Big data, machine learning, image, signal, and  surface 

 

(243) Duc Nguyen, Zixuan Cang, and Guo-Wei Wei, Mathematical methods for protein-ligand binding affinity prediction (Invited perspective by Physical Chemistry Chemical Physics), submitted, (2019).

 

(240) Duc D. Nguyen and Guo-Wei Wei, Manifold learning of activity ligands and decoys (2018)

 

(239) Menglun Wang, Z.  X. Cang, R. Q. Guo, Heedeok Hong and Guo-Wei Wei, Prediction of membrane protein stability changes upon mutation, (2018).

 

(238) Menglun Wang, Z.  X. Cang, and Guo-Wei Wei, TopNetTree: Topology based network tree for the prediction of antibody-antigen binding free energy changes upon mutation,  Nature Machine Intelligence,  (2019).

 

(237)  Kaifu Gao, Duc Duy Nguyen, Vishnu Sresht, Alan M. Mathiowetz, Meihua Tu, and  Guo-Wei Wei, Are 2D  fingerprints still valuable for drug discovery? (2019)

 

(236) Jian Jiang, Rui Wang, Menglun Wang, Kaifu Gao, Duc D Nguyen and Guo-Wei Wei, Boosting tree-assisted multitask deep learning for small scientific datasets. (2019).

 

(235) Rundong Zhao, Menglun Wang, Yiying Tong and Guo-Wei Wei, The de Rham-Hodge analysis and modeling of biomolecules (2019). arXiv:1908.00572

 

(234) Zixuan Cang and Guo-Wei Wei, Persistent cohomology for datasets with heterogeneous information (2018). arXiv:1807.11120

 

(233) Zixuan Cang, Elizabeth Munch, and Guo-Wei Wei, Evolutionary homology on a dynamical system (2018). arXiv:1802.04677

 

(232) Duc Duy Nguyen, Kaifu Gao, Menglun Wang, and Guo-Wei Wei, MathDL: Mathematical deep learning for D3R Grand Challenge 4, Journal of Computer Aided Molecular Design, in press,  (2019).

 

(231) Rundong Zhao, Mathieu Desbrun, Guo-Wei Wei and Yiying Tong, 3D Hodge Decompositions of Edge- and Face-based Vector Fields, in press, SIGGRAPH Asia, 2019

 

(230) Guo-Wei Wei, Protein structure prediction beyond AlphaFold, Nature Machine Intelligence, Vol. 1, 336-337, August (2019).

 

(229) Duc D Nguyen and Guo-Wei Wei, AGL-Score: Algebraic Graph Learning Score for Protein-Ligand Binding Scoring, Ranking, Docking, and Screening, Journal of Chemical Information and Modeling, 59, 3291-3304, (2019).

 

(228) Duc D. Nguyen and Guo-Wei Wei, DG-GL: Differential geometry based geometric learning of molecular datasets, International Journal for Numerical Methods in Biomedical Engineering, 35 (3), e3179 (2019).   

 

(227) Duc Duy Nguyen, Zixuan Cang, Kedi Wu, Menglun Wang, Yin Cao  and Guo-Wei Wei, Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges, Journal of Computer Aided Molecular Design, 33, 71-82   (2019).

 

(226) David Bramer and G. W. Wei, Blind prediction of protein B-factor and flexibility, Journal of Chemical Physics, 149, 134107 (2018).

 

(225) Rundong Zhao, Menglun Wang, Yiying Tong and Guo-Wei Wei, A divide-and-conquer strategy for large-scale Eulerian solvent excluded surface, Communications in Information and Systems, 18, 299-329 (2018).

 

(224) Rundong Zhao, Zixuan Cang, Yiying Tong and Guo-Wei Wei, Protein Pocket Detection via Convex Hull Surface Evolution and Associated Reeb Graph, Bioinformatics, 24 (17), i830-i837 (2018).

 

(223) Kedi Wu, Zhixiong Zhao, Renxiao Wang  and Guo-Wei Wei, TopP–S: Persistent Homology-Based Multi-Task Deep Neural Networks for Simultaneous Predictions of Partition Coefficient and Aqueous Solubility,  Journal of Computational Chemistry,  39, 1444-1454  (2018).  

 

(222) Kedi Wu and Guo-Wei Wei, Quantitative toxicity prediction using topology based multi-task deep neural networks,  Journal of Chemical Information and Modeling,   58, 520-531 (2018).  

 

(219) Z. X. Cang, Lin Mu and Guo-Wei Wei, Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening, PLOS Computational Biology,  14(1), e100592 (2018).

