Related papers: Assembling sequences of DNA using an on-line algor…
We develop a new sampling method to estimate eigenvector centrality on incomplete networks. Our goal is to estimate this global centrality measure having at disposal a limited amount of data. This is the case in many real-world scenarios…
Algorithms to find optimal alignments among strings, or to find a parsimonious summary of a collection of strings, are well studied in a variety of contexts, addressing a wide range of interesting applications. In this paper, we consider…
We introduce a new distributed algorithm for aligning graphs or finding substructures within a given graph. It is based on the cavity method and is used to study the maximum-clique and the graph-alignment problems in random graphs. The…
This paper studies two problems that are motivated by the novel recent approach of composite DNA that takes advantage of the DNA synthesis property which generates a huge number of copies for every synthesized strand. Under this paradigm,…
Whole brain segmentation using deep learning (DL) is a very challenging task since the number of anatomical labels is very high compared to the number of available training images. To address this problem, previous DL methods proposed to…
Graphs are used in many disciplines to model the relationships that exist between objects in a complex discrete system. Researchers may wish to compare a network of interest to a "typical" graph from a family (or ensemble) of graphs which…
Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into one consensus copy or fail to cleanly separate the…
Matching, a task to optimally assign limited resources under constraints, is a fundamental technology for society. The task potentially has various objectives, conditions, and constraints; however, the efficient neural network architecture…
The deep neural networks (DNNs) have been enormously successful in tasks that were hitherto in the human-only realm such as image recognition, and language translation. Owing to their success the DNNs are being explored for use in ever more…
Complex networks have become powerful mechanisms for studying a variety of realworld systems. Consequently, many human-designed network models are proposed that reproduce nontrivial properties of complex networks, such as long-tail degree…
The problem of storing large amounts of information safely for a long period of time has become essential. One of the most promising new data storage mediums are the polymer-based data storage systems, like the DNA-storage system. These…
The 0/1 knapsack problem is weakly NP-hard in that there exist pseudo-polynomial time algorithms based on dynamic programming that can solve it exactly. There are also the core branch and bound algorithms that can solve large randomly…
Recent advancements in microbiology have motivated the study of the production of nanostructures with applications such as biomedical computing and molecular robotics. One way to construct these structures is to construct branched DNA…
Pairwise alignment of DNA sequencing data is a ubiquitous task in bioinformatics and typically represents a heavy computational burden. State-of-the-art approaches to speed up this task use hashing to identify short segments (k-mers) that…
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…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…
Transcriptome assembly from RNA-Seq reads is an active area of bioinformatics research. The ever-declining cost and the increasing depth of RNA-Seq have provided unprecedented opportunities to better identify expressed transcripts. However,…
The paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…
Analysis of DNA samples is an important step in forensics, and the speed of analysis can impact investigations. Comparison of DNA sequences is based on the analysis of short tandem repeats (STRs), which are short DNA sequences of 2-5 base…
Graph matching, also known as network alignment, refers to finding a bijection between the vertex sets of two given graphs so as to maximally align their edges. This fundamental computational problem arises frequently in multiple fields…