arXiv subjects

Grigorios Loukides

Publications and source records attributed to Grigorios Loukides.

17 recordsLinked to original sources

arXiv2026

Subtree Mode and Applications

The mode of a collection of values (i.e., the most frequent value in the collection) is a key summary statistic. Finding the mode in a given range of an array of values is thus of great importance, and constructing a data structure to solve this problem is in fact the well-known Range Mode problem. In this work, we introduce the Subtree Mode (SM) problem, the analogous problem in a leaf-colored tree, where the task is to compute the most frequent color in the leaves of the subtree of a given node. SM is motivated by several applications in domains such as text analytics and biology, where the data are hierarchical and can thus be represented as a (leaf-colored) tree. Our central contribution is a time-optimal algorithm for SM that computes the answer for every node of an input $N$-node tree in $O(N)$ time. We further show how our solution can be adapted for node-colored trees, or for computing the $k$ most frequent colors, for any given $k=O(1)$, in the optimal $O(N)$ time. Moreover, we prove that a similarly fast solution for when the input is a sink-colored directed acyclic graph instead of a leaf-colored tree is highly unlikely. Our experiments on real datasets with trees of up to $7.3$ billion nodes demonstrate that our algorithm is faster than baselines by at least one order of magnitude and much more space efficient. They also show that it is effective in pattern mining, sequence-to-database search, and biology applications.

cs.DS↗

arXiv2025

Contextual Pattern Mining and Counting

Given a string $P$ of length $m$, a longer string $T$ of length $n>m$, and two integers $l\geq 0$ and $r\geq 0$, the context of $P$ in $T$ is the set of all string pairs $(L,R)$, with $|L|=l$ and $|R|=r$, such that the string $LPR$ occurs in $T$. We introduce two problems related to the notion of context: (1) the Contextual Pattern Mining (CPM) problem, which given $T$, $(m,l,r)$, and an integer $τ>0$, asks for outputting the context of each substring $P$ of length $m$ of $T$, provided that the size of the context of $P$ is at least $τ$; and (2) the Contextual Pattern Counting (CPC) problem, which asks for preprocessing $T$ so that the size of the context of a given query string $P$ of length $m$ can be found efficiently. For CPM, we propose a linear-work algorithm that either uses only internal memory, or a bounded amount of internal memory and external memory, which allows much larger datasets to be handled. For CPC, we propose an $\widetilde{\mathcal{O}}(n)$-space index that can be constructed in $\widetilde{\mathcal{O}}n)$ time and answers queries in $\mathcal{O}(m)+\widetilde{\mathcal{O}}(1)$ time. We further improve the practical performance of the CPC index by optimizations that exploit the LZ77 factorization of $T$ and an upper bound on the query length. Using billion-letter datasets from different domains, we show that the external memory version of our CPM algorithm can deal with very large datasets using a small amount of internal memory while its runtime is comparable to that of the internal memory version. Interestingly, we also show that our optimized index for CPC outperforms an approach based on the state of the art for the reporting version of CPC [Navarro, SPIRE 2020] in terms of query time, index size, construction time, and construction space, often by more than an order of magnitude.

cs.DS↗

arXiv2025

Resilient Pattern Mining

Frequent pattern mining is a flagship problem in data mining. In its most basic form, it asks for the set of substrings of a given string $S$ of length $n$ that occur at least $τ$ times in $S$, for some integer $τ\in[1,n]$. We introduce a resilient version of this classic problem, which we term the $(τ, k)$-Resilient Pattern Mining (RPM) problem. Given a string $S$ of length $n$ and two integers $τ, k\in[1,n]$, RPM asks for the set of substrings of $S$ that occur at least $τ$ times in $S$, even when the letters at any $k$ positions of $S$ are substituted by other letters. Unlike frequent substrings, resilient ones account for the fact that changes to string $S$ are often expensive to handle or are unknown. We propose an exact $\mathcal{O}(n\log n)$-time and $\mathcal{O}(n)$-space algorithm for RPM, which employs advanced data structures and combinatorial insights. We then present experiments on real large-scale datasets from different domains demonstrating that: (I) The notion of resilient substrings is useful in analyzing genomic data and is more powerful than that of frequent substrings, in scenarios where resilience is required, such as in the case of versioned datasets; (II) Our algorithm is several orders of magnitude faster and more space-efficient than a baseline algorithm that is based on dynamic programming; and (III) Clustering based on resilient substrings is effective.

