Efficient Summing over Sliding Windows

This paper considers the problem of maintaining statistic aggregates over the last W elements of a data stream. First, the problem of counting the number of 1's in the last W bits of a binary stream is considered. A lower bound of {\Omega}(1/{\epsilon} + log W) memory bits for W{\epsilon}-additive approximations is derived. This is followed by an algorithm whose memory consumption is O(1/{\epsilon} + log W) bits, indicating that the algorithm is optimal and that the bound is tight. Next, the more general problem of maintaining a sum of the last W integers, each in the range of {0,1,...,R}, is addressed. The paper shows that approximating the sum within an additive error of RW{\epsilon} can also be done using {\Theta}(1/{\epsilon} + log W) bits for {\epsilon}={\Omega}(1/W). For {\epsilon}=o(1/W), we present a succinct algorithm which uses B(1 + o(1)) bits, where B={\Theta}(Wlog(1/W{\epsilon})) is the derived lower bound. We show that all lower bounds generalize to randomized algorithms as well. All algorithms process new elements and answer queries in O(1) worst-case time.Comment: A shorter version appears in SWAT 201

Approximate Query Processing over Static Sets and Sliding Windows

Indexing of static and dynamic sets is fundamental to a large set of applications such as information retrieval and caching. Denoting the characteristic vector of the set by B, we consider the problem of encoding sets and multisets to support approximate versions of the operations rank(i) (i.e., computing sum_{j = i}) queries. We study multiple types of approximations (allowing an error in the query or the result) and present lower bounds and succinct data structures for several variants of the problem. We also extend our model to sliding windows, in which we process a stream of elements and compute suffix sums. This is a generalization of the window summation problem that allows the user to specify the window size at query time. Here, we provide an algorithm that supports updates and queries in constant time while requiring just (1+o(1)) factor more space than the fixed-window summation algorithms

Improved Algorithms for Time Decay Streams

In the time-decay model for data streams, elements of an underlying data set arrive sequentially with the recently arrived elements being more important. A common approach for handling large data sets is to maintain a coreset, a succinct summary of the processed data that allows approximate recovery of a predetermined query. We provide a general framework that takes any offline-coreset and gives a time-decay coreset for polynomial time decay functions. We also consider the exponential time decay model for k-median clustering, where we provide a constant factor approximation algorithm that utilizes the online facility location algorithm. Our algorithm stores O(k log(h Delta)+h) points where h is the half-life of the decay function and Delta is the aspect ratio of the dataset. Our techniques extend to k-means clustering and M-estimators as well

Recency Queries with Succinct Representation

In the context of the sliding-window set membership problem, and caching policies that require knowledge of item recency, we formalize the problem of Recency on a stream. Informally, the query asks, "when was the last time I saw item x?" Existing structures, such as hash tables, can support a recency query by augmenting item occurrences with timestamps. To support recency queries on a window of W items, this might require ?(W log W) bits. We propose a succinct data structure for Recency. By combining sliding-window dictionaries in a hierarchical structure, and careful design of the underlying hash tables, we achieve a data structure that returns a 1+? approximation to the recency of every item in O(log(? W)) time, in only (1+o(1))(1+?)(?+Wlog(?^(-1))) bits. Here, ? is the information-theoretic lower bound on the number of bits for a set of size W, in a universe of cardinality N

Handling Massive N-Gram Datasets Efficiently

This paper deals with the two fundamental problems concerning the handling of large n-gram language models: indexing, that is compressing the n-gram strings and associated satellite data without compromising their retrieval speed; and estimation, that is computing the probability distribution of the strings from a large textual source. Regarding the problem of indexing, we describe compressed, exact and lossless data structures that achieve, at the same time, high space reductions and no time degradation with respect to state-of-the-art solutions and related software packages. In particular, we present a compressed trie data structure in which each word following a context of fixed length k, i.e., its preceding k words, is encoded as an integer whose value is proportional to the number of words that follow such context. Since the number of words following a given context is typically very small in natural languages, we lower the space of representation to compression levels that were never achieved before. Despite the significant savings in space, our technique introduces a negligible penalty at query time. Regarding the problem of estimation, we present a novel algorithm for estimating modified Kneser-Ney language models, that have emerged as the de-facto choice for language modeling in both academia and industry, thanks to their relatively low perplexity performance. Estimating such models from large textual sources poses the challenge of devising algorithms that make a parsimonious use of the disk. The state-of-the-art algorithm uses three sorting steps in external memory: we show an improved construction that requires only one sorting step thanks to exploiting the properties of the extracted n-gram strings. With an extensive experimental analysis performed on billions of n-grams, we show an average improvement of 4.5X on the total running time of the state-of-the-art approach.Comment: Published in ACM Transactions on Information Systems (TOIS), February 2019, Article No: 2

Compressing and indexing aligned readsets

Compressed full-text indexes are one of the main success stories of bioinformatics data structures but even they struggle to handle some DNA readsets. This may seem surprising since, at least when dealing with short reads from the same individual, the readset will be highly repetitive and, thus, highly compressible. If we are not careful, however, this advantage can be more than offset by two disadvantages: first, since most base pairs are included in at least tens reads each, the uncompressed readset is likely to be at least an order of magnitude larger than the individual's uncompressed genome; second, these indexes usually pay some space overhead for each string they store, and the total overhead can be substantial when dealing with millions of reads. The most successful compressed full-text indexes for readsets so far are based on the Extended Burrows-Wheeler Transform (EBWT) and use a sorting heuristic to try to reduce the space overhead per read, but they still treat the reads as separate strings and thus may not take full advantage of the readset's structure. For example, if we have already assembled an individual's genome from the readset, then we can usually use it to compress the readset well: e.g., we store the gap-coded list of reads' starting positions; we store the list of their lengths, which is often highly compressible; and we store information about the sequencing errors, which are rare with short reads. There is nowhere, however, where we can plug an assembled genome into the EBWT. In this paper we show how to use one or more assembled or partially assembled genome as the basis for a compressed full-text index of its readset. Specifically, we build a labelled tree by taking the assembled genome as a trunk and grafting onto it the reads that align to it, at the starting positions of their alignments. Next, we compute the eXtended Burrows-Wheeler Transform (XBWT) of the resulting labelled tree and build a compressed full-text index on that. Although this index can occasionally return false positives, it is usually much more compact than the alternatives. Following the established practice for datasets with many repetitions, we compare different full-text indices by looking at the number of runs in the transformed strings. For a human Chr19 readset our preliminary experiments show that eliminating separators characters from the EBWT reduces the number of runs by 19%, from 220 million to 178 million, and using the XBWT reduces it by a further 15%, to 150 million