Related papers: Extending the Overlap Graph for Gene Assembly in C…
Random intersection graphs model networks with communities, assuming an underlying bipartite structure of groups and individuals, where these groups may overlap. Group memberships are generated through the bipartite configuration model.…
The weak-to-strong generalization phenomenon is the driver for important machine learning applications including highly data-efficient learning and, most recently, performing superalignment. While decades of research have resulted in…
Graph signals are functions of the underlying graph. When the edge-weight between a pair of nodes is high, the corresponding signals generally have a higher correlation. As a result, the signals can be represented in terms of a graph-based…
The conception of multi-alphabetical genetics is represented. Matrix forms of the representation of the multi-level system of molecular-genetic alphabets have revealed algebraic properties of this system. These properties are connected with…
Shape graphs are complex geometrical structures commonly found in biological and anatomical systems. A shape graph is a collection of nodes, some connected by curvilinear edges with arbitrary shapes. Their high complexity stems from the…
The inference of gene regulatory networks (GRNs) is a foundational stride towards deciphering the fundamentals of complex biological systems. Inferring a possible regulatory link between two genes can be formulated as a link prediction…
Graph-based semantic representations are valuable in natural language processing, where it is often simple and effective to represent linguistic concepts as nodes, and relations as edges between them. Several attempts has been made to find…
Hypergraphs are structures that can be decomposed or described; in other words they are recursively countable. Here, we get exact and asymptotic enumeration results on hypergraphs by means of exponential generating functions. The number of…
A splicing system is a formal model of a recombinant behaviour of sets of double stranded DNA molecules when acted on by restriction enzymes and ligase. In this survey we will concentrate on a specific behaviour of a type of splicing…
A Genetic Algorithm (GA) is proposed in which each member of the population can change schemata only with its neighbors according to a rule. The rule methodology and the neighborhood structure employ elements from the Cellular Automata (CA)…
Fitch graphs $G=(X,E)$ are di-graphs that are explained by $\{\otimes,1\}$-edge-labeled rooted trees with leaf set $X$: there is an arc $xy\in E$ if and only if the unique path in $T$ that connects the least common ancestor…
A typed model of strategic term rewriting is developed. The key innovation is that generic traversal is covered. To this end, we define a typed rewriting calculus S'_{gamma}. The calculus employs a many-sorted type system extended by…
Reconstructing components of a genomic mixture from data obtained by means of DNA sequencing is a challenging problem encountered in a variety of applications including single individual haplotyping and studies of viral communities.…
Many models of genome rearrangement involve operations (e.g. inversions and translocations) that are self-inverse, and hence generate a group acting on the space of genomes. This gives a correspondence between genome arrangements and the…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
Graph rewrite formalisms are a powerful approach to modeling complex molecular systems. They capture the intrinsic concurrency of molecular interactions, thereby enabling a formal notion of mechanism (a partially ordered set of events) that…
This Letter introduces a generalization of known duplication-divergence models for growing random graphs. This general duplication-divergence model includes a new coupled divergence asymmetry rate, which allows to obtain the structure of…
Regulatory interactions between genes show a large amount of cross-species variability, even when the underlying functions are conserved: There are many ways to achieve the same function. Here we investigate the ability of regulatory…
Understanding how genes interact and relate to each other is a fundamental question in biology. However, current practices for describing these relationships, such as drawing diagrams or graphs in a somewhat arbitrary manner, limit our…
Replication helps ensure that a genotype-phenotype association observed in a genome-wide association (GWA) study represents a credible association and is not a chance finding or an artifact due to uncontrolled biases. We discuss…