Related papers: Fast genomic optical map assembly algorithm using …
Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine. However, existing techniques for {\it de novo} genome assembly,…
Binary code similarity comparison is a methodology for identifying similar or identical code fragments in binary programs. It is indispensable in fields of software engineering and security, which has many important applications (e.g.,…
Optical neural networks (ONNs), or optical neuromorphic hardware accelerators, have the potential to dramatically enhance the computing power and energy efficiency of mainstream electronic processors, due to their ultralarge bandwidths of…
We formulate genome assembly problem as an optimization problem in which the objective function is the likelihood of the assembly given the reads.
In many applications, we need algorithms which can align partially overlapping point sets and are invariant to the corresponding transformations. In this work, a method possessing such properties is realized by minimizing the objective of…
Genome assembly is a fundamental problem in Bioinformatics, where for a given set of overlapping substrings of a genome, the aim is to reconstruct the source genome. The classical approaches to solving this problem use assembly graphs, such…
The ever-increasing data demand craves advancements in high-speed and energy-efficient computing hardware. Analog optical neural network (ONN) processors have emerged as a promising solution, offering benefits in bandwidth and energy…
The advent of high-throughput sequencing technologies constituted a major advance in genomic studies, offering new prospects in a wide range of applications. We propose a rigorous and flexible algorithmic solution to mapping SOLiD…
In this paper we develop optimal algorithms in the binary-forking model for a variety of fundamental problems, including sorting, semisorting, list ranking, tree contraction, range minima, and ordered set union, intersection and difference.…
Assessing the correctness of genome assemblies is an important step in any genome project. Several methods exist, but most are computationally intensive and, in some cases, inappropriate. Here I present baa.pl, a fast and easy-to-use…
The compact genetic algorithm is an Estimation of Distribution Algorithm for binary optimisation problems. Unlike the standard Genetic Algorithm, no cross-over or mutation is involved. Instead, the compact Genetic Algorithm uses a virtual…
Recombining trinomial trees are a workhorse for modeling discrete-event systems in option pricing, logistics, and feedback control. Because each node stores a state-dependent quantity, a depth-$D$ tree naively yields $\mathcal{O}(3^{D})$…
Binary code similarity detection is a core task in reverse engineering. It supports malware analysis and vulnerability discovery by identifying semantically similar code in different contexts. Modern methods have progressed from manually…
Optimal modulation (OM) schemes for Gaussian channels with peak and average power constraints are known to require nonuniform probability distributions over signal points, which presents practical challenges. An established way to map…
Most current sampling algorithms for high-dimensional distributions are based on MCMC techniques and are approximate in the sense that they are valid only asymptotically. Rejection sampling, on the other hand, produces valid samples, but is…
Genome sequence analysis has enabled significant advancements in medical and scientific areas such as personalized medicine, outbreak tracing, and the understanding of evolution. Unfortunately, it is currently bottlenecked by the…
Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…
DNA sequencing, especially of microbial genomes and metagenomes, has been at the core of recent research advances in large-scale comparative genomics. The data deluge has resulted in exponential growth in genomic datasets over the past…
Adequate read filtering is critical when processing high-throughput data in marker-gene-based studies. Sequencing errors can cause the mis-clustering of otherwise similar reads, artificially increasing the number of retrieved Operational…
In the large-scale image retrieval task, the two most important requirements are the discriminability of image representations and the efficiency in computation and storage of representations. Regarding the former requirement, Convolutional…