Related papers: Extending the Overlap Graph for Gene Assembly in C…
Dominant sequence models like the Transformer represent structure implicitly through dense attention weights, incurring quadratic complexity. We propose RewriteNets, a novel neural architecture built on an alternative paradigm: explicit,…
Ptychography is a well-studied phase imaging method that makes non-invasive imaging possible at a nanometer scale. It has developed into a mainstream technique with various applications across a range of areas such as material science or…
An assembly is a large population of neurons whose synchronous firing is hypothesized to represent a memory, concept, word, and other cognitive categories. Assemblies are believed to provide a bridge between high-level cognitive phenomena…
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
De novo genome assembly, i.e., rebuilding the sequence of an unknown genome from redundant and erroneous short sequences, is a key but computationally intensive step in many genomics pipelines. The exponential growth of genomic data is…
We study a class of growth algorithms for directed graphs that are candidate models for the evolution of genetic regulatory networks. The algorithms involve partial duplication of nodes and their links, together with innovation of new…
Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…
String diagrams are a powerful and intuitive graphical syntax, originated in the study of symmetric monoidal categories. In the last few years, they have found application in the modelling of various computational structures, in fields as…
The \emph{state complexity} of a regular language $L_m$ is the number $m$ of states in a minimal deterministic finite automaton (DFA) accepting $L_m$. The state complexity of a regularity-preserving binary operation on regular languages is…
Graph Neural Networks (GNNs) have enjoyed wide spread applications in graph-structured data. However, existing graph based applications commonly lack annotated data. GNNs are required to learn latent patterns from a limited amount of…
Research shows that gene duplication followed by either repurposing or removal of duplicated genes is an important contributor to evolution of gene and protein interaction networks. We aim to identify which characteristics of a network can…
Compound graphs are networks in which vertices can be grouped into larger subsets, with these subsets capable of further grouping, resulting in a nesting that can be many levels deep. In several applications, including biological workflows,…
Two genes are xenologs in the sense of Fitch if they are separated by at least one horizontal gene transfer event. Horizonal gene transfer is asymmetric in the sense that the transferred copy is distinguished from the one that remains…
Machine Learning methods have of late made significant efforts to solving multidisciplinary problems in the field of cancer classification using microarray gene expression data. Feature subset selection methods can play an important role in…
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…
Genome assembly, the process of reconstructing a long genetic sequence by aligning and merging short fragments, or reads, is known to be NP-hard, either as a version of the shortest common superstring problem or in a Hamiltonian-cycle…
Introgression is an evolutionary process in which genes or other types of genetic material are introduced into a genome. It is an important evolutionary process that can, for example, play a fundamental role in speciation. Recently the…
In complex networks it is common for each node to belong to several communities, implying a highly overlapping community structure. Recent advances in benchmarking indicate that existing community assignment algorithms that are capable of…