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Jonas Fischer

Jonas Fischer

Max-Planck-Institut für Informatik
D5: Databases and Information Systems
Exploratory Data Analysis
 office: E1 7, Room 3.04
Saarland Informatics Campus
66123 Saarbrücken
Germany
 email: Get my email address via email

Research Interests

  • Pattern and Rule mining
  • Interpretable explanations of neural networks
  • Pruning neural networks (Lottery Ticket Hypothesis)
  • Low dimensional embeddings
  • Algorithmic Bioinformatics (read alignment in NGS)
  • Computational Epigenetics

Publications

  • Fischer, J, Burkholz, R, Plant 'n' Seek: Can You Find the Winning Ticket? preprint: arXiv:2111.11153, 2021

  • Marx, A, Fischer, J, Estimating Mutual Information via Geodesic kNN. preprint: arXiv:2110.13883, 2021

  • Hedderich, M*, Fischer, J*, Klakow, D, Vreeken, J, Label-Descriptive Patterns and their Application to Characterizing Classification Errors. preprint: arXiv:2110.09599, 2021

  • Fischer, J, Burkholz, R, Towards strong pruning for lottery tickets with non-zero biases. preprint: arXiv:2110.11150, 2021

  • Kamp, M, Fischer, J, Vreeken, J, Federated Learning from Small Datasets. preprint: arXiv:2110.03469, 2021

  • Fischer, J, Vreeken, J, Differentiable Pattern Set Mining. In: Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD'21), ACM, 2021. (15.4% acceptance rate)

  • Fischer, J, Oláh, A, Vreeken, J, What's in the Box? Explaining Neural Networks with Robust Rules. In: Proceedings of the International Conference on Machine Learning (ICML), PMLR, 2021. (21.4% acceptance rate)

  • Fischer, J, Ardakani, FB, Kattler, K, Walter, J, Schulz, MH, CpG content-dependent associations between transcription factors and histone modifications. Plos ONE 16(4): e0249985, 2021

  • Heiter, E, Fischer, J, Vreeken, J, Factoring out prior knowledge from low-dimensional embeddings. preprint: arXiv:2103.01828, 2021

  • Fischer, J, Vreeken, J, Discovering Succinct Pattern Sets Expressing Co-Occurrence and Mutual Exclusivity. In: Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD'20), ACM, 2020. (16.8% acceptance rate)

  • Fischer, J, Vreeken, J, Sets of Robust Rules, and How to Find Them In: Proceedings of the European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Data (ECMLPKDD), Springer, 2019. (17.7% acceptance rate) Selected plenary talk

  • Fischer, J, Schulz, MH, Fast and accurate bisulfite alignment and methylation calling for mammalian genomes. Talk at ISMB/ECCB, Basel, Switzerland, 2019.

  • Fischer, J, Schulz, MH, Fast and accurate bisulfite alignment and methylation calling for mammalian genomes. Short talk/poster at RECOMB-seq/RECOMB, Paris, France, 2018.

  • Ardakani, FB Kattler, K, Nordström, KJ, Gasparoni, N, Gasparoni, G, Fuchs, S, Sinha, A, Barann, M, Ebert, P, Fischer, J, Hutter, B, Zipprich, G, Imbusch, CD, Felder, B, Eils, J, Brors, B, Lengauer, T, Manke, T, Rosenstiel, P, Walter, J, Schulz, MH, Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters. Epigenetics & Chromatin 11(1): 66, 2018.

  • * equal contribution

Academic Activities

  • Teaching activity

    Elements of Statistical Learning, head TA (2019/2020), Information Retrieval and Data Mining, TA (2017/2018), Bioinformatics 2, TA (2015), Programming 2, TA (2014)

  • Reviewing activity

    Journals: Journal for Knowledge and Information Systems (KAIS), IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)

    Conferences: Advances in Neural InformationProcessing Systems (NeurIPS) 2018, 2019, ACM International Conference on Knowledge Discovery and Data Mining (SIGKDD) 2018, SIAM conference on data mining (SDM) 2021

  • PC for SIAM conference on data mining (SDM) 2021
  • Evaluator for ELLIS PhD Program candidates 2022

Education

  • Dec 2017 - present:

    PhD student in Computer Science at the Max-Planck-Institut für Informatik, Saarbrücken, Germany

  • Oct 2015 - Oct 2017:

    PhD preparatory phase of the Graduate School for Computer Sciene, Saarland University, Saarbrücken, Germany

    Master's degree in Bioinformatics (with Honors), Saarland University, Saarbrücken, Germany

  • Oct 2012 - Oct 2015:

    Bachelor's degree in Bioinformatics, Saarland University, Saarbrücken, Germany

  • 2012:

    Abitur, Stefan-George-Gymnasium, Bingen am Rhein, Germany