Error Tree: A Tree Structure for Hamming and Edit Distances and Wildcards Matching

In the approximate pattern matching problem, given a text $T$ , a pattern $P$ , and a threshold $k$ , the task is to find (the starting positions of) all substrings of $T$ that are at distance at most $k$ from $P$ . We consider the two most fundamental string metrics: Under the Hamming distance, we search for substrings of $T$ that have at most $k$ mismatches with $P$ , while under the edit distance, we search for substrings of $T$ that can be transformed to $P$ with at most $k$ edits. Exact occurrences of $P$ in $T$ have a very simple structure: If we assume for simplicity that $\vert P\vert and that $P$ occurs both as a prefix and as a suffix of $T$ , then both $P$ and $T$ are periodic with a common period. However, an analogous characterization for occurrences with up to $k$ mismatches was proved only recently by Bringmann et al. [SODA'19]: Either there are $\mathcal{O}(k^{2}) k$ -mismatch occurrences of $P$ in $T$ , or both $P$ and $T$ are at Hamming distance $\mathcal{O}(k)$ from strings with a common string period of length $\mathcal{O}(m/k)$ . We tighten this characterization by showing that there are $\mathcal{O}(k) k$ -mismatch occurrences in the non-periodic case, and we lift it to the edit distance setting, where we tightly bound the number of $k$ -edit occurrences by $\mathcal{O}(k^{2})$ in the non-periodic case. Our proofs are constructive and let us obtain a unified framework for approximate pattern matching for both considered distances. In particular, we provide meta-algorithms that only rely on a small set of primitive operations. We showcase the generality of our meta-algorithms with results for the fully compressed setting, the dynamic setting, and the standard setting.

A string S of length n has period P of length p if \(S[i]=S[i+p]\) for all \(1 \le i \le n-p\) and \(n \ge 2p\). The shortest such substring, P, is called the period of S, and the string S is called periodic in P. In this paper we investigate the period recovery problem. Given a string S of length n, find the primitive period(s) P such that the distance between S and the string that is periodic in P is below a threshold \(\tau \). We consider the period recovery problem over both the Hamming distance and the edit distance. For the Hamming distance case, we present an \(O(n \log n)\) time algorithm, where \(\tau \) is given as \(\frac{n}{(2+\epsilon )p}\), for \(0 < \epsilon < 1\). For the edit distance case, \(\tau =\frac{n}{(4+\epsilon )p}\), and we provide an \(O(n^{4/ 3})\) time algorithm.

We consider the streaming complexity of a fundamental task in approximate pattern matching: the $k$-mismatch problem. It asks to compute Hamming distances between a pattern of length $n$ and all length-$n$ substrings of a text for which the Hamming distance does not exceed a given threshold $k$. In our problem formulation, we report not only the Hamming distance but also, on demand, the full \emph{mismatch information}, that is the list of mismatched pairs of symbols and their indices. The twin challenges of streaming pattern matching derive from the need both to achieve small working space and also to guarantee that every arriving input symbol is processed quickly. We present a streaming algorithm for the $k$-mismatch problem which uses $O(k\log{n}\log\frac{n}{k})$ bits of space and spends \ourcomplexity time on each symbol of the input stream, which consists of the pattern followed by the text. The running time almost matches the classic offline solution and the space usage is within a logarithmic factor of optimal. Our new algorithm therefore effectively resolves and also extends an open problem first posed in FOCS'09. En route to this solution, we also give a deterministic $O( k (\log \frac{n}{k} + \log |\Sigma|) )$-bit encoding of all the alignments with Hamming distance at most $k$ of a length-$n$ pattern within a text of length $O(n)$. This secondary result provides an optimal solution to a natural communication complexity problem which may be of independent interest.

