Prof. Dr.

Wrobel, Stefan

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  • 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.
  • Publication
    Context-based clustering of image search results
    ( 2009)
    Wang, H.
    ;
    Missura, Olana
    ;
    Gärtner, Thomas
    ;
    Wrobel, Stefan
    In this work we propose to cluster image search results based on the textual contents of the referring webpages. The natural ambiguity and context-dependence of human languages lead to problems that plague modern image search engines: A user formulating a query usually has in mind just one topic, while the results produced to satisfy this query may (and usually do) belong to the different topics. Therefore, only part of the search results are relevant for a user. One of the possible ways to improve the user's experience is to cluster the results according to the topics they belong to and present the clustered results to the user. As opposed to the clustering based on visual features, an approach utilising the text information in the webpages containing the image is less computationally intensive and provides the resulting clusters with semantically meaningful names.