Prospects and limitations of full-text index structures in genome analysis

The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared

Runtime Optimizations for Prediction with Tree-Based Models

Tree-based models have proven to be an effective solution for web ranking as well as other problems in diverse domains. This paper focuses on optimizing the runtime performance of applying such models to make predictions, given an already-trained model. Although exceedingly simple conceptually, most implementations of tree-based models do not efficiently utilize modern superscalar processor architectures. By laying out data structures in memory in a more cache-conscious fashion, removing branches from the execution flow using a technique called predication, and micro-batching predictions using a technique called vectorization, we are able to better exploit modern processor architectures and significantly improve the speed of tree-based models over hard-coded if-else blocks. Our work contributes to the exploration of architecture-conscious runtime implementations of machine learning algorithms

The CoNLL 2007 shared task on dependency parsing

The Conference on Computational Natural Language Learning features a shared task, in which participants train and test their learning systems on the same data sets. In 2007, as in 2006, the shared task has been devoted to dependency parsing, this year with both a multilingual track and a domain adaptation track. In this paper, we define the tasks of the different tracks and describe how the data sets were created from existing treebanks for ten languages. In addition, we characterize the different approaches of the participating systems, report the test results, and provide a first analysis of these results

Domain transfer for deep natural language generation from abstract meaning representations

Stochastic natural language generation systems that are trained from labelled datasets are often domainspecific in their annotation and in their mapping from semantic input representations to lexical-syntactic outputs. As a result, learnt models fail to generalize across domains, heavily restricting their usability beyond single applications. In this article, we focus on the problem of domain adaptation for natural language generation. We show how linguistic knowledge from a source domain, for which labelled data is available, can be adapted to a target domain by reusing training data across domains. As a key to this, we propose to employ abstract meaning representations as a common semantic representation across domains. We model natural language generation as a long short-term memory recurrent neural network encoderdecoder, in which one recurrent neural network learns a latent representation of a semantic input, and a second recurrent neural network learns to decode it to a sequence of words. We show that the learnt representations can be transferred across domains and can be leveraged effectively to improve training on new unseen domains. Experiments in three different domains and with six datasets demonstrate that the lexical-syntactic constructions learnt in one domain can be transferred to new domains and achieve up to 75-100% of the performance of in-domain training. This is based on objective metrics such as BLEU and semantic error rate and a subjective human rating study. Training a policy from prior knowledge from a different domain is consistently better than pure in-domain training by up to 10%

On the Benefit of Merging Suffix Array Intervals for Parallel Pattern Matching

We present parallel algorithms for exact and approximate pattern matching with suffix arrays, using a CREW-PRAM with $p$ processors. Given a static text of length $n$, we first show how to compute the suffix array interval of a given pattern of length $m$ in $O(\frac{m}{p}+ \lg p + \lg\lg p\cdot\lg\lg n)$ time for $p \le m$. For approximate pattern matching with $k$ differences or mismatches, we show how to compute all occurrences of a given pattern in $O(\frac{m^k\sigma^k}{p}\max\left(k,\lg\lg n\right)\!+\!(1+\frac{m}{p}) \lg p\cdot \lg\lg n + \text{occ})$ time, where $\sigma$ is the size of the alphabet and $p \le \sigma^k m^k$. The workhorse of our algorithms is a data structure for merging suffix array intervals quickly: Given the suffix array intervals for two patterns $P$ and $P'$, we present a data structure for computing the interval of $PP'$ in $O(\lg\lg n)$ sequential time, or in $O(1+\lg_p\lg n)$ parallel time. All our data structures are of size $O(n)$ bits (in addition to the suffix array)

Inbreeding ratio and genetic relationships among strains of the Western clawed frog, Xenopus tropicalis

The Western clawed frog, Xenopus tropicalis, is a highly promising model amphibian, especially in developmental and physiological research, and as a tool for understanding disease. It was originally found in the West African rainforest belt, and was introduced to the research community in the 1990s. The major strains thus far known include the Nigerian and Ivory Coast strains. However, due to its short history as an experimental animal, the genetic relationship among the various strains has not yet been clarified, and establishment of inbred strains has not yet been achieved. Since 2003 the Institute for Amphibian Biology (IAB), Hiroshima University has maintained stocks of multiple X. tropicalis strains and conducted consecutive breeding as part of the National BioResource Project. In the present study we investigated the inbreeding ratio and genetic relationship of four inbred strains at IAB, as well as stocks from other institutions, using highly polymorphic microsatellite markers and mitochondrial haplotypes. Our results show successive reduction of heterozygosity in the genome of the IAB inbred strains. The Ivory Coast strains clearly differed from the Nigerian strains genetically, and three subgroups were identified within both the Nigerian and Ivory Coast strains. It is noteworthy that the Ivory Coast strains have an evolutionary divergent genetic background. Our results serve as a guide for the most effective use of X. tropicalis strains, and the long-term maintenance of multiple strains will contribute to further research efforts