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).