combinatorics (math.CO) #FOS: Mathematics #Topological and Geometric Data Analysis #Tryptophan and brain disorders
  2. Position: Topological Deep Learning is the New Frontier for Relational Learning
    2024/02/14 by Theodore Papamarkou, Tolga Birdal, Papamarkou, Theodore +41 · 18 citations
    Biochemistry, Genetics and Molecular Biology · Computer Science · #Cell Image Analysis Techniques #FOS: Computer and information sciences #Image Retrieval and Classification Techniques #Machine Learning (cs.LG) #Machine Learning (stat.ML) #Topological and Geometric Data Analysis
  3. Evolutionary de Rham-Hodge method
    2019/12/28 by Jiahui Chen, Chen, Jiahui, Rundong Zhao +5 · 8 citations
    Biochemistry, Genetics and Molecular Biology · Computer Science · #Cell Image Analysis Techniques #Differential Geometry (math.DG) #FOS: Mathematics #Topological and Geometric Data Analysis
  4. Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges
    2018/04/27 by Nguyen, Duc Duy, Cang, Zixuan, Wu, Kedi +3 · 7 citations
    #Biomolecules (q-bio.BM) #FOS: Biological sciences
  5. Persistent Laplacian projected Omicron BA.4 and BA.5 to become new dominating variants
    2022/05/01 by Chen, Jiahui, Qiu, Yuchi, Wang, Rui +1 · 8 citations
    #Biomolecules (q-bio.BM) #FOS: Biological sciences
  6. Persistent Topological Laplacians -- a Survey
    2023/12/09 by Xiaoqi Wei, Wei, Xiaoqi, Guo‐Wei Wei +1 · 13 citations
    Computer Science · #Topological and Geometric Data Analysis
  7. Persistent sheaf Laplacians
    2021/12/20 by Xiaoqi Wei, Guo‐Wei Wei, Wei, Xiaoqi +1 · 8 citations
    Computer Science · Engineering · Medicine · #Advanced Neuroimaging Techniques and Applications #Algebraic Topology (math.AT) #FOS: Mathematics #Slime Mold and Myxomycetes Research #Topological and Geometric Data Analysis
  8. MathDL: Mathematical deep learning for D3R Grand Challenge 4
    2019/09/17 by Duc Duy Nguyen, Kaifu Gao, Nguyen, Duc Duy +5 · 6 citations
    Biochemistry, Genetics and Molecular Biology · Computer Science · Materials Science · #Biomolecules (q-bio.BM) #Computational Drug Discovery Methods #Enzyme Structure and Function #FOS: Biological sciences #Protein Structure and Dynamics #Quantitative Methods (q-bio.QM)
  9. Multidimensional persistence in biomolecular data
    2014/12/24 by Kelin Xia, Xia, Kelin, Guo‐Wei Wei +1 · 4 citations
    Biochemistry, Genetics and Molecular Biology · Computer Science · #Biomolecules (q-bio.BM) #Cell Image Analysis Techniques #FOS: Biological sciences #Metabolomics and Mass Spectrometry Studies #Topological and Geometric Data Analysis
  10. Persistent Path Laplacian
    2022/06/08 by Wang, Rui, Wei, Guo-Wei · 7 citations
    #Algebraic Topology (math.AT) #FOS: Mathematics #Spectral Theory (math.SP)
  11. Topological fingerprints reveal protein-ligand binding mechanism
    2017/03/31 by Cang, Zixuan, Wei, Guo-Wei · 3 citations
    #Biomolecules (q-bio.BM) #FOS: Biological sciences #Quantitative Methods (q-bio.QM)
  12. Flexibility-Rigidity Index for Protein-Nucleic Acid Flexibility and Fluctuation Analysis
    2015/10/26 by Kristopher Opron, Opron, Kristopher, Kelin Xia +5 · 3 citations
    Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #Biomolecules (q-bio.BM) #FOS: Biological sciences #Force Microscopy Techniques and Applications #Protein Structure and Dynamics #RNA and protein synthesis mechanisms