cs.DS↗

arXiv2025

U-index: A Universal Indexing Framework for Matching Long Patterns

Text indexing is a fundamental and well-studied problem. Classic solutions either replace the original text with a compressed representation, e.g., the FM-index and its variants, or keep it uncompressed but attach some redundancy - an index - to accelerate matching. The former solutions thus retain excellent compressed space, but are slow in practice. The latter approaches, like the suffix array, instead sacrifice space for speed. We show that efficient text indexing can be achieved using just a small extra space on top of the original text, provided that the query patterns are sufficiently long. More specifically, we develop a new indexing paradigm in which a sketch of a query pattern is first matched against a sketch of the text. Once candidate matches are retrieved, they are verified using the original text. This paradigm is thus universal in the sense that it allows us to use any solution to index the sketched text, like a suffix array, FM-index, or r-index. We explore both the theory and the practice of this universal framework. With an extensive experimental analysis, we show that, surprisingly, universal indexes can be constructed much faster than their unsketched counterparts and take a fraction of the space, as a direct consequence of (i) having a lower bound on the length of patterns and (ii) working in sketch space. Furthermore, these data structures have the potential of retaining or even improving query time, because matching against the sketched text is faster and verifying candidates can be theoretically done in constant time per occurrence (or, in practice, by short and cache-friendly scans of the text). Finally, we discuss some important applications of this novel indexing paradigm to computational biology. We hypothesize that such indexes will be particularly effective when the queries are sufficiently long, and so demonstrate applications in long-read mapping.

cs.DS↗

arXiv2025

Indexing Strings with Utilities

Applications in domains ranging from bioinformatics to advertising feature strings that come with numerical scores (utilities). The utilities quantify the importance, interest, profit, or risk of the letters occurring at every position of a string. Motivated by the ever-increasing rate of generating such data, as well as by their importance in several domains, we introduce Useful String Indexing (USI), a natural generalization of the classic String Indexing problem. Given a string $S$ (the text) of length $n$, USI asks for preprocessing $S$ into a compact data structure supporting the following queries efficiently: given a shorter string $P$ (the pattern), return the global utility $U(P)$ of $P$ in $S$, where $U$ is a function that maps any string $P$ to a utility score based on the utilities of the letters of every occurrence of $P$ in $S$. Our work also makes the following contributions: (1) We propose a novel and efficient data structure for USI based on finding the top-$K$ frequent substrings of $S$. (2) We propose a linear-space data structure that can be used to mine the top-$K$ frequent substrings of $S$ or to tune the parameters of the USI data structure. (3) We propose a novel space-efficient algorithm for estimating the set of the top-$K$ frequent substrings of $S$, thus improving the construction space of the data structure for USI. (4) We show that popular space-efficient top-$K$ frequent item mining strategies employed by state-of-the-art algorithms do not smoothly translate from items to substrings. (5) Using billion-letter datasets, we experimentally demonstrate that: (i) our top-$K$ frequent substring mining algorithms are accurate and scalable, unlike two state-of-the-art methods; and (ii) our USI data structures are up to $15$ times faster in querying than $4$ nontrivial baselines while occupying the same space with them.

