Related papers: Improved Lower Bounds for Constant GC-Content DNA …
Oligonucleotide arrays are used in a wide range of genomic analyses, such as gene expression profiling, comparative genomic hybridization, chromatin immunoprecipitation, SNP detection, etc. During fabrication, the sites of an…
One important feature of complex systems are problem domains that have many local minima and substructure. Biological systems manage these local minima by switching between different subsystems depending on their environmental or…
DNA strands serve as a storage medium for $4$-ary data over the alphabet $\{A,T,G,C\}$. DNA data storage promises formidable information density, long-term durability, and ease of replicability. However, information in this intriguing…
Gravitational-wave detection strategies are based on a signal analysis technique known as matched filtering. Despite the success of matched filtering, due to its computational cost, there has been recent interest in developing deep…
We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…
We consider the problem of sampling from a strongly log-concave density in $\mathbb{R}^d$, and prove an information theoretic lower bound on the number of stochastic gradient queries of the log density needed. Several popular sampling…
Graph-structured data is central to many scientific and industrial domains, where the goal is often to optimize objectives defined over graph structures. Given the combinatorial complexity of graph spaces, such optimization problems are…
The locally repairable codes (LRCs) were introduced to correct erasures efficiently in distributed storage systems. LRCs are extensively studied recently. In this paper, we first deal with the open case remained in \cite{q} and derive an…
In this paper, we consider a concatenated coding based class of DNA storage codes in which the selected molecules are constrained to be taken from an ``inner'' codebook associated with the sequencing channel. This codebook is used in a…
In this paper, based on the limited memory techniques and subspace minimization conjugate gradient (SMCG) methods, a regularized limited memory subspace minimization conjugate gradient method is proposed, which contains two types of…
The last five years of research on distributed graph algorithms have seen huge leaps of progress, both regarding algorithmic improvements and impossibility results: new strong lower bounds have emerged for many central problems and…
In real-time trajectory planning for unmanned vehicles, on-board sensors, radars and other instruments are used to collect information on possible obstacles to be avoided and pathways to be followed. Since, in practice, observations of the…
Genetic algorithm (GA) is typically used to solve nonlinear model predictive control's optimization problem. However, the size of the search space in which the GA searches for the optimal control inputs is crucial for its applicability to…
In this paper, we construct linear codes over $\mathbb{Z}_4$ with bounded $GC$-content. The codes are obtained using a greedy algorithm over $\mathbb{Z}_4$. Further, upper and lower bounds are derived for the maximum size of DNA codes of…
In this thesis, I study the minimax oracle complexity of distributed stochastic optimization. First, I present the "graph oracle model", an extension of the classic oracle complexity framework that can be applied to study distributed…
Modern biological science produces vast amounts of genomic sequence data. This is fuelling the need for efficient algorithms for sequence compression and analysis. Data compression and the associated techniques coming from information…
In this paper the approach to solving several combinatorial optimization problems using the local search and the genetic algorithm techniques is proposed. Initially this approach was developed in purpose to overcome some difficulties…
Quantum search algorithms are considered in the context of protein sequence comparison in biocomputing. Given a sample protein sequence of length m (i.e m residues), the problem considered is to find an optimal match in a large database…
The coverage depth problem in DNA data storage is about minimizing the expected number of reads until all data is recovered. When they exist, MDS codes offer the best performance in this context. This paper focuses on the scenario where the…
We show that a large fraction of the data-structure lower bounds known today in fact follow by reduction from the communication complexity of lopsided (asymmetric) set disjointness. This includes lower bounds for: * high-dimensional…