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Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
In this paper, we propose an original manner to employ a tangential cover algorithm - minDSS - in order to geometrically reconstruct noisy digital contours. To do so, we exploit the representation of graphical objects by maximal primitives…
While achieving a compression ratio of 2.0 bits/base, the new algorithm codes non-N bases in fixed length. It dramatically reduces the time of coding and decoding than previous DNA compression algorithms and some universal compression…
We present a novel sparse signal reconstruction method "ISD", aiming to achieve fast reconstruction and a reduced requirement on the number of measurements compared to the classical l_1 minimization approach. ISD addresses failed…
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…
In this paper, soft-decision (SD) decoders of permutation trellis code (PTC) with $M$-ary frequency shift keying are designed using three optimization algorithms and presented in four decoding schemes. In a concatenated code such as PTC,…
Mean-based reconstruction is a fundamental, natural approach to worst-case trace reconstruction over channels with synchronization errors. It is known that $\exp(O(n^{1/3}))$ traces are necessary and sufficient for mean-based worst-case…
Building particle tracks is the most computationally intense step of event reconstruction at the LHC. With the increased instantaneous luminosity and associated increase in pileup expected from the High-Luminosity LHC, the computational…
Next-generation sequencing (NGS) technologies have enabled affordable sequencing of billions of short DNA fragments at high throughput, paving the way for population-scale genomics. Genomics data analytics at this scale requires overcoming…
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.…
Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…
Peer-to-peer distributed storage systems provide reliable access to data through redundancy spread over nodes across the Internet. A key goal is to minimize the amount of bandwidth used to maintain that redundancy. Storing a file using an…
Neuron reconstruction is essential to generate exquisite neuron connectivity map for understanding brain function. Despite the significant amount of effect that has been made on automatic reconstruction methods, manual tracing by…
In this paper, we discuss the reduction of error-trellises for tail-biting convolutional codes. In the case where some column of a parity-check matrix has a monomial factor (with indeterminate D), we show that the associated tail-biting…
We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…
Motivated by mutation processes occurring in in-vivo DNA-storage applications, a channel that mutates stored strings by duplicating substrings as well as substituting symbols is studied. Two models of such a channel are considered: one in…
The DNA storage channel is considered, in which a codeword is comprised of $M$ unordered DNA molecules. At reading time, $N$ molecules are sampled with replacement, and then each molecule is sequenced. A coded-index concatenated-coding…
Regenerating codes provide an efficient way to recover data at failed nodes in distributed storage systems. It has been shown that regenerating codes can be designed to minimize the per-node storage (called MSR) or minimize the…
DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…
Empirically observed time series in physics, biology, or medicine, are commonly generated by some underlying dynamical system (DS) which is the target of scientific interest. There is an increasing interest to harvest machine learning…