André Müller, Dipl.-Phys.

Müller, André

High Performance Computing
Academic Staff Member

Phone: +49 6131 39 23704

Email: muellan@uni-mainz.de

Website: https://www.hpc.informatik.uni-mainz.de/people/andre-mueller/

Portrait Müller, André

 

Research Interests

  • Stochastic Optimization
  • Packing & Layout Optimization, Geometric Algorithms
  • Metagenomic Short Read Classification
  • C++ Library Design
  • Generic Programming
  • Functional Programming
  • Parallelization Techniques

Research

Current: Bioinformatics DSLs with Hardware Accelerator Support (using AnyDSL/Impala)

Packing & Layout Optimization

Benchmark results for various packing problem instances

Metagenomic Read Mapping

Links

GitHub Repositories: C++ generic programming utilities, C++ numeric classes & utilities, some useful C++ generic containers

Teaching Materials

Collection of (some of) my C++ Learning & Teaching Materials

I aimed at providing a broad, yet not too shallow overview of the C++ programming language (originally for people with a beginner level Java or Python background). If you find any bug please drop me an e-mail. The stuff is for personal use only and may not be used in a commercial context without my permission.

Teaching

  • WT 2018: 1-week C++ Crash Course
  • WT 2016: 1-week C++ Crash Course
  • ST 2016: Exercises for "Programming Languages"
  • ST 2015: 1-week C++ Crash Course
  • WT 2014/15 Exercises for "Data Structures and Efficient Algorithms", Lecture on AVL Trees
  • ST 2014: Exercises, Tutorial & Lecture Sessions on C++ for "Programming Languages"
  • ST 2014: 1-week "C++ Crash Course" for Java/Python Programmers
  • WT 2013/14 Exercises & Tutorial for "Data Structures and Efficient Algorithms"
  • ST 2013 Exercises, Tutorial & Lecture Sessions on C++ for "Programming Languages"
  • WT 2012/13: Tutor for "Data Structures and Efficient Algorithms"
  • ST 2012: Exercises & Tutorial for "Programming Languages"
  • WT 2011/12: Exercises & Tutorial for "Databases II"
  • ST 2011: Exercises & Tutorial for "Databases I"

Publlications

2023

Wichmann, A., Buschong, E., Mueller, A., et al. (2023). MetaTransformer: deep metagenomic sequencing read classification using self-attention models. NAR GENOMICS AND BIOINFORMATICS, 5(3). DOI Author/Publisher URL
Yan, L., Yin, Z., Zhang, H., et al. (2023). RabbitQCPlus 2.0: More efficient and versatile quality control for sequencing data. METHODS, 216, 39-50. DOI Author/Publisher URL

2022

Yan, L., Yin, Z., Zhang, H., et al. (2022). RabbitQCPlus: More Efficient Quality Control for Sequencing Data. 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 619-626. DOI
Cascitti, J., Niebler, S., Mueller, A., Schmidt, B. (2022). RNACache: A scalable approach to rapid transcriptomic read mapping using locality sensitive hashing. JOURNAL OF COMPUTATIONAL SCIENCE, 60. DOI Author/Publisher URL
Juenger, D., Kobus, R., Mueller, A., et al. (2022). General-purpose GPU hashing data structures and their application in accelerated genomics. JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING, 163, 256-268. DOI Author/Publisher URL
Müller, A., Schmidt, B., Membarth, R., et al. (2022). AnySeq/GPU: a novel approach for faster sequence alignment on GPUs. In L. Rauchwerger, K. W. Cameron, D. S. Nikolopoulos, and D. N. Pnevmatikatos (eds.), ICS (pp. 20:1-20:1). ACM. Author/Publisher URL
Müller, A., Schmidt, B., Membarth, R., et al. (2022). AnySeq/GPU: A Novel Approach for Faster Sequence Alignment on GPUs. CoRR, abs/2205.07610.
Xu, K., Duan, X., Muller, A., et al. (2022). FMapper: Scalable read mapper based on succinct hash index on SunWay TaihuLight. JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING, 161, 72-82. DOI Author/Publisher URL

