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1Unstable cores are the source of instability in chemical reaction networks
N. Vassena, and P. Stadler. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 480 (2285): 20230694 (2024)
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1Notation3 as an Existential Rule Language
D. Arndt, and S. Mennicke. Rules and Reasoning - 7th International Joint Conference on Rules and Reasoning, RuleML+RR 2023, Proceedings, Springer, (October 2023)
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1On Over-Squashing in Message Passing Neural Networks: The Impact of Width, Depth, and Topology
F. Giovanni, L. Giusti, F. Barbero, G. Luise, P. Lio', and M. Bronstein. (2023)
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1Neural Networks as Black-Box Benchmark Functions Optimized for Exploratory Landscape Features
{. Prager, K. Dietrich, L. Schneider, L. Schäpermeier, B. Bischl, P. Kerschke, H. Trautmann, and O. Mersmann. FOGA 2023, page 129--139. United States, Association for Computing Machinery, (Aug 30, 2023)Publisher Copyright: © 2023 ACM.; 17th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, FOGA 2023, FOGA 2023 ; Conference date: 30-08-2023 Through 01-09-2023.
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2024_OA_procedureBenchmarkingBlack-box_continuous_optimizationExploratory_landscape_analysisInstance_generatorNeural_networks
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1Deep-ELA: Deep Exploratory Landscape Analysis with Self-Supervised Pretrained Transformers for Single- and Multi-Objective Continuous Optimization Problems
M. Seiler, P. Kerschke, and H. Trautmann. (2024)
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1Geometry of Data
P. Joharinad, and J. Jost. (2022)
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1Dancing to the State of the Art? How Candidate Lists Influence LKH for Solving the Traveling Salesperson Problem
J. Heins, L. Schäpermeier, P. Kerschke, and D. Whitley. (2024)
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1Fuzzy simplicial sets and their application to geometric data analysis
L. Barth, Fatemeh, Fahimi, P. Joharinad, J. Jost, J. Keck, and T. Mikhail. (2024)
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1Marine cloud base height retrieval from MODIS cloud properties using machine learning
J. Lenhardt, J. Quaas, and D. Sejdinovic. Atmospheric Measurement Techniques, (2024)
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1A Bayesian hierarchical model to estimate DNA methylation conservation in colorectal tumors
K. Murgas, Y. Ma, L. Shahidi, S. Mukherjee, A. Allen, D. Shibata, and M. Ryser. Bioinformatics, 38 (1): 22--29 (September 2021)
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1Semantic Characterizations of AGM Revision for Tarskian Logics
F. Falakh, S. Rudolph, and K. Sauerwald. Proceedings of the 6th International Joint Conference on Rules and Reasoning (RuleML+RR 2022), volume 13752 of LNCS, page 95--110. Springer, (September 2022)
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1Towards Ontology Construction with Language Models
M. Funk, S. Hosemann, J. Jung, and C. Lutz. (2023)
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1Asymptotics of Bayesian Uncertainty Estimation in Random Features Regression
Y. Baek, S. Berchuck, and S. Mukherjee. Advances in Neural Information Processing Systems, 36, page 40140--40153. Curran Associates, Inc., (2023)
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1Community Detection on Networks with Ricci Flow
C. Ni, Y. Lin, F. Luo, and J. Gao. (2019)
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1Synchrony and idiosyncrasy in the gut microbiome of wild baboons
{. Björk, {. Dasari, K. Roche, L. Grieneisen, {. Gould, {. Grenier, V. Yotova, N. Gottel, D. Jansen, {. Gesquiere and 13 other author(s). Nature Ecology and Evolution, 6 (7): 955--964 (July 2022)Funding Information: We thank J. Altmann for her essential role in stewarding the Amboseli Baboon Project and in collecting and maintaining the faecal samples used in this manuscript. This work was supported by the National Science Foundation (NSF) and the National Institutes of Health (NIH), especially NSF Rules of Life Award DEB1840223 (E.A.A. and J.A.G.) and the National Institute on Aging R21AG055777 (E.A.A. and R.B.) and NIH R01AG053330 (E.A.A.), NIH R01AG071684 (E.A.A.) and NIHR35 GM128716 (R.B.), the Duke University Population Research Institute P2C-HD065563 (pilot to J.T.), the University of Notre Dame’s Eck Institute for Global Health (E.A.A.) and the Notre Dame Environmental Change Initiative (E.A.A.). Since 2000, long-term data collection in Amboseli has been supported by NSF and NIH, including IOS1456832 (S.C.A.), IOS1053461 (E.A.A.), DEB1405308 (J.T.), IOS0919200 (S.C.A.), DEB0846286 (S.C.A.), DEB0846532 (S.C.A.), IBN0322781 (S.C.A.), IBN0322613 (S.C.A.), BCS0323553 (S.C.A.), BCS0323596 (S.C.A.), P01AG031719 (S.C.A.), R21AG049936 (J.T. and S.C.A.), R03AG045459 (J.T. and S.C.A.), R01AG034513 (S.C.A.), R01HD088558 (J.T.) and P30AG024361 (S.C.A.). We also especially thank the members of the Maasai pastoralist communities in the Amboseli-Longido areas. We thank the Kenya Wildlife Service, Kenya’s Wildlife Research & Training Institute, the National Council for Science, Technology and Innovation and the National Environment Management Authority for permission to conduct research and collect biological samples in Kenya. We also thank the University of Nairobi, Institute of Primate Research, National Museums of Kenya, the Enduimet Wildlife Management Area, Ker & Downey Safaris, Air Kenya and Safarilink for their cooperation and assistance in the field. We thank K. Pinc for managing and designing the database. We also thank T. Voyles, A. Dumaine, Y. Zhang, M. Rao, T. Vilgalys, A. Lea, N. Snyder-Mackler, P. Durst, J. Zussman, G. Chavez and R. Debray for contributing to faecal sample processing. Complete acknowledgements for the ABRP can be found online at https://amboselibaboons.nd.edu/acknowledgements/ . Publisher Copyright: © 2022, The Author(s), under exclusive licence to Springer Nature Limited..
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1Tailored machine learning models for functional RNA detection in genome-wide screens (Version 1)
C. Klapproth, S. Zöztsche, F. Kühnl, J. Fallmann, P. Stadler, and S. Findeiß. https://doi.org/10.5281/zenodo.8120827, (July 2023)Accessed on YYYY-MM-DD..
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1Partial Fitch Graphs: Characterization, Satisfiability and Complexity*
M. Hellmuth, A. Korchmaros, J. Ram\'ırez-Rafael, B. Schmidt, P. Stadler, and S. Thekkumpadan Puthiyaveedu. bioRxiv, (2024)
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1Higher Order Bipartiteness vs Bi-Partitioning in Simplicial Complexes
M. Eidi, and S. Mukherjee. (2024)
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1Concentration inequalities and optimal number of layers for stochastic deep neural networks
M. Caprio, and S. Mukherjee. (2023)
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1Planar median graphs and cubesquare-graphs
{. Seemann, V. Moulton, {. Stadler, and M. Hellmuth. Discrete Applied Mathematics, (May 31, 2023)
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1Unstable cores are the source of instability in chemical reaction networks

