Related papers: Extending the Overlap Graph for Gene Assembly in C…
A construction described by the current author in 2017 uses two linear `prototype' graphs to build a compound graph with Ramsey properties inherited from the prototypes. This paper describes a generalisation of that construction which has…
We introduce the concept of an abstract evolution system, which provides a convenient framework for studying generic mathematical structures and their properties. Roughly speaking, an evolution system is a category endowed with a selected…
String rewriting systems have proved very useful to study monoids. In good cases, they give finite presentations of monoids, allowing computations on those and their manipulation by a computer. Even better, when the presentation is…
Some recent results have introduced external-memory algorithms to compute self-indexes of a set of strings, mainly via computing the Burrows-Wheeler Transform (BWT) of the input strings. The motivations for those results stem from…
Natural genomes sometimes encode two different proteins in staggered reading frames of the same DNA sequence. Despite the prevalence of these 'overlapping genes' across the tree of life, it remains unknown whether arbitrary protein pairs…
We investigate the new, Turing-complete class of layered systems, whose lefthand sides of rules can only be overlapped at a multiset of disjoint or equal positions. Layered systems define a natural notion of rank for terms: the maximal…
We introduce a parallel algorithmic architecture for metagenomic sequence assembly, termed MetaPar, which allows for significant reductions in assembly time and consequently enables the processing of large genomic datasets on computers with…
LAGE is a systematic framework developed in Java. The motivation of LAGE is to provide a scalable and parallel solution to reconstruct Gene Regulatory Networks (GRNs) from continuous gene expression data for very large amount of genes. The…
Graph convolutions have gained popularity due to their ability to efficiently operate on data with an irregular geometric structure. However, graph convolutions cause over-smoothing, which refers to representations becoming more similar…
Generative models of graph structure have applications in biology and social sciences. The state of the art is GraphRNN, which decomposes the graph generation process into a series of sequential steps. While effective for modest sizes, it…
We introduce bonding grammars, a graph grammar formalism developed to model DNA computation by means of graph transformations. It is a modification of fusion grammars introduced by Kreowski, Kuske and Lye in 2017. Bonding is a graph…
Reaction mechanisms are often presented as sequences of elementary steps, such as codified by arrow pushing. We propose an approach for representing such mechanisms using graph transformation. In this framework, each elementary step is a…
We recently reported that the simple genetic algorithm (SGA) is capable of performing a remarkable form of sublinear computation which has a straightforward connection with the general problem of interacting attributes in data-mining. In…
Graphs are a powerful tool for analyzing large data sets, but many real-world phenomena involve interactions that go beyond the simple pairwise relationships captured by a graph. In this paper we introduce and study a simple combinatorial…
Genetic Programming has been very successful in solving a large area of problems but its use as a machine learning algorithm has been limited so far. One of the reasons is the problem of overfitting which cannot be solved or suppresed as…
Biomedical networks (or graphs) are universal descriptors for systems of interacting elements, from molecular interactions and disease co-morbidity to healthcare systems and scientific knowledge. Advances in artificial intelligence,…
Converting a set of sequencing reads into a lossless compact data structure that encodes all the relevant biological information is a major challenge. The classical approaches are to build the string graph or the de Bruijn graph. Each has…
Covering alignment problems arise from recent developments in genomics; so called pan-genome graphs are replacing reference genomes, and advances in haplotyping enable full content of diploid genomes to be used as basis of sequence…
We generalize the problem of reconstructing strings from their substring compositions first introduced by Acharya et al. in 2015 motivated by polymer-based advanced data storage systems utilizing mass spectrometry. Namely, we see strings as…
In this paper we present a model containing modifications to the Signal-passing Tile Assembly Model (STAM), a tile-based self-assembly model whose tiles are capable of activating and deactivating glues based on the binding of other glues.…