相关论文: Exact and Approximation Algorithms for DNA Tag Set…

DNA is not only the genetic material of life, but also a favorable material for a new computing model. Various research works based on DNA computing have been carried out in recent years. DNA sequence design is the foundation of such…

We introduce exponential search trees as a novel technique for converting static polynomial space search structures for ordered sets into fully-dynamic linear space data structures. This leads to an optimal bound of O(sqrt(log n/loglog n))…

The branch-and-bound algorithm based on decision diagrams introduced by Bergman et al. in 2016 is a framework for solving discrete optimization problems with a dynamic programming formulation. It works by compiling a series of bounded-width…

In this paper, a general algorithm is proposed for rate analysis and code design of linear index coding problems. Specifically a solution for minimum rank matrix completion problem over finite fields representing the linear index coding…

We study ranked enumeration of join-query results according to very general orders defined by selective dioids. Our main contribution is a framework for ranked enumeration over a class of dynamic programming problems that generalizes…

Within biology, it is of interest to construct DNA complexes of a certain shape. These complexes can be represented through graph theory, using edges to model strands of DNA joined at junctions, represented by vertices. Because guided…

Aligning sequencing reads on graph representations of genomes is an important ingredient of pan-genomics. Such approaches typically find a set of local anchors that indicate plausible matches between substrings of a read to subpaths of the…

Estimating the structure of directed acyclic graphs (DAGs, also known as Bayesian networks) is a challenging problem since the search space of DAGs is combinatorial and scales superexponentially with the number of nodes. Existing approaches…

Model trees provide an appealing way to perform interpretable machine learning for both classification and regression problems. In contrast to ``classic'' decision trees with constant values in their leaves, model trees can use linear…

Graph augmentation is a fundamental and well-studied problem that arises in network optimization. We consider a new variant of this model motivated by reconfigurable communication networks. In this variant, we consider a given physical…

In this work, we present a new iterative exact solution algorithm for the weighted fair sequences problem, which is a recently introduced NP-hard sequencing problem with applications in diverse areas such as TV advertisement scheduling,…

This paper introduces a new solution to DNA storage that integrates all three steps of retrieval, namely clustering, reconstruction, and error correction. DNA-correcting codes are presented as a unique solution to the problem of ensuring…

Motivation: Microarray data has been recently been shown to be efficacious in distinguishing closely related cell types that often appear in the diagnosis of cancer. It is useful to determine the minimum number of genes needed to do such a…

We consider the problem of optimizing the interconnection graphs of complex networks to promote synchronization. When traditional optimization methods are inapplicable, due to uncertain or unknown node dynamics, we propose a data-driven…

In this paper, we consider recommender systems with side information in the form of graphs. Existing collaborative filtering algorithms mainly utilize only immediate neighborhood information and have a hard time taking advantage of deeper…

An alphabetic binary tree formulation applies to problems in which an outcome needs to be determined via alphabetically ordered search prior to the termination of some window of opportunity. Rather than finding a decision tree minimizing…

Statistical design of experiments is widely used in scientific and industrial investigations. A generalized minimum aberration (GMA) orthogonal array is optimum under the well-established, so-called GMA criterion, and such an array can…

In many situations, it would be useful to know not just the best phylogenetic tree for a given data set, but the collection of high-quality trees. This goal is typically addressed using Bayesian techniques, however, current Bayesian methods…

Listing triangles is a fundamental graph problem with many applications, and large graphs require fast algorithms. Vertex ordering allows the orientation of edges from lower to higher vertex indices, and state-of-the-art triangle listing…

DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…