Prof. Dr.

Wrobel, Stefan

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  • Publication
    HOPS: Probabilistic Subtree Mining for Small and Large Graphs
    ( 2020)
    Welke, Pascal
    ;
    Seiffahrt, Florian
    ;
    Kamp, Michael
    ;
    Wrobel, Stefan
    Frequent subgraph mining, i.e., the identification of relevant patterns in graph databases, is a well-known data mining problem with high practical relevance, since next to summarizing the data, the resulting patterns can also be used to define powerful domain-specific similarity functions for prediction. In recent years, significant progress has been made towards subgraph mining algorithms that scale to complex graphs by focusing on tree patterns and probabilistically allowing a small amount of incompleteness in the result. Nonetheless, the complexity of the pattern matching component used for deciding subtree isomorphism on arbitrary graphs has significantly limited the scalability of existing approaches. In this paper, we adapt sampling techniques from mathematical combinatorics to the problem of probabilistic subtree mining in arbitrary databases of many small to medium-size graphs or a single large graph. By restricting on tree patterns, we provide an algorithm tha t approximately counts or decides subtree isomorphism for arbitrary transaction graphs in sub-linear time with one-sided error. Our empirical evaluation on a range of benchmark graph datasets shows that the novel algorithm substantially outperforms state-of-the-art approaches both in the task of approximate counting of embeddings in single large graphs and in probabilistic frequent subtree mining in large databases of small to medium sized graphs.
  • Publication
    Effcient Decentralized Deep Learning by Dynamic Model Averaging
    ( 2019)
    Kamp, Michael
    ;
    Adilova, Linara
    ;
    Sicking, Joachim
    ;
    Hüger, Fabian
    ;
    Schlicht, Peter
    ;
    Wirtz, Tim
    ;
    Wrobel, Stefan
    We propose an efficient protocol for decentralized training of deep neural networks from distributed data sources. The proposed protocol allows to handle different phases of model training equally well and to quickly adapt to concept drifts. This leads to a reduction of communication by an order of magnitude compared to periodically communicating state-of-the-art approaches. Moreover, we derive a communication bound that scales well with the hardness of the serialized learning problem. The reduction in communication comes at almost no cost, as the predictive performance remains virtually unchanged. Indeed, the proposed protocol retains loss bounds of periodically averaging schemes. An extensive empirical evaluation validates major improvement of the trade-off between model performance and communication which could be beneficial for numerous decentralized learning applications, such as autonomous driving, or voice recognition and image classification on mobile phones.
  • Publication
    Co-regularised support vector regression
    ( 2017)
    Ullrich, Katrin
    ;
    Kamp, Michael
    ;
    Gärtner, Thomas
    ;
    Vogt, Martin
    ;
    Wrobel, Stefan
    We consider a semi-supervised learning scenario for regression, where only few labelled examples, many unlabelled instances and different data representations (multiple views) are available. For this setting, we extend support vector regression with a co-regularisation term and obtain co-regularised support vector regression (CoSVR). In addition to labelled data, co-regularisation includes information from unlabelled examples by ensuring that models trained on different views make similar predictions. Ligand affinity prediction is an important real-world problem that fits into this scenario. The characterisation of the strength of protein-ligand bonds is a crucial step in the process of drug discovery and design. We introduce variants of the base CoSVR algorithm and discuss their theoretical and computational properties. For the CoSVR function class we provide a theoretical bound on the Rademacher complexity. Finally, we demonstrate the usefulness of CoSVR for the affinity prediction task and evaluate its performance empirically on different protein-ligand datasets. We show that CoSVR outperforms co-regularised least squares regression as well as existing state-of-the-art approaches for affinity prediction. Code and data related to this chapter are available at: https://doi.org/10.6084/m9.figshare.5427241.
  • Publication
    Ligand-based virtual screening with co-regularised support vector regression
    ( 2016)
    Ullrich, Katrin
    ;
    Kamp, Michael
    ;
    Gärtner, Thomas
    ;
    Vogt, Martin
    ;
    Wrobel, Stefan
    We consider the problem of ligand affinity prediction as a regression task, typically with few labelled examples, many unlabelled instances, and multiple views on the data. In chemoinformatics, the prediction of binding affinities for protein ligands is an important but also challenging task. As protein-ligand bonds trigger biochemical reactions, their characterisation is a crucial step in the process of drug discovery and design. However, the practical determination of ligand affinities is very expensive, whereas unlabelled compounds are available in abundance. Additionally, many different vectorial representations for compounds (molecular fingerprints) exist that cover different sets of features. To this task we propose to apply a co-regularisation approach, which extracts information from unlabelled examples by ensuring that individual models trained on different fingerprints make similar predictions. We extend support vector regression similarly to the existing co-regularised least squares regression (CoRLSR) and obtain a co-regularised support vector regression (CoSVR). We empirically evaluate the performance of CoSVR on various protein-ligand datasets. We show that CoSVR outperforms CoRLSR as well as existing state-of-the- art approaches that do not take unlabelled molecules into account. Additionally, we provide a theoretical bound on the Rademacher complexity for CoSVR.