  13. Persistent cohomology for data with multicomponent heterogeneous information
    2018/07/29 by Cang, Zixuan, Wei, Guo-Wei · 3 citations
    #Algebraic Topology (math.AT) #FOS: Biological sciences #FOS: Mathematics #Quantitative Methods (q-bio.QM)
  14. A topological approach for protein classification
    2015/10/04 by Cang, Zixuan, Mu, Lin, Wu, Kedi +3 · 3 citations
    #Biomolecules (q-bio.BM) #FOS: Biological sciences
  15. Mutations strengthened SARS-CoV-2 infectivity
    2020/05/27 by Jiahui Chen, Rui Wang, Chen, Jiahui +5 · 4 citations
    Medicine · Biochemistry, Genetics and Molecular Biology · Computer Science · #SARS-CoV-2 and COVID-19 Research #vaccines and immunoinformatics approaches #Computational Drug Discovery Methods
  16. Atom-specific persistent homology and its application to protein flexibility analysis
    2019/03/26 by David Bramer, Bramer, David, Guo‐Wei Wei +1 · 3 citations
    Biochemistry, Genetics and Molecular Biology · Computer Science · #Bioinformatics and Genomic Networks #Biomolecules (q-bio.BM) #Computational Drug Discovery Methods #FOS: Biological sciences #Quantitative Methods (q-bio.QM) #Topological and Geometric Data Analysis
  17. SVSBI: Sequence-based virtual screening of biomolecular interactions
    2022/12/27 by Li Shen, Shen, Li, Hongsong Feng +5 · 5 citations
    Computer Science · Materials Science · Biochemistry, Genetics and Molecular Biology · #Computational Drug Discovery Methods #Machine Learning in Materials Science #Protein Structure and Dynamics
  18. Persistent hyperdigraph homology and persistent hyperdigraph Laplacians
    2023/04/01 by Chen, Dong, Liu, Jian, Wu, Jie +1 · 5 citations
    #Algebraic Topology (math.AT) #FOS: Mathematics
  19. Persistent topology for cryo-EM data analysis
    2014/12/07 by Xia, Kelin, Wei, Guo-Wei · 2 citations
    #Biomolecules (q-bio.BM) #FOS: Biological sciences
  20. HERMES: Persistent spectral graph software
    2020/12/21 by Wang, Rui, Zhao, Rundong, Ribando-Gros, Emily +3 · 3 citations
    #Algebraic Topology (math.AT) #FOS: Mathematics
  21. DG-GL: Differential geometry based geometric learning of molecular datasets
    2018/06/11 by Duc Duy Nguyen, Nguyen, Duc Duy, Guo‐Wei Wei +1 · 2 citations
    Biochemistry, Genetics and Molecular Biology · Computer Science · Medicine · #Biomolecules (q-bio.BM) #Computational Drug Discovery Methods #FOS: Biological sciences #Microbial Natural Products and Biosynthesis #Protein Structure and Dynamics #Quantitative Methods (q-bio.QM)
  22. Multiresolution topological simplification
    2015/03/31 by Xia, Kelin, Zhao, Zhixiong, Wei, Guo-Wei · 2 citations
    #Biomolecules (q-bio.BM) #FOS: Biological sciences
  23. Persistent topological Laplacian analysis of SARS-CoV-2 variants
    2023/01/25 by Xiaoqi Wei, Wei, Xiaoqi, Jiahui Chen +3 · 3 citations
    Computer Science · Medicine · #Topological and Geometric Data Analysis #Clusterin in disease pathology #Computational Drug Discovery Methods
  24. Evolutionary homology on coupled dynamical systems
    2018/02/13 by Cang, Zixuan, Munch, Elizabeth, Wei, Guo-Wei · 2 citations
    #Algebraic Topology (math.AT) #Dynamical Systems (math.DS) #FOS: Biological sciences #FOS: Mathematics #Quantitative Methods (q-bio.QM)
