Publications

Mikael Vejdemo-Johansson, and Sayan Mukherjee. Multiple hypothesis testing with persistent homology. Foundations of Data Science, (4)4:667--705, 2022. [PUMA: topic_mathfoundation Persistent_homology false_discovery_rate family-wise_error_rate hypothesis_testing multiple_hypothesis_control] URL

Brian St. Thomas, Kisung You, Lizhen Lin, Lek-Heng Lim, and Sayan Mukherjee. Learning Subspaces of Different Dimensions. Journal of Computational and Graphical Statistics, (31)2:337--350, ASA Website, 2022. [PUMA: topic_mathfoundation imported] URL

Youngsoo Baek, Samuel Berchuck, and Sayan Mukherjee. Asymptotics of Bayesian Uncertainty Estimation in Random Features Regression. In A. Oh, T. Naumann, A. Globerson, K. Saenko, M. Hardt, and S. Levine (Eds.), Advances in Neural Information Processing Systems, (36):40140--40153, Curran Associates, Inc., 2023. [PUMA: topic_mathfoundation imported] URL

Michele Caprio, Andrea Aveni, and Sayan Mukherjee. Concerning Two Classes of Non-Diophantine Arithmetics. Proceedings, (81):33, March 2022. [PUMA: topic_mathfoundation imported]

Youngsoo Baek, Wilkins Aquino, and Sayan Mukherjee. Generalized Bayes approach to inverse problems with model misspecification. Inverse Problems, (39)10:105011, IOP Publishing, September 2023. [PUMA: topic_mathfoundation imported] URL

Sayan Mukherjee, and Vorapong Suppakitpaisarn. Robustness for Spectral Clustering of General Graphs under Local Differential Privacy. 2023. [PUMA: topic_mathfoundation imported] URL

Lukas Silvester Barth, Fatemeh, Fahimi, Parvaneh Joharinad, Jürgen Jost, and Janis Keck. IsUMap: Manifold Learning and Data Visualization leveraging Vietoris-Rips filtrations. 2024. [PUMA: topic_mathfoundation topic_lifescience imported] URL

Parvaneh Joharinad, and Jürgen Jost. Geometry of Data. 2022. [PUMA: topic_mathfoundation topic_lifescience imported] URL

Lukas Silvester Barth, Fatemeh, Fahimi, Parvaneh Joharinad, Jürgen Jost, Janis Keck, and Thomas Jan Mikhail. Fuzzy simplicial sets and their application to geometric data analysis. 2024. [PUMA: topic_mathfoundation topic_lifescience imported] URL

Jan Engelhardt, Oliver Scheer, Peter Stadler, and Sonja Prohaska. Evolution of DNA Methylation Across Ecdysozoa. Journal of Molecular Evolution, (90)January 2022. [PUMA: topic_mathfoundation zno]

Toralf Kirsten, Frank Meineke, Henry Löffler-Wirth, Alexandr Uciteli, Christoph Beger, Sebastian Stäubert, Matthias Löbe, René Hänsel, Franziska Rauscher, Judith Schuster, Thomas Peschel, Heinrich Herre, Jonas Wagner, Silke Zachariae, Christoph Engel, Markus Scholz, Erhard Rahm, Hans Binder, and Markus Löffler. The Leipzig Health Atlas - An open platform to present, archive and share bio-medical data, analyses and models online. Methods of Information in Medicine, (61)August 2022. [PUMA: area_bigdata topic_mathfoundation topic_lifescience imported]

Michèle Nebe, Stephanie Kehr, Samuel Schmitz, Jana Breitfeld, Judith Lorenz, Diana Le Duc, Peter Stadler, Jens Meiler, Wieland Kiess, Antje Garten, and Anna Kirstein. Small integral membrane protein 10 like 1 enhances differentiation of adipose progenitor cells. Biochemical and Biophysical Research Communications, (604)March 2022. [PUMA: topic_mathfoundation topic_lifescience imported]

Sarah von Löhneysen, Mario Mörl, and Peter F. Stadler. Limits of experimental evidence in RNA secondary structure prediction. Frontiers in Bioinformatics, (4)2024. [PUMA: topic_mathfoundation imported] URL

Annachiara Korchmaros, David Schaller, Marc Hellmuth, and Peter F. Stadler. Quasi-best match graphs. Discrete Applied Mathematics, (331):104--125, 2023. [PUMA: topic_mathfoundation Best Colored Hierarchies, Phylogenetic Rooted combinatorics, directed graphs, matches trees,] URL

Michele Caprio, and Sayan Mukherjee. Extended probabilities and their application to statistical inference. 2023. [PUMA: topic_mathfoundation imported] URL

