Selected Publications

2021

Refereed Journal Articles

M. Bollhöfer, O. Schenk, F. Verbosio
High Performance Block Incomplete LU Factorization
Applied Numerical Mathematics, Volume 162, April 2021, Pages 265-2021, doi.org/10.1016/j.apnum.2020.12.023
A. Eftekhari, D. Pasadakis, S. Scheidegger, M. Bollhöfer, O. Schenk
Block-Enhanced Precision Matrix Estimation for Large-Scale Datasets
Journal of Computational Science, Volume 53, July 2021, Pages 1-39, doi.org/10.1016/j.jocs.2021.101389

Refereed Conference Articles

T. Holt, J. Kardoš, V. Fazio, L. Fabietti, F. Spazzini, O. Schenk
High-Performance Data Analytics Techniques for Power Markets Simulation
2021 International Conference on Smart Energy Systems and Technologies (SEST) Mon, Sep 6, 2021 – Wed, Sep 8, 2021

2020

Refereed Journal Articles

A. Buetti-Dinh, M. Herold, S. Christel, M.E. Hajjami, S. Bellenberg, O. Ilie, P. Wilmes, A. Poetsch, W. Sand, M. Vera, I.V. Pivkin, M. Dopson
Systems biology of acidophile biofilms for efficient metal extraction
Scientific Data, 2020 doi.org/10.1038/s41597-020-0519-2
S. Bellenberg , A. Buetti-Dinh, V. Galli, O. Ilie, M. Herold, S. Christel, M. Boretska, I.V. Pivkin, P. Wilmes, W. Sand, M. Vera, M. Dopson
Automated microscopic analysis of metal sulfide colonization by acidophilic microorganisms
Applied and Environmental Microbiology, 6-86, 2020 doi.org/10.1128/AEM.02702-19
A. Buetti-Dinh, M. Herold, S. Christel , M.E.Hajjami, F. Delogu, O. Ilie, S. Bellenberg, P. Wilmes, A. Poetsch, W. Sand, M. Vera, I.V. Pivkin, R. Friedman, M. Dopson
Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations
BMC Bioinformatics, 1-21, 2020 doi.org/10.1186/s12859-019-3337-9
I. Horenko, G. Marchenko, P. Gagliardini
On a computationally-scalable sparse formulation of the multidimensional and non-stationary maximum entropy principle
Communications in Applied Mathematics and Computational Science, Volume 15, Number 2, Pages 1-38, 2020 https://msp.org/soon/coming.php?jpath=camcos
I. Horenko, D. Rodrigues, T. O'Kane, K. Everschor-Sitte
Physically-inspired computational tools for sharp detection of material inhomogeneities in magnetic imaging
ArXiv:1907.04601v2 arxiv.org/abs/1907.04601
I. Horenko
On a scalable entropic breaching of the overfitting barrier in machine learning
Neural Computation, Volume 32, Number 8, pages 1563-1579, 2020 www.mitpressjournals.org/toc/neco/32/8
S. Gerber, L. Pospisil, M. Navandar, I. Horenko
Low-cost scalable discretization, prediction and feature selection for complex systems.
Science Advances, Volume 6, Number 5, eaaw0961, 2020 DOI: 10.1126/sciadv.aaw0961
R. Užupytė, E. C. Wit
Test for triadic closure and triadic protection in temporal relational event data
Social Network Analysis and Mining, 1-21(10), 2020 scopus.com
V. Vinciotti, E. C. Wit
Statistica Neerlandica special issue on Statistical Network Science
Statistica Neerlandica, 74(3), 220-221, 2020. doi.org/10.1111/stan.12212
F. Richter, B. Haegeman, R. S. Etienne, E. C. Wit
Introducing a general class of species diversification models for phylogenetic trees
Statistica Neerlandica, 74(3), 261-274, 2020 doi.org/10.1111/stan.12205
S. Ranciati., E.C. Wit, C. Viroli
Bayesian smooth-and-match inference for ordinary differential equations models linear in the parameters
Statistica Neerlandica, 74(3), 125-144, 2020 scopus.com
E. C. Wit, L. Augugliaro, H. Pazira, J. González, F. Abegaz
Sparse relative risk regression models
