Related papers: Combinatorial RNA Design: Designability and Struct…
Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…
In recent years, there has been a growing interest in using learning-based approaches for solving combinatorial problems, either in an end-to-end manner or in conjunction with traditional optimization algorithms. In both scenarios, the…
The design of fusion devices is typically based on computationally expensive simulations. This can be alleviated using high aspect ratio models that employ a reduced number of free parameters, especially in the case of stellarator…
We provide a randomized linear time approximation scheme for a generic problem about clustering of binary vectors subject to additional constrains. The new constrained clustering problem encompasses a number of problems and by solving it,…
Despite nearly two scores of research on RNA secondary structure and RNA-RNA interaction prediction, the accuracy of the state-of-the-art algorithms are still far from satisfactory. Researchers have proposed increasingly complex energy…
We study the complexity of the problem of searching for a set of patterns that separate two given sets of strings. This problem has applications in a wide variety of areas, most notably in data mining, computational biology, and in…
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…
Assembly Theory, as developed by Cronin and co-workers, assigns to an object an assembly index: the minimal number of binary join operations required to build at least one copy of the object from a specified set of basic building blocks,…
Using an off-lattice model, we fully enumerate folded conformations of polypeptide chains of up to N = 19 monomers. Structures are found to differ markedly in designability, defined as the number of sequences with that structure as a unique…
Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex…
Suffix trees have recently become very successful data structures in handling large data sequences such as DNA or Protein sequences. Consequently parallel architectures have become ubiquitous. We present a novel alphabet-dependent parallel…
Cluster deletion is an NP-hard graph clustering objective with applications in computational biology and social network analysis, where the goal is to delete a minimum number of edges to partition a graph into cliques. We first provide a…
Biological processes, including cell differentiation, organism development, and disease progression, can be interpreted as attractors (fixed points or limit cycles) of an underlying networked dynamical system. In this paper, we study the…
We consider partially ordered sets of combinatorial structures under consecutive orders, meaning that two structures are related when one embeds in the other such that `consecutive' elements remain consecutive in the image. Given such a…
Ribonucleic acid (RNA) binds to molecules to achieve specific biological functions. While generative models are advancing biomolecule design, existing methods for designing RNA that target specific ligands face limitations in capturing…
We consider Convolutional Neural Networks (CNNs) with 2D structured features that are symmetric in the spatial dimensions. Such networks arise in modeling pairwise relationships for a sequential recommendation problem, as well as secondary…
In recent years, deep neural networks have had great success in machine learning and pattern recognition. Architecture size for a neural network contributes significantly to the success of any neural network. In this study, we optimize the…
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…
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…
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…