Related papers: Combinatorial RNA Design Designability and Structu…
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…
The function of protein, RNA, and DNA is modulated by fast, dynamic exchanges between three-dimensional conformations. Conformational sampling of biomolecules with exact and nullspace inverse kinematics, using rotatable bonds as revolute…
Constrained least squares problems arise in many applications. Their memory and computation costs are expensive in practice involving high-dimensional input data. We employ the so-called "sketching" strategy to project the least squares…
In this work, we investigate a challenging problem, which has been considered to be an important criterion in designing codewords for DNA computing purposes, namely secondary structure avoidance in single-stranded DNA molecules. In short,…
Combinatorial designs provide an interesting source of optimization problems. Among them, permutation codes are particularly interesting given their applications in powerline communications, flash memories, and block ciphers. This paper…
Test response compaction for integrated circuits (ICs) with scan-based design-for-testability (DFT) support in the presence of unknown logic values (Xs) is investigated from a combinatorial viewpoint. The theoretical foundations of X-codes,…
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…
The secondary structure of ribonucleic acid (RNA) is more stable and accessible in the cell than its tertiary structure, making it essential for functional prediction. Although deep learning has shown promising results in this field,…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
Jain's iterative rounding theorem is a well-known result in the area of approximation algorithms and, more broadly, in combinatorial optimization. The theorem asserts that LP relaxations of several problems in network design and…
We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for…
We argue that most commonly used models for nuclear scattering at ultra-relativistic energies do not treat energy conservation in a consistent fashion. Demanding theoretical consistency as a minimal requirement for a realistic model, we…
Background: Genotype-phenotype maps provide a meaningful filtration of sequence space and RNA secondary structures are particular such phenotypes. Compatible sequences i.e.~sequences that satisfy the base pairing constraints of a given RNA…
Optical orthogonal signature pattern codes (OOSPCs) play an important role in a novel type of optical code-division multiple-access (CDMA) network for 2-dimensional image transmission. There is a one-to-one correspondence between an $(m, n,…
This paper introduces a combinatorial optimization approach to register allocation and instruction scheduling, two central compiler problems. Combinatorial optimization has the potential to solve these problems optimally and to exploit…
We review connections between coding-theoretic objects and sparse learning problems. In particular, we show how seemingly different combinatorial objects such as error-correcting codes, combinatorial designs, spherical codes, compressed…
Tandem duplication is an evolutionary process whereby a segment of DNA is replicated and proximally inserted. The different configurations that can arise from this process give rise to some interesting combinatorial questions. Firstly, we…
Ribonucleic Acid (RNA) can fold into shapes that perform functions in the cell. These foldings are governed by Watson-Crick base pairing, namely Adenine to Uracil and Cytosine to Guanine (A-U and G-C). The properties of the H-P…
This paper addresses problems on the robust structural design of complex networks. More precisely, we address the problem of deploying the minimum number of dedicated sensors, i.e., those measuring a single state variable, that ensure the…
Powerful yet complex deep neural networks (DNNs) have fueled a booming demand for efficient DNN solutions to bring DNN-powered intelligence into numerous applications. Jointly optimizing the networks and their accelerators are promising in…