cs.DS↗

arXiv2024

Scalable Order-Preserving Pattern Mining

Time series are ubiquitous in domains ranging from medicine to marketing and finance. Frequent Pattern Mining (FPM) from a time series has thus received much attention. Recently, it has been studied under the order-preserving (OP) matching relation stating that a match occurs when two time series have the same relative order on their elements. Here, we propose exact, highly scalable algorithms for FPM in the OP setting. Our algorithms employ an OP suffix tree (OPST) as an index to store and query time series efficiently. Unfortunately, there are no practical algorithms for OPST construction. Thus, we first propose a novel and practical $\mathcal{O}(nσ\log σ)$-time and $\mathcal{O}(n)$-space algorithm for constructing the OPST of a length-$n$ time series over an alphabet of size $σ$. We also propose an alternative faster OPST construction algorithm running in $\mathcal{O}(n\log σ)$ time using $\mathcal{O}(n)$ space; this algorithm is mainly of theoretical interest. Then, we propose an exact $\mathcal{O}(n)$-time and $\mathcal{O}(n)$-space algorithm for mining all maximal frequent OP patterns, given an OPST. This significantly improves on the state of the art, which takes $Ω(n^3)$ time in the worst case. We also formalize the notion of closed frequent OP patterns and propose an exact $\mathcal{O}(n)$-time and $\mathcal{O}(n)$-space algorithm for mining all closed frequent OP patterns, given an OPST. We conducted experiments using real-world, multi-million letter time series showing that our $\mathcal{O}(nσ\log σ)$-time OPST construction algorithm runs in $\mathcal{O}(n)$ time on these datasets despite the $\mathcal{O}(nσ\log σ)$ bound; that our frequent pattern mining algorithms are up to orders of magnitude faster than the state of the art and natural Apriori-like baselines; and that OP pattern-based clustering is effective.

cs.DS↗

arXiv2024

Text Indexing for Long Patterns using Locally Consistent Anchors

In many real-world database systems, a large fraction of the data is represented by strings: sequences of letters over some alphabet. This is because strings can easily encode data arising from different sources. It is often crucial to represent such string datasets in a compact form but also to simultaneously enable fast pattern matching queries. This is the classic text indexing problem. The four absolute measures anyone should pay attention to when designing or implementing a text index are: (i) index space; (ii) query time; (iii) construction space; and (iv) construction time. Unfortunately, however, most (if not all) widely-used indexes (e.g., suffix tree, suffix array, or their compressed counterparts) are not optimized for all four measures simultaneously, as it is difficult to have the best of all four worlds. Here, we take an important step in this direction by showing that text indexing with sampling based on locally consistent anchors (lc-anchors) offers remarkably good performance in all four measures, when we have at hand a lower bound $\ell$ on the length of the queried patterns -- which is arguably a quite reasonable assumption in practical applications. Our index offers average-case guarantees. In our experiments using real benchmark datasets, we show that it compares favorably based on the four measures to all classic indexes: (compressed) suffix tree; (compressed) suffix array; and the FM-index. Notably, we also present a counterpart of our index with worst-case guarantees based on the lc-anchors notion of partitioning sets. To the best of our knowledge, this is the first index achieving the best of all worlds in the regime where we have at hand a lower bound $\ell$ on the length of the queried patterns.

cs.DS↗

arXiv2024

Sparse Suffix and LCP Array: Simple, Direct, Small, and Fast

Sparse suffix sorting is the problem of sorting $b=o(n)$ suffixes of a string of length $n$. Efficient sparse suffix sorting algorithms have existed for more than a decade. Despite the multitude of works and their justified claims for applications in text indexing, the existing algorithms have not been employed by practitioners. Arguably this is because there are no simple, direct, and efficient algorithms for sparse suffix array construction. We provide two new algorithms for constructing the sparse suffix and LCP arrays that are simultaneously simple, direct, small, and fast. In particular, our algorithms are: simple in the sense that they can be implemented using only basic data structures; direct in the sense that the output arrays are not a byproduct of constructing the sparse suffix tree or an LCE data structure; fast in the sense that they run in $\mathcal{O}(n\log b)$ time, in the worst case, or in $\mathcal{O}(n)$ time, when the total number of suffixes with an LCP value greater than $2^{\lfloor \log \frac{n}{b} \rfloor + 1}-1$ is in $\mathcal{O}(b/\log b)$, matching the time of the optimal yet much more complicated algorithms [Gawrychowski and Kociumaka, SODA 2017; Birenzwige et al., SODA 2020]; and small in the sense that they can be implemented using only $8b+o(b)$ machine words. Our algorithms are non-trivial space-efficient adaptations of the Monte Carlo algorithm by I et al. for constructing the sparse suffix tree in $\mathcal{O}(n\log b)$ time [STACS 2014]. We provide extensive experiments to justify our claims on simplicity and on efficiency.

