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Given a subset of active nodes in a network can we re- construct the cascade that has generated these observa- tions? This is a problem that has been studied in the literature, but here we focus in the case that tempo- ral information is…

Branched molecules of deoxyribonucleic acid (DNA) can self-assemble into nanostructures through complementary cohesive strand base pairing. The production of DNA nanostructures is valuable in targeted drug delivery and biomolecular…

We consider the problem of storing and retrieving information from synthetic DNA media. The mathematical basis of the problem is the construction and design of sequences that may be discriminated based on their collection of substrings…

A genetic algorithm procedure is demonstrated that refines the selection of interpolation points of the discrete empirical interpolation method (DEIM) when used for constructing reduced order models for time dependent and/or parametrized…

In this article we show that the reconstructions of semiconductor surfaces can be determined using a genetic procedure. Coupled with highly optimized interatomic potentials, the present approach represents an efficient tool for finding and…

Motivation: Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining the sequences for a large number of genes from an organism with no reference genome. With the rapidly increasing throughputs and…

Next-generation sequencing (NGS) technologies allow new methodologies for alternative splicing (AS) analysis. Current computational methods for AS from NGS data are mainly focused on predicting splice site junctions or de novo assembly of…

By using the Jensen-Shannon divergence, genomic DNA can be divided into compositionally distinct domains through a standard recursive segmentation procedure. Each domain, while significantly different from its neighbours, may however share…

Self-assembly is a phenomenon observed in nature at all scales where autonomous entities build complex structures, without external influences nor centralised master plan. Modelling such entities and programming correct interactions among…

Hypergraphs, increasingly utilised to model complex and diverse relationships in modern networks, have gained significant attention for representing intricate higher-order interactions. Among various challenges, cohesive subgraph discovery…

Metagenomics research has accelerated the studies of microbial organisms, providing insights into the composition and potential functionality of various microbial communities. Metatranscriptomics (studies of the transcripts from a mixture…

We introduce a novel method to analyse complete genomes and recognise some distinctive features by means of an adaptive compression algorithm, which is not DNA-oriented. We study the Information Content as a function of the number of…

Exploring statistics of locally connected subgraph patterns (also known as network motifs) has helped researchers better understand the structure and function of biological and online social networks (OSNs). Nowadays the massive size of…

Minimizers and convolutional neural networks (CNNs) are two quite distinct popular techniques that have both been employed to analyze categorical biological sequences. At face value, the methods seem entirely dissimilar. Minimizers use…

Code generation maps a program description to executable source code in a programming language. Existing approaches mainly rely on a recurrent neural network (RNN) as the decoder. However, we find that a program contains significantly more…

Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking…

Each human genome is a 3 billion base pair set of encoding instructions. Decoding the genome using deep learning fundamentally differs from most tasks, as we do not know the full structure of the data and therefore cannot design…

We describe a strategy for constructing codes for DNA-based information storage by serial composition of weighted finite-state transducers. The resulting state machines can integrate correction of substitution errors; synchronization by…

Deep neural network-based architectures give promising results in various domains including pattern recognition. Finding the optimal combination of the hyper-parameters of such a large-sized architecture is tedious and requires a large…

Decoding sequences that stem from multiple transmissions of a codeword over an insertion, deletion, and substitution channel is a critical component of efficient deoxyribonucleic acid (DNA) data storage systems. In this paper, we consider a…