Related papers: Exact and Approximation Algorithms for DNA Tag Set…

In this paper we address two optimization problems arising in the design of genomic assays based on universal tag arrays. First, we address the universal array tag set design problem. For this problem, we extend previous formulations to…

We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…

Many information systems use tags and keywords to describe and annotate content. These allow for efficient organization and categorization of items, as well as facilitate relevant search queries. As such, the selected set of tags for an…

DNA pattern matching is essential for many widely used bioinformatics applications. Disease diagnosis is one of these applications, since analyzing changes in DNA sequences can increase our understanding of possible genetic diseases. The…

The paper "Stack-based Algorithms for Pattern Matching on DAGs" generalizes the classical holistic twig join algorithms and proposes PathStackD, TwigStackD and DagStackD to respectively evaluate path, twig and DAG pattern queries on…

Working with exhaustive search on large dataset is infeasible for several reasons. Recently, developed techniques that made pattern set mining feasible by a general solver with long execution time that supports heuristic search and are…

We propose generative neural network methods to generate DNA sequences and tune them to have desired properties. We present three approaches: creating synthetic DNA sequences using a generative adversarial network; a DNA-based variant of…

In the problems of image retrieval and annotation, complete textual tag lists of images play critical roles. However, in real-world applications, the image tags are usually incomplete, thus it is important to learn the complete tags for…

This paper leverages the framework of algorithms-with-predictions to design data structures for two fundamental dynamic graph problems: incremental topological ordering and cycle detection. In these problems, the input is a directed graph…

Dynamic programming on tree decompositions is a frequently used approach to solve otherwise intractable problems on instances of small treewidth. In recent work by Bodlaender et al., it was shown that for many connectivity problems, there…

Graphs are extremely versatile and ubiquitous mathematical structures with potential to model a wide range of domains. For this reason, graph problems have been of interest since the early days of computer science. Some of these problems…

Using author provided tags to predict tags for a new document often results in the overgeneration of tags. In the case where the author doesn't provide any tags, our documents face the severe under-tagging issue. In this paper, we present a…

Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic relationships. This paper…

Tagging items with descriptive annotations or keywords is a very natural way to compress and highlight information about the properties of the given entity. Over the years several methods have been proposed for extracting a hierarchy…

The problem of fast items retrieval from a fixed collection is often encountered in most computer science areas, from operating system components to databases and user interfaces. We present an approach based on hash tables that focuses on…

We are concerned with the problem of designing large families of subsets over a common labeled ground set that have small pairwise intersections and the property that the maximum discrepancy of the label values within each of the sets is…

RNA design aims to identify RNA sequences that fold into a target secondary structure. This task is challenging in terms of computational efficiency. Most existing methods focus on either minimum free energy (MFE)-based or ensemble-based…

While most methods for solving mixed-integer optimization problems compute a single optimal solution, a diverse set of near-optimal solutions can often lead to improved outcomes. We present a new method for finding a set of diverse…

A critical problem in the emerging high-throughput genotyping protocols is to minimize the number of polymerase chain reaction (PCR) primers required to amplify the single nucleotide polymorphism loci of interest. In this paper we study PCR…

Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…