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We study algorithms for solving three problems on strings. The first one is the Most Frequently String Search Problem. The problem is the following. Assume that we have a sequence of $n$ strings of length $k$. The problem is finding the…
State-of-the-art parallel sorting algorithms for distributed-memory architectures are based on computing a balanced partitioning via sampling and histogramming. By finding samples that partition the sorted keys into evenly-sized chunks,…
We propose an exact algorithm for solving the longest simple path problem between two given vertices in undirected weighted graphs. By using graph partitioning and dynamic programming, we obtain an algorithm that is significantly faster…
It has recently been shown that starting with a classical query algorithm (decision tree) and a guessing algorithm that tries to predict the query answers, we can design a quantum algorithm with query complexity $O(\sqrt{GT})$ where $T$ is…
Dispersion of mobile robots over the nodes of an anonymous graph is an important problem and turns out to be a crucial subroutine for designing efficient algorithms for many fundamental graph problems via mobile robots. In this problem,…
We present an implementation of a recent algorithm to compute shortest-path trees in unit disk graphs in $O(n\log n)$ worst-case time, where $n$ is the number of disks. In the minimum-separation problem, we are given $n$ unit disks and two…
Given a graph $G$, a proper $k$-coloring of $G$ is a partition $c = (S_i)_{i\in [1,k]}$ of $V(G)$ into $k$ stable sets $S_1,\ldots, S_{k}$. Given a weight function $w: V(G) \to \mathbb{R}^+$, the weight of a color $S_i$ is defined as $w(i)…
Max-k-Cut and correlation clustering are fundamental graph partitioning problems. For a graph with G=(V,E) with n vertices, the methods with the best approximation guarantees for Max-k-Cut and the Max-Agree variant of correlation clustering…
We present an $m^{4/3+o(1)}\log W$-time algorithm for solving the minimum cost flow problem in graphs with unit capacity, where $W$ is the maximum absolute value of any edge weight. For sparse graphs, this improves over the best known…
Partitioning a region into districts to favor a particular candidate or a party is commonly known as gerrymandering. In this paper, we investigate the gerrymandering problem in graph theoretic setting as proposed by Cohen-Zemach et al.…
This paper presents the results of an experimental study of graph partitioning. We describe a new heuristic technique, path optimization, and its application to two variations of graph partitioning: the max_cut problem and the…
Graph partitioning schedules parallel calculations like sparse matrix-vector multiply (SpMV). We consider contiguous partitions, where the $m$ rows (or columns) of a sparse matrix with $N$ nonzeros are split into $K$ parts without…
Given a signed permutation on $n$ elements, we need to sort it with the fewest reversals. This is a fundamental algorithmic problem motivated by applications in comparative genomics, as it allows to accurately model rearrangements in small…
There has recently been much progress on exact algorithms for the (un)weighted graph (bi)partitioning problem using branch-and-bound and related methods. In this note we present and improve an easily computable, purely combinatorial lower…
A common way of partitioning graphs is through minimum cuts. One drawback of classical minimum cut methods is that they tend to produce small groups, which is why more balanced variants such as normalized and ratio cuts have seen more…
We show that many classical optimization problems --- such as $(1\pm\epsilon)$-approximate maximum flow, shortest path, and transshipment --- can be computed in $\newcommand{\tmix}{{\tau_{\text{mix}}}}\tmix(G)\cdot n^{o(1)}$ rounds of…
We present a set of rules to guide the design of GPU algorithms. These rules are grounded on the principle of reducing waste in GPU utility to achieve good speed up. In accordance to these rules, we propose GPU algorithms for 2D…
Solving exactly Combinatorial Optimization Problems (COPs) using a Branch-and-Bound (B&B) algorithm requires a huge amount of computational resources. Therefore, we recently investigated designing B&B algorithms on top of graphics…
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…
Random reshuffling, which randomly permutes the dataset each epoch, is widely adopted in model training because it yields faster convergence than with-replacement sampling. Recent studies indicate greedily chosen data orderings can further…