cs.DS↗

arXiv2024

Minimizing the Minimizers via Alphabet Reordering

Minimizers sampling is one of the most widely-used mechanisms for sampling strings [Roberts et al., Bioinformatics 2004]. Let $S=S[1]\ldots S[n]$ be a string over a totally ordered alphabet $Σ$. Further let $w\geq 2$ and $k\geq 1$ be two integers. The minimizer of $S[i\mathinner{.\,.} i+w+k-2]$ is the smallest position in $[i,i+w-1]$ where the lexicographically smallest length-$k$ substring of $S[i\mathinner{.\,.} i+w+k-2]$ starts. The set of minimizers over all $i\in[1,n-w-k+2]$ is the set $\mathcal{M}_{w,k}(S)$ of the minimizers of $S$. We consider the following basic problem: Given $S$, $w$, and $k$, can we efficiently compute a total order on $Σ$ that minimizes $|\mathcal{M}_{w,k}(S)|$? We show that this is unlikely by proving that the problem is NP-hard for any $w\geq 2$ and $k\geq 1$. Our result provides theoretical justification as to why there exist no exact algorithms for minimizing the minimizers samples, while there exists a plethora of heuristics for the same purpose.

cs.DS↗

arXiv2024

Space-Efficient Indexes for Uncertain Strings

Strings in the real world are often encoded with some level of uncertainty. In the character-level uncertainty model, an uncertain string $X$ of length $n$ on an alphabet $Σ$ is a sequence of $n$ probability distributions over $Σ$. Given an uncertain string $X$ and a weight threshold $\frac{1}{z}\in(0,1]$, we say that pattern $P$ occurs in $X$ at position $i$, if the product of probabilities of the letters of $P$ at positions $i,\ldots,i+|P|-1$ is at least $\frac{1}{z}$. While indexing standard strings for online pattern searches can be performed in linear time and space, indexing uncertain strings is much more challenging. Specifically, the state-of-the-art index for uncertain strings has $\mathcal{O}(nz)$ size, requires $\mathcal{O}(nz)$ time and $\mathcal{O}(nz)$ space to be constructed, and answers pattern matching queries in the optimal $\mathcal{O}(m+|\text{Occ}|)$ time, where $m$ is the length of $P$ and $|\text{Occ}|$ is the total number of occurrences of $P$ in $X$. For large $n$ and (moderate) $z$ values, this index is completely impractical to construct, which outweighs the benefit of the supported optimal pattern matching queries. We were thus motivated to design a space-efficient index at the expense of slower yet competitive pattern matching queries. We propose an index of $\mathcal{O}(\frac{nz}{\ell}\log z)$ expected size, which can be constructed using $\mathcal{O}(\frac{nz}{\ell}\log z)$ expected space, and supports very fast pattern matching queries in expectation, for patterns of length $m\geq \ell$. We have implemented and evaluated several versions of our index. The best-performing version of our index is up to two orders of magnitude smaller than the state of the art in terms of both index size and construction space, while offering faster or very competitive query and construction times.

cs.DS↗

arXiv2024

Pattern Masking for Dictionary Matching

In the Pattern Masking for Dictionary Matching (PMDM) problem, we are given a dictionary $\mathcal{D}$ of $d$ strings, each of length $\ell$, a query string $q$ of length $\ell$, and a positive integer $z$, and we are asked to compute a smallest set $K\subseteq\{1,\ldots,\ell\}$, so that if $q[i]$, for all $i\in K$, is replaced by a wildcard, then $q$ matches at least $z$ strings from $\mathcal{D}$. The PMDM problem lies at the heart of two important applications featured in large-scale real-world systems: record linkage of databases that contain sensitive information, and query term dropping. In both applications, solving PMDM allows for providing data utility guarantees as opposed to existing approaches. We first show, through a reduction from the well-known $k$-Clique problem, that a decision version of the PMDM problem is NP-complete, even for strings over a binary alphabet. We present a data structure for PMDM that answers queries over $\mathcal{D}$ in time $\mathcal{O}(2^{\ell/2}(2^{\ell/2}+τ)\ell)$ and requires space $\mathcal{O}(2^{\ell}d^2/τ^2+2^{\ell/2}d)$, for any parameter $τ\in[1,d]$. We also approach the problem from a more practical perspective. We show an $\mathcal{O}((d\ell)^{k/3}+d\ell)$-time and $\mathcal{O}(d\ell)$-space algorithm for PMDM if $k=|K|=\mathcal{O}(1)$. We generalize our exact algorithm to mask multiple query strings simultaneously. We complement our results by showing a two-way polynomial-time reduction between PMDM and the Minimum Union problem [Chlamtáč et al., SODA 2017]. This gives a polynomial-time $\mathcal{O}(d^{1/4+ε})$-approximation algorithm for PMDM, which is tight under plausible complexity conjectures.

