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1. Ranked Document Retrieval in External Memory

   https://doi.org/10.1145/3559763  

   Shah, Rahul ; Sheng, Cheng ; Thankachan, Sharma ; Vitter, Jeffrey ( January 2023 , ACM Transactions on Algorithms)

   The ranked (or top-k) document retrieval problem is defined as follows: preprocess a collection{T₁,T₂,… ,T_d}ofdstrings (called documents) of total lengthninto a data structure, such that for any given query(P,k), wherePis a string (called pattern) of lengthp ≥ 1andk ∈ [1,d]is an integer, the identifiers of thosekdocuments that are most relevant toPcan be reported, ideally in the sorted order of their relevance. The seminal work by Hon et al. [FOCS 2009 and Journal of the ACM 2014] presented anO(n)-space (in words) data structure withO(p+klogk)query time. The query time was later improved toO(p+k)[SODA 2012] and further toO(p/log_σn+k)[SIAM Journal on Computing 2017] by Navarro and Nekrich, whereσis the alphabet size. We revisit this problem in the external memory model and present three data structures. The first one takesO(n)-space and answer queries inO(p/B+ log_Bn + k/B+log^*(n/B)) I/Os, whereBis the block size. The second one takesO(nlog^*(n/B)) space and answer queries in optimalO(p/B+ log_Bn + k/B)I/Os. In both cases, the answers are reported in the unsorted order of relevance. To handle sorted top-kdocument retrieval, we present anO(nlog(d/B))space data structure with optimal query cost.

    

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2. 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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3. Fully Functional Parameterized Suffix Trees in Compact Space

   Ganguly, Arnab ; Shah, Rahul ; Thankachan, Sharma V. ( June 2022 , 49th International Colloquium on Automata, Languages, and Programming (ICALP 2022))

   Mikolaj Bojanczyk ; Emanuela Merelli ; David P. Woodruff (Ed.)

   Two equal length strings are a parameterized match (p-match) iff there exists a one-to-one function that renames the symbols in one string to those in the other. The Parameterized Suffix Tree (PST) [Baker, STOC' 93] is a fundamental data structure that handles various string matching problems under this setting. The PST of a text T[1,n] over an alphabet Σ of size σ takes O(nlog n) bits of space. It can report any entry in (parameterized) (i) suffix array, (ii) inverse suffix array, and (iii) longest common prefix (LCP) array in O(1) time. Given any pattern P as a query, a position i in T is an occurrence iff T[i,i+|P|-1] and P are a p-match. The PST can count the number of occurrences of P in T in time O(|P|log σ) and then report each occurrence in time proportional to that of accessing a suffix array entry. An important question is, can we obtain a compressed version of PST that takes space close to the text’s size of nlogσ bits and still support all three functionalities mentioned earlier? In SODA' 17, Ganguly et al. answered this question partially by presenting an O(nlogσ) bit index that can support (parameterized) suffix array and inverse suffix array operations in O(log n) time. However, the compression of the (parameterized) LCP array and the possibility of faster suffix array and inverse suffix array queries in compact space were left open. In this work, we obtain a compact representation of the (parameterized) LCP array. With this result, in conjunction with three new (parameterized) suffix array representations, we obtain the first set of PST representations in o(nlog n) bits (when logσ = o(log n)) as follows. Here ε > 0 is an arbitrarily small constant. - Space O(n logσ) bits and query time O(log_σ^ε n); - Space O(n logσlog log_σ n) bits and query time O(log log_σ n); and - Space O(n logσ log^ε_σ n) bits and query time O(1). The first trade-off is an improvement over Ganguly et al.’s result, whereas our third trade-off matches the optimal time performance of Baker’s PST while squeezing the space by a factor roughly log_σ n. We highlight that our trade-offs match the space-and-time bounds of the best-known compressed text indexes for exact pattern matching and further improvement is highly unlikely. 

