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

Noisy-parallel and comparable corpora filtering methodology for the extraction of bi-lingual equivalent data at sentence level

Text alignment and text quality are critical to the accuracy of Machine Translation (MT) systems, some NLP tools, and any other text processing tasks requiring bilingual data. This research proposes a language independent bi-sentence filtering approach based on Polish (not a position-sensitive language) to English experiments. This cleaning approach was developed on the TED Talks corpus and also initially tested on the Wikipedia comparable corpus, but it can be used for any text domain or language pair. The proposed approach implements various heuristics for sentence comparison. Some of them leverage synonyms and semantic and structural analysis of text as additional information. Minimization of data loss was ensured. An improvement in MT system score with text processed using the tool is discussed.Comment: arXiv admin note: text overlap with arXiv:1509.09093, arXiv:1509.0888

Real-Time Statistical Speech Translation

This research investigates the Statistical Machine Translation approaches to translate speech in real time automatically. Such systems can be used in a pipeline with speech recognition and synthesis software in order to produce a real-time voice communication system between foreigners. We obtained three main data sets from spoken proceedings that represent three different types of human speech. TED, Europarl, and OPUS parallel text corpora were used as the basis for training of language models, for developmental tuning and testing of the translation system. We also conducted experiments involving part of speech tagging, compound splitting, linear language model interpolation, TrueCasing and morphosyntactic analysis. We evaluated the effects of variety of data preparations on the translation results using the BLEU, NIST, METEOR and TER metrics and tried to give answer which metric is most suitable for PL-EN language pair.Comment: machine translation, polish englis

Learning Bilingual Word Representations by Marginalizing Alignments

We present a probabilistic model that simultaneously learns alignments and distributed representations for bilingual data. By marginalizing over word alignments the model captures a larger semantic context than prior work relying on hard alignments. The advantage of this approach is demonstrated in a cross-lingual classification task, where we outperform the prior published state of the art.Comment: Proceedings of ACL 2014 (Short Papers