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1. An Ultra-Fast and Parallelizable Algorithm for Finding $$k$$-Mismatch Shortest Unique Substrings

   https://doi.org/10.1109/TCBB.2020.2968531  

   Allen, Daniel R.; Thankachan, Sharma V.; Xu, Bojian (January 2021, IEEE/ACM Transactions on Computational Biology and Bioinformatics)

   null (Ed.)

   This paper revisits the k-mismatch shortest unique substring finding problem and demonstrates that a technique recently presented in the context of solving the k-mismatch average common substring problem can be adapted and combined with parts of the existing solution, resulting in a new algorithm which has expected time complexity of O(n log^k n), while maintaining a practical space complexity at O(kn), where n is the string length. When , which is the hard case, our new proposal significantly improves the any-case O(n^2) time complexity of the prior best method for k-mismatch shortest unique substring finding. Experimental study shows that our new algorithm is practical to implement and demonstrates significant improvements in processing time compared to the prior best solution's implementation when k is small relative to n. For example, our method processes a 200 KB sample DNA sequence with k=1 in just 0.18 seconds compared to 174.37 seconds with the prior best solution. Further, it is observed that significant portions of the adapted technique can be executed in parallel, using two different simple concurrency models, resulting in further significant practical performance improvement. As an example, when using 8 cores, the parallel implementations both achieved processing times that are less than 1/4 of the serial implementation's time cost, when processing a 10 MB sample DNA sequence with k=2. In an age where instances with thousands of gigabytes of RAM are readily available for use through Cloud infrastructure providers, it is likely that the trade-off of additional memory usage for significantly improved processing times will be desirable and needed by many users. For example, the best prior solution may spend years to finish a DNA sample of 200MB for any , while this new proposal, using 24 cores, can finish processing a sample of this size with k=1 in 206.376 seconds with a peak memory usage of 46 GB, which is both easily available and affordable on Cloud. It is expected that this new efficient and practical algorithm for k-mismatch shortest unique substring finding will prove useful to those using the measure on long sequences in fields such as computational biology. We also give a theoretical bound that the k-mismatch shortest unique substring finding problem can be solved using O(n log^k n) time and O(n) space, asymptotically much better than the one we implemented, serving as a new discovery of interest. 

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2. Counting Simplices in Hypergraph Streams

   Chakrabarti, Amit; Haris, Themistoklis (October 2022, Leibniz international proceedings in informatics)

   We consider the problem of space-efficiently estimating the number of simplices in a hypergraph stream. This is the most natural hypergraph generalization of the highly-studied problem of estimating the number of triangles in a graph stream. Our input is a k-uniform hypergraph H with n vertices and m hyperedges, each hyperedge being a k-sized subset of vertices. A k-simplex in H is a subhypergraph on k+1 vertices X such that all k+1 possible hyperedges among X exist in H. The goal is to process the hyperedges of H, which arrive in an arbitrary order as a data stream, and compute a good estimate of T_k(H), the number of k-simplices in H. We design a suite of algorithms for this problem. As with triangle-counting in graphs (which is the special case k = 2), sublinear space is achievable but only under a promise of the form T_k(H) ≥ T. Under such a promise, our algorithms use at most four passes and together imply a space bound of O(ε^{-2} log δ^{-1} polylog n ⋅ min{(m^{1+1/k})/T, m/(T^{2/(k+1)})}) for each fixed k ≥ 3, in order to guarantee an estimate within (1±ε)T_k(H) with probability ≥ 1-δ. We also give a simpler 1-pass algorithm that achieves O(ε^{-2} log δ^{-1} log n⋅ (m/T) (Δ_E + Δ_V^{1-1/k})) space, where Δ_E (respectively, Δ_V) denotes the maximum number of k-simplices that share a hyperedge (respectively, a vertex), which generalizes a previous result for the k = 2 case. We complement these algorithmic results with space lower bounds of the form Ω(ε^{-2}), Ω(m^{1+1/k}/T), Ω(m/T^{1-1/k}) and Ω(mΔ_V^{1/k}/T) for multi-pass algorithms and Ω(mΔ_E/T) for 1-pass algorithms, which show that some of the dependencies on parameters in our upper bounds are nearly tight. Our techniques extend and generalize several different ideas previously developed for triangle counting in graphs, using appropriate innovations to handle the more complicated combinatorics of hypergraphs. 

