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Abstract. This paper describes the application of the perceptron algorithm to the morphological disambiguation of Turkish text. Turkish has a productive derivational morphology. Due to the ambiguity caused by complex morphology, a word may have multiple morphological parses, each with a different stem or sequence of morphemes. The methodology employed is based on ranking with perceptron algorithm which has been successful in some NLP tasks in English. We use a baseline statistical trigram-based model of a previous work to enumerate an n-best list of candidate morphological parse sequences for each sentence. We then apply the perceptron algorithm to rerank the n-best list using a set of 23 features. The perceptron trained to do morphological disambiguation improves the accuracy of the baseline model from 93.61% to 96.80%. When we train the perceptron as a POS tagger, the accuracy is 98.27%. Turkish morphological disambiguation and POS tagging results that we obtained is the best reported so far.

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BackgroundTurkey is a crossroads of major population movements throughout history and has been a hotspot of cultural interactions. Several studies have investigated the complex population history of Turkey through a limited set of genetic markers. However, to date, there have been no studies to assess the genetic variation at the whole genome level using whole genome sequencing. Here, we present whole genome sequences of 16 Turkish individuals resequenced at high coverage (32 × -48×).ResultsWe show that the genetic variation of the contemporary Turkish population clusters with South European populations, as expected, but also shows signatures of relatively recent contribution from ancestral East Asian populations. In addition, we document a significant enrichment of non-synonymous private alleles, consistent with recent observations in European populations. A number of variants associated with skin color and total cholesterol levels show frequency differentiation between the Turkish populations and European populations. Furthermore, we have analyzed the 17q21.31 inversion polymorphism region (MAPT locus) and found increased allele frequency of 31.25% for H1/H2 inversion polymorphism when compared to European populations that show about 25% of allele frequency.ConclusionThis study provides the first map of common genetic variation from 16 western Asian individuals and thus helps fill an important geographical gap in analyzing natural human variation and human migration. Our data will help develop population-specific experimental designs for studies investigating disease associations and demographic history in Turkey.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-963) contains supplementary material, which is available to authorized users.

This work proposes a sequential tagger for named entity recognition in morphologically rich languages. Several schemes for representing the morphological analysis of a word in the context of named entity recognition are examined. Word representations are formed by concatenating word and character embeddings with the morphological embeddings based on these schemes. The impact of these representations is measured by training and evaluating a sequential tagger composed of a conditional random field layer on top of a bidirectional long short-term memory layer. Experiments with Turkish, Czech, Hungarian, Finnish and Spanish produce the state-of-the-art results for all these languages, indicating that the representation of morphological information improves performance.

MotivationDespite recent advances in algorithms design to characterize structural variation using high-throughput short read sequencing (HTS) data, characterization of novel sequence insertions longer than the average read length remains a challenging task. This is mainly due to both computational difficulties and the complexities imposed by genomic repeats in generating reliable assemblies to accurately detect both the sequence content and the exact location of such insertions. Additionally, de novo genome assembly algorithms typically require a very high depth of coverage, which may be a limiting factor for most genome studies. Therefore, characterization of novel sequence insertions is not a routine part of most sequencing projects.There are only a handful of algorithms that are specifically developed for novel sequence insertion discovery that can bypass the need for the whole genome de novo assembly. Still, most such algorithms rely on high depth of coverage, and to our knowledge there is only one method (PopIns) that can use multi-sample data to “collectively” obtain a very high coverage dataset to accurately find insertions common in a given population.ResultHere, we present Pamir, a new algorithm to efficiently and accurately discover and genotype novel sequence insertions using either single or multiple genome sequencing datasets. Pamir is able to detect breakpoint locations of the insertions and calculate their zygosity (i.e. heterozygous versus homozygous) by analyzing multiple sequence signatures, matching one-end-anchored sequences to small-scale de novo assemblies of unmapped reads, and conducting strand-aware local assembly. We test the efficacy of Pamir on both simulated and real data, and demonstrate its potential use in accurate and routine identification of novel sequence insertions in genome projects.Availability and implementationPamir is available at https://github.com/vpc-ccg/pamir.Supplementary information Supplementary data are available at Bioinformatics online.

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We present a set of language resources and tools-a morphological parser, a morphological disambiguator, and a text corpus-for exploiting Turkish morphology in natural language processing applications. The morphological parser is a state-of-the-art finite-state transducer-based implementation of Turkish morphology. The disambiguator is based on the averaged perceptron algorithm and has the best accuracy reported for Turkish in the literature. The text corpus has been compiled from the web and contains about 500 million tokens. This is the largest Turkish web corpus published.