arXiv subjects

Blair D. Sullivan

Publications and source records attributed to Blair D. Sullivan.

53 records · Page 3Linked to original sources

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

Optimizing Adiabatic Quantum Program Compilation using a Graph-Theoretic Framework

Adiabatic quantum computing has evolved in recent years from a theoretical field into an immensely practical area, a change partially sparked by D-Wave System's quantum annealing hardware. These multimillion-dollar quantum annealers offer the potential to solve optimization problems millions of times faster than classical heuristics, prompting researchers at Google, NASA and Lockheed Martin to study how these computers can be applied to complex real-world problems such as NASA rover missions. Unfortunately, compiling (embedding) an optimization problem into the annealing hardware is itself a difficult optimization problem and a major bottleneck currently preventing widespread adoption. Additionally, while finding a single embedding is difficult, no generalized method is known for tuning embeddings to use minimal hardware resources. To address these barriers, we introduce a graph-theoretic framework for developing structured embedding algorithms. Using this framework, we introduce a biclique virtual hardware layer to provide a simplified interface to the physical hardware. Additionally, we exploit bipartite structure in quantum programs using odd cycle transversal (OCT) decompositions. By coupling an OCT-based embedding algorithm with new, generalized reduction methods, we develop a new baseline for embedding a wide range of optimization problems into fault-free D-Wave annealing hardware. To encourage the reuse and extension of these techniques, we provide an implementation of the framework and embedding algorithms.

quant-ph↗

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↗

arXiv2017

Hyperbolicity, degeneracy, and expansion of random intersection graphs

We establish the conditions under which several algorithmically exploitable structural features hold for random intersection graphs, a natural model for many real-world networks where edges correspond to shared attributes. Specifically, we fully characterize the degeneracy of random intersection graphs, and prove that the model asymptotically almost surely produces graphs with hyperbolicity at least $\log{n}$. Further, we prove that in the parametric regime where random intersection graphs are degenerate an even stronger notion of sparseness, so called bounded expansion, holds with high probability. We supplement our theoretical findings with experimental evaluations of the relevant statistics.

cs.SI↗

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↗

arXiv2016

A Fast Parameterized Algorithm for Co-Path Set

The k-CO-PATH SET problem asks, given a graph G and a positive integer k, whether one can delete k edges from G so that the remainder is a collection of disjoint paths. We give a linear-time fpt algorithm with complexity O^*(1.588^k) for deciding k-CO-PATH SET, significantly improving the previously best known O^*(2.17^k) of Feng, Zhou, and Wang (2015). Our main tool is a new O^*(4^{tw(G)}) algorithm for CO-PATH SET using the Cut&Count framework, where tw(G) denotes treewidth. In general graphs, we combine this with a branching algorithm which refines a 6k-kernel into reduced instances, which we prove have bounded treewidth.

cs.DS↗

arXiv2016

Tree decompositions and social graphs

Recent work has established that large informatics graphs such as social and information networks have non-trivial tree-like structure when viewed at moderate size scales. Here, we present results from the first detailed empirical evaluation of the use of tree decomposition (TD) heuristics for structure identification and extraction in social graphs. Although TDs have historically been used in structural graph theory and scientific computing, we show that---even with existing TD heuristics developed for those very different areas---TD methods can identify interesting structure in a wide range of realistic informatics graphs. Our main contributions are the following: we show that TD methods can identify structures that correlate strongly with the core-periphery structure of realistic networks, even when using simple greedy heuristics; we show that the peripheral bags of these TDs correlate well with low-conductance communities (when they exist) found using local spectral computations; and we show that several types of large-scale "ground-truth" communities, defined by demographic metadata on the nodes of the network, are well-localized in the large-scale and/or peripheral structures of the TDs. Our other main contributions are the following: we provide detailed empirical results for TD heuristics on toy and synthetic networks to establish a baseline to understand better the behavior of the heuristics on more complex real-world networks; and we prove a theorem providing formal justification for the intuition that the only two impediments to low-distortion hyperbolic embedding are high tree-width and long geodesic cycles. Our results suggest future directions for improved TD heuristics that are more appropriate for realistic social graphs.

cs.DS↗

arXiv2015

On the Threshold of Intractability

We study the computational complexity of the graph modification problems Threshold Editing and Chain Editing, adding and deleting as few edges as possible to transform the input into a threshold (or chain) graph. In this article, we show that both problems are NP-complete, resolving a conjecture by Natanzon, Shamir, and Sharan (Discrete Applied Mathematics, 113(1):109--128, 2001). On the positive side, we show the problem admits a quadratic vertex kernel. Furthermore, we give a subexponential time parameterized algorithm solving Threshold Editing in $2^{O(\surd k \log k)} + \text{poly}(n)$ time, making it one of relatively few natural problems in this complexity class on general graphs. These results are of broader interest to the field of social network analysis, where recent work of Brandes (ISAAC, 2014) posits that the minimum edit distance to a threshold graph gives a good measure of consistency for node centralities. Finally, we show that all our positive results extend to the related problem of Chain Editing, as well as the completion and deletion variants of both problems.

