Related papers: Extending the Overlap Graph for Gene Assembly in C…
Rewriting is a formalism widely used in computer science and mathematical logic. The classical formalism has been extended, in the context of functional languages, with an order over the rules and, in the context of rewrite based languages,…
We study and compare different Graph Neural Network extensions that increase the expressive power of GNNs beyond the Weisfeiler-Leman test. We focus on (i) GNNs based on higher order WL methods, (ii) GNNs that preprocess small substructures…
In the field of empirical modeling using Genetic Programming (GP), it is important to evolve solution with good generalization ability. Generalization ability of GP solutions get affected by two important issues: bloat and over-fitting. We…
Multiset rewriting systems provide a formalism particularly suitable for the description of biological systems. We present an extension of this formalism with additional controls on the derivations as a tool for reducing possible…
We present a new and powerful algebraic framework for graph rewriting, based on drags, a class of graphs enjoying a novel composition operator. Graphs are embellished with roots and sprouts, which can be wired together to form edges. Drags…
A quest to determine the complete sequence of a human DNA from telomere to telomere started three decades ago and was finally completed in 2021. This accomplishment was a result of a tremendous effort of numerous experts who engineered…
De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…
Gene expression analysis aims at identifying the genes able to accurately predict biological parameters like, for example, disease subtyping or progression. While accurate prediction can be achieved by means of many different techniques,…
DNA self-assembly is an important tool that has a wide range of applications such as building nanostructures, the transport of target virotherapies, and nano-circuitry. Tools from graph theory can be used to encode the biological process of…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
Gene expression programming, a genotype/phenotype genetic algorithm (linear and ramified), is presented here for the first time as a new technique for the creation of computer programs. Gene expression programming uses character linear…
We introduce a new concept of a subgraph class called a superbubble for analyzing assembly graphs, and propose an efficient algorithm for detecting it. Most assembly algorithms utilize assembly graphs like the de Bruijn graph or the overlap…
Over the past two decades, a series of works have aimed at studying the problem of genome assembly: the process of reconstructing a genome from sequence reads. An early formulation of the genome assembly problem showed that genome…
The complicated syntax structure of natural language is hard to be explicitly modeled by sequence-based models. Graph is a natural structure to describe the complicated relation between tokens. The recent advance in Graph Neural Networks…
So far, a very large amount of work in Natural Language Processing (NLP) rely on trees as the core mathematical structure to represent linguistic informations (e.g. in Chomsky's work). However, some linguistic phenomena do not cope properly…
The simple connected graphs may be classified by their cycle composition (number and lengths of cycles). This work derives the counting series of the simple connected graphs that have cycles of unrestricted number and length, but no…
In the presence of recombination, the evolutionary relationships between a set of sampled genomes cannot be described by a single genealogical tree. Instead, the genomes are related by a complex, interwoven collection of genealogies…
A rewriting system is a set of equations over a given set of terms called rules that characterize a system of computation and is a powerful general method for providing decision procedures of equational theories, based upon the principle of…
Higher-dimensional rewriting is founded on a duality of rewrite systems and cell complexes, connecting computational mathematics to higher categories and homotopy theory: the two sides of a rewrite rule are two halves of the boundary of an…
Graphs and networks are common ways of depicting biological information. In biology, many different biological processes are represented by graphs, such as regulatory networks, metabolic pathways and protein--protein interaction networks.…