Graph operationsIn the mathematical field of graph theory, graph operations are operations which produce new graphs from initial ones. They include both unary (one input) and binary (two input) operations. Unary operations create a new graph from a single initial graph. Elementary operations or editing operations, which are also known as graph edit operations, create a new graph from one initial one by a simple local change, such as addition or deletion of a vertex or of an edge, merging and splitting of vertices, edge contraction, etc.
Directed graphIn mathematics, and more specifically in graph theory, a directed graph (or digraph) is a graph that is made up of a set of vertices connected by directed edges, often called arcs. In formal terms, a directed graph is an ordered pair where V is a set whose elements are called vertices, nodes, or points; A is a set of ordered pairs of vertices, called arcs, directed edges (sometimes simply edges with the corresponding set named E instead of A), arrows, or directed lines.
Protein–protein interaction predictionProtein–protein interaction prediction is a field combining bioinformatics and structural biology in an attempt to identify and catalog physical interactions between pairs or groups of proteins. Understanding protein–protein interactions is important for the investigation of intracellular signaling pathways, modelling of protein complex structures and for gaining insights into various biochemical processes.
Independent set (graph theory)In graph theory, an independent set, stable set, coclique or anticlique is a set of vertices in a graph, no two of which are adjacent. That is, it is a set of vertices such that for every two vertices in , there is no edge connecting the two. Equivalently, each edge in the graph has at most one endpoint in . A set is independent if and only if it is a clique in the graph's complement. The size of an independent set is the number of vertices it contains. Independent sets have also been called "internally stable sets", of which "stable set" is a shortening.
Matrix (mathematics)In mathematics, a matrix (plural matrices) is a rectangular array or table of numbers, symbols, or expressions, arranged in rows and columns, which is used to represent a mathematical object or a property of such an object. For example, is a matrix with two rows and three columns. This is often referred to as a "two by three matrix", a " matrix", or a matrix of dimension . Without further specifications, matrices represent linear maps, and allow explicit computations in linear algebra.
Structural alignmentStructural alignment attempts to establish homology between two or more polymer structures based on their shape and three-dimensional conformation. This process is usually applied to protein tertiary structures but can also be used for large RNA molecules. In contrast to simple structural superposition, where at least some equivalent residues of the two structures are known, structural alignment requires no a priori knowledge of equivalent positions.
Vertex (geometry)In geometry, a vertex (: vertices or vertexes) is a point where two or more curves, lines, or edges meet. As a consequence of this definition, the point where two lines meet to form an angle and the corners of polygons and polyhedra are vertices. The vertex of an angle is the point where two rays begin or meet, where two line segments join or meet, where two lines intersect (cross), or any appropriate combination of rays, segments, and lines that result in two straight "sides" meeting at one place.
Adjacency listIn graph theory and computer science, an adjacency list is a collection of unordered lists used to represent a finite graph. Each unordered list within an adjacency list describes the set of neighbors of a particular vertex in the graph. This is one of several commonly used representations of graphs for use in computer programs. An adjacency list representation for a graph associates each vertex in the graph with the collection of its neighbouring vertices or edges.
Analysis of varianceAnalysis of variance (ANOVA) is a collection of statistical models and their associated estimation procedures (such as the "variation" among and between groups) used to analyze the differences among means. ANOVA was developed by the statistician Ronald Fisher. ANOVA is based on the law of total variance, where the observed variance in a particular variable is partitioned into components attributable to different sources of variation.
Multiple edgesIn graph theory, multiple edges (also called parallel edges or a multi-edge), are, in an undirected graph, two or more edges that are incident to the same two vertices, or in a directed graph, two or more edges with both the same tail vertex and the same head vertex. A simple graph has no multiple edges and no loops. Depending on the context, a graph may be defined so as to either allow or disallow the presence of multiple edges (often in concert with allowing or disallowing loops): Where graphs are defined so as to allow multiple edges and loops, a graph without loops or multiple edges is often distinguished from other graphs by calling it a simple graph.
Dominating setIn graph theory, a dominating set for a graph G is a subset D of its vertices, such that any vertex of G is either in D, or has a neighbor in D. The domination number γ(G) is the number of vertices in a smallest dominating set for G. The dominating set problem concerns testing whether γ(G) ≤ K for a given graph G and input K; it is a classical NP-complete decision problem in computational complexity theory. Therefore it is believed that there may be no efficient algorithm that can compute γ(G) for all graphs G.
Complement graphIn the mathematical field of graph theory, the complement or inverse of a graph G is a graph H on the same vertices such that two distinct vertices of H are adjacent if and only if they are not adjacent in G. That is, to generate the complement of a graph, one fills in all the missing edges required to form a complete graph, and removes all the edges that were previously there. The complement is not the set complement of the graph; only the edges are complemented. Let G = (V, E) be a simple graph and let K consist of all 2-element subsets of V.
