Related papers: Combinatorial RNA Design: Designability and Struct…
Combinatorial problems are formulated to find optimal designs within a fixed set of constraints. They are commonly found across diverse engineering and scientific domains. Understanding how to best use quantum computers for combinatorial…
Many combinatorial optimization problems can be phrased in the language of constraint satisfaction problems. We introduce a graph neural network architecture for solving such optimization problems. The architecture is generic; it works for…
RNA design consists of discovering a nucleotide sequence that folds into a target secondary structure. It is useful for synthetic biology, medicine, and nanotechnology. We propose Montparnasse, a Multi Objective Generalized Nested Rollout…
Longest Run Subsequence is a problem introduced recently in the context of the scaffolding phase of genome assembly (Schrinner et al., WABI 2020). The problem asks for a maximum length subsequence of a given string that contains at most one…
RNA secondary structure prediction and classification are two important problems in the field of RNA biology. Here, we propose a new permutation based approach to create logical non-disjoint clusters of different secondary structures of a…
The simplest possible informational heteropolymer requires only a two-letter alphabet to be able to store information. The evolutionary choice of four monomers in the informational biomolecules RNA/DNA or their progenitors is intriguing,…
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…
RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two…
We investigate block designs, under the A- and MV-criteria, when each treatment can have only one or two replications due to resource constraints, as can happen, for example, in early generation varietal trials. While these are commonly…
This paper considers the construction of minimum aberration (MA) blocked factorial designs. Based on coding theory, the concept of minimum moment aberration due to Xu [Statist. Sinica 13 (2003) 691--708] for unblocked designs is extended to…
The rapidly evolving field of Artificial Intelligence necessitates automated approaches to co-design neural network architecture and neural accelerators to maximize system efficiency and address productivity challenges. To enable joint…
We consider the problem of making a quick decision in favor of one of two possible physical signal models while the numerical measurements are acquired by sensing devices featuring minimal digitization complexity. Therefore, the digital…
Dual graphs have been applied to model RNA secondary structures. The purpose of the paper is two-fold: we present new graph-theoretic properties of dual graphs to validate the further analysis and classification of RNAs using these…
A typical protein structure is a compact packing of connected alpha-helices and/or beta-strands. We have developed a method for generating the ensemble of compact structures a given set of helices and strands can form. The method is tested…
Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…
This work investigates the structure of rank-metric codes in connection with concepts from finite geometry, most notably the $q$-analogues of projective systems and blocking sets. We also illustrate how to associate a classical…
When designing distributed controllers for large-scale systems, the actuation, sensing and communication architectures of the controller can no longer be taken as given. In particular, controllers implemented using dense architectures…
Dual graphs have been applied to model RNA secondary structures with pseudoknots, or intertwined base pairs. In previous works, a linear-time algorithm was introduced to partition dual graphs into maximally connected components called…
In this paper we propose new solution methods for designing tag sets for use in universal DNA arrays. First, we give integer linear programming formulations for two previous formalizations of the tag set design problem, and show that these…
We study the theoretical problem of synthesizing multiple DNA strands under spatial constraints, motivated by large-scale DNA synthesis technologies. In this setting, strands are arranged in an array and synthesized according to a fixed…