Cleveland, Electa; Zhu, Angela; Sandstede, Björn; Volkening, Alexandria Quantifying different modeling frameworks using topological data analysis: a case study with zebrafish patterns. (English) Zbl 07773365 SIAM J. Appl. Dyn. Syst. 22, No. 4, 3233-3266 (2023). MSC: 92C15 37B15 55N31 PDFBibTeX XMLCite \textit{E. Cleveland} et al., SIAM J. Appl. Dyn. Syst. 22, No. 4, 3233--3266 (2023; Zbl 07773365) Full Text: DOI arXiv
Mang, Andreas; He, Jiwen; Azencott, Robert An operator-splitting approach for variational optimal control formulations for diffeomorphic shape matching. (English) Zbl 07748049 J. Comput. Phys. 493, Article ID 112463, 32 p. (2023). MSC: 65Kxx 92Cxx 68Uxx PDFBibTeX XMLCite \textit{A. Mang} et al., J. Comput. Phys. 493, Article ID 112463, 32 p. (2023; Zbl 07748049) Full Text: DOI arXiv
Manin, Fedor; Roldán, Érika; Schweinhart, Benjamin Topology and local geometry of the Eden model. (English) Zbl 1509.82066 Discrete Comput. Geom. 69, No. 3, 771-799 (2023). MSC: 82B43 62R40 60K35 55N31 05B50 92B05 PDFBibTeX XMLCite \textit{F. Manin} et al., Discrete Comput. Geom. 69, No. 3, 771--799 (2023; Zbl 1509.82066) Full Text: DOI arXiv
Conceição, Pedro; Morimoto, Juliano ‘Holey’ niche! finding holes in niche hypervolumes using persistence homology. (English) Zbl 1493.92088 J. Math. Biol. 84, No. 7, Paper No. 58, 13 p. (2022). MSC: 92D40 55N31 PDFBibTeX XMLCite \textit{P. Conceição} and \textit{J. Morimoto}, J. Math. Biol. 84, No. 7, Paper No. 58, 13 p. (2022; Zbl 1493.92088) Full Text: DOI
Jimenez, Maria-Jose On topological analysis of cells organization in biological images. (English) Zbl 1486.92099 Lindblad, Joakim (ed.) et al., Discrete geometry and mathematical morphology. First international joint conference, DGMM 2021, Uppsala, Sweden, May 24–27, 2021. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 12708, 58-63 (2021). MSC: 92C55 92C37 62R40 PDFBibTeX XMLCite \textit{M.-J. Jimenez}, Lect. Notes Comput. Sci. 12708, 58--63 (2021; Zbl 1486.92099) Full Text: DOI
Wang, Bruce; Sudijono, Timothy; Kirveslahti, Henry; Gao, Tingran; Boyer, Douglas M.; Mukherjee, Sayan; Crawford, Lorin A statistical pipeline for identifying physical features that differentiate classes of 3D shapes. (English) Zbl 1478.62390 Ann. Appl. Stat. 15, No. 2, 638-661 (2021). MSC: 62R40 62P10 62H35 60G15 92D15 PDFBibTeX XMLCite \textit{B. Wang} et al., Ann. Appl. Stat. 15, No. 2, 638--661 (2021; Zbl 1478.62390) Full Text: DOI
Ciocanel, Maria-Veronica; Juenemann, Riley; Dawes, Adriana T.; McKinley, Scott A. Topological data analysis approaches to uncovering the timing of ring structure onset in filamentous networks. (English) Zbl 1460.92063 Bull. Math. Biol. 83, No. 3, Paper No. 21, 25 p. (2021). MSC: 92C37 92C42 62P15 62R40 PDFBibTeX XMLCite \textit{M.-V. Ciocanel} et al., Bull. Math. Biol. 83, No. 3, Paper No. 21, 25 p. (2021; Zbl 1460.92063) Full Text: DOI arXiv