 

(216) Bao Wang, Chengzhang Wang, Kedi Wu and Guo-Wei Wei, Breaking the polar-nonpolar division in solvation free energy prediction, Journal of Computational Chemistry, 39, 217–232 (2018).

 

(215) Z. X. Cang and Guo-Wei Wei, Integration of element specific persistent homology and machine learning for protein-ligand binding affinity prediction, International Journal for Numerical Methods in Biomedical Engineering, 34 (2), e2914  (2018).

 

(212) Z. X. Cang and Guo-Wei Wei, TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions

, PLOS Computational Biology, 13(7), e1005690 (2017).

 

(211) Z. X. Cang and Guo-Wei Wei, Element specific persistent homology for the analysis and prediction of protein folding stability upon mutation, Bioinformatics,   33, 3549-3557 (2017).

 

(210) Duc D Nguyen, Tian Xiao, Menglun Wang  and Guo-Wei Wei, Rigidity strengthening: A  mechanism for protein-ligand binding,  Journal of Chemical Information and Modeling, 57, 1715-1721 (2017).

 

(209) Bao Wang, Zhixiong Zhao, Duc Nguyen and Guo-Wei Wei, Feature functional theory - binding predictor (FFT-BP) for the blind prediction of binding free energy, Theoretical Chemistry Account, 136, 55 (2017).

 

 

(207) Duc D Nguyen, Bao Wang and Guo-Wei Wei, Accurate,  robust and  reliable  calculations of Poisson-Boltzmann binding energies,  Journal of Computational Chemistry, 38,  941-948 (2017).

 

 

(204) Beibei Liu, Bao Wang, Rundong Zhao, Yiying Tong and Guo-Wei Wei, ESES:  software for Eulerian solvent excluded surface, Journal of Computational Chemistry, 38, 446-466 (2017).

 

(199) Bao Wang, Zhixiong Zhao and Guo-Wei Wei, Automatic parametrization of non-polar implicit solvent models for the blind prediction of solvation free energies, Journal of Chemical Physics, 145, 124110 (2016).

 

(195) Bao Wang and   Guo-Wei Wei,  Object-oriented persistent homology,  Journal of Computational Physics, 305, 276-299 (2016).

 

(194) Zixuan Cang, Lin Mu, Kedi Wu, Kris Opron, Kelin Xia and Guo-Wei Wei, A topological approach to protein classification, Molecular based Mathematical Biology, 3, 140-162 (2015)   

 

(191) Kelin  Xia, Zhixiong Zhao   and    Guo-Wei Wei,  Multiresolution persistent homology for excessively large biomolecular datasets, Journal of Chemical Physics, 143, 134103 (2015).

 

(188) Kelin  Xia   and    Guo-Wei Wei,  Multidimensional persistence in  biomolecular data,   Journal of Computational Chemistry, 36, 1502-1520 (2015).

 

(187) Kelin  Xia, Zhixiong Zhao  and   Guo-Wei Wei,  Multiresolution topological simplification, Journal of Computational Biology, 22, 9, 1-5 (2015).

 

(185) Kelin  Xia   and    Guo-Wei    Wei,  Persistent topology for cryo-EM data analysis,    International  Journal  for  Numerical    Methods  in    Biomedical    Engineering,  31, e02719 (2015).

 

(182) Kelin  Xia, X.  Feng,  Yiying  Tong  and    Guo-Wei    Wei,  Persistent homology for the quantitative prediction of fullerene stability, Journal of Computational Chemistry, 36, 408-422 (2015).

 

(178) Kelin  Xia   and    Guo-Wei    Wei,  Persistent homology  analysis of protein structure, flexibility and folding,    International  Journal  for  Numerical    Methods  in    Biomedical    Engineering, 30, 814-844 (2014).

 

(176) Kelin Xia and Guo-Wei Wei, Molecular nonlinear dynamics and protein thermal uncertainty quantification, Chaos, 24, 013103 (2014).

 

(173)  Kelin Xia, and Guo-Wei Wei, A stochastic model for protein flexibility analysis, Physical Review E, 88, 062709 (2013).

 

(172) X.  Feng,  Kelin  Xia, Zhan Chen, Yiying  Tong  and    Guo-Wei    Wei, Multiscale  geometric modeling of macromolecules II: Lagrangian representation, Journal of Computational Chemistry,  34, 2100-2120  (2013).

 

(163)  Langhua    Hu,  Duan  Chen  and  Guo-Wei  Wei,    High-order  fractional  partial  differential equations for molecular surface  construction, Molecular  Based  Mathematical  Biology,  1-25  (2012).

