arXiv subjects

Michael P. O'Brien

Publications and source records attributed to Michael P. O'Brien.

7 recordsLinked to original sources

arXiv2018

Polynomial Treedepth Bounds in Linear Colorings

Low-treedepth colorings are an important tool for algorithms that exploit structure in classes of bounded expansion; they guarantee subgraphs that use few colors have bounded treedepth. These colorings have an implicit tradeoff between the total number of colors used and the treedepth bound, and prior empirical work suggests that the former dominates the run time of existing algorithms in practice. We introduce $p$-linear colorings as an alternative to the commonly used $p$-centered colorings. They can be efficiently computed in bounded expansion classes and use at most as many colors as $p$-centered colorings. Although a set of $k<p$ colors from a $p$-centered coloring induces a subgraph of treedepth at most $k$, the same number of colors from a $p$-linear coloring may induce subgraphs of larger treedepth. We establish a polynomial upper bound on the treedepth in general graphs, and give tighter bounds in trees and interval graphs via constructive coloring algorithms. We also give a co-NP-completeness reduction for recognizing $p$-linear colorings and discuss ways to overcome this limitation in practice. This preprint extends results that appeared in [9]; for full proofs omitted from [9], see previous versions of this preprint.

cs.DS↗

arXiv2018

An Experimental Evaluation of a Bounded Expansion Algorithmic Pipeline

Previous work has suggested that the structural restrictions of graphs from classes of bounded expansion--locally dense pockets in a globally sparse graph--naturally coincide with common properties of real-world networks such as clustering and heavy-tailed degree distributions. As such, fixed-parameter tractable algorithms for bounded expansion classes may offer a promising framework for network analysis where other approaches have struggled to scale. However, there has been little work done in implementing and evaluating the performance of these structure-based algorithms. To this end we introduce CONCUSS, a proof-of-concept implementation of a generic algorithmic pipeline for classes of bounded expansion. In particular, we focus on using CONCUSS for subgraph isomorphism counting (also called motif or graphlet counting), which has been used extensively as a tool for analyzing biological and social networks. Through a broad set of experiments we first evaluate the interactions between implementation/engineering choices at multiple stages of the pipeline and their effects on overall run time. From there, we establish viability of the bounded expansion framework by demonstrating that in some scenarios CONCUSS achieves run times competitive with a popular algorithm for subgraph isomorphism counting that does not exploit graph structure. Finally, we empirically identify two particular ways in which future theoretical advances could alleviate bottlenecks in the algorithmic pipeline.

cs.DS↗

arXiv2017

A practical fpt algorithm for Flow Decomposition and transcript assembly

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.

cs.DS↗

arXiv2017

Being even slightly shallow makes life hard

We study the computational complexity of identifying dense substructures, namely $r/2$-shallow topological minors and $r$-subdivisions. Of particular interest is the case when $r=1$, when these substructures correspond to very localized relaxations of subgraphs. Since Densest Subgraph can be solved in polynomial time, we ask whether these slight relaxations also admit efficient algorithms. In the following, we provide a negative answer: Dense $r/2$-Shallow Topological Minor and Dense $r$-Subdivsion are already NP-hard for $r = 1$ in very sparse graphs. Further, they do not admit algorithms with running time $2^{o(\mathbf{tw}^2)} n^{O(1)}$ when parameterized by the treewidth of the input graph for $r \geq 2$ unless ETH fails.

cs.CC↗

arXiv2016

Asymptotic Analysis of Equivalences and Core-Structures in Kronecker-Style Graph Models

Growing interest in modeling large, complex networks has spurred significant research into generative graph models. Kronecker-style models (SKG and R-MAT) are often used due to their scalability and ability to mimic key properties of real-world networks. Although a few papers theoretically establish these models' behavior for specific parameters, many claims used to justify their use are supported only empirically. In this work, we prove several results using asymptotic analysis which illustrate that empirical studies may not fully capture the true behavior of the models. Paramount to the widespread adoption of Kronecker-style models was the introduction of a linear-time edge-sampling variant (R-MAT), which existing literature typically treats as interchangeable with SKG. We prove that although several R-MAT formulations are asymptotically equivalent, their behavior diverges from that of SKG. Further, we show these results are observable even at relatively small graph sizes. Second, we consider a case where asymptotic analysis reveals unexpected behavior within a given model.

cs.SI↗

arXiv2014

Locally Estimating Core Numbers

Graphs are a powerful way to model interactions and relationships in data from a wide variety of application domains. In this setting, entities represented by vertices at the "center" of the graph are often more important than those associated with vertices on the "fringes". For example, central nodes tend to be more critical in the spread of information or disease and play an important role in clustering/community formation. Identifying such "core" vertices has recently received additional attention in the context of {\em network experiments}, which analyze the response when a random subset of vertices are exposed to a treatment (e.g. inoculation, free product samples, etc). Specifically, the likelihood of having many central vertices in any exposure subset can have a significant impact on the experiment. We focus on using $k$-cores and core numbers to measure the extent to which a vertex is central in a graph. Existing algorithms for computing the core number of a vertex require the entire graph as input, an unrealistic scenario in many real world applications. Moreover, in the context of network experiments, the subgraph induced by the treated vertices is only known in a probabilistic sense. We introduce a new method for estimating the core number based only on the properties of the graph within a region of radius $δ$ around the vertex, and prove an asymptotic error bound of our estimator on random graphs. Further, we empirically validate the accuracy of our estimator for small values of $δ$ on a representative corpus of real data sets. Finally, we evaluate the impact of improved local estimation on an open problem in network experimentation posed by Ugander et al.

cs.SI↗

arXiv2014

Zig-Zag Numberlink is NP-Complete

When can $t$ terminal pairs in an $m \times n$ grid be connected by $t$ vertex-disjoint paths that cover all vertices of the grid? We prove that this problem is NP-complete. Our hardness result can be compared to two previous NP-hardness proofs: Lynch's 1975 proof without the ``cover all vertices'' constraint, and Kotsuma and Takenaga's 2010 proof when the paths are restricted to have the fewest possible corners within their homotopy class. The latter restriction is a common form of the famous Nikoli puzzle \emph{Numberlink}; our problem is another common form of Numberlink, sometimes called \emph{Zig-Zag Numberlink} and popularized by the smartphone app \emph{Flow Free}.

cs.CC↗