1Notation3 as an Existential Rule Language

1On Over-Squashing in Message Passing Neural Networks: The Impact of Width, Depth, and Topology

1Neural Networks as Black-Box Benchmark Functions Optimized for Exploratory Landscape Features

1Deep-ELA: Deep Exploratory Landscape Analysis with Self-Supervised Pretrained Transformers for Single- and Multi-Objective Continuous Optimization Problems

1Geometry of Data

1Dancing to the State of the Art? How Candidate Lists Influence LKH for Solving the Traveling Salesperson Problem

1Fuzzy simplicial sets and their application to geometric data analysis

1Marine cloud base height retrieval from MODIS cloud properties using machine learning

1A Bayesian hierarchical model to estimate DNA methylation conservation in colorectal tumors

1Semantic Characterizations of AGM Revision for Tarskian Logics

1Towards Ontology Construction with Language Models

1Asymptotics of Bayesian Uncertainty Estimation in Random Features Regression

1Community Detection on Networks with Ricci Flow

1Synchrony and idiosyncrasy in the gut microbiome of wild baboons

1Tailored machine learning models for functional RNA detection in genome-wide screens (Version 1)

1Partial Fitch Graphs: Characterization, Satisfiability and Complexity*

1Higher Order Bipartiteness vs Bi-Partitioning in Simplicial Complexes

1Concentration inequalities and optimal number of layers for stochastic deep neural networks

1Planar median graphs and cubesquare-graphs

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