JGraphT -- A Java library for graph data structures and algorithms

Mathematical software and graph-theoretical algorithmic packages to efficiently model, analyze and query graphs are crucial in an era where large-scale spatial, societal and economic network data are abundantly available. One such package is JGraphT, a programming library which contains very efficient and generic graph data-structures along with a large collection of state-of-the-art algorithms. The library is written in Java with stability, interoperability and performance in mind. A distinctive feature of this library is the ability to model vertices and edges as arbitrary objects, thereby permitting natural representations of many common networks including transportation, social and biological networks. Besides classic graph algorithms such as shortest-paths and spanning-tree algorithms, the library contains numerous advanced algorithms: graph and subgraph isomorphism; matching and flow problems; approximation algorithms for NP-hard problems such as independent set and TSP; and several more exotic algorithms such as Berge graph detection. Due to its versatility and generic design, JGraphT is currently used in large-scale commercial, non-commercial and academic research projects. In this work we describe in detail the design and underlying structure of the library, and discuss its most important features and algorithms. A computational study is conducted to evaluate the performance of JGraphT versus a number of similar libraries. Experiments on a large number of graphs over a variety of popular algorithms show that JGraphT is highly competitive with other established libraries such as NetworkX or the BGL.Comment: Major Revisio

Algorithms for the Maximum Independent Set Problem

This thesis focuses mainly on the Maximum Independent Set (MIS) problem. Some related graph theoretical combinatorial problems are also considered. As these problems are generally NP-hard, we study their complexity in hereditary graph classes, i.e. graph classes defined by a set F of forbidden induced subgraphs. We revise the literature about the issue, for example complexity results, applications, and techniques tackling the problem. Through considering some general approach, we exhibit several cases where the problem admits a polynomial-time solution. More specifically, we present polynomial-time algorithms for the MIS problem in: + some subclasses of $S_{2;j;k}$-free graphs (thus generalizing the classical result for $S_{1;2;k}$-free graphs); + some subclasses of $tree_{k}$-free graphs (thus generalizing the classical results for subclasses of P5-free graphs); + some subclasses of $P_{7}$-free graphs and $S_{2;2;2}$-free graphs; and various subclasses of graphs of bounded maximum degree, for example subcubic graphs. Our algorithms are based on various approaches. In particular, we characterize augmenting graphs in a subclass of $S_{2;k;k}$-free graphs and a subclass of $S_{2;2;5}$-free graphs. These characterizations are partly based on extensions of the concept of redundant set [125]. We also propose methods finding augmenting chains, an extension of the method in [99], and finding augmenting trees, an extension of the methods in [125]. We apply the augmenting vertex technique, originally used for $P_{5}$-free graphs or banner-free graphs, for some more general graph classes. We consider a general graph theoretical combinatorial problem, the so-called Maximum -Set problem. Two special cases of this problem, the so-called Maximum F-(Strongly) Independent Subgraph and Maximum F-Induced Subgraph, where F is a connected graph set, are considered. The complexity of the Maximum F-(Strongly) Independent Subgraph problem is revised and the NP-hardness of the Maximum F-Induced Subgraph problem is proved. We also extend the augmenting approach to apply it for the general Maximum Π -Set problem. We revise on classical graph transformations and give two unified views based on pseudo-boolean functions and αff-redundant vertex. We also make extensive uses of α-redundant vertices, originally mainly used for $P_{5}$-free graphs, to give polynomial solutions for some subclasses of $S_{2;2;2}$-free graphs and $tree_{k}$-free graphs. We consider some classical sequential greedy heuristic methods. We also combine classical algorithms with αff-redundant vertices to have new strategies of choosing the next vertex in greedy methods. Some aspects of the algorithms, for example forbidden induced subgraph sets and worst case results, are also considered. Finally, we restrict our attention on graphs of bounded maximum degree and subcubic graphs. Then by using some techniques, for example ff-redundant vertex, clique separator, and arguments based on distance, we general these results for some subclasses of $S_{i;j;k}$-free subcubic graphs

Performance Guarantees for Distributed Reachability Queries

In the real world a graph is often fragmented and distributed across different sites. This highlights the need for evaluating queries on distributed graphs. This paper proposes distributed evaluation algorithms for three classes of queries: reachability for determining whether one node can reach another, bounded reachability for deciding whether there exists a path of a bounded length between a pair of nodes, and regular reachability for checking whether there exists a path connecting two nodes such that the node labels on the path form a string in a given regular expression. We develop these algorithms based on partial evaluation, to explore parallel computation. When evaluating a query Q on a distributed graph G, we show that these algorithms possess the following performance guarantees, no matter how G is fragmented and distributed: (1) each site is visited only once; (2) the total network traffic is determined by the size of Q and the fragmentation of G, independent of the size of G; and (3) the response time is decided by the largest fragment of G rather than the entire G. In addition, we show that these algorithms can be readily implemented in the MapReduce framework. Using synthetic and real-life data, we experimentally verify that these algorithms are scalable on large graphs, regardless of how the graphs are distributed.Comment: VLDB201

Efficient training algorithms for HMMs using incremental estimation

Typically, parameter estimation for a hidden Markov model (HMM) is performed using an expectation-maximization (EM) algorithm with the maximum-likelihood (ML) criterion. The EM algorithm is an iterative scheme that is well-defined and numerically stable, but convergence may require a large number of iterations. For speech recognition systems utilizing large amounts of training material, this results in long training times. This paper presents an incremental estimation approach to speed-up the training of HMMs without any loss of recognition performance. The algorithm selects a subset of data from the training set, updates the model parameters based on the subset, and then iterates the process until convergence of the parameters. The advantage of this approach is a substantial increase in the number of iterations of the EM algorithm per training token, which leads to faster training. In order to achieve reliable estimation from a small fraction of the complete data set at each iteration, two training criteria are studied; ML and maximum a posteriori (MAP) estimation. Experimental results show that the training of the incremental algorithms is substantially faster than the conventional (batch) method and suffers no loss of recognition performance. Furthermore, the incremental MAP based training algorithm improves performance over the batch versio