Related papers: Combinatorial RNA Design: Designability and Struct…

We propose and discuss a novel strategy for protein design. The method is based on recent theoretical advancements which showed the importance to treat carefully the conformational free energy of designed sequences. In this work we show how…

Targeting RNA with small molecules offers significant therapeutic potential. Machine learning could substantially accelerate preclinical drug discovery, from hit identification to lead optimization. Yet a fundamental limitation emerges:…

Combinatorial samplers are algorithmic schemes devised for the approximate- and exact-size generation of large random combinatorial structures, such as context-free words, various tree-like data structures, maps, tilings, RNA molecules.…

The binary string matching problem consists in finding all the occurrences of a pattern in a text where both strings are built on a binary alphabet. This is an interesting problem in computer science, since binary data are omnipresent in…

A heapable sequence is a sequence of numbers that can be arranged in a "min-heap data structure". Finding a longest heapable subsequence of a given sequence was proposed by Byers, Heeringa, Mitzenmacher, and Zervas (ANALCO 2011) as a…

Motivated by mass-spectrometry protein sequencing, we consider a simply-stated problem of reconstructing a string from the multiset of its substring compositions. We show that all strings of length 7, one less than a prime, or one less than…

Convolutional Neural Network (CNN) has gained state-of-the-art results in many pattern recognition and computer vision tasks. However, most of the CNN structures are manually designed by experienced researchers. Therefore, auto- matically…

Neural architecture search (NAS) aims to produce the optimal sparse solution from a high-dimensional space spanned by all candidate connections. Current gradient-based NAS methods commonly ignore the constraint of sparsity in the search…

We propose a model-based, automated, bottom-up approach for design, which is applicable to various physical domains, but in this work we focus on the electrical domain. This bottom-up approach is based on a meta-topology in which each link…

In post-transcriptional regulation, an mRNA molecule is bound by many proteins and/or miRNAs to modulate its function. To enable combinatorial gene regulation, these binding partners of an RNA must communicate with each other, exhibiting…

Covers being one of the most popular form of regularities in strings, have drawn much attention over time. In this paper, we focus on the problem of linear time inference of strings from cover arrays using the least sized alphabet possible.…

We are interested in the design of generative networks. The training of these mathematical structures is mostly performed with the help of adversarial (min-max) optimization problems. We propose a simple methodology for constructing such…

We describe properties and constructions of constraint-based codes for DNA-based data storage which account for the maximum repetition length and AT/GC balance. We present algorithms for computing the number of sequences with maximum…

The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…

Many approaches to transform classification problems from non-linear to linear by feature transformation have been recently presented in the literature. These notably include sparse coding methods and deep neural networks. However, many of…

Variational Quantum Algorithms are one of the most promising candidates to yield the first industrially relevant quantum advantage. Being capable of arbitrary function approximation, they are often referred to as Quantum Neural Networks…

This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…

String data are often disseminated to support applications such as location-based service provision or DNA sequence analysis. This dissemination, however, may expose sensitive patterns that model confidential knowledge. In this paper, we…

Motivated by the study of matrix elimination orderings in combinatorial scientific computing, we utilize graph sketching and local sampling to give a data structure that provides access to approximate fill degrees of a matrix undergoing…

Electronic Phased-Array Radars offer new possibilities for Optimization of Radar Search Pattern by using bi-dimensional beam forming and beam steering, along both elevation and azimuth axes. The minimization of the Time-Budget required for…