On the Succinct Representation of Equivalence Classes

Given a set of n elements that are partitioned into equivalence classes, we study the problem of assigning unique labels to these elements in order to support the query that asks whether the elements corresponding to two given labels belong to the same equivalence class. This problem has been studied by Katz et al., Alstrup et al., and Lewenstein et al.. Lewenstein et al. showed that with no auxiliary data structure, a label space of size nlg(n) is necessary and sufficient to represent the equivalence relation. They also showed that if the labels were to be assigned from the set [n], a data structure of square root of n bits is necessary and sufficient to represent the equivalence relation and to answer the equivalence query in O(lg(n)) time. In this thesis, we give an improved data structure that uses O(square root of n) bits and can answer queries in constant time, when the label space is of size n. Moreover, we study the case where we allow the label space to be of size cn for any constant c > 1. We show that with such a label space, a data structure of O(lg(n)) bits is necessary and sufficient to represent the equivalence relation and to answer the equivalence query in constant time. We believe that our work can trigger further work on tradeoffs between label space and auxiliary data structure space for other labeling problems

Space Efficient Data Structures and Algorithms in the Word-RAM Model

In modern computation the volume of data-sets has increased dramatically. Since the majority of these data-sets are stored in internal memory, reducing their storage requirement is an important research topic. One way of reducing storage is using succinct and compact data structures which maintain the data in compressed form with extra data structures over it in a way that allows efficient access and query of the data. In this thesis we study space-efficient data structures for various combinatorial objects. We focus on succinct and compact data structures. Succinct data structures are data structures whose size is within the information theoretic lower bound plus a lower order term, whereas compact data structures are data structures whose size is a constant factor from the information theoretic lower bound

Raising Permutations to Powers in Place

Given a permutation of n elements, stored as an array, we address the problem of replacing the permutation by its kth power. We aim to perform this operation quickly using o(n) bits of extra storage. To this end, we first present an algorithm for inverting permutations that uses O(lg^2 n) additional bits and runs in O(n lg n) worst case time. This result is then generalized to the situation in which the permutation is to be replaced by its kth power. An algorithm whose worst case running time is O(n lg n) and uses O(lg^2 n + min{k lg n, n^{3/4 + epsilon}}) additional bits is presented

Succinct Dynamic One-Dimensional Point Reporting

In this paper we present a succinct data structure for the dynamic one-dimensional range reporting problem. Given an interval [a,b] for some a,b in [m], the range reporting query on an integer set S subseteq [m] asks for all points in S cap [a,b]. We describe a data structure that answers reporting queries in optimal O(k+1) time, where k is the number of points in the answer, and supports updates in O(lg^epsilon m) expected time. Our data structure uses B(n,m) + o(B(n,m)) bits where B(n,m) is the minimum number of bits required to represent a set of size n from a universe of m elements. This is the first dynamic data structure for this problem that uses succinct space and achieves optimal query time

Succinct Color Searching in One Dimension

In this paper we study succinct data structures for one-dimensional color reporting and color counting problems. We are given a set of n points with integer coordinates in the range [1,m] and every point is assigned a color from the set {1,...sigma}. A color reporting query asks for the list of distinct colors that occur in a query interval [a,b] and a color counting query asks for the number of distinct colors in [a,b]. We describe a succinct data structure that answers approximate color counting queries in O(1) time and uses mathcal{B}(n,m) + O(n) + o(mathcal{B}(n,m)) bits, where mathcal{B}(n,m) is the minimum number of bits required to represent an arbitrary set of size n from a universe of m elements. Thus we show, somewhat counterintuitively, that it is not necessary to store colors of points in order to answer approximate color counting queries. In the special case when points are in the rank space (i.e., when n=m), our data structure needs only O(n) bits. Also, we show that Omega(n) bits are necessary in that case. Then we turn to succinct data structures for color reporting. We describe a data structure that uses mathcal{B}(n,m) + nH_d(S) + o(mathcal{B}(n,m)) + o(nlgsigma) bits and answers queries in O(k+1) time, where k is the number of colors in the answer, and nH_d(S) (d=log_sigma n) is the d-th order empirical entropy of the color sequence. Finally, we consider succinct color reporting under restricted updates. Our dynamic data structure uses nH_d(S)+o(nlgsigma) bits and supports queries in O(k+1) time