Quasiperiodicity in strings was introduced almost 30 years ago as an extension of string periodicity. The basic notions of quasiperiodicity are cover and seed. A cover of a text T is a string whose occurrences in T cover all positions of T. A seed of text T is a cover of a superstring of T. In various applications exact quasiperiodicity is still not sufficient due to the presence of errors. We consider approximate notions of quasiperiodicity, for which we allow approximate occurrences in T with a small Hamming, Levenshtein or weighted edit distance. In previous work Sim et al. (J Korea Inf Sci Soc 29(1):16–21, 2002) and Christodoulakis et al. (J Autom Lang Comb 10(5/6), 609–626, 2005) showed that computing approximate covers and seeds, respectively, under weighted edit distance is NP-hard. They, therefore, considered restricted approximate covers and seeds which need to be factors of the original string T and presented polynomial-time algorithms for computing them. Further algorithms, considering approximate occurrences with Hamming distance bounded by k, were given in several contributions by Guth et al. They also studied relaxed approximate quasiperiods. We present more efficient algorithms for computing restricted approximate covers and seeds. In particular, we improve upon the complexities of many of the aforementioned algorithms, also for relaxed quasiperiods. Our solutions are especially efficient if the number (or total cost) of allowed errors is small. We also show conditional lower bounds for computing restricted approximate covers and prove NP-hardness of computing non-restricted approximate covers and seeds under the Hamming distance.

In a 2-dimensional (2D) pattern matching problem, the text is arranged as a matrix 𝖬[1..n, 1..n] and consists of N = n × n symbols drawn from alphabet set Σ of size σ. The query consists of a m × m square matrix 𝖯[1..m, 1..m] drawn from the same alphabet set Σ and the task is to find all the locations in 𝖬 where 𝖯 appears as a (contiguous) submatrix. The patterns can be of any size, but as long as they are square in shape data structures like suffix trees and suffix array exist [Raffaele Giancarlo, 1995; Dong Kyue Kim et al., 1998] for the task of efficient pattern matching. These are essentially 2D counterparts of classic suffix trees and arrays known for traditional 1-dimensional (1D) pattern matching. They work based on linearization of 2D suffixes which would preserve the prefix match property (i.e., every pattern match is a prefix of some suffix). The main limitation of the suffix trees and the suffix arrays (in 1D) was their space utilization of O(N log N) bits, where N is the size of the text. This was suboptimal compared to Nlog σ bits of space, which is information theoretic optimal for the text. With the advent of the field of succinct/compressed data structures, it was possible to develop compressed variants of suffix trees and array based on Burrows-Wheeler Tansform and LF-mapping (or Φ function) [Roberto Grossi and Jeffrey Scott Vitter, 2005; Paolo Ferragina and Giovanni Manzini, 2005; Kunihiko Sadakane, 2007]. These data structures indeed achieve O(N log σ) bits of space or better. This gives rise to the question: analogous to 1D case, can we design a succinct or compressed index for 2D pattern matching? Can there be a 2D compressed suffix tree? Are there analogues of Burrows-Wheeler Transform or LF-mapping? The problem has been acknowledged for over a decade now and there have been a few attempts at applying Φ function [Ankur Gupta, 2004] and achieving entropy based compression [Veli Mäkinen and Gonzalo Navarro, 2008]. However, achieving the complexity breakthrough akin to 1D case has yet to be found. In this paper, we still do not know how to answer suffix array queries in O(N log σ) bits of space - which would have led to efficient pattern matching. However, for the first time, we show an interesting result that it is indeed possible to compute inverse suffix array (ISA) queries in near compact space in O(polylog n) time. Our 2D succinct text index design is based on two 1D compressed suffix trees and it takes O(N log log N + N logσ) bits of space which is much smaller than its naive design that takes O(N log N) bits. Although the main problem is still evasive, this index gives a hope on the existence of a full 2D succinct index with all functionalities similar to that of 1D case.