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3. Improved Algorithms for Maximum Coverage in Dynamic and Random Order Streams

   https://doi.org/10.4230/LIPICS.ESA.2024.40  

   Chakrabarti, Amit; McGregor, Andrew; Wirth, Anthony (January 2024, Schloss Dagstuhl – Leibniz-Zentrum für Informatik)

   Chan, Timothy; Fischer, Johannes; Iacono, John; Herman, Grzegorz (Ed.)

   The maximum coverage problem is to select k sets, from a collection of m sets, such that the cardinality of their union, in a universe of size n, is maximized. We consider (1-1/e-ε)-approximation algorithms for this NP-hard problem in three standard data stream models. 1) Dynamic Model. The stream consists of a sequence of sets being inserted and deleted. Our multi-pass algorithm uses ε^{-2} k ⋅ polylog(n,m) space. The best previous result (Assadi and Khanna, SODA 2018) used (n +ε^{-4} k) polylog(n,m) space. While both algorithms use O(ε^{-1} log m) passes, our analysis shows that, when ε ≤ 1/log log m, it is possible to reduce the number of passes by a 1/log log m factor without incurring additional space. 2) Random Order Model. In this model, there are no deletions, and the sets forming the instance are uniformly randomly permuted to form the input stream. We show that a single pass and k polylog(n,m) space suffices for arbitrary small constant ε. The best previous result, by Warneke et al. (ESA 2023), used k² polylog(n,m) space. 3) Insert-Only Model. Lastly, our results, along with numerous previous results, use a sub-sampling technique introduced by McGregor and Vu (ICDT 2017) to sparsify the input instance. We explain how this technique and others used in the paper can be implemented such that the amortized update time of our algorithm is polylogarithmic. This also implies an improvement of the state-of-the-art insert only algorithms in terms of the update time: polylog(m,n) update time suffices, whereas the best previous result by Jaud et al. (SEA 2023) required update time that was linear in k. 

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4. A New Algorithm for Euclidean Shortest Paths in the Plane

   https://doi.org/10.1145/3580475  

   Wang, Haitao (April 2023, Journal of the ACM)

   Given a set of pairwise disjoint polygonal obstacles in the plane, finding an obstacle-avoiding Euclidean shortest path between two points is a classical problem in computational geometry and has been studied extensively. Previously, Hershberger and Suri (in SIAM Journal on Computing , 1999) gave an algorithm of O(n log n ) time and O(n log n ) space, where n is the total number of vertices of all obstacles. Recently, by modifying Hershberger and Suri’s algorithm, Wang (in SODA’21) reduced the space to O(n) while the runtime of the algorithm is still O(n log n ). In this article, we present a new algorithm of O(n+h log h ) time and O(n) space, provided that a triangulation of the free space is given, where h is the number of obstacles. The algorithm is better than the previous work when h is relatively small. Our algorithm builds a shortest path map for a source point s so that given any query point t , the shortest path length from s to t can be computed in O (log n ) time and a shortest s - t path can be produced in additional time linear in the number of edges of the path. 

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5. Subtrajectory Clustering: Finding Set Covers for Set Systems of Subcurves

   Brüning, F.; Akitaya, H.; Chambers, E; Driemel, A (February 2023, Computing in geometry and topology)

   We study subtrajectory clustering under the Fréchet distance. Given one or more trajectories, the task is to split the trajectories into several parts, such that the parts have a good clustering structure. We approach this problem via a new set cover formulation, which we think provides a natural formalization of the problem as it is studied in many applications. Given a polygonal curve P with n vertices in fixed dimension, integers k, ℓ ≥ 1, and a real value Δ > 0, the goal is to find k center curves of complexity at most ℓ such that every point on P is covered by a subtrajectory that has small Fréchet distance to one of the k center curves (≤ Δ). In many application scenarios, one is interested in finding clusters of small complexity, which is controlled by the parameter ℓ. Our main result is a bicriterial approximation algorithm: if there exists a solution for given parameters k, ℓ, and Δ, then our algorithm finds a set of k' center curves of complexity at most ℓ with covering radius Δ' with k' in O(kℓ2 log (kℓ)), and Δ' ≤ 19Δ. Moreover, within these approximation bounds, we can minimize k while keeping the other parameters fixed. If ℓ is a constant independent of n, then, the approximation factor for the number of clusters k is O(log k) and the approximation factor for the radius Δ is constant. In this case, the algorithm has expected running time in Õ(km2 + mn) and uses space in O(n + m), where m=⌈L/Δ⌉ and L is the total arclength of the curve P. 

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