相关论文: Data structures to represent a set of k-long DNA s…

Given a set of $k$ strings $I$, their longest common subsequence (LCS) is the string with the maximum length that is a subset of all the strings in $I$. A data-structure for this problem preprocesses $I$ into a data-structure such that the…

Despite the availability of various sequence analysis models, comparative genomic analysis remains a challenge in genomics, genetics, and phylogenetics. Commutative algebra, a fundamental tool in algebraic geometry and number theory, has…

Given a dynamic set $K$ of $k$ strings of total length $n$ whose characters are drawn from an alphabet of size $\sigma$, a keyword dictionary is a data structure built on $K$ that provides locate, prefix search, and update operations on…

De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…

DNA-based storage is an emerging technology that enables digital information to be archived in DNA molecules. This method enjoys major advantages over magnetic and optical storage solutions such as exceptional information density, enhanced…

Since about 100 years ago, to learn the intrinsic structure of data, many representation learning approaches have been proposed, including both linear ones and nonlinear ones, supervised ones and unsupervised ones. Particularly, deep…

The paper surveys the evolution of main algorithmic techniques to compare and search biological sequences. We highlight key algorithmic ideas emerged in response to several interconnected factors: shifts of biological analytical paradigm,…

We give the first data structure for the problem of maintaining a dynamic set of n elements drawn from a partially ordered universe described by a tree. We define the Line-Leaf Tree, a linear-sized data structure that supports the…

Data storage is one of the main computing issues of this century. Not only storage devices are converging to strict physical limits, but also the amount of data generated by users is growing at an unbelievable rate. To face these…

Data represented as strings abounds in biology, linguistics, document mining, web search and many other fields. Such data often have a hierarchical structure, either because they were artificially designed and composed in a hierarchical…

The Binary Search Tree (BST) is average in computer science which supports a compact data structure in memory and oneself even conducts a row of quick algorithms, by which people often apply it in dynamical circumstance. Besides these…

Graph kernels have attracted a lot of attention during the last decade, and have evolved into a rapidly developing branch of learning on structured data. During the past 20 years, the considerable research activity that occurred in the…

High-throughput computational materials design promises to greatly accelerate the process of discovering new materials and compounds, and of optimizing their properties. The large databases of structures and properties that result from…

We study possible applications of artificial neural networks to examine the string landscape. Since the field of application is rather versatile, we propose to dynamically evolve these networks via genetic algorithms. This means that we…

In this work, we propose a framework to store and manage spatial data, which includes new efficient algorithms to perform operations accepting as input a raster dataset and a vector dataset. More concretely, we present algorithms for…

The yearly global production of data is growing exponentially, outpacing the capacity of existing storage media, such as tape and disk, and surpassing our ability to store it. DNA storage - the representation of arbitrary information as…

In computational biology, $k$-mers and edit distance are fundamental concepts. However, little is known about the metric space of all $k$-mers equipped with the edit distance. In this work, we explore the structure of the $k$-mer space by…

As the global need for large-scale data storage is rising exponentially, existing storage technologies are approaching their theoretical and functional limits in terms of density and energy consumption, making DNA based storage a potential…

The domains of data mining and knowledge discovery make use of large amounts of textual data, which need to be handled efficiently. Specific problems, like finding the maximum weight ordered common subset of a set of ordered sets or…

String barcoding is a recently introduced technique for genomic-based identification of microorganisms. In this paper we describe the engineering of highly scalable algorithms for robust string barcoding. Our methods enable distinguisher…