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The main objective of this paper is to solve the optimization problem that is associated with the classification of DNA samples in PCR plates for Sanger sequencing. To achieve this goal, we design an integer linear programming model. Given…
Generalizations of plain strings have been proposed as a compact way to represent a collection of nearly identical sequences or to express uncertainty at specific text positions by enumerating all possibilities. While a plain string stores…
Information leaks are a significant problem in modern computer systems and string manipulation is prevalent in modern software. We present techniques for automated synthesis of side-channel attacks that recover secret string values based on…
The problem of reconstructing strings from substring information has found many applications due to its importance in genomic data sequencing and DNA- and polymer-based data storage. One practically important and challenging paradigm…
Subset selection in multiple linear regression aims to choose a subset of candidate explanatory variables that tradeoff fitting error (explanatory power) and model complexity (number of variables selected). We build mathematical programming…
The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…
In this paper, we present a toolbox for a specific optimization problem that frequently arises in bioinformatics or genomics. In this specific optimisation problem, the state space is a set of words of specified length over a finite…
String matching is the problem of finding all the occurrences of a pattern in a text. We propose improved versions of the fast family of string matching algorithms based on hashing $q$-grams. The improvement consists of considering minimal…
String analysis is the problem of reasoning about how strings are manipulated by a program. It has numerous applications including automatic detection of cross-site scripting (XSS). A popular string analysis technique includes symbolic…
Repeat finding in strings has important applications in subfields such as computational biology. The challenge of finding the longest repeats covering particular string positions was recently proposed and solved by \.{I}leri et al., using a…
Recently, Tensor Ring Networks (TRNs) have been applied in deep networks, achieving remarkable successes in compression ratio and accuracy. Although highly related to the performance of TRNs, rank selection is seldom studied in previous…
An elastic-degenerate (ED) string is a sequence of $n$ sets of strings of total length $N$, which was recently proposed to model a set of similar sequences. The ED string matching (EDSM) problem is to find all occurrences of a pattern of…
Relative compression, where a set of similar strings are compressed with respect to a reference string, is a very effective method of compressing DNA datasets containing multiple similar sequences. Relative compression is fast to perform…
An elastic-degenerate string is a sequence of $n$ finite sets of strings of total length $N$, introduced to represent a set of related DNA sequences, also known as a pangenome. The ED string matching (EDSM) problem consists in reporting all…
Discrete biological sequence optimization requires iterative refinement under strict syntactic constraints. Diffusion models offer progressive refinement but do not naturally expose controllable discrete edit operations, while…
Deep neural networks (DNNs) frequently contain far more weights, represented at a higher precision, than are required for the specific task which they are trained to perform. Consequently, they can often be compressed using techniques such…
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…
Compressed indexing is a powerful technique that enables efficient querying over data stored in compressed form, significantly reducing memory usage and often accelerating computation. While extensive progress has been made for…
Strings are widely used in programs, especially in web applications. Integer data type occurs naturally in string-manipulating programs, and is frequently used to refer to lengths of, or positions in, strings. Analysis and testing of…
Reduction of combinatorial filters involves compressing state representations that robots use. Such optimization arises in automating the construction of minimalist robots. But exact combinatorial filter reduction is an NP-complete problem…