Biostatistics, 21(2), e131–e147, 2020 scopus.com
W. Kruijer, P. Behrouzi, D. Bustos-Korts, M. X. Rodríguez-Álvarez, S. M. Mahmoudi, B. Yandell, E. C. Wit, F. A. van Eeuwijk
Reconstruction of Networks with Direct and Indirect Genetic Effects
Genetics, 214(4), 781-807, 2020 doi.org/10.1534/GENETICS.119.302949
M. Signorelli, E. C. Wit
Model-based clustering for populations of networks
Statistical Modelling, 20(1), 9-29, 2020 doi.org/10.1177/1471082X19871128
S. de Vos, S. Patten, E. C. Wit, E. H. Bos, K. J. Wardenaar, P. de Jonge
Subtyping psychological distress in the population: A semi-parametric network approach
Epidemiology and psychiatric sciences, 29, 1-8, 2020 doi.org/10.1017/S204579601900026X
S. N. Wood, E. C. Wit, M.Fasiolo, P. J. Green
COVID-19 and the difficulty of inferring epidemiological parameters from clinical data
Lancet Infectious Diseases, 2020 doi.org/10.1016/S1473-3099(20)30437-0
I. Artico, I. Smolyarenko, V. Vinciotti, E. C. Wit
How rare are power-law networks really?
Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 476(2241), 2020 doi.org/10.1098/rspa.2019.0742
P. Arbenz, L. Giraud, O. Schenk.W. Vanroose
Guest editorial: Special Issue on Parallel Matrix Algorithms and Applications (PMAA’18)
Parallel Computing, Volume 84, December 2020, Pages 1-2 doi.org/10.1016/j.parco.2018.01.003
P. Sanan. D. May, B. Bollhöfer, O. Schenk
Pragmatic Solvers for 3D Stokes and Elasticity Problems with Heterogeneous Coefficients: Evaluating Modern Incomplete LDLT Preconditioners
Solid Earth Discussions, 1-23, 2020, doi.org/10.5194/se-2020-79
A. Klawonn, M. Lanser, M. Uran, O. Rheinbach, S. Köhler, J. Schröder, L. Scheunemann, D. Brands, D. Balzani, A. Gandhi, G. Wellein, M. Wittmann, O. Schenk, R. Janalík
Towards A Virtual Laboratory - Computation of Forming Limit Curves
In: Bungartz HJ., Reiz S., Uekermann B., Neumann P., Nagel W. (eds) Software for Exascale Computing - SPPEXA 2016-2019. Lecture Notes in Computational Science and Engineering, vol 136. Springer, Cham, doi.org/10.1007/978-3-030-47956-5_13
J. van Niekerk, H. Bakka, H. Rue, and O. Schenk
New frontiers in Bayesian modeling using the INLA package in R
Journal of Statistical Software, accepted, in press.
J. Kardos, D. Kourounis, and O. Schenk
Two-Level Parallel Augmented Schur Complement Interior-Point Algorithms for the Solution of Security Constrained Optimal Power Flow Problems
IEEE Transactions on Power Systems, 1340 - 1350, Volume: 35 , Issue: 2 , March 2020, doi.org/10.1109/TPWRS.2019.2942964
C. Alappat, G. Hager, O. Schenk, J. Thies, A. Basermann, A. Bischop, H. Fehske, G. Wellein
A Recursive Algebraic Coloring Technique for Hardware-Efficient Symmetric Sparse Matrix-Vector Multiplication
ACM Transactions on Parallel Computing, Vol. 7, No. 3, Article 19, June 2020 doi.org/10.1145/3399732

2019

Book Contributions

M. Bollhöfer, O. Schenk , R. Janalik, S. Hamm, and K. Gullapalli
State-of-The-Art Sparse Direct Solvers
In: Grama A., Sameh A. (eds) Parallel Algorithms in Computational Science and Engineering. Modeling and Simulation in Science, Engineering and Technology. pp 1-32, Birkhäuser, Cham. doi.org/10.1007/978-3-030-43736-7_1
J. Kardos, D. Kourounis, and O. Schenk
Parallel Structure Exploiting Interior Point Methods
In: Grama A., Sameh A. (eds) Parallel Algorithms in Computational Science and Engineering. Modeling and Simulation in Science, Engineering and Technology. pp 63-93, Birkhäuser, Cham. doi.org/10.1007/978-3-030-43736-7_3