  25. Artificial intelligence-aided protein engineering: from topological data analysis to deep protein language models
    2023/07/27 by Qiu, Yuchi, Wei, Guo-Wei · 3 citations
    #Biomolecules (q-bio.BM) #FOS: Biological sciences
  26. Multiscale Laplacian Learning
    2021/09/08 by Merkurjev, Ekaterina, Nguyen, Duc DUy, Wei, Guo-Wei · 2 citations
    #FOS: Computer and information sciences #Machine Learning (cs.LG)
  27. Persistent de Rham-Hodge Laplacians in Eulerian representation for manifold topological learning
    2024/08/01 by Zhe Su, Yiying Tong, Su, Zhe +3 · 5 citations
    Mathematics · #Advanced Algebra and Geometry #Geometric Analysis and Curvature Flows #Algebraic Geometry and Number Theory
  28. Topological Data Analysis and Topological Deep Learning Beyond Persistent Homology -- A Review
    2025/07/12 by Zhe Su, Xiang Liu, Su, Zhe +11 · 13 citations
    Computer Science · Mathematics · #55-08 #57K18 #57R19 #62R40 #Differential Geometry (math.DG) #Digital Image Processing Techniques #FOS: Mathematics #Geometric Topology (math.GT) #History and Overview (math.HO) #Homotopy and Cohomology in Algebraic Topology #Topological and Geometric Data Analysis
  29. Persistent Mayer homology and persistent Mayer Laplacian
    2023/12/03 by Li Shen, Shen, Li, Jian Liu +3 · 4 citations
    Computer Science · Medicine · #Advanced Neuroimaging Techniques and Applications #Algebraic Topology (math.AT) #FOS: Mathematics #Topological and Geometric Data Analysis
  30. Persistent interaction topology in data analysis
    2024/04/17 by Jian Liu, Dong Chen, Liu, Jian +3 · 5 citations
    Biochemistry, Genetics and Molecular Biology · Computer Science · Physics and Astronomy · #Advanced Clustering Algorithms Research #Algebraic Topology (math.AT) #Bioinformatics and Genomic Networks #Complex Network Analysis Techniques #FOS: Mathematics
  31. Multiscale Topology in Interactomic Network: From Transcriptome to Antiaddiction Drug Repurposing
    2023/12/03 by Hongyan Du, Guo‐Wei Wei, Du, Hongyan +3 · 3 citations
    Biochemistry, Genetics and Molecular Biology · Computer Science · #Bioinformatics and Genomic Networks #Biomolecules (q-bio.BM) #Computational Drug Discovery Methods #FOS: Biological sciences #FOS: Computer and information sciences #Genomics (q-bio.GN) #Machine Learning (cs.LG) #Topological and Geometric Data Analysis
  32. Mutations on COVID-19 diagnostic targets
    2020/05/05 by Rui Wang, Wang, Rui, Yuta Hozumi +5 · 2 citations
    Medicine · #Biomolecules (q-bio.BM) #COVID-19 Clinical Research Studies #FOS: Biological sciences #Genomics (q-bio.GN) #SARS-CoV-2 and COVID-19 Research #SARS-CoV-2 detection and testing
  33. Knot data analysis using multiscale Gauss link integral
    2023/10/03 by Shen, Li, Feng, Hongsong, Li, Fengling +3 · 3 citations
    #Biomolecules (q-bio.BM) #FOS: Biological sciences #FOS: Mathematics #Geometric Topology (math.GT)
  34. Analysis and prediction of protein folding energy changes upon mutation by element specific persistent homology
    2017/03/31 by Zixuan Cang, Guo‐Wei Wei, Cang, Zixuan +1 · 1 citation
    Biochemistry, Genetics and Molecular Biology · #FOS: Biological sciences #Genomics and Chromatin Dynamics #Protein Structure and Dynamics #Quantitative Methods (q-bio.QM) #RNA and protein synthesis mechanisms