Mandal, Sayan; Guzmán-Sáenz, Aldo; Haiminen, Niina; Basu, Saugata; Parida, Laxmi A topological data analysis approach on predicting phenotypes from gene expression data. (English) Zbl 1500.92079 Martín-Vide, Carlos (ed.) et al., Algorithms for computational biology. 7th international conference, AlCoB 2020, Missoula, MT, USA, April 13–15, 2020. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 12099, 178-187 (2020). MSC: 92D20 92C40 62R40 PDFBibTeX XMLCite \textit{S. Mandal} et al., Lect. Notes Comput. Sci. 12099, 178--187 (2020; Zbl 1500.92079) Full Text: DOI
Paluzo-Hidalgo, Eduardo; Gonzalez-Diaz, Rocio; Gutiérrez-Naranjo, Miguel A. Two-hidden-layer feed-forward networks are universal approximators: a constructive approach. (English) Zbl 1491.41009 Neural Netw. 131, 29-36 (2020). MSC: 41A30 68T05 92B20 PDFBibTeX XMLCite \textit{E. Paluzo-Hidalgo} et al., Neural Netw. 131, 29--36 (2020; Zbl 1491.41009) Full Text: DOI arXiv
Mcguirl, Melissa R.; Volkening, Alexandria; Sandstede, Björn Topological data analysis of zebrafish patterns. (English) Zbl 1456.92004 Proc. Natl. Acad. Sci. USA 117, No. 10, 5113-5124 (2020). MSC: 92-08 55N31 PDFBibTeX XMLCite \textit{M. R. Mcguirl} et al., Proc. Natl. Acad. Sci. USA 117, No. 10, 5113--5124 (2020; Zbl 1456.92004) Full Text: DOI arXiv
Cang, Zixuan; Munch, Elizabeth; Wei, Guo-Wei Evolutionary homology on coupled dynamical systems with applications to protein flexibility analysis. (English) Zbl 1460.55007 J. Appl. Comput. Topol. 4, No. 4, 481-507 (2020). Reviewer: Jonathan Hodgson (Swarthmore) MSC: 55N31 62R40 37N25 92E10 PDFBibTeX XMLCite \textit{Z. Cang} et al., J. Appl. Comput. Topol. 4, No. 4, 481--507 (2020; Zbl 1460.55007) Full Text: DOI Link
Lesnick, Michael; Rabadán, Raúl; Rosenbloom, Daniel I. S. Quantifying genetic innovation: mathematical foundations for the topological study of reticulate evolution. (English) Zbl 1433.92030 SIAM J. Appl. Algebra Geom. 4, No. 1, 141-184 (2020). MSC: 92D15 55N31 PDFBibTeX XMLCite \textit{M. Lesnick} et al., SIAM J. Appl. Algebra Geom. 4, No. 1, 141--184 (2020; Zbl 1433.92030) Full Text: DOI arXiv
Rybakken, Erik; Baas, Nils; Dunn, Benjamin Decoding of neural data using cohomological feature extraction. (English) Zbl 1471.92034 Neural Comput. 31, No. 1, 68-93 (2019). MSC: 92B20 PDFBibTeX XMLCite \textit{E. Rybakken} et al., Neural Comput. 31, No. 1, 68--93 (2019; Zbl 1471.92034) Full Text: DOI arXiv Link
Maroulas, Vasileios; Mike, Joshua L.; Oballe, Christopher Nonparametric estimation of probability density functions of random persistence diagrams. (English) Zbl 1446.62113 J. Mach. Learn. Res. 20, Paper No. 151, 49 p. (2019). MSC: 62G07 62R40 62P10 92C55 PDFBibTeX XMLCite \textit{V. Maroulas} et al., J. Mach. Learn. Res. 20, Paper No. 151, 49 p. (2019; Zbl 1446.62113) Full Text: arXiv Link
Wu, Dongqing; Gao, Jian; Hu, Xiaoli; Xiao, Zhengtao; Huang, Zhuwei; Zhang, Lanyu; Chen, Xin; He, Yunbo Evaluation algorithm of root canal shape based on Steklov spectrum analysis. (English) Zbl 1428.92068 Comput. Math. Methods Med. 2019, Article ID 4830914, 16 p. (2019). MSC: 92C55 PDFBibTeX XMLCite \textit{D. Wu} et al., Comput. Math. Methods Med. 2019, Article ID 4830914, 16 p. (2019; Zbl 1428.92068) Full Text: DOI
