Mining Brain Networks using Multiple Side Views for Neurological Disorder Identification

Mining discriminative subgraph patterns from graph data has attracted great interest in recent years. It has a wide variety of applications in disease diagnosis, neuroimaging, etc. Most research on subgraph mining focuses on the graph representation alone. However, in many real-world applications, the side information is available along with the graph data. For example, for neurological disorder identification, in addition to the brain networks derived from neuroimaging data, hundreds of clinical, immunologic, serologic and cognitive measures may also be documented for each subject. These measures compose multiple side views encoding a tremendous amount of supplemental information for diagnostic purposes, yet are often ignored. In this paper, we study the problem of discriminative subgraph selection using multiple side views and propose a novel solution to find an optimal set of subgraph features for graph classification by exploring a plurality of side views. We derive a feature evaluation criterion, named gSide, to estimate the usefulness of subgraph patterns based upon side views. Then we develop a branch-and-bound algorithm, called gMSV, to efficiently search for optimal subgraph features by integrating the subgraph mining process and the procedure of discriminative feature selection. Empirical studies on graph classification tasks for neurological disorders using brain networks demonstrate that subgraph patterns selected by the multi-side-view guided subgraph selection approach can effectively boost graph classification performances and are relevant to disease diagnosis.Comment: in Proceedings of IEEE International Conference on Data Mining (ICDM) 201

Mining Representative Unsubstituted Graph Patterns Using Prior Similarity Matrix

One of the most powerful techniques to study protein structures is to look for recurrent fragments (also called substructures or spatial motifs), then use them as patterns to characterize the proteins under study. An emergent trend consists in parsing proteins three-dimensional (3D) structures into graphs of amino acids. Hence, the search of recurrent spatial motifs is formulated as a process of frequent subgraph discovery where each subgraph represents a spatial motif. In this scope, several efficient approaches for frequent subgraph discovery have been proposed in the literature. However, the set of discovered frequent subgraphs is too large to be efficiently analyzed and explored in any further process. In this paper, we propose a novel pattern selection approach that shrinks the large number of discovered frequent subgraphs by selecting the representative ones. Existing pattern selection approaches do not exploit the domain knowledge. Yet, in our approach we incorporate the evolutionary information of amino acids defined in the substitution matrices in order to select the representative subgraphs. We show the effectiveness of our approach on a number of real datasets. The results issued from our experiments show that our approach is able to considerably decrease the number of motifs while enhancing their interestingness

Significant Subgraph Mining with Multiple Testing Correction

The problem of finding itemsets that are statistically significantly enriched in a class of transactions is complicated by the need to correct for multiple hypothesis testing. Pruning untestable hypotheses was recently proposed as a strategy for this task of significant itemset mining. It was shown to lead to greater statistical power, the discovery of more truly significant itemsets, than the standard Bonferroni correction on real-world datasets. An open question, however, is whether this strategy of excluding untestable hypotheses also leads to greater statistical power in subgraph mining, in which the number of hypotheses is much larger than in itemset mining. Here we answer this question by an empirical investigation on eight popular graph benchmark datasets. We propose a new efficient search strategy, which always returns the same solution as the state-of-the-art approach and is approximately two orders of magnitude faster. Moreover, we exploit the dependence between subgraphs by considering the effective number of tests and thereby further increase the statistical power.Comment: 18 pages, 5 figure, accepted to the 2015 SIAM International Conference on Data Mining (SDM15

ProtNN: Fast and Accurate Nearest Neighbor Protein Function Prediction based on Graph Embedding in Structural and Topological Space

Studying the function of proteins is important for understanding the molecular mechanisms of life. The number of publicly available protein structures has increasingly become extremely large. Still, the determination of the function of a protein structure remains a difficult, costly, and time consuming task. The difficulties are often due to the essential role of spatial and topological structures in the determination of protein functions in living cells. In this paper, we propose ProtNN, a novel approach for protein function prediction. Given an unannotated protein structure and a set of annotated proteins, ProtNN finds the nearest neighbor annotated structures based on protein-graph pairwise similarities. Given a query protein, ProtNN finds the nearest neighbor reference proteins based on a graph representation model and a pairwise similarity between vector embedding of both query and reference protein-graphs in structural and topological spaces. ProtNN assigns to the query protein the function with the highest number of votes across the set of k nearest neighbor reference proteins, where k is a user-defined parameter. Experimental evaluation demonstrates that ProtNN is able to accurately classify several datasets in an extremely fast runtime compared to state-of-the-art approaches. We further show that ProtNN is able to scale up to a whole PDB dataset in a single-process mode with no parallelization, with a gain of thousands order of magnitude of runtime compared to state-of-the-art approaches

FS^3: A Sampling based method for top-k Frequent Subgraph Mining

Mining labeled subgraph is a popular research task in data mining because of its potential application in many different scientific domains. All the existing methods for this task explicitly or implicitly solve the subgraph isomorphism task which is computationally expensive, so they suffer from the lack of scalability problem when the graphs in the input database are large. In this work, we propose FS^3, which is a sampling based method. It mines a small collection of subgraphs that are most frequent in the probabilistic sense. FS^3 performs a Markov Chain Monte Carlo (MCMC) sampling over the space of a fixed-size subgraphs such that the potentially frequent subgraphs are sampled more often. Besides, FS^3 is equipped with an innovative queue manager. It stores the sampled subgraph in a finite queue over the course of mining in such a manner that the top-k positions in the queue contain the most frequent subgraphs. Our experiments on database of large graphs show that FS^3 is efficient, and it obtains subgraphs that are the most frequent amongst the subgraphs of a given size