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Register a new userLightweight Data Indexing and Compression in External Memory
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Travis Gagie
Publication date
2009
fields
Informatics Engineering
and research's language is
English
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In this paper we describe algorithms for computing the BWT and for building (compressed) indexes in external memory. The innovative feature of our algorithms is that they are lightweight in the sense that, for an input of size $n$, they use only ${n}$ bits of disk working space while all previous approaches use $Th{n log n}$ bits of disk working space. Moreover, our algorithms access disk data only via sequential scans, thus they take full advantage of modern disk features that make sequential disk accesses much faster than random accesses. We also present a scan-based algorithm for inverting the BWT that uses $Th{n}$ bits of working space, and a lightweight {em internal-memory} algorithm for computing the BWT which is the fastest in the literature when the available working space is $os{n}$ bits. Finally, we prove {em lower} bounds on the complexity of computing and inverting the BWT via sequential scans in terms of the classic product: internal-memory space $times$ number of passes over the disk data.
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Data series similarity search is a core operation for several data series analysis applications across many different domains. However, the state-of-the-art techniques fail to deliver the time performance required for interactive exploration, or analysis of large data series collections. In this work, we propose MESSI, the first data series index designed for in-memory operation on modern hardware. Our index takes advantage of the modern hardware parallelization opportunities (i.e., SIMD instructions, multi-core and multi-socket architectures), in order to accelerate both index construction and similarity search processing times. Moreover, it benefits from a careful design in the setup and coordination of the parallel workers and data structures, so that it maximizes its performance for in-memory operations. Our experiments with synthetic and real datasets demonstrate that overall MESSI is up to 4x faster at index construction, and up to 11x faster at query answering than the state-of-the-art parallel approach. MESSI is the first to answer exact similarity search queries on 100GB datasets in _50msec (30-75msec across diverse datasets), which enables real-time, interactive data exploration on very large data series collections.
In the unit-cost comparison model, a black box takes an input two items and outputs the result of the comparison. Problems like sorting and searching have been studied in this model, and it has been generalized to include the concept of priced information, where different pairs of items (say database records) have different comparison costs. These comparison costs can be arbitrary (in which case no algorithm can be close to optimal (Charikar et al. STOC 2000)), structured (for example, the comparison cost may depend on the length of the databases (Gupta et al. FOCS 2001)), or stochastic (Angelov et al. LATIN 2008). Motivated by the database setting where the cost depends on the sizes of the items, we consider the problems of sorting and batched predecessor where two non-uniform sets of items $A$ and $B$ are given as input. (1) In the RAM setting, we consider the scenario where both sets have $n$ keys each. The cost to compare two items in $A$ is $a$, to compare an item of $A$ to an item of $B$ is $b$, and to compare two items in $B$ is $c$. We give upper and lower bounds for the case $a le b le c$. Notice that the case $b=1, a=c=infty$ is the famous ``nuts and bolts problem. (2) In the Disk-Access Model (DAM), where transferring elements between disk and internal memory is the main bottleneck, we consider the scenario where elements in $B$ are larger than elements in $A$. The larger items take more I/Os to be brought into memory, consume more space in internal memory, and are required in their entirety for comparisons. We first give output-sensitive lower and upper bounds on the batched predecessor problem, and use these to derive bounds on the complexity of sorting in the two models. Our bounds are tight in most cases, and require novel generalizations of the classical lower bound techniques in external memory to accommodate the non-uniformity of keys.
We study the problem of validating XML documents of size $N$ against general DTDs in the context of streaming algorithms. The starting point of this work is a well-known space lower bound. There are XML documents and DTDs for which $p$-pass streaming algorithms require $Omega(N/p)$ space. We show that when allowing access to external memory, there is a deterministic streaming algorithm that solves this problem with memory space $O(log^2 N)$, a constant number of auxiliary read/write streams, and $O(log N)$ total number of passes on the XML document and auxiliary streams. An important intermediate step of this algorithm is the computation of the First-Child-Next-Sibling (FCNS) encoding of the initial XML document in a streaming fashion. We study this problem independently, and we also provide memory efficient streaming algorithms for decoding an XML document given in its FCNS encoding. Furthermore, validating XML documents encoding binary trees in the usual streaming model without external memory can be done with sublinear memory. There is a one-pass algorithm using $O(sqrt{N log N})$ space, and a bidirectional two-pass algorithm using $O(log^2 N)$ space performing this task.
We study dynamic planar point location in the External Memory Model or Disk Access Model (DAM). Previous work in this model achieves polylog query and polylog amortized update time. We present a data structure with $O( log_B^2 N)$ query time and $O(frac{1}{ B^{1-epsilon}} log_B N)$ amortized update time, where $N$ is the number of segments, $B$ the block size and $epsilon$ is a small positive constant, under the assumption that all faces have constant size. This is a $B^{1-epsilon}$ factor faster for updates than the fastest previous structure, and brings the cost of insertion and deletion down to subconstant amortized time for reasonable choices of $N$ and $B$. Our structure solves the problem of vertical ray-shooting queries among a dynamic set of interior-disjoint line segments; this is well-known to solve dynamic planar point location for a connected subdivision of the plane with faces of constant size.
The recent introduction of learned indexes has shaken the foundations of the decades-old field of indexing data structures. Combining, or even replacing, classic design elements such as B-tree nodes with machine learning models has proven to give outstanding improvements in the space footprint and time efficiency of data systems. However, these novel approaches are based on heuristics, thus they lack any guarantees both in their time and space requirements. We propose the Piecewise Geometric Model index (shortly, PGM-index), which achieves guaranteed I/O-optimality in query operations, learns an optimal number of linear models, and its peculiar recursive construction makes it a purely learned data structure, rather than a hybrid of traditional and learned indexes (such as RMI and FITing-tree). We show that the PGM-index improves the space of the FITing-tree by 63.3% and of the B-tree by more than four orders of magnitude, while achieving their same or even better query time efficiency. We complement this result by proposing three variants of the PGM-index. First, we design a compressed PGM-index that further reduces its space footprint by exploiting the repetitiveness at the level of the learned linear models it is composed of. Second, we design a PGM-index that adapts itself to the distribution of the queries, thus resulting in the first known distribution-aware learned index to date. Finally, given its flexibility in the offered space-time trade-offs, we propose the multicriteria PGM-index that efficiently auto-tune itself in a few seconds over hundreds of millions of keys to the possibly evolving space-time constraints imposed by the application of use. We remark to the reader that this paper is an extended and improved version of our previous paper titled Superseding traditional indexes by orchestrating learning and geometry (arXiv:1903.00507).
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