2021

Cascitti, J., Niebler, S., Müller, A., Schmidt, B. (2021). RNACache: Fast Mapping of RNA-Seq Reads to Transcriptomes Using MinHashing. 367-381. DOI
Kobus, R., Mueller, A., Juenger, D., et al. (2021). MetaCache-GPU: Ultra-Fast Metagenomic Classification. 50TH INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING. Published. DOI Author/Publisher URL
Kobus, R., Müller, A., Jünger, D., et al. (2021). MetaCache-GPU: Ultra-Fast Metagenomic Classification.

2020

Juenger, D., Kobus, R., Mueller, A., et al. (2020). WarpCore: A Library for fast Hash Tables on GPUs. 2020 IEEE 27TH INTERNATIONAL CONFERENCE ON HIGH PERFORMANCE COMPUTING, DATA, AND ANALYTICS (HIPC 2020), 11-20. DOI Author/Publisher URL
Jünger, D., Kobus, R., Müller, A., et al. (2020). WarpCore: A Library for fast Hash Tables on GPUs. CoRR, abs/2009.07914.
Kobus, R., Abuin, J. M., Mueller, A., et al. (2020). A big data approach to metagenomics for all-food-sequencing. BMC BIOINFORMATICS, 21(1). DOI Author/Publisher URL
Müller, A., Schmidt, B., Hildebrandt, A., et al. (2020). AnySeq: A High Performance Sequence Alignment Library based on Partial Evaluation. arXiv preprint arXiv:2002.04561.
Müller, A., Schmidt, B., Hildebrandt, A., et al. (2020). AnySeq: A High Performance Sequence Alignment Library based on Partial Evaluation. IPDPS, 1030-1040. Author/Publisher URL
Niebler, S., Mueller, A., Hankeln, T., Schmidt, B. (2020). RainDrop: Rapid activation matrix computation for droplet-based single-cell RNA-seq reads. BMC BIOINFORMATICS, 21(1). DOI Author/Publisher URL

2019

Yin, Z., Zhang, T., Muller, A., et al. (2019). Efficient Parallel Sort on AVX-512-Based Multi-Core and Many-Core Architectures. 2019 IEEE 21st International Conference on High Performance Computing and Communications; IEEE 17th International Conference on Smart City; IEEE 5th International Conference on Data Science and Systems (HPCC/SmartCity/DSS), 12, 168-176. DOI

2018

Leißa, R., Boesche, K., Hack, S., et al. (2018). AnyDSL: a partial evaluation framework for programming high-performance libraries. Proceedings of the ACM on Programming Languages, 2(OOPSLA), 1-30. DOI
Kobus, R., Lamoth, A., Müller, A., et al. (2018). cuBool: bit-parallel Boolean Matrix Factorization on CUDA-enabled accelerators. Seiten: 465-472. Author/Publisher URL
Leissa, R., Boesche, K., Hack, S., et al. (2018). AnyDSL: A Partial Evaluation Framework for Programming High-Performance Libraries. PROCEEDINGS OF THE ACM ON PROGRAMMING LANGUAGES-PACMPL, 2. DOI Author/Publisher URL

2017

Kobus, R., Hundt, C., Müller, A., Schmidt, B. (2017). Accelerating metagenomic read classification on CUDA-enabled GPUs. BMC Bioinformatics, 18(11), 10 S. Author/Publisher URL
Müller, A., Hundt, C., Hildebrandt, A., et al. (2017). MetaCache: context-aware classification of metagenomic reads using minhashing. Bioinformatics, 33, 3740-3748.

2009

Mueller, A., Schneider, J. J., and Schoemer, E. (2009). Packing a multidisperse system of hard disks in a circular environment. PHYSICAL REVIEW E, 79(2). DOI Author/Publisher URL
Schneider, J. J., Mueller, A., and Schoemer, E. (2009). Ultrametricity property of energy landscapes of multidisperse packing problems. PHYSICAL REVIEW E, 79(3). DOI Author/Publisher URL