Monod, Anthea; Kališnik, Sara; Patiño-Galindo, Juan Ángel; Crawford, Lorin Tropical sufficient statistics for persistent homology. (English) Zbl 1443.62018 SIAM J. Appl. Algebra Geom. 3, No. 2, 337-371 (2019). MSC: 62B05 62R40 55N31 14T90 62P10 92D30 PDFBibTeX XMLCite \textit{A. Monod} et al., SIAM J. Appl. Algebra Geom. 3, No. 2, 337--371 (2019; Zbl 1443.62018) Full Text: DOI arXiv
Mémoli, Facundo; Singhal, Kritika A primer on persistent homology of finite metric spaces. (English) Zbl 1417.62013 Bull. Math. Biol. 81, No. 7, 2074-2116 (2019). MSC: 62-07 62H30 62P10 92C20 55N35 PDFBibTeX XMLCite \textit{F. Mémoli} and \textit{K. Singhal}, Bull. Math. Biol. 81, No. 7, 2074--2116 (2019; Zbl 1417.62013) Full Text: DOI arXiv
Jordan, K. E.; Marinelli, K.; Peters, T. J.; Roulier, J. A.; Zaffetti, P. Subdivision of Bézier curves for ambient isotopy in molecular modeling. (English) Zbl 1412.65012 Topology Appl. 259, 311-322 (2019). MSC: 65D18 65D17 57M25 68U05 92C40 PDFBibTeX XMLCite \textit{K. E. Jordan} et al., Topology Appl. 259, 311--322 (2019; Zbl 1412.65012) Full Text: DOI
Beketayev, Kenes; Yeliussizov, Damir; Morozov, Dmitriy; Weber, Gunther H.; Hamann, Bernd Measuring the error in approximating the sub-level set topology of sampled scalar data. (English) Zbl 1433.55002 Int. J. Comput. Geom. Appl. 28, No. 1, 57-77 (2018). MSC: 55N20 05C90 52B55 65D99 68U05 92E10 PDFBibTeX XMLCite \textit{K. Beketayev} et al., Int. J. Comput. Geom. Appl. 28, No. 1, 57--77 (2018; Zbl 1433.55002) Full Text: DOI
Xia, Kelin; Li, Zhiming; Mu, Lin Multiscale persistent functions for biomolecular structure characterization. (English) Zbl 1385.92021 Bull. Math. Biol. 80, No. 1, 1-31 (2018). MSC: 92C40 92D20 PDFBibTeX XMLCite \textit{K. Xia} et al., Bull. Math. Biol. 80, No. 1, 1--31 (2018; Zbl 1385.92021) Full Text: DOI arXiv
Kovacev-Nikolic, Violeta; Bubenik, Peter; Nikolić, Dragan; Heo, Giseon Using persistent homology and dynamical distances to analyze protein binding. (English) Zbl 1343.92380 Stat. Appl. Genet. Mol. Biol. 15, No. 1, 19-38 (2016). MSC: 92D20 92B15 62P10 PDFBibTeX XMLCite \textit{V. Kovacev-Nikolic} et al., Stat. Appl. Genet. Mol. Biol. 15, No. 1, 19--38 (2016; Zbl 1343.92380) Full Text: DOI arXiv
Giusti, Chad; Pastalkova, Eva; Curto, Carina; Itskov, Vladimir Clique topology reveals intrinsic geometric structure in neural correlations. (English) Zbl 1355.92015 Proc. Natl. Acad. Sci. USA 112, No. 44, 13455-13460 (2015). MSC: 92C20 92B20 PDFBibTeX XMLCite \textit{C. Giusti} et al., Proc. Natl. Acad. Sci. USA 112, No. 44, 13455--13460 (2015; Zbl 1355.92015) Full Text: DOI arXiv
Cang, Zixuan; Mu, Lin; Wu, Kedi; Opron, Kristopher; Xia, Kelin; Wei, Guo-Wei A topological approach for protein classification. (English) Zbl 1347.92054 Mol. Based Math. Biol. 3, 140-162 (2015). MSC: 92D20 PDFBibTeX XMLCite \textit{Z. Cang} et al., Mol. Based Math. Biol. 3, 140--162 (2015; Zbl 1347.92054) Full Text: DOI arXiv