cs.DS↗

arXiv2022

Differentially Private Top-k Selection via Canonical Lipschitz Mechanism

Selecting the top-$k$ highest scoring items under differential privacy (DP) is a fundamental task with many applications. This work presents three new results. First, the exponential mechanism, permute-and-flip and report-noisy-max, as well as their oneshot variants, are unified into the Lipschitz mechanism, an additive noise mechanism with a single DP-proof via a mandated Lipschitz property for the noise distribution. Second, this new generalized mechanism is paired with a canonical loss function to obtain the canonical Lipschitz mechanism, which can directly select k-subsets out of $d$ items in $O(dk+d \log d)$ time. The canonical loss function assesses subsets by how many users must change for the subset to become top-$k$. Third, this composition-free approach to subset selection improves utility guarantees by an $Ω(\log k)$ factor compared to one-by-one selection via sequential composition, and our experiments on synthetic and real-world data indicate substantial utility improvements.

cs.LG↗

arXiv2021

String Sampling with Bidirectional String Anchors

The minimizers sampling mechanism is a popular mechanism for string sampling introduced independently by Schleimer et al. [SIGMOD 2003] and by Roberts et al. [Bioinf. 2004]. Given two positive integers $w$ and $k$, it selects the lexicographically smallest length-$k$ substring in every fragment of $w$ consecutive length-$k$ substrings (in every sliding window of length $w + k - 1$). Minimizers samples are approximately uniform, locally consistent, and computable in linear time. Two main disadvantages of minimizers sampling mechanisms are: first, they do not have good guarantees on the expected size of their samples for every combination of $w$ and $k$; and, second, indexes that are constructed over their samples do not have good worst-case guarantees for on-line pattern searches. We introduce bidirectional string anchors (bd-anchors), a new string sampling mechanism. Given a positive integer $\ell$, our mechanism selects the lexicographically smallest rotation in every length-$\ell$ fragment (in every sliding window of length $\ell$). We show that bd-anchors samples are also approximately uniform, locally consistent, and computable in linear time. In addition, our experiments using several datasets demonstrate that the bd-anchors sample sizes decrease proportionally to $\ell$; and that these sizes are competitive to or smaller than the minimizers sample sizes using the analogous sampling parameters. We provide theoretical justification for these results by analyzing the expected size of bd-anchors samples. As a negative result, we show that computing a total order $\leq$ on the input alphabet, which minimizes the bd-anchors sample size, is NP-hard. We also show that by using any bd-anchors sample, we can construct, in near-linear time, an index which requires linear (extra) space in the size of the sample and answers on-line pattern searches in near-optimal time.

cs.DS↗

arXiv2021

Maximizing approximately k-submodular functions

We introduce the problem of maximizing approximately $k$-submodular functions subject to size constraints. In this problem, one seeks to select $k$-disjoint subsets of a ground set with bounded total size or individual sizes, and maximum utility, given by a function that is "close" to being $k$-submodular. The problem finds applications in tasks such as sensor placement, where one wishes to install $k$ types of sensors whose measurements are noisy, and influence maximization, where one seeks to advertise $k$ topics to users of a social network whose level of influence is uncertain. To deal with the problem, we first provide two natural definitions for approximately $k$-submodular functions and establish a hierarchical relationship between them. Next, we show that simple greedy algorithms offer approximation guarantees for different types of size constraints. Last, we demonstrate experimentally that the greedy algorithms are effective in sensor placement and influence maximization problems.

