Related papers: Partial DNA Assembly: A Rate-Distortion Perspectiv…
A crucial problem in genome assembly is the discovery and correction of misassembly errors in draft genomes. We develop a method that will enhance the quality of draft genomes by identifying and removing misassembly errors using paired…
DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics.…
For a number of lossy source coding problems it is shown that even if the usual single-letter sum-rate-distortion expressions may become invalid for non-infinite distortion functions, they can be approached, to any desired accuracy, via the…
Genomics is changing our understanding of humans, evolution, diseases, and medicines to name but a few. As sequencing technology is developed collecting DNA sequences takes less time thereby generating more genetic data every day. Today the…
DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are…
Motivation: New long read sequencers promise to transform sequencing and genome assembly by producing reads tens of kilobases long. However their high error rate significantly complicates assembly and requires expensive correction steps to…
DNA computing, a nontraditional computing mechanism, provides a feasible and effective method for solving NP-hard problems because of the vast parallelism and high-density storage of DNA molecules. Although DNA computing has been exploited…
A causal rate distortion function with a general fidelity criterion is formulated on abstract alphabets and a coding theorem is derived. Existence of the minimizing kernel is shown using the topology of weak convergence of probability…
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…
A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex…
In this paper, we study rate-distortion theory for general sources with an emphasis on the existence of optimal reconstruction distributions on noncompact alphabets. Classical attainability results typically rely on compactness of the…
We simulate the assembly of DNA copolymers from two types of short duplexes (short double strands with a single-stranded overhang at each end), as described by the oxDNA model. We find that the statistics of chain lengths can be well…
We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations…
Symmetry breaking for graphs and other combinatorial objects is notoriously hard. On the one hand, complete symmetry breaks are exponential in size. On the other hand, current, state-of-the-art, partial symmetry breaks are often considered…
Gene assembly in ciliates is one of the most involved DNA processings going on in any organism. This process transforms one nucleus (the micronucleus) into another functionally different nucleus (the macronucleus). We continue the…
Trees have long been used as a graphical representation of species relationships. However complex evolutionary events, such as genetic reassortments or hybrid speciations which occur commonly in viruses, bacteria and plants, do not fit into…
A large driver of the complexity of graph learning is the interplay between structure and features. When analyzing the expressivity of graph neural networks, however, existing approaches ignore features in favor of structure, making it…
Most existing algorithms for dictionary learning assume that all entries of the (high-dimensional) input data are fully observed. However, in several practical applications (such as hyper-spectral imaging or blood glucose monitoring), only…
This paper studies the haplotype assembly problem from an information theoretic perspective. A haplotype is a sequence of nucleotide bases on a chromosome, often conveniently represented by a binary string, that differ from the bases in the…
We define the complexity of a continuous-time linear system to be the minimum number of bits required to describe its forward increments to a desired level of fidelity, and compute this quantity using the rate distortion function of a…