  35. Integration of persistent Laplacian and pre-trained transformer for protein solubility changes upon mutation
    2023/10/28 by JunJie Wee, Wee, JunJie, Jiahui Chen +5 · 1 voice · 2 citations
    Biochemistry, Genetics and Molecular Biology · Mathematics · #Algebraic Topology (math.AT) #Biomolecules (q-bio.BM) #FOS: Biological sciences #FOS: Mathematics #math.AT #q-bio.BM
  36. TopP-S: Persistent homology based multi-task deep neural networks for simultaneous predictions of partition coefficient and aqueous solubility
    2017/12/09 by Kedi Wu, Zhixiong Zhao, Wu, Kedi +5 · 1 citation
    Biochemistry, Genetics and Molecular Biology · Computer Science · #Bioinformatics and Genomic Networks #Computational Drug Discovery Methods #FOS: Biological sciences #Quantitative Methods (q-bio.QM) #Topological and Geometric Data Analysis
  37. Quantitative toxicity prediction using topology based multi-task deep neural networks
    2017/12/09 by Wu, Kedi, Wei, Guo-Wei · 1 citation
    #FOS: Biological sciences #Quantitative Methods (q-bio.QM)
  38. Manifold Topological Deep Learning for Biomedical Data
    2025/02/28 by Liu, Xiang, Su, Zhe, Shi, Yongyi +3 · 4 citations
    #FOS: Computer and information sciences #FOS: Electrical engineering #Image and Video Processing (eess.IV) #Machine Learning (cs.LG) #electronic engineering #information engineering
  39. Persistent Stanley--Reisner Theory
    2025/03/30 by Faisal Suwayyid, Guo‐Wei Wei, Suwayyid, Faisal +1 · 8 citations
    Computer Science · Mathematics · #Topological and Geometric Data Analysis #Homotopy and Cohomology in Algebraic Topology #Polynomial and algebraic computation
  40. Persistent Laplacian-enhanced Algorithm for Scarcely Labeled Data Classification
    2023/05/25 by Gokul Bhusal, Bhusal, Gokul, Ekaterina Merkurjev +3 · 2 citations
    Computer Science · Social Sciences · #Advanced Computing and Algorithms #Advanced Graph Neural Networks #FOS: Computer and information sciences #Machine Learning (cs.LG) #Topological and Geometric Data Analysis
  41. Generative network complex for the automated generation of druglike molecules
    2020/05/28 by Gao, Kaifu, Nguyen, Duc D, Tu, Meihua +1 · 1 citation
    #Biomolecules (q-bio.BM) #FOS: Biological sciences #Quantitative Methods (q-bio.QM)
  42. Analyzing Single Cell RNA Sequencing with Topological Nonnegative Matrix Factorization
    2023/10/24 by Yuta Hozumi, Hozumi, Yuta, Guo‐Wei Wei +1 · 2 citations
    Biochemistry, Genetics and Molecular Biology · #Single-cell and spatial transcriptomics #Gene expression and cancer classification
  43. Topology-preserving Hodge Decomposition in the Eulerian Representation
    2024/08/26 by Su, Zhe, Tong, Yiying, Wei, Guo-Wei · 2 citations
    #Differential Geometry (math.DG) #FOS: Mathematics
  44. UMAP-assisted K-means clustering of large-scale SARS-CoV-2 mutation datasets
    2020/12/30 by Yuta Hozumi, Rui Wang, Hozumi, Yuta +5 · 1 citation
    Medicine · #COVID-19 diagnosis using AI #FOS: Biological sciences #Quantitative Methods (q-bio.QM) #SARS-CoV-2 and COVID-19 Research #SARS-CoV-2 detection and testing
  45. Revealing the Shape of Genome Space via K-mer Topology
    2024/12/28 by Hozumi, Yuta, Wei, Guo-Wei · 7 citations