Given a dictionary ${\mathcal W}$ consisting of n binary strings of length m each, a d-query asks if there exists a string in ${\mathcal W}$ within Hamming distance d of a given binary query string q. The problem was posed by Minsky and Papert in 1969 as a challenge to data structure design. There is a tradeoff between time and space in solving the problem of answering a d-query. Recently developed time-efficient methods for text indexing with errors can be used to answer a d-query in O(m) time. However, these methods use O(nlog d n) (or more) additional space which is not practical for large databases. We present a method for the problem assuming the standard RAM model of computation. We process the dictionary to construct an edge-labelled tree with distinct labels to siblings, and with bounded branching factor and height. Storing the resulting tree does not require asymptotically more space than the size of an ordinary trie that stores the given dictionary. We present an algorithm for the d-query problem that takes O(m(3 log4/3 n – 1) d (log2 n) d + 1) time, and uses only O(m) additional space. We also generalize the results for the case of the problem when a larger alphabet, or edit distance are used. We achieve $O(m(2|\Sigma|-1)^{d}(log_{(2|\Sigma|-1)}{\it n} -1) ^{d}(log_{2}n)^{d+1})$ time complexity for the problem when Hamming distance is used. The time complexity increases by a factor of $O(d(2|\Sigma|-1)^d(log_{2}n)^{d})$ when we use edit distance. The algorithms are efficient when the approximate dictionary look-up involves long words defined over small alphabets. The algorithm can be modified such that it allows for words of different lengths as well as different lengths of query strings.

Recently, Li et al. introduced a fuzzy keyword search over encrypted data in Cloud Computing. Their approach relies on fuzzy keyword sets which are used by a symmetric searchable encryption protocol. The idea behind these fuzzy keyword sets is to index – before the search phase – the exact keywords but also the ones differing slightly according to a fixed bound on the tolerated edit distance. We here suggest a different construction. We exploit a classical embedding of the edit distance into the Hamming distance. This enables us to adapt results on private identification schemes to this new context. This way of doing implies more flexibility on the tolerated edit distance.

The suffix array $SA[1..n]$ of a text $T$ of length $n$ is a permutation of $\{1,\ldots,n\}$ describing the lexicographical ordering of suffixes of $T$, and it is considered to be among of the most important data structures in string algorithms, with dozens of applications in data compression, bioinformatics, and information retrieval. One of the biggest drawbacks of the suffix array is that it is very difficult to maintain under text updates: even a single character substitution can completely change the contents of the suffix array. Thus, the suffix array of a dynamic text is modelled using suffix array queries, which return the value $SA[i]$ given any $i\in[1..n]$. Prior to this work, the fastest dynamic suffix array implementations were by Amir and Boneh. At ISAAC 2020, they showed how to answer suffix array queries in $\tilde{O}(k)$ time, where $k\in[1..n]$ is a trade-off parameter, with $\tilde{O}(\frac{n}{k})$-time text updates. In a very recent preprint [2021], they also provided a solution with $O(\log^5 n)$-time queries and $\tilde{O}(n^{2/3})$-time updates. We propose the first data structure that supports both suffix array queries and text updates in $O({\rm polylog}\,n)$ time (achieving $O(\log^4 n)$ and $O(\log^{3+o(1)} n)$ time, respectively). Our data structure is deterministic and the running times for all operations are worst-case. In addition to the standard single-character edits (character insertions, deletions, and substitutions), we support (also in $O(\log^{3+o(1)} n)$ time) the "cut-paste" operation that moves any (arbitrarily long) substring of $T$ to any place in $T$. We complement our structure by a hardness result: unless the Online Matrix-Vector Multiplication (OMv) Conjecture fails, no data structure with $O({\rm polylog}\,n)$-time suffix array queries can support the "copy-paste" operation in $O(n^{1-\epsilon})$ time for any $\epsilon>0$.

In the literature dealing with patterns with variables, a word, also called string, is a sequence of terminal letters, while a pattern is a sequence of terminal and variable letters. The problem of deciding if there is a substitution for all the variables in a pattern, such that a target word is obtained, is the matching problem for patterns with variables. In many problems related to the processing of textual data, it is essential to model uncertainty in the text, such as, e.g., typos in handwritten texts or mutations in biological data. For this reason, I introduce and present in this thesis our proposals of several settings which model uncertainty in the context of matching patterns with variables and a series of algorithmic and complexity theoretic results developed in these settings. The first setting, approached in Chapter 3, is concerned with matching patterns with variables under Hamming distance, that is, deciding if there is a substitution for all variables in a pattern, such that a word is obtained that is not "too far" from the target word with respect to the Hamming distance. The same problem is analyzed in Chapter 4 for the Edit distance and in Chapter 5 for a similarity measure based on k-Simon's congruence. The final problem in Chapter 6 is concerned with the edit distance of a word to a k-universal word, i.e., a word which contains all possible words of length k as subsequences.