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4. Fast Dynamic Cuts, Distances and Effective Resistances via Vertex Sparsifiers

   https://doi.org/10.1109/FOCS46700.2020.00109  

   Chen, Li ; Goranci, Gramoz ; Henzinger, Monika ; Peng, Richard ; Saranurak, Thatchaphol ( November 2020 , 61st IEEE Annual Symposium on Foundations of Computer Science, FOCS 2020, Durham, NC, USA, November 16-19, 2020)

   null (Ed.)

   We present a general framework of designing efficient dynamic approximate algorithms for optimization on undirected graphs. In particular, we develop a technique that, given any problem that admits a certain notion of vertex sparsifiers, gives data structures that maintain approximate solutions in sub-linear update and query time. We illustrate the applicability of our paradigm to the following problems. (1) A fully-dynamic algorithm that approximates all-pair maximum-flows/minimum-cuts up to a nearly logarithmic factor in $\tilde{O}(n^{2/3})$ amortized time against an oblivious adversary, and $\tilde{O}(m^{3/4})$ time against an adaptive adversary. (2) An incremental data structure that maintains $O(1)$-approximate shortest path in $n^{o(1)}$ time per operation, as well as fully dynamic approximate all-pair shortest path and transshipment in $\tilde{O}(n^{2/3+o(1)})$ amortized time per operation. (3) A fully-dynamic algorithm that approximates all-pair effective resistance up to an $(1+\eps)$ factor in $\tilde{O}(n^{2/3+o(1)} \epsilon^{-O(1)})$ amortized update time per operation. The key tool behind result (1) is the dynamic maintenance of an algorithmic construction due to Madry [FOCS' 10], which partitions a graph into a collection of simpler graph structures (known as j-trees) and approximately captures the cut-flow and metric structure of the graph. The $O(1)$-approximation guarantee of (2) is by adapting the distance oracles by [Thorup-Zwick JACM `05]. Result (3) is obtained by invoking the random-walk based spectral vertex sparsifier by [Durfee et al. STOC `19] in a hierarchical manner, while carefully keeping track of the recourse among levels in the hierarchy. 

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5. Computing β-Stretch Paths in Drawings of Graphs

   Arkin, E ; Darabi, F ; Efrat, A ; Frank, F ; Fulek, R ; Kobourov, S ; Mitchell, J ( October 2020 , 17th Scandinavian Symposium and Workshops on Algorithm Theory (SWAT))

   Let f be a drawing in the Euclidean plane of a graph G, which is understood to be a 1-dimensional simplicial complex. We assume that every edge of G is drawn by f as a curve of constant algebraic complexity, and the ratio of the length of the longest simple path to the the length of the shortest edge is poly(n). In the drawing f, a path P of G, or its image in the drawing π = f(P), is β-stretch if π is a simple (non-self-intersecting) curve, and for every pair of distinct points p ∈ P and q ∈ P , the length of the sub-curve of π connecting f(p) with f(q) is at most β∥f(p) − f(q)∥, where ∥.∥ denotes the Euclidean distance. We introduce and study the β-stretch Path Problem (βSP for short), in which we are given a pair of vertices s and t of G, and we are to decide whether in the given drawing of G there exists a β-stretch path P connecting s and t. We also output P if it exists. The βSP quantifies a notion of “near straightness” for paths in a graph G, motivated by gerrymandering regions in a map, where edges of G represent natural geographical/political boundaries that may be chosen to bound election districts. The notion of a β-stretch path naturally extends to cycles, and the extension gives a measure of how gerrymandered a district is. Furthermore, we show that the extension is closely related to several studied measures of local fatness of geometric shapes. We prove that βSP is strongly NP-complete. We complement this result by giving a quasi-polynomial time algorithm, that for a given ε > 0, β ∈ O(poly(log |V (G)|)), and s, t ∈ V (G), outputs a β-stretch path between s and t, if a (1 − ε)β-stretch path between s and t exists in the drawing. 

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