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In this paper, we first consider the subpath convex hull query problem: Given a simple path $\pi$ of $n$ vertices, preprocess it so that the convex hull of any query subpath of $\pi$ can be quickly obtained. Previously, Guibas, Hershberger,…
The Burrows-Wheeler Transform (BWT) is often taught in undergraduate courses on algorithmic bioinformatics, because it underlies the FM-index and thus important tools such as Bowtie and BWA. Its admirers consider the BWT a thing of beauty…
Efficient structure search is a major challenge in computational materials science. We present a modification of the basin hopping global geometry optimization approach that uses a curvilinear coordinate system to describe global trial…
The need for scalable concurrent ordered set data structures with linearizable range query support is increasing due to the rise of multicore computers, data processing platforms and in-memory databases. This paper presents a new concurrent…
Binary relations are commonly used in Computer Science for modeling data. In addition to classical representations using matrices or lists, some compressed data structures have recently been proposed to represent binary relations in compact…
Finding the minimum distance of linear codes is an NP-hard problem. Traditionally, this computation has been addressed by means of the design of algorithms that find, by a clever exhaustive search, a linear combination of some generating…
In this paper, we show that the LZ77 factorization of a text T {\in\Sigma^n} can be computed in O(R log n) bits of working space and O(n log R) time, R being the number of runs in the Burrows-Wheeler transform of T reversed. For extremely…
Structural decomposition methods offer powerful theoretical guarantees for join evaluation, yet they are rarely used in real-world query optimizers. A major reason is the difficulty of combining cost-based plan search and structure-based…
The NP-complete Permutation Pattern Matching problem asks whether a $k$-permutation $P$ is contained in a $n$-permutation $T$ as a pattern. This is the case if there exists an order-preserving embedding of $P$ into $T$. In this paper, we…
In this paper we study lower bounds for the fundamental problem of text indexing with mismatches and differences. In this problem we are given a long string of length $n$, the "text", and the task is to preprocess it into a data structure…
Despite the performance advantages of modern sampling-based motion planners, solving high dimensional planning problems in near real-time remains a challenge. Applications include hyper-redundant manipulators, snake-like and humanoid…
Prefix-free parsing (PFP) was introduced by Boucher et al. (2019) as a preprocessing step to ease the computation of Burrows-Wheeler Transforms (BWTs) of genomic databases. Given a string $S$, it produces a dictionary $D$ and a parse $P$ of…
Path planning has long been one of the major research areas in robotics, with PRM and RRT being two of the most effective classes of planners. Though generally very efficient, these sampling-based planners can become computationally…
Continuous time quantum walks provide an important framework for designing new algorithms and modelling quantum transport and state transfer problems. Often, the graph representing the structure of a problem contains certain symmetries that…
Simulating fermionic systems on a quantum computer requires representing fermionic states using qubits. The complexity of many simulation algorithms depends on the complexity of implementing rotations generated by fermionic…
In an input-queued switch, a crossbar schedule, or a matching between the input ports and the output ports needs to be computed in each switching cycle, or time slot. Designing switching algorithms with very low computational complexity,…
We consider preprocessing a set $S$ of $n$ points in convex position in the plane into a data structure supporting queries of the following form: given a point $q$ and a directed line $\ell$ in the plane, report the point of $S$ that is…
Compared to basic fork-join queues, a job in (n, k) fork-join queues only needs its k out of all n sub-tasks to be finished. Since (n, k) fork-join queues are prevalent in popular distributed systems, erasure coding based cloud storages,…
Suffix tree (and the closely related suffix array) are fundamental structures capturing all substrings of a given text essentially by storing all its suffixes in the lexicographical order. In some applications, we work with a subset of $b$…
In this paper we present two versions of a parallel working-set map on p processors that supports searches, insertions and deletions. In both versions, the total work of all operations when the map has size at least p is bounded by the…