Refereed Journal Articles

A. Buetti-Dinh, V. Galli, S. Bellenberg, O. Ilie, M. Herold, S. Christel, M. Boretska, I.V. Pivkin, P. Wilmes, W. Sand, M. Vera, M. Dopson
Deep neural networks outperform human expert's capacity in characterizing bioleaching bacterial biofilm composition
Biotechnology Reports, 2019 doi.org/10.1016/j.btre.2019.e00321
D. Pellin, L. Biasco, A. Aiuti, M.C. Di Serio, E.C. Wit
Penalized inference of the hematopoietic cell differentiation network via high-dimensional clonal tracking
Applied Network Science, 1-115, 2019 doi.org/10.1007/s41109-019-0225-1
K. Kamphorst, B.C. Oosterloo, A.M. Vlieger, N.B. Rutten, C.M. Bunkers, E.C. Wit, R.M Van Elburg
Antibiotic Treatment in the First Week of Life Impacts the Growth Trajectory in the First Year of Life in Term Infants
Journal of Pediatric Gastroenterology and Nutrition, 131-136, 2019 doi.org/10.1097/MPG.0000000000002360
A. Abbruzzo , I. Vujačić, A.M. Mineo, E.C. Wit
Selecting the tuning parameter in penalized Gaussian graphical models
Statistics and Computing, 559-569, 2019 doi.org/10.1007/s11222-018-9823-5
P. Behrouzi, E.C. Wit
De novo construction of polyploid linkage maps using discrete graphical models
Bioinformatics, 1-3, 2019 doi.org/10.1093/bioinformatics/bty777
N. Demetrashvili, N. Smidt, H. Snieder, E.R. Van Den Heuvel, E.C. Wit
Variance components models for analysis of big family data of health outcomes in the lifelines cohort study
Twin Research and Human Genetics, 1083-1093, 2019 https://doi.org/10.1017/thg.2019.1
E.C. Wit
Introduction to network inference in genomics
Network Science: An Aerial View, 99-119, 2019 doi.org/10.1007/978-3-030-26814-5_7
R. Mohammadi, E.C. Wit
BDgraph: An R package for Bayesian structure learning in graphical models
Journal of Statistical Software, 1-2, 2019 doi.org/10.18637/jss.v089.i03
S. E. Balafas, W. P. Krijnen, W. J. Post, E. C. Wit
An R Package for Nonparametric IRT Modelling of Unfolding Processes
The R Journal, journal.r-project.org
N. P. Gill, L. D’Arrigo, E. C Wit
Comparison of Postoperative Fever and Effectiveness of Percutaneous Nephrolithotomy (PCNL) Versus Retrograde Intrarenal Surgery (RIRS) for the Treatment of Renal Stones
SN Comprehensive Clinical Medicine, 1(3), 154-159.019, 2019 doi.org/10.1007/s42399-018-0023-6
P. Behrouzi, E. C. Wit
Detecting epistatic selection with partially observed genotype data by using copula graphical models
Journal of the Royal Statistical Society. Series C: Applied Statistics, 68(1), 141-160, 2019 doi.org/10.1111/rssc.12287
M. Rosenau, I. Horenko, F. Corbi, M. Rudolf, R. Kornhuber and O. Oncken
Synchronization of great subduction megathrust earthquakes: Insights from scale model analysis.
Journal of Geophysical Research: Solid Earth, 124(4):3646-3661, 2019 agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JB016597
M. Bollhoefer, A. Eftekhari, S. Scheidegger, and O. Schenk
Large-Scale Sparse Inverse Covariance Matrix Estimation
SIAM J. Sci. Comput., 41(1), A380–A401, January 2019, DOI: doi.org/10.1137/17M1147615