Related papers: Improved Lower Bounds for Constant GC-Content DNA …
We prove lower bounds on the error probability of a quantum algorithm for searching through an unordered list of N items, as a function of the number T of queries it makes. In particular, if T=O(sqrt{N}) then the error is lower bounded by a…
Motivation: Despite significant advances in Third-Generation Sequencing (TGS) technologies, Next-Generation Sequencing (NGS) technologies remain dominant in the current sequencing market. This is due to the lower error rates and richer…
We introduce a stochastic framework into the open--source Core Imaging Library (CIL) which enables easy development of stochastic algorithms. Five such algorithms from the literature are developed, Stochastic Gradient Descent, Stochastic…
Traditional online continual learning (OCL) research has primarily focused on mitigating catastrophic forgetting with fixed and limited storage allocation throughout an agent's lifetime. However, a broad range of real-world applications are…
This thesis develops computational methods in similarity-preserving hashing, classification, and cancer genomics. Standard space partitioning-based hashing relies on Binary Search Trees (BSTs), but their exponential growth and sparsity…
Motivated by applications to DNA storage, we study reconstruction and list-reconstruction schemes for integer vectors that suffer from limited-magnitude errors. We characterize the asymptotic size of the intersection of error balls in…
Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…
This paper uses stochastic dominance principles to construct upper and lower sample path bounds for Hidden Markov Model (HMM) filters. Given a HMM, by using convex optimization methods for nuclear norm minimization with copositive…
Local search is a powerful heuristic in optimization and computer science, the complexity of which has been studied in the white box and black box models. In the black box model, we are given a graph $G = (V,E)$ and oracle access to a…
We study linear codes that maximize minimum distance subject to arbitrary support constraints on the parity-check matrix. Such constraints arise naturally in the design of LDPC codes, locally repairable codes, and hardware-constrained…
As a possible implementation of data storage using DNA, multiple strands of DNA are stored in a liquid container so that, in the future, they can be read by an array of DNA readers in parallel. These readers will sample the strands with…
DNA-based data storage has been attracting significant attention due to its extremely high data storage density, low power consumption, and long duration compared to conventional data storage media. Despite the recent advancements in DNA…
In the study of deterministic distributed algorithms it is commonly assumed that each node has a unique $O(\log n)$-bit identifier. We prove that for a general class of graph problems, local algorithms (constant-time distributed algorithms)…
We investigate the limits of one of the fundamental ideas in data structures: fractional cascading. This is an important data structure technique to speed up repeated searches for the same key in multiple lists and it has numerous…
In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount…
Over the past two decades, a series of works have aimed at studying the problem of genome assembly: the process of reconstructing a genome from sequence reads. An early formulation of the genome assembly problem showed that genome…
High-density oligonucleotide arrays are among the most rapidly expanding technologies in biology today. In the {\sl GeneChip} system, the reconstruction of the target concentration depends upon the differential signal generated from…
We prove that any exact quantum algorithm searching an ordered list of N elements requires more than \frac{1}{\pi}(\ln(N)-1) queries to the list. This improves upon the previously best known lower bound of {1/12}\log_2(N) - O(1). Our proof…
We consider a new family of codes, termed asymmetric Lee distance codes, that arise in the design and implementation of DNA-based storage systems and systems with parallel string transmission protocols. The codewords are defined over a…
The past decade highlighted the usefulness of social network simulations that run on k-regular, n-size, connected graphs. These can be seen as small-scale models of human social networks of large societies. By narrowing down onto k-regular…