    #Algebraic Topology (math.AT) #FOS: Biological sciences #FOS: Mathematics #Genomics (q-bio.GN)
  46. Mathematical artificial intelligence design of mutation-proof COVID-19 monoclonal antibodies
    2022/04/20 by Jiahui Chen, Guo‐Wei Wei, Chen, Jiahui +1 · 1 citation
    Biochemistry, Genetics and Molecular Biology · Computer Science · Medicine · #vaccines and immunoinformatics approaches #Computational Drug Discovery Methods #Chronic Lymphocytic Leukemia Research
  47. Drug Resistance Predictions Based on a Directed Flag Transformer
    2024/03/05 by Chen, Dong, Liu, Gengzhuo, Du, Hongyan +6 · 2 citations
    #FOS: Biological sciences #Quantitative Methods (q-bio.QM)
  48. Emerging dominant SARS-CoV-2 variants
    2022/10/18 by Chen, Jiahui, Wang, Rui, Hozumi, Yuta +4 · 1 citation
    #Biomolecules (q-bio.BM) #FOS: Biological sciences #Populations and Evolution (q-bio.PE)
  49. Topological data analysis hearing the shapes of drums and bells
    2023/01/11 by Wei, Guo-Wei · 1 citation
    #Audio and Speech Processing (eess.AS) #FOS: Computer and information sciences #FOS: Electrical engineering #FOS: Mathematics #History and Overview (math.HO) #Sound (cs.SD) #electronic engineering #information engineering
  50. Multiscale differential geometry learning of networks with applications to single-cell RNA sequencing data
    2023/12/15 by Feng, Hongsong, Cottrell, Sean, Hozumi, Yuta +1 · 2 citations
    #FOS: Biological sciences #Molecular Networks (q-bio.MN)
  51. Superionic Ionic Conductor Discovery via Multiscale Topological Learning
    2024/12/16 by Dong Chen, Bingxu Wang, Chen, Dong +13 · 2 citations
    Engineering · Computer Science · Materials Science · #Surface Chemistry and Catalysis #Topological and Geometric Data Analysis #Machine Learning in Materials Science
  52. Interaction homotopy and interaction homology
    2023/11/27 by Jian Liu, Liu, Jian, Dong Chen +3 · 2 citations
    Computer Science · Mathematics · #Algebraic Topology (math.AT) #FOS: Mathematics #Homotopy and Cohomology in Algebraic Topology #Topological and Geometric Data Analysis
  53. CAML: Commutative algebra machine learning -- a case study on protein-ligand binding affinity prediction
    2025/04/25 by Hongsong Feng, Faisal Suwayyid, Feng, Hongsong +11 · 5 citations
    Computer Science · Biochemistry, Genetics and Molecular Biology · Materials Science · #Computational Drug Discovery Methods #Bioinformatics and Genomic Networks #Machine Learning in Materials Science
  54. ChatGPT in Drug Discovery: A Case Study on Anti-Cocaine Addiction Drug Development with Chatbots
    2023/08/14 by Wang, Rui, Feng, Hongsong, Wei, Guo-Wei · 1 citation
    #Artificial Intelligence (cs.AI) #Biomolecules (q-bio.BM) #FOS: Biological sciences #FOS: Computer and information sciences #Human-Computer Interaction (cs.HC)
  55. Persistent Directed Flag Laplacian (PDFL)-Based Machine Learning for Protein-Ligand Binding Affinity Prediction
    2024/11/04 by Mushal Zia, Zia, Mushal, Benjamin Jones +5 · 2 citations
    Biochemistry, Genetics and Molecular Biology · Computer Science · #Biomolecules (q-bio.BM) #Computational Drug Discovery Methods #FOS: Biological sciences #Machine Learning in Bioinformatics #Protein Structure and Dynamics
  56. Category-Specific Topological Learning of Metal-Organic Frameworks