Gameiro, Marcio; Hiraoka, Yasuaki; Izumi, Shunsuke; Kramar, Miroslav; Mischaikow, Konstantin; Nanda, Vidit A topological measurement of protein compressibility. (English) Zbl 1320.55004 Japan J. Ind. Appl. Math. 32, No. 1, 1-17 (2015). Reviewer: Jonathan Hodgson (Swarthmore) MSC: 55N99 92E10 92B99 PDFBibTeX XMLCite \textit{M. Gameiro} et al., Japan J. Ind. Appl. Math. 32, No. 1, 1--17 (2015; Zbl 1320.55004) Full Text: DOI
Li, Ji; Peters, T. J.; Marinelli, K.; Kovalev, E.; Jordan, K. E. Topological subtleties for molecular movies. (English) Zbl 1325.57005 Topology Appl. 188, 91-96 (2015). MSC: 57M25 92C40 PDFBibTeX XMLCite \textit{J. Li} et al., Topology Appl. 188, 91--96 (2015; Zbl 1325.57005) Full Text: DOI
Poza, María; Domínguez, César; Heras, Jónathan; Rubio, Julio A certified reduction strategy for homological image processing. (English) Zbl 1354.68286 ACM Trans. Comput. Log. 15, No. 3, Article No. 23, 23 p. (2014). MSC: 68U10 03B35 55U15 68T15 92C55 PDFBibTeX XMLCite \textit{M. Poza} et al., ACM Trans. Comput. Log. 15, No. 3, Article No. 23, 23 p. (2014; Zbl 1354.68286) Full Text: DOI arXiv
Berwald, Jesse; Gidea, Marian Critical transitions in a model of a genetic regulatory system. (English) Zbl 1327.92029 Math. Biosci. Eng. 11, No. 4, 723-740 (2014). MSC: 92D10 92C42 34C23 PDFBibTeX XMLCite \textit{J. Berwald} and \textit{M. Gidea}, Math. Biosci. Eng. 11, No. 4, 723--740 (2014; Zbl 1327.92029) Full Text: DOI arXiv
Yaffe, Eitan; Halperin, Dan Approximating the pathway axis and the persistence diagrams for a collection of balls in 3-space. (English) Zbl 1211.52004 Discrete Comput. Geom. 44, No. 3, 660-685 (2010). MSC: 52A15 05C90 52C45 52B55 92E10 68U05 65D18 PDFBibTeX XMLCite \textit{E. Yaffe} and \textit{D. Halperin}, Discrete Comput. Geom. 44, No. 3, 660--685 (2010; Zbl 1211.52004) Full Text: DOI
Cazals, Frédéric; Chazal, Frédéric; Giesen, Joachim Spectral techniques to explore point clouds in Euclidean space, with applications to collective coordinates in structural biology. (English) Zbl 1182.92002 Emiris, Ioannis Z. (ed.) et al., Nonlinear computational geometry. Papers presented at the workshop, Minneapolis, MN, USA, May 29–June 2, 2007. Dordrecht: Springer (ISBN 978-1-4419-0998-5/hbk; 978-1-4419-0999-2/e-book). The IMA Volumes in Mathematics and its Applications 151, 1-34 (2010). MSC: 92B05 92C05 90C40 62H25 PDFBibTeX XMLCite \textit{F. Cazals} et al., IMA Vol. Math. Appl. 151, 1--34 (2010; Zbl 1182.92002) Full Text: DOI HAL
Baldacci, L.; Golfarelli, M.; Lumini, A.; Rizzi, S. Clustering techniques for protein surfaces. (English) Zbl 1103.68745 Pattern Recognition 39, No. 12, 2370-2382 (2006). MSC: 68T10 92C10 PDFBibTeX XMLCite \textit{L. Baldacci} et al., Pattern Recognition 39, No. 12, 2370--2382 (2006; Zbl 1103.68745) Full Text: DOI
Natarajan, Vijay; Wang, Yusu; Bremer, Peer-Timo; Pascucci, Valerio; Hamann, Bernd Segmenting molecular surfaces. (English) Zbl 1098.92029 Comput. Aided Geom. Des. 23, No. 6, 495-509 (2006). MSC: 92C40 92C05 57Q99 57N99 57R70 PDFBibTeX XMLCite \textit{V. Natarajan} et al., Comput. Aided Geom. Des. 23, No. 6, 495--509 (2006; Zbl 1098.92029) Full Text: DOI