 

(162) X.  Feng,  Kelin  Xia,  Yiying  Tong  and    Guo-Wei    Wei,  Geometric  modeling  of  organelles,  subcellular  structures   and  multiprotein  complexes,  International  Journal  for  Numerical    Methods  in    Biomedical    Engineering, 28, 1198-1223 (2012).

 

(157)    Yang  Wang,    Guo-Wei    Wei    and    Siyang    Yang,    Selective    extraction  of  entangled  textures  via    adaptive  PDE  transform,    Int.      J.    Biomed      Imaging,    Volume 2012 (2012), Article ID 958142 (2012).

 

(153)    Yang  Wang,    Guo-Wei    Wei    and    Siyang    Yang,    Model    decomposing  evolution    equations,  Journal  of  Scientific    Computing,    50, 495-518 (2012).

 

(152)      Yang    Wang,    Guo-Wei    Wei    and    Siyang  Yang,  Empirical  model  decomposition    using    local  spectral    evolution    kernels,    Journal  of  Scientific  Computing,   50, 629-664   (2012).

 

(147)  Yang  Wang,    Guo-Wei    Wei    and    Siyang    Yang,  Partial  differential  equation  transform  ---  variational  formulation  and  Fourier  analysis  ,    International  Journal  for      Numerical    Methods  in  Biomedical    Engineering,   27,   1996-2020,  (2011).

 

(142) G. W.  Wei, Lalita Udpa, Yang Wang and Shan Zhao, Editorial: Mathematical  methods  for  images  and surfaces,   International   Journal of  Biomedical  Imaging,  Volume 2010, Article ID 918467, 3 pages (2010).

 

(139) Changjun Chen,  Rishu Saxena, and Guo-Wei Wei,  Differential  geometry  based  multiscale  model  for  virus capsid  dynamics,  Int.   J.  Biomed  Imaging,  Volume 2010, Article ID 308627, 9 pages (2010).

 

(136) G.W. Wei and G. Wang,  Editorial:  Special issue on recent advances in  computational techniques for biomedical  imaging,  Commun. Numer. Methods Engng, 25, 581-582 (2009)

 

(135) P. Bates, Z. Chen, Y.H. Sun, G.W. Wei and S. Zhao,  Geometric and potential  driving   formation and evolution  of  biomolecular surfaces, J. Math. Biol. 59, 193-231 (2009)

 

(133) Duan Chen, G.W. Wei, X. Cong and Ge Wang,  Computational methods for optical  molecular  imaging, Commun. Numer. Methods Engng,  25, 1137-1161(2008).

 

(124) G.W. Wei, Editoral: Recent advances in mathematical methods for the analysis of biomedical image, International Journal of  Biomedical  Imaging, vol. 2006, 70578, 1, (2006).

 

(121)  Ge Wang, Haiou Shen Wenxiang Cong, Shan Zhao and G.W. Wei, Temperature modulated bioluminescence tomography, Optics Express,  14 (17)  7852-7871 (2006).

 

(119) Y.H. Sun, P.R. Wu, G.W. Wei and G. Wang, Evolution operator based single-step method for image processing, Int. J. Biomed. Imaging, 83847, 1-27 (2006).

 

(86) S. Zhao and G.W. Wei,  Jump process analysis for the trend estimation of time series,  Comput. Statist. Data Anal.,  42,  219-241 (2003).

 

(84) G. W. Wei and Y. Q.  Jia,  Synchronization based image edge detection, Europhys.  Lett. 59, 814-819 (2002).

 

(77) G.W. Wei,  Oscillation reduction by anisotropic diffusions, Comput. Phys.  Commun. ,  144 , 417-342 (2002). 

 

(70) Z.J. Hou and G.W. Wei, A new approach for edge detection, Pattern Recognition, 35(7) , 1559-1570 (2002). This article was the most requested paper in Pattern Recognition.

 

(67) S. Guan, C.-H. Lai and G.W. Wei,  A wavelet method for the characterization of spatiotemporal patterns, Physica D , 163 , 49-79 (2002).

 

(60) Z. Shi, G.W. Wei, D.J. Kouri, D.K. Hoffman, Z. Bao,  Lagrange wavelets for signal processing, IEEE T. Image Processing, 10 , 1488-1508 (2001).

 

(50) G.W. Wei,  Wavelets generated by using discrete singular convolution kernels,  J. Phys. A, Mathematical and General, 33 , 8577-8596 (2000).

 

(44)  Zhuoer Shi, D.J.  Kouri, G.W. Wei, and David K. Hoffman, Generalized symmetric interpolating wavelets, Comput. Phys.  Commun. ,  119, 194-218 (1999).

 

(42) G.W. Wei, Generalized  Perona-Malik  equation for Image Restoration, IEEE Signal Processing  Lett. ,  6 , 165-167 (1999).