Now showing 1 - 6 of 6
  • Publication
    A generalized Weisfeiler-Lehman graph kernel
    ( 2022-04-27)
    Schulz, Till Hendrik
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    Welke, Pascal
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    After more than one decade, Weisfeiler-Lehman graph kernels are still among the most prevalent graph kernels due to their remarkable predictive performance and time complexity. They are based on a fast iterative partitioning of vertices, originally designed for deciding graph isomorphism with one-sided error. The Weisfeiler-Lehman graph kernels retain this idea and compare such labels with respect to equality. This binary valued comparison is, however, arguably too rigid for defining suitable graph kernels for certain graph classes. To overcome this limitation, we propose a generalization of Weisfeiler-Lehman graph kernels which takes into account a more natural and finer grade of similarity between Weisfeiler-Lehman labels than equality. We show that the proposed similarity can be calculated efficiently by means of the Wasserstein distance between certain vectors representing Weisfeiler-Lehman labels. This and other facts give rise to the natural choice of partitioning the vertices with the Wasserstein k-means algorithm. We empirically demonstrate on the Weisfeiler-Lehman subtree kernel, which is one of the most prominent Weisfeiler-Lehman graph kernels, that our generalization significantly outperforms this and other state-of-the-art graph kernels in terms of predictive performance on datasets which contain structurally more complex graphs beyond the typically considered molecular graphs.
  • Publication
    Decision Snippet Features
    ( 2021)
    Welke, Pascal
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    Alkhoury, Fouad
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    Decision trees excel at interpretability of their prediction results. To achieve required prediction accuracies, however, often large ensembles of decision trees random forests are considered, reducing interpretability due to large size. Additionally, their size slows down inference on modern hardware and restricts their applicability in low-memory embedded devices. We introduce Decision Snippet Features, which are obtained from small subtrees that appear frequently in trained random forests. We subsequently show that linear models on top of these features achieve comparable and sometimes even better predictive performance than the original random forest, while reducing the model size by up to two orders of magnitude.
  • Publication
    HOPS: Probabilistic Subtree Mining for Small and Large Graphs
    ( 2020)
    Welke, Pascal
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    Seiffarth, Florian
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    Kamp, Michael
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    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
    Mining Tree Patterns with Partially Injective Homomorphisms
    ( 2019)
    Schulz, Till Hendrik
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    Welke, Pascal
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    One of the main differences between inductive logic programming (ILP) and graph mining lies in the pattern matching operator applied: While it is mainly defined by relational homomorphism (i.e., subsumption) in ILP, subgraph isomorphism is the most common pattern matching operator in graph mining. Using the fact that subgraph isomorphisms are injective homomorphisms, we bridge the gap between ILP and graph mining by considering a natural transition from homomorphisms to subgraph isomorphisms that is defined by partially injective homomorphisms, i.e., which require injectivity only for subsets of the vertex pairs in the pattern. Utilizing positive complexity results on deciding homomorphisms from bounded tree-width graphs, we present an algorithm mining frequent trees from arbitrary graphs w.r.t. partially injective homomorphisms. Our experimental results show that the predictive performance of the patterns obtained is comparable to that of ordinary frequent subgraphs. Thus, by preserving much from the advantageous properties of homomorphisms and subgraph isomorphisms, our approach provides a trade-off between efficiency and predictive power.
  • Publication
    Probabilistic and exact frequent subtree mining in graphs beyond forests
    ( 2019)
    Welke, Pascal
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    Motivated by the impressive predictive power of simple patterns, we consider the problem of mining frequent subtrees in arbitrary graphs. Although the restriction of the pattern language to trees does not resolve the computational complexity of frequent subgraph mining, in a recent work we have shown that it gives rise to an algorithm generating probabilistic frequent subtrees, a random subset of all frequent subtrees, from arbitrary graphs with polynomial delay. It is based on replacing each transaction graph in the input database with a forest formed by a random subset of its spanning trees. This simple technique turned out to be quite powerful on molecule classification tasks. It has, however, the drawback that the number of sampled spanning trees must be bounded by a polynomial of the size of the transaction graphs, resulting in less impressive recall even for slightly more complex structures beyond molecular graphs. To overcome this limitation, in this work we propose an algorithm mining probabilistic frequent subtrees also with polynomial delay, but by replacing each graph with a forest formed by an exponentially large implicit subset of its spanning trees. We demonstrate the superiority of our algorithm over the simple one on threshold graphs used e.g. in spectral clustering. In addition, providing sufficient conditions for the completeness and efficiency of our algorithm, we obtain a positive complexity result on exact frequent subtree mining for a novel, practically and theoretically relevant graph class that is orthogonal to all graph classes defined by some constant bound on monotone graph properties.
  • Publication
    Probabilistic frequent subtrees for efficient graph classification and retrieval
    ( 2018)
    Welke, Pascal
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    Frequent subgraphs proved to be powerful features for graph classification and prediction tasks. Their practical use is, however, limited by the computational intractability of pattern enumeration and that of graph embedding into frequent subgraph feature spaces. We propose a simple probabilistic technique that resolves both limitations. In particular, we restrict the pattern language to trees and relax the demand on the completeness of the mining algorithm, as well as on the correctness of the pattern matching operator by replacing transaction and query graphs with small random samples of their spanning trees. In this way we consider only a random subset of frequent subtrees, called probabilistic frequent subtrees, that can be enumerated efficiently. Our extensive empirical evaluation on artificial and benchmark molecular graph datasets shows that probabilistic frequent subtrees can be listed in practically feasible time and that their predictive and retrieval performance is very close even to those of complete sets of frequent subgraphs. We also present different fast techniques for computing the embedding of unseen graphs into (probabilistic frequent) subtree feature spaces. These algorithms utilize the partial order on tree patterns induced by subgraph isomorphism and, as we show empirically, require much less evaluations of subtree isomorphism than the standard brute-force algorithm. We also consider partial embeddings, i.e., when only a part of the feature vector has to be calculated. In particular, we propose a highly effective practical algorithm that significantly reduces the number of pattern matching evaluations required by the classical min-hashing algorithm approximating Jaccard-similarities.