근사문자열매칭 문제는 다양한 분야에서 연구되어 왔다. 최근에는 차세대염기서열분석의 비용과 시간을 줄이기 위해 빠른 근사문자열매칭 알고리즘들이 이용되고 있다. 근사문자열매칭은 문자열들의 오차를 측정하기 위해 편집거리와 같은 거리함수를 이용한다. 알파벳 <TEX>${\Sigma}$</TEX>에 대한 길이가 각각 m, n인 두 문자열 X와 Y의 편집거리는 X를 Y로 변환하기 위해 필요한 최소 편집연산의 수로 정의된다. 두 문자열의 편집거리는 잘 알려진 동적프로그래밍을 이용하여 O(mn) 시간과 공간에 계산할 수 있으며, 4-러시안 알고리즘을 이용해서도 계산할 수 있다. 4-러시안 알고리즘은 블록 크기를 t라 할 때, 전처리 단계에서 <TEX>$O((3{\mid}{\Sigma}{\mid})^{2t}t^2)$</TEX> 시간과 <TEX>$O((3{\mid}{\Sigma}{\mid})^{2t}t)$</TEX> 공간이 필요하며, 계산 단계에서 O(mn/t) 시간과 O(mn) 공간을 이용하여 편집거리를 계산하는 알고리즘이다. 본 논문에서는 4-러시안 알고리즘의 계산 단계를 병렬화하고 실험을 통해 CPU 기반의 순차적 알고리즘과 CUDA로 구현한 GPU 기반의 병렬 알고리즘의 수행시간을 비교한다. 본 논문에서 제시하는 4-러시안 알고리즘의 계산단계는 m/t개의 쓰레드를 사용하여 O(m+n) 시간에 편집거리를 계산한다. GPU 기반의 알고리즘이 CPU 기반의 알고리즘 보다 t = 1일 때 약 10배 빠르고, t = 2일 때 약 3배 빠른 결과를 보였다. Approximate string matching problems have been studied in diverse fields. Recently, fast approximate string matching algorithms are being used to reduce the time and costs for the next generation sequencing. To measure the amounts of errors between two strings, we use a distance function such as the edit distance. Given two strings X(|X| = m) and Y(|Y| = n) over an alphabet <TEX>${\Sigma}$</TEX>, the edit distance between X and Y is the minimum number of edit operations to convert X into Y. The edit distance between X and Y can be computed using the well-known dynamic programming technique in O(mn) time and space. The edit distance also can be computed using the Four-Russians' algorithm whose preprocessing step runs in <TEX>$O((3{\mid}{\Sigma}{\mid})^{2t}t^2)$</TEX> time and <TEX>$O((3{\mid}{\Sigma}{\mid})^{2t}t)$</TEX> space and the computation step runs in O(mn/t) time and O(mn) space where t represents the size of the block. In this paper, we present a parallelized version of the computation step of the Four-Russians' algorithm. Our algorithm computes the edit distance between X and Y in O(m+n) time using m/t threads. Then we implemented both the sequential version and our parallelized version of the Four-Russians' algorithm using CUDA to compare the execution times. When t = 1 and t = 2, our algorithm runs about 10 times and 3 times faster than the sequential algorithm, respectively.

We propose a protocol for the problem of secure two-party pattern matching, where Alice holds a text t?{0,1}? of length n, while Bob has a pattern p?{0,1}? of length m. The goal is for Bob to (only) learn where his pattern occurs in Alice's text, while Alice learns nothing. Private pattern matching is an important problem that has many applications in the area of DNA search, computational biology and more. Our construction guarantees full simulation in the presence of malicious, polynomial-time adversaries (assuming the hardness of DDH assumption) and exhibits computation and communication costs of O(n+m) group elements in a constant round complexity. This improves over previous work by Gennaro et al. (Public Key Cryptography, pp. 145---160, 2010) whose solution requires overhead of O(nm) group elements and exponentiations in O(m) rounds. In addition to the above, we propose a collection of protocols for important variations of the secure pattern matching problem that are significantly more efficient than the current state of art solutions: First, we deal with secure pattern matching with wildcards. In this variant the pattern may contain wildcards that match both 0 and 1. Our protocol requires O(n+m) communication and O(1) rounds using O(nm) computation. Then we treat secure approximate pattern matching. In this variant the matches may be approximated, i.e., have Hamming distance less than some threshold, ?. Our protocol requires O(n?) communication in O(1) rounds using O(nm) computation. Third, we have secure pattern matching with hidden pattern length. Here, the length, m, of Bob's pattern remains a secret. Our protocol requires O(n+M) communication in O(1) rounds using O(n+M) computation, where M is an upper bound on m. Finally, we have secure pattern matching with hidden text length. Finally, in this variant the length, n, of Alice's text remains a secret. Our protocol requires O(N+m) communication in O(1) rounds using O(N+m) computation, where N is an upper bound on n.

