HypergraphIn mathematics, a hypergraph is a generalization of a graph in which an edge can join any number of vertices. In contrast, in an ordinary graph, an edge connects exactly two vertices. Formally, a directed hypergraph is a pair , where is a set of elements called nodes, vertices, points, or elements and is a set of pairs of subsets of . Each of these pairs is called an edge or hyperedge; the vertex subset is known as its tail or domain, and as its head or codomain. The order of a hypergraph is the number of vertices in .
Matching in hypergraphsIn graph theory, a matching in a hypergraph is a set of hyperedges, in which every two hyperedges are disjoint. It is an extension of the notion of matching in a graph. Recall that a hypergraph H is a pair (V, E), where V is a set of vertices and E is a set of subsets of V called hyperedges. Each hyperedge may contain one or more vertices. A matching in H is a subset M of E, such that every two hyperedges e_1 and e_2 in M have an empty intersection (have no vertex in common).
Bipartite graphIn the mathematical field of graph theory, a bipartite graph (or bigraph) is a graph whose vertices can be divided into two disjoint and independent sets and , that is, every edge connects a vertex in to one in . Vertex sets and are usually called the parts of the graph. Equivalently, a bipartite graph is a graph that does not contain any odd-length cycles. The two sets and may be thought of as a coloring of the graph with two colors: if one colors all nodes in blue, and all nodes in red, each edge has endpoints of differing colors, as is required in the graph coloring problem.
Incidence matrixIn mathematics, an incidence matrix is a logical matrix that shows the relationship between two classes of objects, usually called an incidence relation. If the first class is X and the second is Y, the matrix has one row for each element of X and one column for each element of Y. The entry in row x and column y is 1 if x and y are related (called incident in this context) and 0 if they are not. There are variations; see below. Incidence matrix is a common graph representation in graph theory.
Graph (discrete mathematics)In discrete mathematics, and more specifically in graph theory, a graph is a structure amounting to a set of objects in which some pairs of the objects are in some sense "related". The objects correspond to mathematical abstractions called vertices (also called nodes or points) and each of the related pairs of vertices is called an edge (also called link or line). Typically, a graph is depicted in diagrammatic form as a set of dots or circles for the vertices, joined by lines or curves for the edges.
Bipartite hypergraphIn graph theory, the term bipartite hypergraph describes several related classes of hypergraphs, all of which are natural generalizations of a bipartite graph. Property B The weakest definition of bipartiteness is also called 2-colorability. A hypergraph H = (V, E) is called 2-colorable if its vertex set V can be partitioned into two sets, X and Y, such that each hyperedge meets both X and Y. Equivalently, the vertices of H can be 2-colored so that no hyperedge is monochromatic.
Vertex cover in hypergraphsIn graph theory, a vertex cover in a hypergraph is a set of vertices, such that every hyperedge of the hypergraph contains at least one vertex of that set. It is an extension of the notion of vertex cover in a graph. An equivalent term is a hitting set: given a collection of sets, a set which intersects all sets in the collection in at least one element is called a hitting set. The equivalence can be seen by mapping the sets in the collection onto hyperedges. Another equivalent term, used more in a combinatorial context, is transversal.
Transversal (combinatorics)In mathematics, particularly in combinatorics, given a family of sets, here called a collection C, a transversal (also called a cross-section) is a set containing exactly one element from each member of the collection. When the sets of the collection are mutually disjoint, each element of the transversal corresponds to exactly one member of C (the set it is a member of). If the original sets are not disjoint, there are two possibilities for the definition of a transversal: One variation is that there is a bijection f from the transversal to C such that x is an element of f(x) for each x in the transversal.
Protein function predictionProtein function prediction methods are techniques that bioinformatics researchers use to assign biological or biochemical roles to proteins. These proteins are usually ones that are poorly studied or predicted based on genomic sequence data. These predictions are often driven by data-intensive computational procedures. Information may come from nucleic acid sequence homology, gene expression profiles, protein domain structures, text mining of publications, phylogenetic profiles, phenotypic profiles, and protein-protein interaction.
Hall-type theorems for hypergraphsIn the mathematical field of graph theory, Hall-type theorems for hypergraphs are several generalizations of Hall's marriage theorem from graphs to hypergraphs. Such theorems were proved by Ofra Kessler, Ron Aharoni, Penny Haxell, Roy Meshulam, and others. Hall's marriage theorem provides a condition guaranteeing that a bipartite graph (X + Y, E) admits a perfect matching, or - more generally - a matching that saturates all vertices of Y. The condition involves the number of neighbors of subsets of Y.
Protein structure predictionProtein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its secondary and tertiary structure from primary structure. Structure prediction is different from the inverse problem of protein design. Protein structure prediction is one of the most important goals pursued by computational biology; and it is important in medicine (for example, in drug design) and biotechnology (for example, in the design of novel enzymes).
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.
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.
Rainbow matchingIn the mathematical discipline of graph theory, a rainbow matching in an edge-colored graph is a matching in which all the edges have distinct colors. Given an edge-colored graph G = (V,E), a rainbow matching M in G is a set of pairwise non-adjacent edges, that is, no two edges share a common vertex, such that all the edges in the set have distinct colors. A maximum rainbow matching is a rainbow matching that contains the largest possible number of edges. Rainbow matchings are of particular interest given their connection to transversals of Latin squares.
Incidence structureIn mathematics, an incidence structure is an abstract system consisting of two types of objects and a single relationship between these types of objects. Consider the points and lines of the Euclidean plane as the two types of objects and ignore all the properties of this geometry except for the relation of which points are on which lines for all points and lines. What is left is the incidence structure of the Euclidean plane.
Logical matrixA logical matrix, binary matrix, relation matrix, Boolean matrix, or (0, 1)-matrix is a matrix with entries from the Boolean domain B = {0, 1}. Such a matrix can be used to represent a binary relation between a pair of finite sets. It is an important tool in combinatorial mathematics and theoretical computer science.
StatisticsStatistics (from German: Statistik, () "description of a state, a country") is the discipline that concerns the collection, organization, analysis, interpretation, and presentation of data. In applying statistics to a scientific, industrial, or social problem, it is conventional to begin with a statistical population or a statistical model to be studied. Populations can be diverse groups of people or objects such as "all people living in a country" or "every atom composing a crystal".
Statistical inferenceStatistical inference is the process of using data analysis to infer properties of an underlying distribution of probability. Inferential statistical analysis infers properties of a population, for example by testing hypotheses and deriving estimates. It is assumed that the observed data set is sampled from a larger population. Inferential statistics can be contrasted with descriptive statistics. Descriptive statistics is solely concerned with properties of the observed data, and it does not rest on the assumption that the data come from a larger population.
Edge coverIn graph theory, an edge cover of a graph is a set of edges such that every vertex of the graph is incident to at least one edge of the set. In computer science, the minimum edge cover problem is the problem of finding an edge cover of minimum size. It is an optimization problem that belongs to the class of covering problems and can be solved in polynomial time. Formally, an edge cover of a graph G is a set of edges C such that each vertex in G is incident with at least one edge in C.
Adjacency matrixIn graph theory and computer science, an adjacency matrix is a square matrix used to represent a finite graph. The elements of the matrix indicate whether pairs of vertices are adjacent or not in the graph. In the special case of a finite simple graph, the adjacency matrix is a (0,1)-matrix with zeros on its diagonal. If the graph is undirected (i.e. all of its edges are bidirectional), the adjacency matrix is symmetric. The relationship between a graph and the eigenvalues and eigenvectors of its adjacency matrix is studied in spectral graph theory.
