Related papers: Genome assembly, from practice to theory: safe, co…
We introduce the straggler identification problem, in which an algorithm must determine the identities of the remaining members of a set after it has had a large number of insertion and deletion operations performed on it, and now has…
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…
Graph embeddings are low dimensional representations of nodes, edges or whole graphs. Such representations allow for data in a network format to be used along with machine learning models for a variety of tasks (e.g., node classification),…
The repeat content and heterozygosity rate of a target genome are important factors in determining the feasibility of achieving a complete telomere-to-telomere assembly. The mathematical relationship between the required coverage and read…
We introduce a parallel algorithmic architecture for metagenomic sequence assembly, termed MetaPar, which allows for significant reductions in assembly time and consequently enables the processing of large genomic datasets on computers with…
Omics technologies enable unbiased investigation of biological systems through massively parallel sequence acquisition or molecular measurements, bringing the life sciences into the era of Big Data. A central challenge posed by such omics…
Connectivity (or equivalently, unweighted maximum flow) is an important measure in graph theory and combinatorial optimization. Given a graph $G$ with vertices $s$ and $t$, the connectivity $\lambda(s,t)$ from $s$ to $t$ is defined to be…
We give an algorithm for finding the arboricity of a weighted, undirected graph, defined as the minimum number of spanning forests that cover all edges of the graph, in $\sqrt{n} m^{1+o(1)}$ time. This improves on the previous best bound of…
Genome-to-genome comparisons require designating anchor points, which are given by Maximum Exact Matches (MEMs) between their sequences. For large genomes this is a challenging problem and the performance of existing solutions, even in…
In real life, it is always an urge to reach our goal in minimum effort i.e., it should have a minimum constrained path. The path may be shortest route in practical life, either physical or electronic medium. The scenario is to represents…
This paper proposes a new general technique for maximal subgraph enumeration which we call proximity search, whose aim is to design efficient enumeration algorithms for problems that could not be solved by existing frameworks. To support…
We demonstrate that the assembly pathway method underlying assembly theory (AT) is an encoding scheme widely used by popular statistical compression algorithms. We show that in all cases (synthetic or natural) AT performs similarly to other…
Recent advancements in microbiology have motivated the study of the production of nanostructures with applications such as biomedical computing and molecular robotics. One way to construct these structures is to construct branched DNA…
A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…
In the String Matching in Labeled Graphs (SMLG) problem, we need to determine whether a pattern string appears on a given labeled graph or a given automaton. Under the Orthogonal Vectors hypothesis, the SMLG problem cannot be solved in…
A Bayesian network is a directed acyclic graph that represents statistical dependencies between variables of a joint probability distribution. A fundamental task in data science is to learn a Bayesian network from observed data.…
We study ranked enumeration of join-query results according to very general orders defined by selective dioids. Our main contribution is a framework for ranked enumeration over a class of dynamic programming problems that generalizes…
In this paper, we consider tree decompositions, branch decompositions, and clique decompositions. We improve the running time of dynamic programming algorithms on these graph decompositions for a large number of problems as a function of…
We revisit the complexity of approximate pattern matching in an elastic-degenerate string. Such a string is a sequence of $n$ finite sets of strings of total length $N$, and compactly describes a collection of strings obtained by first…
In this paper, we consider two versions of the Text Assembling problem. We are given a sequence of strings $s^1,\dots,s^n$ of total length $L$ that is a dictionary, and a string $t$ of length $m$ that is texts. The first version of the…