cs.DS↗

arXiv2015

Multi-Level Anomaly Detection on Time-Varying Graph Data

This work presents a novel modeling and analysis framework for graph sequences which addresses the challenge of detecting and contextualizing anomalies in labelled, streaming graph data. We introduce a generalization of the BTER model of Seshadhri et al. by adding flexibility to community structure, and use this model to perform multi-scale graph anomaly detection. Specifically, probability models describing coarse subgraphs are built by aggregating probabilities at finer levels, and these closely related hierarchical models simultaneously detect deviations from expectation. This technique provides insight into a graph's structure and internal context that may shed light on a detected event. Additionally, this multi-scale analysis facilitates intuitive visualizations by allowing users to narrow focus from an anomalous graph to particular subgraphs or nodes causing the anomaly. For evaluation, two hierarchical anomaly detectors are tested against a baseline Gaussian method on a series of sampled graphs. We demonstrate that our graph statistics-based approach outperforms both a distribution-based detector and the baseline in a labeled setting with community structure, and it accurately detects anomalies in synthetic and real-world datasets at the node, subgraph, and graph levels. To illustrate the accessibility of information made possible via this technique, the anomaly detector and an associated interactive visualization tool are tested on NCAA football data, where teams and conferences that moved within the league are identified with perfect recall, and precision greater than 0.786.

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↗

arXiv2014

An Integrated Programming and Development Environment for Adiabatic Quantum Optimization

Adiabatic quantum computing is a promising route to the computational power afforded by quantum information processing. The recent availability of adiabatic hardware has raised challenging questions about how to evaluate adiabatic quantum optimization programs. Processor behavior depends on multiple steps to synthesize an adiabatic quantum program, which are each highly tunable. We present an integrated programming and development environment for adiabatic quantum optimization called JADE that provides control over all the steps taken during program synthesis. JADE captures the workflow needed to rigorously specify the adiabatic quantum optimization algorithm while allowing a variety of problem types, programming techniques, and processor configurations. We have also integrated JADE with a quantum simulation engine that enables program profiling using numerical calculation. The computational engine supports plug-ins for simulation methodologies tailored to various metrics and computing resources. We present the design, integration, and deployment of JADE and discuss its potential use for benchmarking adiabatic quantum optimization programs by the quantum computer science community.

quant-ph↗

arXiv2012

Adiabatic Quantum Programming: Minor Embedding With Hard Faults

Adiabatic quantum programming defines the time-dependent mapping of a quantum algorithm into an underlying hardware or logical fabric. An essential step is embedding problem-specific information into the quantum logical fabric. We present algorithms for embedding arbitrary instances of the adiabatic quantum optimization algorithm into a square lattice of specialized unit cells. These methods extend with fabric growth while scaling linearly in time and quadratically in footprint. We also provide methods for handling hard faults in the logical fabric without invoking approximations to the original problem, and illustrate their versatility through numerical studies of embeddabilty versus fault rates in square lattices of complete bipartite unit cells. The studies show these algorithms are more resilient to faulty fabrics than naive embedding approaches, a feature which should prove useful in benchmarking the adiabatic quantum optimization algorithm on existing faulty hardware.

quant-ph↗

arXiv2012

On a Conjecture of Andrica and Tomescu

Let S(n) be the integer sequence which is the coefficient of x^{n(n+1)/4} in the expansion of (1+x)(1+x^2), ..., (1+x^n) for positive integers n congruent to 0 or 3 mod 4. We prove a conjecture of Andrica and Tomescu that S(n) is asymptotic to \sqrt{6/π} 2^n n^{-3/2} as n approaches infinity.

math.CO↗

arXiv2012

Counting paths in digraphs

Say a digraph is k-free if it has no directed cycles of length at most k, for positive integers k. Thomasse conjectured that the number of induced 3-vertex directed paths in a simple 2-free digraph on n vertices is at most (n-1)n(n+1)/15. We present an unpublished result of Bondy proving that there are at most 2n^3/25 such paths, and prove that for the class of circular interval digraphs, an upper bound of n^3/16 holds. We also study the problem of bounding the number of (non-induced) 4-vertex paths in 3-free digraphs. We show an upper bound of 4n^4/75 using Bondy's result for Thomasse's conjecture.

math.CO↗

arXiv2007

Heights in finite projective space, and a problem on directed graphs

Let $\F_p = \Z/p\Z$. The \emph{height} of a point $\mathbf{a}=(a_1,..., a_d) \in \F_p^d$ is $h_p(\mathbf{a}) = \min \left\{\sum_{i=1}^d (ka_i \mod p) : k=1,...,p-1\right\}.$ Explicit formulas and estimates are obtained for the values of the height function in the case $d=2,$ and these results are applied to the problem of determining the minimum number of edges the must be deleted from a finite directed graph so that the resulting subgraph is acyclic.

math.NT↗

arXiv2007

Cycles in dense digraphs

Let G be a digraph (without parallel edges) such that every directed cycle has length at least four; let $β(G)$ denote the size of the smallest subset X in E(G) such that $G\X$ has no directed cycles, and let $γ(G)$ be the number of unordered pairs {u,v} of vertices such that u,v are nonadjacent in G. It is easy to see that if $γ(G) = 0$ then $β(G) = 0$; what can we say about $β(G)$ if $γ(G)$ is bounded? We prove that in general $β(G)$ is at most $γ(G)$. We conjecture that in fact $β(G)$ is at most $γ(G)/2$ (this would be best possible if true), and prove this conjecture in two special cases: 1. when V(G) is the union of two cliques, 2. when the vertices of G can be arranged in a circle such that if distinct u,v,w are in clockwise order and uw is a (directed) edge, then so are both uv and vw.

math.CO↗