cs.DS↗

arXiv2019

Combinatorial Algorithms for String Sanitization

String data are often disseminated to support applications such as location-based service provision or DNA sequence analysis. This dissemination, however, may expose sensitive patterns that model confidential knowledge. In this paper, we consider the problem of sanitizing a string by concealing the occurrences of sensitive patterns, while maintaining data utility, in two settings that are relevant to many common string processing tasks. In the first setting, we aim to generate the minimal-length string that preserves the order of appearance and frequency of all non-sensitive patterns. Such a string allows accurately performing tasks based on the sequential nature and pattern frequencies of the string. To construct such a string, we propose a time-optimal algorithm, TFS-ALGO. We also propose another time-optimal algorithm, PFS-ALGO, which preserves a partial order of appearance of non-sensitive patterns but produces a much shorter string that can be analyzed more efficiently. The strings produced by either of these algorithms are constructed by concatenating non-sensitive parts of the input string. However, it is possible to detect the sensitive patterns by ``reversing'' the concatenation operations. In response, we propose a heuristic, MCSR-ALGO, which replaces letters in the strings output by the algorithms with carefully selected letters, so that sensitive patterns are not reinstated, implausible patterns are not introduced, and occurrences of spurious patterns are prevented. In the second setting, we aim to generate a string that is at minimal edit distance from the original string, in addition to preserving the order of appearance and frequency of all non-sensitive patterns. To construct such a string, we propose an algorithm, ETFS-ALGO, based on solving specific instances of approximate regular expression matching.

cs.DS↗

arXiv2019

Location histogram privacy by sensitive location hiding and target histogram avoidance/resemblance (extended version)

A location histogram is comprised of the number of times a user has visited locations as they move in an area of interest, and it is often obtained from the user in applications such as recommendation and advertising. However, a location histogram that leaves a user's computer or device may threaten privacy when it contains visits to locations that the user does not want to disclose (sensitive locations), or when it can be used to profile the user in a way that leads to price discrimination and unsolicited advertising. Our work introduces two privacy notions to protect a location histogram from these threats: sensitive location hiding, which aims at concealing all visits to sensitive locations, and target avoidance/resemblance, which aims at concealing the similarity/dissimilarity of the user's histogram to a target histogram that corresponds to an undesired/desired profile. We formulate an optimization problem around each notion: Sensitive Location Hiding (SLH), which seeks to construct a histogram that is as similar as possible to the user's histogram but associates all visits with nonsensitive locations, and Target Avoidance/Resemblance (TA/TR), which seeks to construct a histogram that is as dissimilar/similar as possible to a given target histogram but remains useful for getting a good response from the application that analyzes the histogram. We develop an optimal algorithm for each notion and also develop a greedy heuristic for the TA/TR problem. Our experiments demonstrate that all algorithms are effective at preserving the distribution of locations in a histogram and the quality of location recommendation. They also demonstrate that the heuristic produces near-optimal solutions while being orders of magnitude faster than the optimal algorithm for TA/TR.

cs.CR↗

arXiv2010

Towards Utility-driven Anonymization of Transactions

Publishing person-specific transactions in an anonymous form is increasingly required by organizations. Recent approaches ensure that potentially identifying information (e.g., a set of diagnosis codes) cannot be used to link published transactions to persons' identities, but all are limited in application because they incorporate coarse privacy requirements (e.g., protecting a certain set of m diagnosis codes requires protecting all m-sized sets), do not integrate utility requirements, and tend to explore a small portion of the solution space. In this paper, we propose a more general framework for anonymizing transactional data under specific privacy and utility requirements. We model such requirements as constraints, investigate how these constraints can be specified, and propose COAT (COnstraint-based Anonymization of Transactions), an algorithm that anonymizes transactions using a flexible hierarchy-free generalization scheme to meet the specified constraints. Experiments with benchmark datasets verify that COAT significantly outperforms the current state-of-the-art algorithm in terms of data utility, while being comparable in terms of efficiency. The effectiveness of our approach is also demonstrated in a real-world scenario, which requires disseminating a private, patient-specific transactional dataset in a way that preserves both privacy and utility in intended studies.

cs.DB↗