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A block graph is a graph in which every block is a complete graph. Let $G$ be a block graph and let $A(G)$ be its (0,1)-adjacency matrix. Graph $G$ is called nonsingular (singular) if $A(G)$ is nonsingular (singular). Characterizing…
A linear graph is a graph whose vertices are totally ordered. Biological and linguistic sequences with interactions among symbols are naturally represented as linear graphs. Examples include protein contact maps, RNA secondary structures…
We present linear time {\it in-place} algorithms for several basic and fundamental graph problems including the well-known graph search methods (like depth-first search, breadth-first search, maximum cardinality search), connectivity…
The least squares linear filter, also called the Wiener filter, is a popular tool to predict the next element(s) of time series by linear combination of time-delayed observations. We consider observation sequences of deterministic dynamics,…
A Burling graph is an induced subgraph of some graph in Burling's construction of triangle-free high-chromatic graphs. Equivalently, a Burling graph is a graph that admits a so-called strict frame representation. We provide a…
We show how to solve a number of problems in numerical linear algebra, such as least squares regression, $\ell_p$-regression for any $p \geq 1$, low rank approximation, and kernel regression, in time $T(A) \poly(\log(nd))$, where for a…
A system of coupled oscillators on an arbitrary graph is locally driven by the tendency to mutual synchronization between nearby oscillators, but can and often exhibit nonlinear behavior on the whole graph. Understanding such nonlinear…
We present a linear time algorithm for the minimum linear arrangement problem on proper interval graphs. The obtained ordering is a 4-approximation for general interval graphs
Intersection graphs are well-studied in the area of graph algorithms. Some intersection graph classes are known to have algorithms enumerating all unlabeled graphs by reverse search. Since these algorithms output graphs one by one and the…
An interval graph is considered improper if and only if it has a representation such that an interval contains another interval. Previously these have been investigated in terms of balance and minimal forbidden interval subgraphs for the…
We present algorithms that run in linear time on pointer machines for a collection of problems, each of which either directly or indirectly requires the evaluation of a function defined on paths in a tree. These problems previously had…
This paper deals with the problem of finding, for a given graph and a given natural number k, a subgraph of k nodes with a maximum number of edges. This problem is known as the k-cluster problem and it is NP-hard on general graphs as well…
A Helly circular-arc graph is the intersection graph of a set of arcs on a circle having the Helly property. We introduce essential obstacles, which are a refinement of the notion of obstacles, and prove that essential obstacles are…
A fundamental algorithmic problem in computational biology is to find all subgraphs of a given type (superbubbles, snarls, and ultrabubbles) in a directed or bidirected input graph. These correspond to regions of genetic variation and are…
Given graphs $G$ and $H$, we propose a method to implicitly enumerate topological-minor-embeddings of $H$ in $G$ using decision diagrams. We show a useful application of our method to enumerating subgraphs characterized by forbidden…
We recall several known results about minimally 2-connected graphs, and show that they all follow from a decomposition theorem. Starting from an analogy with critically 2-connected graphs, we give structural characterizations of the classes…
Mining subgraphs with interesting structural properties from networks (or graphs) is a computationally challenging task. In this paper, we propose two algorithms for enumerating all connected induced subgraphs of a given cardinality from…
In the study of full bubble model graphs of bounded clique-width and bounded linear clique-width, we determined complete sets of forbidden induced subgraphs, that are minimal in the class of full bubble model graphs. In this note, we show…
The most elusive problem around the class of circular-arc graphs is identifying all minimal graphs that are not in this class. The main obstacle is the lack of a systematic way of enumerating these minimal graphs. McConnell [FOCS 2001]…
We give a strongly polynomial-time algorithm for integer linear programs defined by integer coefficient matrices whose subdeterminants are bounded by a constant and that contain at most two nonzero entries in each row. The core of our…