Multiset Of Colors Research Articles

Finding Path Motifs in Large Temporal Graphs Using Algebraic Fingerprints.

We study a family of pattern-detection problems in vertex-colored temporal graphs. In particular, given a vertex-colored temporal graph and a multiset of colors as a query, we search for temporal paths in the graph that contain the colors specified in the query. These types of problems have several applications, for example, in recommending tours for tourists or detecting abnormal behavior in a network of financial transactions. For the family of pattern-detection problems we consider, we establish complexity results and design an algebraic-algorithmic framework based on constrained multilinear sieving. We demonstrate that our solution scales to massive graphs with up to a billion edges for a multiset query with 5 colors and up to 100 million edges for a multiset query with 10 colors, despite the problems being non-deterministic polynomial time-hard. Our implementation, which is publicly available, exhibits practical edge-linear scalability and is highly optimized. For instance, in a real-world graph dataset with >6 million edges and a multiset query with 10 colors, we can extract an optimal solution in <8 minutes on a Haswell desktop with four cores.

The perfect $2$-colorings of infinite circulant graphs with a continuous set of odd distances

A vertex coloring of a given simple graph $G=(V,E)$ with $k$ colors ($k$-coloring) is a map from its vertex set to the set of integers $\{1,2,3,\dots, k\}$. A coloring is called perfect if the multiset of colors appearing on the neighbours of any vertex depends only on the color of the vertex. We consider perfect colorings of Cayley graphs of the additive group of integers with generating set $\{1,-1,3,-3,5,-5,\dots, 2n-1,1-2n\}$ for a positive integer $n$. We enumerate perfect $2$-colorings of the graphs under consideration and state the conjecture generalizing the main result to an arbitrary number of colors.

Perfect colorings of the infinite circulant graph with distances 1 and 2

A coloring of the vertex set in a graph is called perfect if all its identically colored vertices have identical multisets of colors of their neighbors. Refer as the infinite circulant graph with continuous set of n distances to the Cayley graph of the group ℤ with generator set {1, 2,..., n}. We obtain a description of all perfect colorings with an arbitrary number of colors of this graph with distances 1 and 2. In 2015, there was made a conjecture characterizing perfect colorings for the infinite circulant graphs with a continuous set of n distances. The obtained result confirms the conjecture for n = 2. The problem is still open in the case of n > 2.

Parameterized algorithms for the Module Motif problem

Module Motif is a pattern matching problem that was introduced in the context of biological networks. Informally, given a multiset of colors P and a graph H in which each node is associated with a set of colors, it asks if P occurs in a module of H (i.e., in a set of nodes that have the same neighborhood outside the set). We present three parameterized algorithms for this problem, which both measure similarity between matched colors and handle deletions and insertions of colors to P. Moreover, we observe that the running times of two of them might be essentially tight, and prove that the problem is unlikely to admit a polynomial kernel.

CeFunMO: A centrality based method for discovering functional motifs with application in biological networks

Detecting functional motifs in biological networks is one of the challenging problems in systems biology. Given a multiset of colors as query and a list-colored graph (an undirected graph with a set of colors assigned to each of its vertices), the problem is reduced to finding connected subgraphs, which best cover the multiset of query. To solve this NP-complete problem, we propose a new color-based centrality measure for list-colored graphs. Based on this newly-defined measure of centrality, a novel polynomial time algorithm is developed to discover functional motifs in list-colored graphs, using a greedy strategy. This algorithm, called CeFunMO, has superior running time and acceptable accuracy in comparison with other well-known algorithms, such as RANGI and GraMoFoNe.

Counting dominating sets and related structures in graphs

We first consider some problems related to the maximum number of dominating (or total dominating) sets in a regular graph. Our techniques, centered around Shearer’s entropy lemma, extend to a reasonably broad class of graph parameters enumerating vertex colorings that satisfy conditions on the multiset of colors appearing in neighborhoods (either open or closed). Dominating sets and total dominating sets are examples, as are graph colorings in which each vertex’s neighborhood is not monochromatic (or rainbow). In the final section, we think about a generalization of dominating sets in a slightly different direction. Just as independent sets are homomorphisms into K2 with one vertex looped, we think of dominating sets as an example of what we call an existence homomorphism. Here our results are substantially less complete, though we do solve some natural problems.