Saiyam B. Jain, Shao Zongru, Sachin K. T. Veettil, and Michael Hecht. Adversarial attacks for machine learning denoisers and how to resisit them. In Giovanni Volpe, Joana B. Pereira, Daniel Brunner, and Aydogan Ozcan (Eds.), Emerging Topics in Artificial Intelligence (ETAI) 2022, (12204):1220402, SPIE, October 2022. [PUMA: topic_mathfoundation]

Anita Behme, and Apostolos Sideris. Markov-modulated generalized Ornstein-Uhlenbeck processes and an application in risk theory. Bernoulli (Andover.), (28)2Bernoulli Society for Mathematical Statistics and Probability, May 2022. [PUMA: topic_mathfoundation]

John Anders, and Peter F. Stadler. RNAcode\_Web -- Convenient Identification of Evolutionary Conserved Protein Coding Regions. J. Integrative Bioinf., ():, 2023. [PUMA: topic_mathfoundation]

Johannes R Björk, Mauna R Dasari, Kim Roche, Laura Grieneisen, Trevor J Gould, Jean-Christophe Grenier, Vania Yotova, Neil Gottel, David Jansen, Laurence R Gesquiere, Jacob B Gordon, Niki H Learn, Tim L Wango, Raphael S Mututua, J Kinyua Warutere, Long'ida Siodi, Sayan Mukherjee, Luis B Barreiro, Susan C Alberts, Jack A Gilbert, Jenny Tung, Ran Blekhman, and Elizabeth A Archie. Synchrony and idiosyncrasy in the gut microbiome of wild baboons. Nat. Ecol. Evol., (6)7:955--964, Springer Science and Business Media LLC, July 2022. [PUMA: topic_mathfoundation]

Kimberly E Roche, and Sayan Mukherjee. The accuracy of absolute differential abundance analysis from relative count data. PLoS Comput. Biol., (18)7:e1010284, Public Library of Science (PLoS), July 2022. [PUMA: topic_mathfoundation]

Wai Shing Tang, Gabriel Monteiro da Silva, Henry Kirveslahti, Erin Skeens, Bibo Feng, Timothy Sudijono, Kevin K Yang, Sayan Mukherjee, Brenda Rubenstein, and Lorin Crawford. A topological data analytic approach for discovering biophysical signatures in protein dynamics. PLoS Comput. Biol., (18)5:e1010045, Public Library of Science (PLoS), May 2022. [PUMA: topic_mathfoundation]

Michelle Pistner Nixon, Jeffrey Letourneau, Lawrence A David, Nicole A Lazar, Sayan Mukherjee, and Justin D Silverman. Scale Reliant Inference. arXiv, 2022. [PUMA: topic_mathfoundation]

Michele Caprio, and Sayan Mukherjee. Concentration inequalities and optimal number of layers for stochastic deep neural networks. arXiv, 2022. [PUMA: topic_mathfoundation]

Shreya Arya, Justin Curry, and Sayan Mukherjee. A sheaf-theoretic construction of shape space. arXiv, 2022. [PUMA: topic_mathfoundation]

Muhammad Kabiru Nata'ala, Anderson P Avila Santos, Jonas Coelho Kasmanas, Alexander Bartholomäus, João Pedro Saraiva, Sandra Godinho Silva, Tina Keller-Costa, Rodrigo Costa, Newton C M Gomes, André Carlos Ponce de Leon Ferreira de Carvalho, Peter F Stadler, Danilo Sipoli Sanches, and Ulisses Nunes da Rocha. MarineMetagenomeDB: a public repository for curated and standardized metadata for marine metagenomes. Environ. Microbiome, (17)1:57, Springer Science and Business Media LLC, November 2022. [PUMA: topic_mathfoundation Database; Marine Metadata; Metagenomics; Microbial ecology microbiomes; topic_lifescience]

Marie Steinacker, Yuri Kheifetz, and Markus Scholz. Individual modelling of haematotoxicity with NARX neural networks: A knowledge transfer approach. Heliyon, (9)7:e17890, Elsevier BV, July 2023. [PUMA: topic_neuroinspired topic_mathfoundation Haematopoiesis; Precision Recurrent System Transfer identification; learning medicine; networks; neural unit_transfer]

Pascal Mettes, Mina Ghadimi Atigh, Martin Keller-Ressel, Jeffrey Gu, and Serena Yeung. Hyperbolic deep learning in computer vision: A survey. arXiv, 2023. [PUMA: topic_mathfoundation topic_lifescience]

Interdisciplinary Center for Bioinformatics & Leipzig University, Leipzig, Germany, Marcos E Gonzalez Laffitte, Nora Beier, Nico Domschke, and Peter F Stadler. Comparison of atom maps. Match (Mulh.), (90)1:75--102, University Library in Kragujevac, 2023. [PUMA: topic_mathfoundation topic_lifescience]