pBWT: Achieving succinct data structures for parameterized pattern matching and related problems

The fields of succinct data structures and compressed text indexing have seen quite a bit of progress over the last two decades. An important achievement, primarily using techniques based on the Burrows-Wheeler Transform (BWT), was obtaining the full functionality of the suffix tree in the optimal number of bits. A crucial property that allows the use of BWT for designing compressed indexes is order-preserving suffix links. Specifically, the relative order between two suffixes in the subtree of an internal node is same as that of the suffixes obtained by truncating the furst character of the two suffixes. Unfortunately, in many variants of the text-indexing problem, for e.g., parameterized pattern matching, 2D pattern matching, and order-isomorphic pattern matching, this property does not hold. Consequently, the compressed indexes based on BWT do not directly apply. Furthermore, a compressed index for any of these variants has been elusive throughout the advancement of the field of succinct data structures. We achieve a positive breakthrough on one such problem, namely the Parameterized Pattern Matching problem. Let T be a text that contains n characters from an alphabet , which is the union of two disjoint sets: containing static characters (s-characters) and containing parameterized characters (p-characters). A pattern P (also over ) matches an equal-length substring S of T i the s-characters match exactly, and there exists a one-to-one function that renames the p-characters in S to that in P. The task is to find the starting positions (occurrences) of all such substrings S. Previous index [Baker, STOC 1993], known as Parameterized Suffix Tree, requires (n log n) bits of space, and can find all occ occurrences in time O(jPj log +occ), where = jj. We introduce an n log +O(n)-bit index with O(jPj log +occlog n log ) query time. At the core, lies a new BWT-like transform, which we call the Parame- terized Burrows-Wheeler Transform (pBWT). The techniques are extended to obtain a succinct index for the Parameterized Dictionary Matching problem of Idury and Schaer [CPM, 1994]

Succinct Data Structures for Parameterized Pattern Matching and Related Problems

Let T be a fixed text-string of length n and P be a varying pattern-string of length |P| \u3c= n. Both T and P contain characters from a totally ordered alphabet Sigma of size sigma \u3c= n. Suffix tree is the ubiquitous data structure for answering a pattern matching query: report all the positions i in T such that T[i + k - 1] = P[k], 1 \u3c= k \u3c= |P|. Compressed data structures support pattern matching queries, using much lesser space than the suffix tree, mainly by relying on a crucial property of the leaves in the tree. Unfortunately, in many suffix tree variants (such as parameterized suffix tree, order-preserving suffix tree, and 2-dimensional suffix tree), this property does not hold. Consequently, compressed representations of these suffix tree variants have been elusive. We present the first compressed data structures for two important variants of the pattern matching problem: (1) Parameterized Matching -- report a position i in T if T[i + k - 1] = f(P[k]), 1 \u3c= k \u3c= |P|, for a one-to-one function f that renames the characters in P to the characters in T[i,i+|P|-1], and (2) Order-preserving Matching -- report a position i in T if T[i + j - 1] and T[i + k -1] have the same relative order as that of P[j] and P[k], 1 \u3c= j \u3c k \u3c= |P|. For each of these two problems, the existing suffix tree variant requires O(n*log n) bits of space and answers a query in O(|P|*log sigma + occ) time, where occ is the number of starting positions where a match exists. We present data structures that require O(n*log sigma) bits of space and answer a query in O((|P|+occ) poly(log n)) time. As a byproduct, we obtain compressed data structures for a few other variants, as well as introduce two new techniques (of independent interest) for designing compressed data structures for pattern matching

Indexing large genome collections on a PC

Motivation: The availability of thousands of invidual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key operation useful in such analyses is aligning sequencing reads against a collection of genomes, which is costly with the use of existing algorithms due to their large memory requirements. Results: We present MuGI, Multiple Genome Index, which reports all occurrences of a given pattern, in exact and approximate matching model, against a collection of thousand(s) genomes. Its unique feature is the small index size fitting in a standard computer with 16--32\,GB, or even 8\,GB, of RAM, for the 1000GP collection of 1092 diploid human genomes. The solution is also fast. For example, the exact matching queries are handled in average time of 39\,$\mu$s and with up to 3 mismatches in 373\,$\mu$s on the test PC with the index size of 13.4\,GB. For a smaller index, occupying 7.4\,GB in memory, the respective times grow to 76\,$\mu$s and 917\,$\mu$s. Availability: Software and Suuplementary material: \url{http://sun.aei.polsl.pl/mugi}