Ochem, Rampersad, and Shallit gave various examples of infinite words avoiding what they called approximate repetitions. An approximate repetition is a factor of the form xx', where x and x' are close to being identical. In their work, they measured the similarity of x and x' using either the Hamming distance or the edit distance. In this paper, we show the existence of words avoiding approximate repetitions, where the measure of similarity between adjacent factors is based on the length of the longest common subsequence. Our principal technique is the so-called "entropy compression" method, which has its origins in Moser and Tardos's algorithmic version of the Lovasz local lemma.

Prevention and detection of plagiarism are crucial. There are several algorithms that can be used to detect plagiarism in documents, including the Cosine Similarity, Rabin-Karp, Levenshtein Distance, Hamming Distance, Euclidean Distance, Edit Distance, Ratcliff/Obershelp, etc. Based on the literature review from previous research, three best algorithms were identified: Cosine Similarity, Rabin-Karp, and Levenshtein Distance. However, there has been no study analyzing the comparison of these three algorithms. Therefore, this study will compare the performance of each algorithm and determine the best algorithm for plagiarism detection in documents based on similarity scores and execution time. The research objects use a sample of documents consisting of titles and abstracts from Indonesian-language informatics journals. Cosine Similarity algorithm is superior to others for plagiarism detection in documents, as it produces the highest average similarity score with a relatively fast execution time. The similarity values of Cosine Similarity, Rabin-Karp with 4 k-grams, and Levenshtein Distance are 48.80%, 47.13%, 20.61%, respectively. The average execution time of Cosine Similarity, Rabin-Karp with 4 k-grams, and Levenshtein Distance are 0.22 s, 0.45 s, and 39.15 s, respectively

Implementing approximate regularities

Recently, there has been a growing focus in solving approximate pattern matching problems in the streaming model. Of particular interest are the pattern matching with k-mismatches (KMM) problem and the pattern matching with w-wildcards (PMWC) problem. Motivated by reductions from these problems in the streaming model to the dictionary matching problem, this paper focuses on designing algorithms for the dictionary matching problem in the multi-stream model where there are several independent streams of data (as opposed to just one in the streaming model), and the memory complexity of an algorithm is expressed using two quantities: (1) a read-only shared memory storage area which is shared among all the streams, and (2) local stream memory that each stream stores separately. In the dictionary matching problem in the multi-stream model the goal is to preprocess a dictionary D={P_1,P_2,...,P_d} of d=|D| patterns (strings with maximum length m over alphabet Sigma) into a data structure stored in shared memory, so that given multiple independent streaming texts (where characters arrive one at a time) the algorithm reports occurrences of patterns from D in each one of the texts as soon as they appear. We design two efficient algorithms for the dictionary matching problem in the multi-stream model. The first algorithm works when all the patterns in D have the same length m and costs O(d log m) words in shared memory, O(log m log d) words in stream memory, and O(log m) time per character. The second algorithm works for general D, but the time cost per character becomes O(log m+log d log log d). We also demonstrate the usefulness of our first algorithm in solving both the KMM problem and PMWC problem in the streaming model. In particular, we obtain the first almost optimal (up to poly-log factors) algorithm for the PMWC problem in the streaming model. We also design a new algorithm for the KMM problem in the streaming model that, up to poly-log factors, has the same bounds as the most recent results that use different techniques. Moreover, for most inputs, our algorithm for KMM is significantly faster on average.