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1. 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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2. Tiny Pointers

   Michael A. Bender; Alex Conway; Martín Farach-Colton; William Kuszmaul; Guido Tagliavini (January 2023, Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA))

   This paper introduces a new data-structural object that we call the tiny pointer. In many applications, traditional log n-bit pointers can be replaced with o(log n)-bit tiny pointers at the cost of only a constant-factor time overhead and a small probability of failure. We develop a comprehensive theory of tiny pointers, and give optimal constructions for both fixed-size tiny pointers (i.e., settings in which all of the tiny pointers must be the same size) and variable-size tiny pointers (i.e., settings in which the average tiny-pointer size must be small, but some tiny pointers can be larger). If a tiny pointer references an element in an array filled to load factor 1 — δ, then the optimal tiny-pointer size is Θ(log log log n + log δ-1) bits in the fixed-size case, and Θ(log δ-1) expected bits in the variable-size case. Our tiny-pointer constructions also require us to revisit several classic problems having to do with balls and bins; these results may be of independent interest. Using tiny pointers, we revisit five classic data-structure problems. We show that: • A data structure storing n v-bit values for n keys with constant-time modifications/queries can be implemented to take space nv + O(n log(r) n) bits, for any constant r > 0, as long as the user stores a tiny pointer of expected size O(1) with each key—here, log(r) n is the r-th iterated logarithm. • Any binary search tree can be made succinct with constant-factor time overhead, and can even be made to be within O(n) bits of optimal if we allow for O(log* n)-time modifications—this holds even for rotation-based trees such as the splay tree and the red-black tree. • Any fixed-capacity key-value dictionary can be made stable (i.e., items do not move once inserted) with constant-time overhead and 1 + o(1) space overhead. • Any key-value dictionary that requires uniform-size values can be made to support arbitrary-size values with constant-time overhead and with an additional space consumption of log(r) n + O(log j) bits per j-bit value for an arbitrary constant r > 0 of our choice. • Given an external-memory array A of size (1 + ε)n containing a dynamic set of up to n key-value pairs, it is possible to maintain an internal-memory stash of size O(n log ε-1) bits so that the location of any key-value pair in A can be computed in constant time (and with no IOs). These are all well studied and classic problems, and in each case tiny pointers allow for us to take a natural space-inefficient solution that uses pointers and make it space-efficient for free. 

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3. Repetition Aware Text Indexing for Matching Patterns with Wildcards

   https://doi.org/10.4230/LIPICS.ICALP.2025.88  

   Gibney, Daniel; Huffstutler, Jackson; Parthasarathi, Mano Prakash; Thankachan, Sharma V (January 2025, Schloss Dagstuhl – Leibniz-Zentrum für Informatik)

   Censor-Hillel, Keren; Grandoni, Fabrizio; Ouaknine, Joel; Puppis, Gabriele (Ed.)

   We study the problem of indexing a text T[1..n] to support pattern matching with wildcards. The input of a query is a pattern P[1..m] containing h ∈ [0, k] wildcard (a.k.a. don't care) characters and the output is the set of occurrences of P in T (i.e., starting positions of substrings of T that matches P), where k = o(log n) is fixed at index construction. A classic solution by Cole et al. [STOC 2004] provides an index with space complexity O(n ⋅ (clog n)^k/k!)) and query time O(m+2^h log log n+occ), where c > 1 is a constant, and occ denotes the number of occurrences of P in T. We introduce a new data structure that significantly reduces space usage for highly repetitive texts while maintaining efficient query processing. Its space (in words) and query time are as follows: O(δ log (n/δ)⋅ c^k (1+(log^k (δ log n))/k!)) and O((m+2^h +occ)log n)) The parameter δ, known as substring complexity, is a recently introduced measure of repetitiveness that serves as a unifying and lower-bounding metric for several popular measures, including the number of phrases in the LZ77 factorization (denoted by z) and the number of runs in the Burrows-Wheeler Transform (denoted by r). Moreover, O(δ log (n/δ)) represents the optimal space required to encode the data in terms of n and δ, helping us see how close our space is to the minimum required. In another trade-off, we match the query time of Cole et al.’s index using O(n+δ log (n/δ) ⋅ (clogδ)^{k+ε}/k!) space, where ε > 0 is an arbitrarily small constant. We also demonstrate how these techniques can be applied to a more general indexing problem, where the query pattern includes k-gaps (a gap can be interpreted as a contiguous sequence of wildcard characters). 

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4. Trace Reconstruction from Local Statistical Queries

   https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2024.52  

   Chen, Xi; De, Anindya; Lee, Chin Ho; Servedio, Rocco A (January 2024, Schloss Dagstuhl – Leibniz-Zentrum für Informatik)

   Kumar, Amit; Ron-Zewi, Noga (Ed.)

   The goal of trace reconstruction is to reconstruct an unknown n-bit string x given only independent random traces of x, where a random trace of x is obtained by passing x through a deletion channel. A Statistical Query (SQ) algorithm for trace reconstruction is an algorithm which can only access statistical information about the distribution of random traces of x rather than individual traces themselves. Such an algorithm is said to be 𝓁-local if each of its statistical queries corresponds to an 𝓁-junta function over some block of 𝓁 consecutive bits in the trace. Since several - but not all - known algorithms for trace reconstruction fall under the local statistical query paradigm, it is interesting to understand the abilities and limitations of local SQ algorithms for trace reconstruction. In this paper we establish nearly-matching upper and lower bounds on local Statistical Query algorithms for both worst-case and average-case trace reconstruction. For the worst-case problem, we show that there is an Õ(n^{1/5})-local SQ algorithm that makes all its queries with tolerance τ ≥ 2^{-Õ(n^{1/5})}, and also that any Õ(n^{1/5})-local SQ algorithm must make some query with tolerance τ ≤ 2^{-Ω̃(n^{1/5})}. For the average-case problem, we show that there is an O(log n)-local SQ algorithm that makes all its queries with tolerance τ ≥ 1/poly(n), and also that any O(log n)-local SQ algorithm must make some query with tolerance τ ≤ 1/poly(n). 

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5. Explicit two-source extractors and resilient functions

   Chattopadhyay, E; Zuckerman, D (May 2019, Annals of mathematics)

   We explicitly construct an extractor for two independent sources on n bits, each with min-entropy at least log^C n for a large enough constant C. Our extractor outputs one bit and has error n^{-\Omega(1)}. The best previous extractor, by Bourgain, required each source to have min-entropy .499n. A key ingredient in our construction is an explicit construction of a monotone, almost-balanced boolean function on n bits that is resilient to coalitions of size n^{1-delta}, for any delta>0. In fact, our construction is stronger in that it gives an explicit extractor for a generalization of non-oblivious bit-fixing sources on n bits, where some unknown n-q bits are chosen almost polylog(n)-wise independently, and the remaining q=n^{1-\delta} bits are chosen by an adversary as an arbitrary function of the n-q bits. The best previous construction, by Viola, achieved q=n^{1/2 - \delta}. Our explicit two-source extractor directly implies an explicit construction of a 2^{(log log N)^{O(1)}}-Ramsey graph over N vertices, improving bounds obtained by Barak et al. and matching independent work by Cohen. 

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