    2024/12/16 by Dong Chen, Chen, Dong, Chun‐Long Chen +3 · 3 citations
    Arts and Humanities · Materials Science · #Biomolecules (q-bio.BM) #Computational Physics (physics.comp-ph) #Corrosion Behavior and Inhibition #Cultural Heritage Materials Analysis #FOS: Biological sciences #FOS: Physical sciences #Materials Science (cond-mat.mtrl-sci) #X-ray Diffraction in Crystallography
  57. Persistent Khovanov homology of tangles
    2024/09/26 by Jian Liu, Li Shen, Liu, Jian +3 · 4 citations
    Computer Science · Engineering · Mathematics · #57K18 #Advanced Numerical Analysis Techniques #FOS: Mathematics #Geometric Topology (math.GT) #Geometric and Algebraic Topology #Primary 55N31 #Secondary 57M10 #Topological and Geometric Data Analysis
  58. Mayer-homology learning prediction of protein-ligand binding affinities
    2024/08/23 by Hongsong Feng, Li Shen, Feng, Hongsong +5 · 2 citations
    Biochemistry, Genetics and Molecular Biology · Computer Science · #Algebraic Topology (math.AT) #Biomolecules (q-bio.BM) #Computational Drug Discovery Methods #FOS: Biological sciences #FOS: Mathematics #Genetics, Bioinformatics, and Biomedical Research
  59. Benchmarking AlphaFold3's protein-protein complex accuracy and machine learning prediction reliability for binding free energy changes upon mutation
    2024/06/06 by JunJie Wee, Guo-Wei Wei, Wee, JunJie +1 · 1 citation
    Biochemistry, Genetics and Molecular Biology · #Algebraic Topology (math.AT) #Biomolecules (q-bio.BM) #FOS: Biological sciences #FOS: Mathematics #Genetics, Bioinformatics, and Biomedical Research #Machine Learning in Bioinformatics #Protein Structure and Dynamics #Quantitative Methods (q-bio.QM)
  60. CAKL: Commutative algebra k-mer learning of genomics
    2025/08/13 by Suwayyid, Faisal, Hozumi, Yuta, Feng, Hongsong +3 · 6 citations
    #13P25 #92D20 #Commutative Algebra (math.AC) #FOS: Biological sciences #FOS: Mathematics #Quantitative Methods (q-bio.QM)
  61. Topological Sequence Analysis of Genomes: Delta Complex approaches
    2025/07/07 by Liu, Jian, Shen, Li, Chen, Dong +1 · 3 citations
    #68Q07 #Algebraic Topology (math.AT) #FOS: Biological sciences #FOS: Mathematics #Primary 55N31 #Quantitative Methods (q-bio.QM) #Secondary 62R40
  62. Persistent Sheaf Laplacian Analysis of Protein Flexibility
    2025/02/12 by Hayes, Nicole, Wei, Xiaoqi, Feng, Hongsong +2 · 2 citations
    #Biomolecules (q-bio.BM) #FOS: Biological sciences #Quantitative Methods (q-bio.QM)
  63. Topological Machine Learning for Protein-Nucleic Acid Binding Affinity Changes Upon Mutation
    2025/05/28 by Xiang Liu, JunJie Wee, Liu, Xiang +3 · 2 citations
    Biochemistry, Genetics and Molecular Biology · Computer Science · #Bioinformatics and Genomic Networks #FOS: Biological sciences #Machine Learning in Bioinformatics #Quantitative Methods (q-bio.QM) #Topological and Geometric Data Analysis
  64. Multiscale differential geometry learning for protein flexibility analysis
    2024/11/05 by Hongsong Feng, J. Y. Zhao, Feng, Hongsong +3 · 1 citation
    Biochemistry, Genetics and Molecular Biology · Computer Science · Physics and Astronomy · #Biomolecules (q-bio.BM) #Computational Drug Discovery Methods #FOS: Biological sciences #Force Microscopy Techniques and Applications #Protein purification and stability