Research Interest: Scalable Evolutionary Bioinformatics

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Software

KaMPIng (Karlsruhe MPI Next Generation): (Near) zero-overhead modern C++ abstraction over the Message Passing Interface
gfkit (Genealogical Forest Kit): Compute-efficient statistics in population genetics
ReStore An in-memory REplicated STORagE for rapid recovery of data in fault-tolerant HPC-algorithms
Fault-Tolerant RAxML-NG (FT-RAxML-NG) Fault-tolerant version of the popular RAxML-NG phylogenetic inference tool
Coraxlib (COre RAXml LIBrary) encapsulates common routines used by likelihood-based phylogenetic software

Technical Reports
Title	Author(s)	Source	Date
ReStore: In-Memory REplicated STORagE for Rapid Recovery in Fault-Tolerant Algorithms	Lukas Hübner, Demian Hespe, Peter Sanders, Alexandros Stamatakis	arXiv	January 2023
Exploring Parallel MPI Fault Tolerance Mechanisms for Phylogenetic Inference with RAxML-NG	Lukas Hübner, Alexey M. Kozlov, Demian Hespe, Peter Sanders, Alexandros Stamatakis	bioRxiv	January 2021
Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests	Lukas Hübner, Alexandros Stamatakis	bioRxiv	27th of Mai 2024
The Free Lunch is not over yet - Systematic Exploration of Numerical Thresholds in Phylogenetic Inference	Julia Haag, Lukas Hübner, Alexey M. Kozlov, Alexandros Stamatakis	bioRxiv	July 2022
Data Distribution for Phylogenetic Inference with Site Repeats via Judicious Hypergraph Partitioning	Ivo Baar, Lukas Hübner, Peter Oettig, Adrian Zapletal, Sebastian Schlag, Alexandros Stamatakis, Benoit Morel	bioRxiv	March 2019
KaMPIng: Flexible and (Near) Zero-overhead C++ Bindings for MPI	Demian Hespe, Lukas Hübner, Florian Kurpicz, Peter Sanders, Matthias Schimek, Daniel Seemaier, Christoph Stelz, Tim Niklas Uhl	arXiv	April 2024
Phylogenetic analysis of SARS-CoV-2 data is difficult	Benoit Morel, Pierre Barbera, Lucas Czech, Ben Bettisworth, Lukas Hübner, Sarah Lutteropp, Dora Serdari, Evangelia-Georgia Kostaki, Ioannis Mamais, Alexey M. Kozlov, Pavlos Pavlidis, Dimitrios Paraskevis, Alexandros Stamatakis	bioRxiv	August 2020

Presentations
Title	Conference	Author(s)	Speaker
Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests	WABI 2024	Lukas Hübner & Alexandros Stamatakis	Lukas Hübner
The Computational Stumbling Blocks: Fault-Tolerance and Reproducibility	Biodiversity Bioinformatics Workshop 2023	Lukas Hübner	Lukas Hübner
ReStore: In-Memory REplicated STORagE for Rapid Recovery	Fault-Tolerance at eXtreme Scale (FTXS) 2022	Lukas Hübner, Demian Hespe, Peter Sanders, Alexandros Stamatakis	Lukas Hübner

Courses, Seminars, Practicals
Title	Type	Semester	Location
Where can I go in hours? Isochrone routing	Praxis der Softwareentwicklung (PSE)	SS 2023
Can we accelerate Maximum-Likelihood Computations on GPUs?	Praxis der Forschung	WS 23/24 + SS 24
Parallel Algorithms	lecture	WS 23/24	Building 50.34, Lecture Hall -101
Parallel Algorithms	Vorlesung (V)	WS 24/25	Building 50.34, Lecture Hall -101
Hands-on Bioinformatics Practical	lab course	SS 21
Parallel Algorithms	lecture	WS 21/22	Building 50.34, Lecture Hall -101
Parallel Algorithms	lecture	WS 22/23	Building 50.34, Lecture Hall -101

Available Thesis
Titel	Forschungsthema	Typ
Scalable Fault-Tolerant MapReduce	Fault-Tolerance, Map Reduce, HPC	Masterarbeit
Data-Redistribution for Malleable Algorithms	Malleability, HPC	Masterarbeit

Supervised Theses
Title	Subject	Supervisor	Student
Lightweight Checkpointing and Recovery for Iterative Converging Algorithms	Fault-Tolerance	Demian Hespe, Lukas Hübner, Peter Sanders	Guido Zeitzmann
Faster Sorting of Aligned DNA-Read Files	Efficient Evolutionary Bioinformatics	Lukas Hübner, Alexandros Stamatakis	Dominik Siebelt
Re-Engineering Genomic Tree Sequence Inference Algorithms	Efficient Evolutionary Bioinformatics	Lukas Hübner, Alexandros Stamatakis	Johannes Hengstler
Core-Count Independent Reproducible Reduce	Fault-Tolerance, Computational Reproducibility	Lukas Hübner, Alexandros Stamatakis, Peter Sanders	Christoph Stelz
Empirical Numerical Properties of Maximum Likelihood Phylogenetic Inference	Phylogenetic Inference, Efficient Evolutionary Bioinformatics	Lukas Hübner, Alexandros Stamatakis	Julia Haag
Scalable Decentralized Fault-Tolerant MapReduce for Iterative Algorithms	Fault-Tolerance	Demian Hespe, Lukas Hübner, Peter Sanders	Charel Mercatoris