Sentiment analysis using averaged weighted word vector features.

People use the World Wide Web heavily to share their experiences with entities such as products, services or travel destinations. Texts that provide online feedback through reviews and comments are essential for consumer decisions. These comments create a valuable source that may be used to measure satisfaction related to products or services. Sentiment analysis is the task of identifying opinions expressed in such text fragments. In this work, we develop two methods that combine different types of word vectors to learn and estimate the polarity of reviews. We create average review vectors from word vectors and add weights to these review vectors using word frequencies in positive and negative sensitivity-tagged reviews. We applied the methods to several datasets from different domains used as standard sentiment analysis benchmarks. We ensemble the techniques with each other and existing methods, and we compare them with the approaches in the literature. The results show that the performances of our approaches outperform the state-of-the-art success rates.

EXSEQREG: Explaining sequence-based NLP tasks with regions with a case study using morphological features for named entity recognition.

The state-of-the-art systems for most natural language engineering tasks employ machine learning methods. Despite the improved performances of these systems, there is a lack of established methods for assessing the quality of their predictions. This work introduces a method for explaining the predictions of any sequence-based natural language processing (NLP) task implemented with any model, neural or non-neural. Our method named EXSEQREG introduces the concept of region that links the prediction and features that are potentially important for the model. A region is a list of positions in the input sentence associated with a single prediction. Many NLP tasks are compatible with the proposed explanation method as regions can be formed according to the nature of the task. The method models the prediction probability differences that are induced by careful removal of features used by the model. The output of the method is a list of importance values. Each value signifies the impact of the corresponding feature on the prediction. The proposed method is demonstrated with a neural network based named entity recognition (NER) tagger using Turkish and Finnish datasets. A qualitative analysis of the explanations is presented. The results are validated with a procedure based on the mutual information score of each feature. We show that this method produces reasonable explanations and may be used for i) assessing the degree of the contribution of features regarding a specific prediction of the model, ii) exploring the features that played a significant role for a trained model when analyzed across the corpus.

Discovery and genotyping of novel sequence insertions in many sequenced individuals.

MOTIVATION: Despite 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. RESULT: Here, 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 IMPLEMENTATION: Pamir is available at https://github.com/vpc-ccg/pamir . CONTACT: fhach@{sfu.ca, prostatecentre.com } or calkan@cs.bilkent.edu.tr. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Robustness of Massively Parallel Sequencing Platforms.

The improvements in high throughput sequencing technologies (HTS) made clinical sequencing projects such as ClinSeq and Genomics England feasible. Although there are significant improvements in accuracy and reproducibility of HTS based analyses, the usability of these types of data for diagnostic and prognostic applications necessitates a near perfect data generation. To assess the usability of a widely used HTS platform for accurate and reproducible clinical applications in terms of robustness, we generated whole genome shotgun (WGS) sequence data from the genomes of two human individuals in two different genome sequencing centers. After analyzing the data to characterize SNPs and indels using the same tools (BWA, SAMtools, and GATK), we observed significant number of discrepancies in the call sets. As expected, the most of the disagreements between the call sets were found within genomic regions containing common repeats and segmental duplications, albeit only a small fraction of the discordant variants were within the exons and other functionally relevant regions such as promoters. We conclude that although HTS platforms are sufficiently powerful for providing data for first-pass clinical tests, the variant predictions still need to be confirmed using orthogonal methods before using in clinical applications.

Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa.

BACKGROUND: Turkey 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×). RESULTS: We 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. CONCLUSION: This 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.