相关论文: Generation of acyclic biological diagrams
Datasets from several domains, such as life-sciences, semantic web, machine learning, natural language processing, etc. are naturally structured as acyclic graphs. These datasets, particularly those in bio-informatics and computational…
A modification of Merino-Mi\v{c}ka-M\"utze's solution to a combinatorial generation problem of Knuth is proposed in this survey. The resulting alternate form to such solution is compatible with a reinterpretation by the author of a proof of…
We study directed random graphs (random graphs whose edges are directed) as they evolve in discrete time by the addition of nodes and edges. For two distinct evolution strategies, one that forces the graph to a condition of near acyclicity…
Recent investigations in computational biology have focused on a family of 2-colored digraphs, called 2-colored best match graphs, which naturally arise from rooted phylogenetic trees. Actually the defining properties of such graphs are…
The pathway is a biological term that refers to a series of interactions between molecules in a cell that causes a certain product or a change in the cell. Pathway analysis is a powerful method for gene expression analysis. Through pathway…
In this paper we study a mapping from permutations to Dyck paths. A Dyck path gives rise to a (Young) diagram and we give relationships between statistics on permutations and statistics on their corresponding diagrams. The distribution of…
Directed acyclic graphs are a fundamental class of networks that includes citation networks, food webs, and family trees, among others. Here we define a random graph model for directed acyclic graphs and give solutions for a number of the…
We study random graph models for directed acyclic graphs, an important class of networks that includes citation networks, food webs, and feed-forward neural networks among others. We propose two specific models, roughly analogous to the…
We describe a simple algorithm based on a Markov chain process to generate simply connected acyclic directed graphs over a fixed set of vertices. This algorithm is an extension of a previous one, designed to generate acyclic digraphs, non…
In this dissertation, we explore the structure of inversion graphs of permutations--a class of graphs that naturally arises by representing each permutation as a graph, where vertices correspond to entries and edges encode inversions.…
A permutation can be locally classified according to the four local types: peaks, valleys, double rises and double falls. The corresponding classification of binary increasing trees uses four different types of nodes. Flajolet demonstrated…
Graphs with given k vertices generate an (acyclic) simplicial complex. We describe the homology of its quotient complex, formed by all connected graphs, and demonstrate its applications to the topology of braid groups, knot theory,…
Recent investigations in computational biology focus on a family of 2-colored digraphs, called 2-colored best match graphs, which naturally arise from rooted phylogenetic trees. Actually the defining properties of such graphs are…
It is described the group of arrowy permutations (that is extension of symmetric group) and the consequent process of generation of GL(n) and some its subgroups by this combinatoric group and its subgroups.
Building on previous work by Cameron et al. in [3], we give a recurrence for computing the number of acyclic orientations of complete $k$-partite graphs, which can be implemented to obtain a dynamic programming algorithm running in time…
In this paper we study termination of term graph rewriting, where we restrict our attention to acyclic term graphs. Motivated by earlier work by Plump we aim at a definition of the notion of simplification order for acyclic term graphs. For…
Because of the huge number of graphs possible even with a small number of nodes, inference on network structure is known to be a challenging problem. Generating large random directed graphs with prescribed probabilities of occurrences of…
We introduce a model for a growing random graph based on simultaneous reproduction of the vertices. The model can be thought of as a generalisation of the reproducing graphs of Southwell and Cannings and Bonato et al to allow for a random…
The derived graph of a voltage graph consisting of a single vertex and two loops of different voltages is a circulant graph with two generators. We characterize the automorphism groups of connected, two-generator circulant graphs, and give…
We develop the theory of linear evolution equations associated with the adjacency matrix of a graph, focusing in particular on infinite graphs of two kinds: uniformly locally finite graphs as well as locally finite line graphs. We discuss…