Covering the basic techniques used in the latest research work, the author consolidates progress made so far, including some very recent and promising results, and conveys the beauty and excitement of work in the field. He gives clear, lucid explanations of key results and ideas, with intuitive proofs, and provides critical examples and numerous illustrations to help elucidate the algorithms. Many of the results presented have been simplified and new insights provided. Of interest to theoretical computer scientists, operations researchers, and discrete mathematicians.

Approximation Algorithms

The success of the von Neumann model of sequential computation is attributable to the fact that it is an efficient bridge between software and hardware: high-level languages can be efficiently compiled on to this model; yet it can be effeciently implemented in hardware. The author argues that an analogous bridge between software and hardware in required for parallel computation if that is to become as widely used. This article introduces the bulk-synchronous parallel (BSP) model as a candidate for this role, and gives results quantifying its efficiency both in implementing high-level language features and algorithms, as well as in being implemented in hardware.

A bridging model for parallel computation

We survey the current techniques to cope with the problem of string matching that allows errors. This is becoming a more and more relevant issue for many fast growing areas such as information retrieval and computational biology. We focus on online searching and mostly on edit distance, explaining the problem and its relevance, its statistical behavior, its history and current developments, and the central ideas of the algorithms and their complexities. We present a number of experiments to compare the performance of the different algorithms and show which are the best choices. We conclude with some directions for future work and open problems.

/pdf/a-guided-tour-to-approximate-string-matching-22fowlmq5b.pdf

A guided tour to approximate string matching

An edited volume containing data structures and algorithms for information retrieved including a disk with examples written in C. For programmers and students interested in parsing text, automated indexing, its the first collection in book form of the basic data structures and algorithms that are critical to the storage and retrieval of documents.

https://hornad.fei.tuke.sk/~genci/Vyucba/OOBDS/Archiv/Podklady/TExtoveIS&IR/Information%20Retrieval%20Data%20Structures%20&%20Algorithms.PDF

Information Retrieval: Data Structures and Algorithms

Often, in the real world, entities have two or more representations in databases. Duplicate records do not share a common key and/or they contain errors that make duplicate matching a difficult task. Errors are introduced as the result of transcription errors, incomplete information, lack of standard formats, or any combination of these factors. In this paper, we present a thorough analysis of the literature on duplicate record detection. We cover similarity metrics that are commonly used to detect similar field entries, and we present an extensive set of duplicate detection algorithms that can detect approximately duplicate records in a database. We also cover multiple techniques for improving the efficiency and scalability of approximate duplicate detection algorithms. We conclude with coverage of existing tools and with a brief discussion of the big open problems in the area

/pdf/duplicate-record-detection-a-survey-4crkywvv1d.pdf

Duplicate Record Detection: A Survey

∗Copyright 2007, Uzi Vishkin. These class notes reflect the theorertical part in the Parallel Algorithms course at UMD. The parallel programming part and its computer architecture context within the PRAM-On-Chip Explicit Multi-Threading (XMT) platform is provided through the XMT home page www.umiacs.umd.edu/users/vishkin/XMT and the class home page. Comments are welcome: please write to me using my last name at umd.edu

/pdf/thinking-in-parallel-some-basic-data-parallel-algorithms-and-28l46jj529.pdf

Thinking in Parallel: Some Basic Data-Parallel Algorithms and Techniques

There are a few algorithms designed to solve the problem of the optimal alignment of one sequence, the pattern, of length m, with another, longer sequence the text, of length n. These algorithms allow mismatches, deletions and insertions. Algorithms to date run in O(mn) time. Let us define an integer, k, which is the maximal number of differences allowed. We present a simple algorithm showing that sequences can be optimally aligned in O(k2n) time. For long sequences the gain factor over the currently used algorithms is very large.

