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

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

Context-aware visual exploration of molecular databases

Facilitating the visual exploration of scientific data has received increasing attention in the past decade or so. Especially in life science related application areas the amount of available data has grown at a breath taking pace. In this paper we describe an approach that allows for visual inspection of large collections of molecular compounds. In contrast to classical visualizations of such spaces we incorporate a specific focus of analysis, for example the outcome of a biological experiment such as high throughout screening results. The presented method uses this experimental data to select molecular fragments of the underlying molecules that have interesting properties and uses the resulting space to generate a two dimensional map based on a singular value decomposition algorithm and a self organizing map. Experiments on real datasets show that the resulting visual landscape groups molecules of similar chemical properties in densely connected regions

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

Inductive queries for a drug designing robot scientist

It is increasingly clear that machine learning algorithms need to be integrated in an iterative scientific discovery loop, in which data is queried repeatedly by means of inductive queries and where the computer provides guidance to the experiments that are being performed. In this chapter, we summarise several key challenges in achieving this integration of machine learning and data mining algorithms in methods for the discovery of Quantitative Structure Activity Relationships (QSARs). We introduce the concept of a robot scientist, in which all steps of the discovery process are automated; we discuss the representation of molecular data such that knowledge discovery tools can analyse it, and we discuss the adaptation of machine learning and data mining algorithms to guide QSAR experiments

Reductions for Frequency-Based Data Mining Problems

Studying the computational complexity of problems is one of the - if not the - fundamental questions in computer science. Yet, surprisingly little is known about the computational complexity of many central problems in data mining. In this paper we study frequency-based problems and propose a new type of reduction that allows us to compare the complexities of the maximal frequent pattern mining problems in different domains (e.g. graphs or sequences). Our results extend those of Kimelfeld and Kolaitis [ACM TODS, 2014] to a broader range of data mining problems. Our results show that, by allowing constraints in the pattern space, the complexities of many maximal frequent pattern mining problems collapse. These problems include maximal frequent subgraphs in labelled graphs, maximal frequent itemsets, and maximal frequent subsequences with no repetitions. In addition to theoretical interest, our results might yield more efficient algorithms for the studied problems.Comment: This is an extended version of a paper of the same title to appear in the Proceedings of the 17th IEEE International Conference on Data Mining (ICDM'17

High performance subgraph mining in molecular compounds

Structured data represented in the form of graphs arises in several fields of the science and the growing amount of available data makes distributed graph mining techniques particularly relevant. In this paper, we present a distributed approach to the frequent subgraph mining problem to discover interesting patterns in molecular compounds. The problem is characterized by a highly irregular search tree, whereby no reliable workload prediction is available. We describe the three main aspects of the proposed distributed algorithm, namely a dynamic partitioning of the search space, a distribution process based on a peer-to-peer communication framework, and a novel receiver-initiated, load balancing algorithm. The effectiveness of the distributed method has been evaluated on the well-known National Cancer Institute’s HIV-screening dataset, where the approach attains close-to linear speedup in a network of workstations