We develop a framework for generalizing approximation algorithms from the structural graph algorithm literature so that they apply to graphs somewhat close to that class (a scenario we expect is common when working with real-world networks) while still guaranteeing approximation ratios. The idea is to edit a given graph via vertex- or edge-deletions to put the graph into an algorithmically tractable class, apply known approximation algorithms for that class, and then lift the solution to apply to the original graph. We give a general characterization of when an optimization problem is amenable to this approach, and show that it includes many well-studied graph problems, such as Independent Set, Vertex Cover, Feedback Vertex Set, Minimum Maximal Matching, Chromatic Number, (l-)Dominating Set, Edge (l-)Dominating Set, and Connected Dominating Set. To enable this framework, we develop new editing algorithms that find the approximately-fewest edits required to bring a given graph into one of a few important graph classes (in some cases these are bicriteria algorithms which simultaneously approximate both the number of editing operations and the target parameter of the family). For bounded degeneracy, we obtain an O(r log{n})-approximation and a bicriteria (4,4)-approximation which also extends to a smoother bicriteria trade-off. For bounded treewidth, we obtain a bicriteria (O(log^{1.5} n), O(sqrt{log w}))-approximation, and for bounded pathwidth, we obtain a bicriteria (O(log^{1.5} n), O(sqrt{log w} * log n))-approximation. For treedepth 2 (related to bounded expansion), we obtain a 4-approximation. We also prove complementary hardness-of-approximation results assuming P != NP: in particular, these problems are all log-factor inapproximable, except the last which is not approximable below some constant factor 2 (assuming UGC).

Many common graph data mining tasks take the form of identifying dense subgraphs (e.g. clustering, clique-finding, etc). In biological applications, the natural model for these dense substructures is often a complete bipartite graph (biclique), and the problem requires enumerating all maximal bicliques (instead of identifying just the largest or densest). The best known algorithm in general graphs is due to Dias et al., and runs in time O(M|V|4), where M is the number of maximal induced bicliques (MIBs) in the graph. When the graph being searched is itself bipartite, Zhang et al. give a faster algorithm where the time per MIB depends on the number of edges in the graph. In this work, we present a new algorithm for enumerating MIBs in general graphs, whose run time depends on how “close to bipartite” the input is. Specifically, the runtime is parameterized by the size k of an odd cycle transversal (OCT), a vertex set whose deletion results in a bipartite graph. Our algorithm runs in time O(M|V‖E|k23k/3), which is an improvement on Dias et al. whenever k ≤ 3 log3 |V|. We implement our algorithm alongside a variant of Dias et al.'s in open-source C++ code, and experimentally verify that the OCT-based approach is faster in practice on graphs with a wide variety of sizes, densities, and OCT decompositions.

The Flow Decomposition problem, which asks for the smallest set of weighted paths that “covers” a flow on a DAG, has recently been used as an important computational step in transcript assembly. We prove the problem is in FPT when parameterized by the number of paths by giving a practical linear fpt algorithm. Further, we implement and engineer a Flow Decomposition solver based on this algorithm, and evaluate its performance on RNA-sequence data. Crucially, our solver finds exact solutions while achieving runtimes competitive with a state-of-the-art heuristic. Finally, we contextualize our design choices with two hardness results related to preprocessing and weight recovery. Specifically, k-Flow Decomposition does not admit polynomial kernels under standard complexity assumptions, and the related problem of assigning (known) weights to a given set of paths is NP-hard.

Large graphs arise in a number of contexts and understanding their structure and extracting information from them is an important research area. Early algorithms for mining communities have focused on global graph structure, and often run in time proportional to the size of the entire graph. As we explore networks with millions of vertices and find communities of size in the hundreds, it becomes important to shift our attention from macroscopic structure to microscopic structure in large networks. A growing body of work has been adopting local expansion methods in order to identify communities from a few exemplary seed members. In this article, we propose a novel approach for finding overlapping communities called L emon ( L ocal E xpansion via M inimum O ne N orm). Provided with a few known seeds , the algorithm finds the community by performing a local spectral diffusion. The core idea of L emon is to use short random walks to approximate an invariant subspace near a seed set, which we refer to as local spectra . Local spectra can be viewed as the low-dimensional embedding that captures the nodes’ closeness in the local network structure. We show that L emon ’s performance in detecting communities is competitive with state-of-the-art methods. Moreover, the running time scales with the size of the community rather than that of the entire graph. The algorithm is easy to implement and is highly parallelizable. We further provide theoretical analysis of the local spectral properties, bounding the measure of tightness of extracted community using the eigenvalues of graph Laplacian. We thoroughly evaluate our approach using both synthetic and real-world datasets across different domains, and analyze the empirical variations when applying our method to inherently different networks in practice. In addition, the heuristics on how the seed set quality and quantity would affect the performance are provided.

MOTIVATION: Diffusion-based network models are widely used for protein function prediction using protein network data and have been shown to outperform neighborhood-based and module-based methods. Recent studies have shown that integrating the hierarchical structure of the Gene Ontology (GO) data dramatically improves prediction accuracy. However, previous methods usually either used the GO hierarchy to refine the prediction results of multiple classifiers, or flattened the hierarchy into a function-function similarity kernel. No study has taken the GO hierarchy into account together with the protein network as a two-layer network model. RESULTS: We first construct a Bi-relational graph (Birg) model comprised of both protein-protein association and function-function hierarchical networks. We then propose two diffusion-based methods, BirgRank and AptRank, both of which use PageRank to diffuse information on this two-layer graph model. BirgRank is a direct application of traditional PageRank with fixed decay parameters. In contrast, AptRank utilizes an adaptive diffusion mechanism to improve the performance of BirgRank. We evaluate the ability of both methods to predict protein function on yeast, fly and human protein datasets, and compare with four previous methods: GeneMANIA, TMC, ProteinRank and clusDCA. We design four different validation strategies: missing function prediction, de novo function prediction, guided function prediction and newly discovered function prediction to comprehensively evaluate predictability of all six methods. We find that both BirgRank and AptRank outperform the previous methods, especially in missing function prediction when using only 10% of the data for training. AVAILABILITY AND IMPLEMENTATION: The MATLAB code is available at https://github.rcac.purdue.edu/mgribsko/aptrank . CONTACT: [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The heat kernel is a type of graph diffusion that, like the much-used personalized PageRank diffusion, is useful in identifying a community nearby a starting seed node. We present the first deterministic, local algorithm to compute this diffusion and use that algorithm to study the communities that it produces. Our algorithm is formally a relaxation method for solving a linear system to estimate the matrix exponential in a degree-weighted norm. We prove that this algorithm stays localized in a large graph and has a worst-case constant runtime that depends only on the parameters of the diffusion, not the size of the graph. On large graphs, our experiments indicate that the communities produced by this method have better conductance than those produced by PageRank, although they take slightly longer to compute. On a real-world community identification task, the heat kernel communities perform better than those from the PageRank diffusion.