Sublinear Computation Paradigm

This open access book gives an overview of cutting-edge work on a new paradigm called the “sublinear computation paradigm,” which was proposed in the large multiyear academic research project “Foundations of Innovative Algorithms for Big Data.” That project ran from October 2014 to March 2020, in Japan. To handle the unprecedented explosion of big data sets in research, industry, and other areas of society, there is an urgent need to develop novel methods and approaches for big data analysis. To meet this need, innovative changes in algorithm theory for big data are being pursued. For example, polynomial-time algorithms have thus far been regarded as “fast,” but if a quadratic-time algorithm is applied to a petabyte-scale or larger big data set, problems are encountered in terms of computational resources or running time. To deal with this critical computational and algorithmic bottleneck, linear, sublinear, and constant time algorithms are required. The sublinear computation paradigm is proposed here in order to support innovation in the big data era. A foundation of innovative algorithms has been created by developing computational procedures, data structures, and modelling techniques for big data. The project is organized into three teams that focus on sublinear algorithms, sublinear data structures, and sublinear modelling. The work has provided high-level academic research results of strong computational and algorithmic interest, which are presented in this book. The book consists of five parts: Part I, which consists of a single chapter on the concept of the sublinear computation paradigm; Parts II, III, and IV review results on sublinear algorithms, sublinear data structures, and sublinear modelling, respectively; Part V presents application results. The information presented here will inspire the researchers who work in the field of modern algorithms

Amortized Dynamic Cell-Probe Lower Bounds from Four-Party Communication

This paper develops a new technique for proving amortized, randomized cell-probe lower bounds on dynamic data structure problems. We introduce a new randomized nondeterministic four-party communication model that enables "accelerated", error-preserving simulations of dynamic data structures. We use this technique to prove an $\Omega(n(\log n/\log\log n)^2)$ cell-probe lower bound for the dynamic 2D weighted orthogonal range counting problem (2D-ORC) with $n/\mathrm{poly}\log n$ updates and $n$ queries, that holds even for data structures with $\exp(-\tilde{\Omega}(n))$ success probability. This result not only proves the highest amortized lower bound to date, but is also tight in the strongest possible sense, as a matching upper bound can be obtained by a deterministic data structure with worst-case operational time. This is the first demonstration of a "sharp threshold" phenomenon for dynamic data structures. Our broader motivation is that cell-probe lower bounds for exponentially small success facilitate reductions from dynamic to static data structures. As a proof-of-concept, we show that a slightly strengthened version of our lower bound would imply an $\Omega((\log n /\log\log n)^2)$ lower bound for the static 3D-ORC problem with $O(n\log^{O(1)}n)$ space. Such result would give a near quadratic improvement over the highest known static cell-probe lower bound, and break the long standing $\Omega(\log n)$ barrier for static data structures

Watching You: Systematic Federal Surveillance of Ordinary Americans

To combat terrorism, Attorney General John Ashcroft has asked Congress to "enhance" the government's ability to conduct domestic surveillance of citizens. The Justice Department's legislative proposals would give federal law enforcement agents new access to personal information contained in business and school records. Before acting on those legislative proposals, lawmakers should pause to consider the extent to which the lives of ordinary Americans already are monitored by the federal government. Over the years, the federal government has instituted a variety of data collection programs that compel the production, retention, and dissemination of personal information about every American citizen. Linked through an individual's Social Security number, these labor, medical, education and financial databases now empower the federal government to obtain a detailed portrait of any person: the checks he writes, the types of causes he supports, and what he says "privately" to his doctor. Despite widespread public concern about preserving privacy, these data collection systems have been enacted in the name of "reducing fraud" and "promoting efficiency" in various government programs. Having exposed most areas of American life to ongoing government scrutiny and recording, Congress is now poised to expand and universalize federal tracking of citizen life. The inevitable consequence of such constant surveillance, however, is metastasizing government control over society. If that happens, our government will have perverted its most fundamental mission and destroyed the privacy and liberty that it was supposed to protect

The Complexity of Symmetry

One of the main goals of theoretical computer science is to prove limits on how efficiently certain Boolean functions can be computed. The study of the algebraic complexity of polynomials provides an indirect approach to exploring these questions, which may prove fruitful since much is known about polynomials already from the field of algebra. This paper explores current research in establishing lower bounds on invariant rings and polynomial families. It explains the construction of an invariant ring for whom a succinct encoding would imply that NP is in P/poly. It then states a theorem about the circuit complexity partial derivatives, and its implications for elementary symmetric function complexity, and proposes potential implications for other classes of functions