Related papers: Randomized Fast Design of Short DNA Words
Efficient algorithms for searching for optimal saturated designs are widely available. They maximize a given efficiency measure (such as D-optimality) and provide an optimum design. Nevertheless, they do not guarantee a \emph{global}…
This paper concerns non-overlapping codes, block codes motivated by synchronisation and DNA-based storage applications. Most existing constructions of these codes do not account for the restrictions posed by the physical properties of…
Genetic Algorithms have established their capability for solving many complex optimization problems. Even as good solutions are produced, the user's understanding of a problem is not necessarily improved, which can lead to a lack of…
In this paper, we consider the ``Shortest Superstring Problem''(SSP) or the ``Shortest Common Superstring Problem''(SCS). The problem is as follows. For a positive integer $n$, a sequence of n strings $S=(s^1,\dots,s^n)$ is given. We should…
We present a detailed study of the performance and reliability of design procedures based on energy minimization. The analysis is carried out for model proteins where exact results can be obtained through exhaustive enumeration. The…
Given a pattern string $P$ of length $n$ consisting of $\delta$ distinct characters and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet $\Sigma$ of size $\Delta$, the {\em exact string…
Genomic expression depends critically both on the ability of regulatory proteins to locate specific target sites on a DNA within seconds and on the formation of long lived (many minutes) complexes between these proteins and the DNA.…
Tandem duplication is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain et al. (2017) proposed the study of codes that correct tandem…
Designing regulatory DNA sequences that achieve precise cell-type-specific gene expression is crucial for advancements in synthetic biology, gene therapy and precision medicine. Although transformer-based language models (LMs) can…
Given a set of pattern strings $\mathcal{P}=\{P_1, P_2,\ldots P_k\}$ and a text string $S$, the classic dictionary matching problem is to report all occurrences of each pattern in $S$. We study the dictionary problem in the compressed…
We study the problem of coded information retrieval for block-structured data, motivated by DNA-based storage systems where a database is partitioned into multiple files that must each be recoverable as an atomic unit. We initiate and…
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…
Algorithms to find optimal alignments among strings, or to find a parsimonious summary of a collection of strings, are well studied in a variety of contexts, addressing a wide range of interesting applications. In this paper, we consider…
String matching is the problem of finding all the substrings of a text which match a given pattern. It is one of the most investigated problems in computer science, mainly due to its very diverse applications in several fields. Recently,…
The approximate string matching is a fundamental and recurrent problem that arises in most computer science fields. This problem can be defined as follows: Let $D=\{x_1,x_2,\ldots x_d\}$ be a set of $d$ words defined on an alphabet…
We initiate a systematic study of utilizing predictions to improve over approximation guarantees of classic algorithms, without increasing the running time. We propose a systematic method for a wide class of optimization problems that ask…
We describe an implementation of a genetic algorithm on partially commutative groups and apply it to the double coset search problem on a subclass of groups. This transforms a combinatorial group theory problem to a problem of combinatorial…
DNA code design aims to generate a set of DNA sequences (codewords) with minimum likelihood of undesired hybridizations among sequences and their reverse-complement (RC) pairs (cross-hybridization). Inspired by the distinct hybridization…
Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…
The genetic selection of keywords set, the text frequencies of which are considered as attributes in text classification analysis, has been analyzed. The genetic optimization was performed on a set of words, which is the fraction of the…