An Efficient String Matching Algorithm With K Differences for Nucleotide and Amino Acid Sequences

A mesh of trees (MoT) on-chip interconnection network has been proposed recently to provide high throughput between memory units and processors for single-chip parallel processing (Balkan et al., 2006). In this paper, we report our findings in bringing this concept to silicon. Specifically, we conduct cycle-accurate Verilog simulations to verify the analytical results claimed in (Balkan et al., 2006). We synthesize and obtain the layout of the MoT interconnection networks of various sizes. To further improve throughput, we investigate different arbitration primitives to handle load and store, the two most common memory operations. We also study the use of pipeline registers in large networks when there are long wires. Simulation based on full network layout demonstrates that significant throughput improvement can be achieved over the original proposed MoT interconnection network. The importance of this work lies in its validation of performance features of the MoT interconnection network, as they were previously shown to be competitive with traditional network solutions. The MoT network is currently used in an eXplicit multi-threading (XMT) on-chip parallel processor, which is engineered to support parallel programming. In that context, a 32-terminal MoT network could support up to 512 on-chip XMT processors. Our 8-terminal network that could serve 8 processor clusters (or 128 total processors), was also accepted recently for fabrication.

http://www.umiacs.umd.edu/users/vishkin/XMT/hotI07-paper.pdf

Layout-Accurate Design and Implementation of a High-Throughput Interconnection Network for Single-Chip Parallel Processing

The resource discovery problem was introduced by Harchol-Balter,
Leighton, and Lewin. They developed a number of algorithms
for the problem in the weakly connected directed graph model. This model is a
directed logical graph that represents the vertices’ knowledge about the topology
of the underlying communication network.

The current paper proposes a deterministic algorithm for the
problem in the same model,
with improved time, message, and communication complexities.
Each previous algorithm had a complexity that was higher at least in one of the
measures. Specifically, previous deterministic solutions required either time linear
in the diameter of the initial network, or communication complexity $O(n^3)$ (with
message complexity $O(n^2)$), or message complexity $O(|E_0| \log n)$ (where $E_0$
is the arc set of the initial graph $G_0$). Compared with the main randomized
algorithm of Harchol-Balter, Leighton, and Lewin, the time complexity is reduced
from $O(\log^2n)$ to\pagebreak[4] $O(\log n )$, the message complexity from $O(n \log^2 n)$ to
$O(n \log n )$, and the communication complexity from $O(n^2 \log^3 n)$ to
$O(|E_0|\log ^2 n )$.
\par
Our work significantly extends the connectivity algorithm of Shiloach
and Vishkin which was originally given for a parallel model of computation.
Our result also confirms a conjecture of Harchol-Balter, Leighton, and
Lewin, and addresses an open question due to Lipton.

Deterministic Resource Discovery in Distributed Networks

We study the effect of limited communication throughput on parallel computation in a setting where the number of processors is much smaller than the length of the input. Our model haspprocessors that communicate through a shared memory of sizem. The input has sizenand can be read directly by all the processors. We will be primarily interested in studying cases wheren?p?m. As a test case we study the list reversal problem. For this problem we prove a time lower bound of?(n/mp). (A similar lower bound holds also for the problems of sorting, finding all unique elements, convolution, and universal hashing.) This result demonstrates that limiting the communication (i.e., smallm) could have significant effect on parallel computation. We show an almost matching upper bound ofO((n/mp)logO(1)n). The upper bound requires the development of a few interesting techniques which can alleviate the limited communication in some general settings. Specifically, we show how to emulate a large shared memory on a limited shared memory efficiently. The lower bound applies even to randomized machines, and the upper bound is a randomized algorithm. We also argue that some standard methodology for designing parallel algorithms appears to require a relatively high level of communication throughput. Our results suggest that new alternative methodologies that need a lower such level must be invented for parallel machines that enable a low level of communication throughput, since otherwise those machines will be severly handicapped as general purpose parallel machines. Although we do not rule that out, we cannot offer any encouraging evidence to suggest that such new methodologies are likely to be found.

Uzi Vishkin

Papers

Thinking in Parallel: Some Basic Data-Parallel Algorithms and Techniques

An Efficient String Matching Algorithm With K Differences for Nucleotide and Amino Acid Sequences

Layout-Accurate Design and Implementation of a High-Throughput Interconnection Network for Single-Chip Parallel Processing

Deterministic Resource Discovery in Distributed Networks

Trade-offs between communication throughput and parallel time