Preprocess and data analysis techniques for affymetrix DNA microarrays using bioconductor: a case study in Alzheimer disease

DNA microarray, or DNA chip, is a technology that allows us to obtain the expression level of many genes in a single experiment. The fact that numerical expression values can be easily obtained gives us the possibility to use multiple statistical techniques of data analysis. In this project microarray data is obtained from Gene Expression Omnibus, the repository of National Center for Biotechnology Information (NCBI). Then, the noise is removed and data is normalized, also we use hypothesis tests to find the most relevant genes that may be involved in a disease and use machine learning methods like KNN, Random Forest or Kmeans. For performing the analysis we use Bioconductor, packages in R for the analysis of biological data, and we conduct a case study in Alzheimer disease. The complete code can be found in https://github.com/alberto-poncelas/ bioc-alzheime

Selecting artificially-generated sentences for fine-tuning neural machine translation

Neural Machine Translation (NMT) models tend to achieve best performance when larger sets of parallel sentences are provided for trai- ning. For this reason, augmenting the training set with artificially-generated sentence pairs can boost performance. Nonetheless, the performance can also be im- proved with a small number of sentences if they are in the same domain as the test set. Accordingly, we want to explore the use of artificially-generated sentences along with data-selection algorithms to improve German- to-English NMT models trained solely with authentic data. In this work, we show how artificially- generated sentences can be more beneficial than authentic pairs, and demonstrate their ad- vantages when used in combination with data- selection algorithms

Extracting correctly aligned segments from unclean parallel data using character n-gram matching

Training of Neural Machine Translation systems is a time- and resource-demanding task, especially when large amounts of parallel texts are used. In addition, it is sensitive to unclean parallel data. In this work, we explore a data cleaning method based on character n-gram matching. The method is particularly convenient for closely related language since the n-gram matching scores can be calculated directly on the source and the target parts of the training corpus. For more distant languages, a translation step is needed and then the MT output is compared with the corresponding original part. We show that the proposed method not only reduces the amount of training corpus, but also can increase the system’s performance

Transductive data-selection algorithms for fine-tuning neural machine translation

Machine Translation models are trained to translate a variety of documents from one language into another. However, models specifically trained for a particular characteristics of the documents tend to perform better. Fine-tuning is a technique for adapting an NMT model to some domain. In this work, we want to use this technique to adapt the model to a given test set. In particular, we are using transductive data selection algorithms which take advantage the information of the test set to retrieve sentences from a larger parallel set

A tool for facilitating OCR postediting in historical documents

Optical character recognition (OCR) for historical documents is a complex procedure subject to a unique set of material issues, including inconsistencies in typefaces and low quality scanning. Consequently, even the most sophisticated OCR engines produce errors. This paper reports on a tool built for postediting the output of Tesseract, more specifically for correcting common errors in digitized historical documents. The proposed tool suggests alternatives for word forms not found in a specified vocabulary. The assumed error is replaced by a presumably correct alternative in the post-edition based on the scores of a Language Model (LM). The tool is tested on a chapter of the book An Essay Towards Regulating the Trade and Employing the Poor of this Kingdom. As demonstrated below, the tool is successful in correcting a number of common errors. If sometimes unreliable, it is also transparent and subject to human intervention

Improving transductive data selection algorithms for machine translation

In this work, we study different ways of improving Machine Translation models by using the subset of training data that is the most relevant to the test set. This is achieved by using Transductive Algoritms (TA) for data selection. In particular, we explore two methods: Infrequent N-gram Recovery (INR) and Feature Decay Algorithms (FDA). Statistical Machine Translation (SMT) models do not always perform better when more data are used for training. Using these techniques to extract the training sentences leads to a better performance of the models for translating a particular test set than using the complete training dataset. Neural Machine Translation (NMT) can outperform SMT models, but they require more data to achieve the best performance. In this thesis, we explore how INR and FDA can also be beneficial to improving NMT models with just a fraction of the available data. On top of that, we propose several improvements for these data-selection methods by exploiting the information on the target side. First, we use the alignment between words in the source and target sides to modify the selection criteria of these methods. Those sentences containing n-grams that are more difficult to translate should be promoted so that more occurrences of these n-grams are selected. Another extension proposed is to select sentences based not on the test set but on an MT-generated approximated translation (so the target-side of the sentences are considered in the selection criteria). Finally, target-language sentences can be translated into the source-language so that INR and FDA have more candidates to select sentences from

Multiple segmentations of Thai sentences for neural machine translation

Thai is a low-resource language, so it is often the case that data is not available in sufficient quantities to train an Neural Machine Translation (NMT) model which perform to a high level of quality. In addition, the Thai script does not use white spaces to delimit the boundaries between words, which adds more complexity when building sequence to sequence models. In this work, we explore how to augment a set of English–Thai parallel data by replicating sentence-pairs with different word segmentation methods on Thai, as training data for NMT model training. Using different merge operations of Byte Pair Encoding, different segmentations of Thai sentences can be obtained. The experiments show that combining these datasets, performance is improved for NMT models trained with a dataset that has been split using a supervised splitting tool

The ADAPT system description for the IWSLT 2018 Basque to English translation task

In this paper we present the ADAPT system built for the Basque to English Low Resource MT Evaluation Campaign. Basque is a low-resourced, morphologically-rich language. This poses a challenge for Neural Machine Translation models which usually achieve better performance when trained with large sets of data. Accordingly, we used synthetic data to improve the translation quality produced by a model built using only authentic data. Our proposal uses back-translated data to: (a) create new sentences, so the system can be trained with more data; and (b) translate sentences that are close to the test set, so the model can be fine-tuned to the document to be translated