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Graphs are a powerful tool for analyzing large data sets, but many real-world phenomena involve interactions that go beyond the simple pairwise relationships captured by a graph. In this paper we introduce and study a simple combinatorial…
We study the classic set cover problem from the perspective of sub-linear algorithms. Given access to a collection of $m$ sets over $n$ elements in the query model, we show that sub-linear algorithms derived from existing techniques have…
Recently, Marcus et al. (Bioinformatics 2014) proposed to use a compressed de Bruijn graph to describe the relationship between the genomes of many individuals/strains of the same or closely related species. They devised an $O(n \log g)$…
Term unification plays an important role in many areas of computer science, especially in those related to logic. The universal mechanism of grammar-based compression for terms, in particular the so-called Singleton Tree Grammars (STG),…
A major challenge in next-generation genome sequencing (NGS) is to assemble massive overlapping short reads that are randomly sampled from DNA fragments. To complete assembling, one needs to finish a fundamental task in many leading…
Given a set of strings, the shortest common superstring problem is to find the shortest possible string that contains all the input strings. The problem is NP-hard, but a lot of work has gone into designing approximation algorithms for…
Spectral graph sparsification is a classical tool for reducing graph complexity while preserving Laplacian quadratic forms. In graph neural networks (GNNs), sparsification is often used to accelerate computation while maintaining predictive…
This paper describes the adaptation of a well-scaling parallel algorithm for computing Morse-Smale segmentations based on path compression to a distributed computational setting. Additionally, we extend the algorithm to efficiently compute…
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 research, we apply ensembles of Fourier encoded spectra to capture and mine recurring concepts in a data stream environment. Previous research showed that compact versions of Decision Trees can be obtained by applying the Discrete…
Background Next Generation Sequencing (NGS) has dramatically enhanced our ability to sequence genomes, but not to assemble them. In practice, many published genome sequences remain in the state of a large set of contigs. Each contig…
The decision problem of perfect matchings in uniform hypergraphs is famously an NP-complete problem. It has been shown by Keevash--Knox--Mycroft [STOC, 2013] that for every $\varepsilon>0$, such decision problem restricted to $k$-uniform…
Coverage problems are central in optimization and have a wide range of applications in data mining and machine learning. While several distributed algorithms have been developed for coverage problems, the existing methods suffer from…
In this thesis, we address the problem of identifying and quantifying variants (alternative splicing and genomic polymorphism) in RNA-seq data when no reference genome is available, without assembling the full transcripts. Based on the…
Genome assembly tools based on the de Bruijn graph framework rely on a parameter k, which represents a trade-off between several competing effects that are difficult to quantify. There is currently a lack of tools that would automatically…
The k-truss is a type of cohesive subgraphs proposed recently for the study of networks. While the problem of computing most cohesive subgraphs is NP-hard, there exists a polynomial time algorithm for computing k-truss. Compared with k-core…
To develop effective and efficient graph similarity learning (GSL) models, a series of data-driven neural algorithms have been proposed in recent years. Although GSL models are frequently deployed in privacy-sensitive scenarios, the user…
Quantum compilation requires the development of new algorithms that optimise the cost of implementing quantum computations on physical hardware. Often this gives rise to problems which are asymptotically hard to solve classically, and for…
Finding spanning trees under various constraints is a classic problem with applications in many fields. Recently, a novel notion of "dense" ("sparse") tree, and in particular spanning tree (DST and SST respectively), is introduced as the…
In the context of algorithm theory, various studies have been conducted on spanning trees with desirable properties. In this paper, we consider the \textsc{Minimum Cover Spanning Tree} problem (MCST for short). Given a graph $G$ and a…