RANGI: A Fast List-Colored Graph Motif Finding Algorithm

Given a multiset of colors as the query and a list-colored graph, i.e., an undirected graph with a set of colors assigned to each of its vertices, in the NP-hard list-colored graph motif problem the goal is to find the largest connected subgraph such that one can select a color from the set of colors assigned to each of its vertices to obtain a subset of the query. This problem was introduced to find functional motifs in biological networks. We present a branch-and-bound algorithm named RANGI for finding and enumerating list-colored graph motifs. As our experimental results show, RANGI's pruning methods and heuristics make it quite fast in practice compared to the algorithms presented in the literature. We also present a parallel version of RANGI that achieves acceptable scalability.

Finding approximate and constrained motifs in graphs

One of the most relevant topics in the analysis of biological networks is the identification of functional motifs inside a network. A recent approach introduced in literature, called Graph Motif, represents the network as a vertex-colored graph, and the motif M as a multiset of colors. An occurrence of a motif M in a vertex-colored graph G is a connected induced subgraph of G whose vertex set is colored exactly as M. In this paper we investigate three different variants of the Graph Motif problem. The first two variants, Minimum Adding Motif (Min-Add Graph Motif) and Minimum Substitution Motif (Min-Sub Graph Motif), deal with approximate occurrences of a motif in the graph, while the third variant, Constrained Graph Motif (CGM), constrains the motif to contain a given set of vertices. We investigate the computational and parameterized complexity of the three problems. We show that Min-Add Graph Motifand Min-Sub Graph Motifare both NP-hard, even when M is a set, and the graph is a tree with maximum degree 4 in which each color appears at most twice. Then, we show that Min-Sub Graph Motifis fixed-parameter tractable when parameterized by the size of M. Finally, we consider the parameterized complexity of the CGMproblem; we give a fixed-parameter algorithm for graphs of bounded treewidth, and show that the problem is W[2]-hard when parameterized by ∣M∣, even if the input graph has diameter 2.

Constrained multilinear detection for faster functional motif discovery

The Graph Motif problem asks whether a given multiset of colors appears on a connected subgraph of a vertex-colored graph. The fastest known parameterized algorithm for this problem is based on a reduction to the k-Multilinear Detection (k-MlD) problem: the detection of multilinear terms of total degree k in polynomials presented as circuits. We revisit k-MlD and define k-CMlD, a constrained version of it which reflects Graph Motif more faithfully. We then give a fast algorithm for k-CMlD. As a result we obtain faster parameterized algorithms for Graph Motif and variants of it.

Finding and Counting Vertex-Colored Subtrees

The problems studied in this article originate from the Graph Motif problem introduced by Lacroix et al. in the context of biological networks. The problem is to decide if a vertex-colored graph has a connected subgraph whose colors equal a given multiset of colors $M$. It is a graph pattern-matching problem variant, where the structure of the occurrence of the pattern is not of interest but the only requirement is the connectedness. Using an algebraic framework recently introduced by Koutis et al., we obtain new FPT algorithms for Graph Motif and variants, with improved running times. We also obtain results on the counting versions of this problem, proving that the counting problem is FPT if M is a set, but becomes W[1]-hard if M is a multiset with two colors. Finally, we present an experimental evaluation of this approach on real datasets, showing that its performance compares favorably with existing software.

Irregular edge coloring of 2-regular graphs

Graphs and Algorithms Let G be a simple graph and let us color its edges so that the multisets of colors around each vertex are distinct. The smallest number of colors for which such a coloring exists is called the irregular coloring number of G and is denoted by c(G). We determine the exact value of the irregular coloring number for almost all 2-regular graphs. The results obtained provide new examples demonstrating that a conjecture by Burris is false. As another consequence, we also determine the value of a graph invariant called the point distinguishing index (where sets, instead of multisets, are required to be distinct) for the same family of graphs.

Vertex-distinguishing edge-colorings of linear forests

In the PhD thesis by Burris (Memphis (1993)), a conjecture was made concerning the number of colors c(G) required to edge-color a simple graph G so that no two distinct vertices are incident to the same multiset of colors. We nd the exact value of c(G) | the irregular coloring number, and hence verify the conjecture when G is a vertexdisjoint union of paths. We also investigate the point-distinguishing chromatic index, 0(G), where sets, instead of multisets, are required to be distinct, and determine its value for the same family of graphs.