Storage and retrieval of individual genomes

A repetitive sequence collection is one where portions of a base sequence of length n are repeated many times with small variations, forming a collection of total length N. Examples of such collections are version control data and genome sequences of individuals, where the differences can be expressed by lists of basic edit operations. Flexible and efficient data analysis on a such typically huge collection is plausible using suffix trees. However, suffix tree occupies O(N log N) bits, which very soon inhibits in-memory analyses. Recent advances in full-text self-indexing reduce the space of suffix tree to O(N log σ) bits, where σ is the alphabet size. In practice, the space reduction is more than 10-fold, for example on suffix tree of Human Genome. However, this reduction factor remains constant when more sequences are added to the collection. We develop a new family of self-indexes suited for the repetitive sequence collection setting. Their expected space requirement depends only on the length n of the base sequence and the number s of variations in its repeated copies. That is, the space reduction factor is no longer constant, but depends on N / n. We believe the structures developed in this work will provide a fundamental basis for storage and retrieval of individual genomes as they become available due to rapid progress in the sequencing technologies.

Fast distributed approximation algorithms for vertex cover and set cover in anonymous networks

We present a distributed algorithm that finds a maximal edge packing in O(Δ + log* W) synchronous communication rounds in a weighted graph, independent of the number of nodes in the network; here Δ is the maximum degree of the graph and W is the maximum weight. As a direct application, we have a distributed 2-approximation algorithm for minimum-weight vertex cover, with the same running time. We also show how to find an f-approximation of minimum-weight set cover in O(f2k2 + fk log* W) rounds; here k is the maximum size of a subset in the set cover instance, f is the maximum frequency of an element, and W is the maximum weight of a subset. The algorithms are deterministic, and they can be applied in anonymous networks.

A Reference Architecture for Electronic Business-to-Business Collaboration Setup and Enactment Systems

The question what a business-to-business (B2B) collaboration setup and enactment application-system should look like remains open. An important element of such collaboration constitutes the inter-organizational disclosure of business-process details so that the opposing parties may protect their business secrets. For that purpose, eSourcing [37] has been developed as a general businessprocess collaboration concept in the framework of the EU research project Cross- Work. The eSourcing characteristics are guiding for the design and evaluation of an eSourcing Reference Architecture (eSRA) that serves as a starting point for software developers of B2B-collaboration systems. In this paper we present the results of a scenario-based evaluation method conducted with the earlier specified eSourcing Architecture (eSA) that generates as results risks, sensitivity, and tradeoff points that must be paid attention to if eSA is implemented. Additionally, the evaluation method detects shortcomings of eSA in terms of integrated components that are required for electronic B2B-collaboration. The evaluation results are used for the specification of eSRA, which comprises all extensions for incorporating the results of the scenario-based evaluation, on three refinement levels.

Local approximability of max-min and min-max linear programs

In a max-min LP, the objective is to maximise ω subject to Ax ≤ 1, Cx ≥ ω1, and x ≥ 0. In a min-max LP, the objective is to minimise ρ subject to Ax ≤ ρ1, Cx ≥ 1, and x ≥ 0. The matrices A and C are nonnegative and sparse: each row ai of A has at most ΔI positive elements, and each row ck of C has at most ΔK positive elements. We study the approximability of max-min LPs and min-max LPs in a distributed setting; in particular, we focus on local algorithms (constant-time distributed algorithms). We show that for any ΔI ≥ 2, ΔK ≥ 2, and ε > 0 there exists a local algorithm that achieves the approximation ratio ΔI (1 − 1/ΔK) + ε. We also show that this result is the best possible: no local algorithm can achieve the approximation ratio ΔI (1 − 1/ΔK) for any ΔI ≥ 2 and ΔK ≥ 2.

Building and Using Existing Hunspell Dictionaries and TEX Hyphenators as Finite-State Automata

There are numerous formats for writing spellcheckers for open-source systems and there are many descriptions for languages written in these formats. Similarly, for word hyphenation by computer there are TEX rules for many languages. In this paper we demonstrate a method for converting these spell-checking lexicons and hyphenation rule sets into finite-state automata, and present a new finite-state based system for writer’s tools used in current open-source software such as Firefox, OpenOffice.org and enchant via the spell-checking library voikko.

Common Infrastructure for Finite-State Based Methods and Linguistics Descriptions

Finite-state methods have been adopted widely in computational morphology and related linguistic applications. To enable efficient development of finite-state based linguistic descriptions, these methods should be a freely available resource for academic language research and the language technology industry. The following needs can be identified: (i) a registry that maps the existing approaches, implementations and descriptions, (ii) managing the incompatibilities of the existing tools, (iii) increasing synergy and complementary functionality of the tools, (iv) persistent availability of the tools used to manipulate the archived descriptions, (v) an archive for free finite-state based tools and linguistic descriptions. Addressing these challenges contributes to building a common research infrastructure for advanced language technology.