Improved Time and Space Bounds for Dynamic Range Mode

Given an array A of n elements, we wish to support queries for the most frequent and least frequent element in a subrange [l, r] of A. We also wish to support updates that change a particular element at index i or insert/ delete an element at index i. For the range mode problem, our data structure supports all operations in O(n^{2/3}) deterministic time using only O(n) space. This improves two results by Chan et al. [Timothy M. Chan et al., 2014]: a linear space data structure supporting update and query operations in O~(n^{3/4}) time and an O(n^{4/3}) space data structure supporting update and query operations in O~(n^{2/3}) time. For the range least frequent problem, we address two variations. In the first, we are allowed to answer with an element of A that may not appear in the query range, and in the second, the returned element must be present in the query range. For the first variation, we develop a data structure that supports queries in O~(n^{2/3}) time, updates in O(n^{2/3}) time, and occupies O(n) space. For the second variation, we develop a Monte Carlo data structure that supports queries in O(n^{2/3}) time, updates in O~(n^{2/3}) time, and occupies O~(n) space, but requires that updates are made independently of the results of previous queries. The Monte Carlo data structure is also capable of answering k-frequency queries; that is, the problem of finding an element of given frequency in the specified query range. Previously, no dynamic data structures were known for least frequent element or k-frequency queries

On Approximate Range Mode and Range Selection

For any epsilon in (0,1), a (1+epsilon)-approximate range mode query asks for the position of an element whose frequency in the query range is at most a factor (1+epsilon) smaller than the true mode. For this problem, we design a data structure occupying O(n/epsilon) bits of space to answer queries in O(lg(1/epsilon)) time. This is an encoding data structure which does not require access to the input sequence; the space cost of this structure is asymptotically optimal for constant epsilon as we also prove a matching lower bound. Furthermore, our solution improves the previous best result of Greve et al. (Cell Probe Lower Bounds and Approximations for Range Mode, ICALP\u2710) by saving the space cost by a factor of lg n while achieving the same query time. In dynamic settings, we design an O(n)-word data structure that answers queries in O(lg n /lg lg n) time and supports insertions and deletions in O(lg n) time, for any constant epsilon in (0,1); the bounds for non-constant epsilon = o(1) are also given in the paper. This is the first result on dynamic approximate range mode; it can also be used to obtain the first static data structure for approximate 3-sided range mode queries in two dimensions. Another problem we consider is approximate range selection. For any alpha in (0,1/2), an alpha-approximate range selection query asks for the position of an element whose rank in the query range is in [k - alpha s, k + alpha s], where k is a rank given by the query and s is the size of the query range. When alpha is a constant, we design an O(n)-bit encoding data structure that can answer queries in constant time and prove this space cost is asymptotically optimal. The previous best result by Krizanc et al. (Range Mode and Range Median Queries on Lists and Trees, Nordic Journal of Computing, 2005) uses O(n lg n) bits, or O(n) words, to achieve constant approximation for range median only. Thus we not only improve the space cost, but also provide support for any arbitrary k given at query time. We also analyse our solutions for non-constant alpha

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

New occurrences for the flora of Lebanon: Sideritis syriaca subsp. nusairiensis (Post) Hub.-Mor. (Lamiaceae) and Thymus sipyleus Boiss. (Lamiaceae) and consideration on their distribution, natural habitats, and conservation status

Investigations carried out during 2019 on the vascular flora of Jabal Akroum, the northernmost part of the Mount Lebanon range near the Syrian border, yielded two new records of Lamiaceae species for the flora of Lebanon: Sideritis syriaca subsp. nusairiensis (Post) Hub.-Mor. and Thymus sipyleus Boiss. We present findings on the distribution and ecology of these species as well as their conservation status at the national level in accordance with International Union for the Conservation of Nature guidelines. We also report on the natural habitats of Jabal Akroum