Biomedical ontology alignment: An approach based on representation learning

While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through which semantic similarity information becomes inscribed onto fields of pre-trained word vectors. The resulting framework also incorporates a novel outlier detection mechanism based on a denoising autoencoder that is shown to improve performance. An ontology matching system derived using the proposed framework achieved an F-score of 94% on an alignment scenario involving the Adult Mouse Anatomical Dictionary and the Foundational Model of Anatomy ontology (FMA) as targets. This compares favorably with the best performing systems on the Ontology Alignment Evaluation Initiative anatomy challenge. We performed additional experiments on aligning FMA to NCI Thesaurus and to SNOMED CT based on a reference alignment extracted from the UMLS Metathesaurus. Our system obtained overall F-scores of 93.2% and 89.2% for these experiments, thus achieving state-of-the-art results

Ontology alignment based on word embedding and random forest classification.

Ontology alignment is crucial for integrating heterogeneous data sources and forms an important component for realising the goals of the semantic web. Accordingly, several ontology alignment techniques have been proposed and used for discovering correspondences between the concepts (or entities) of different ontologies. However, these techniques mostly depend on string-based similarities which are unable to handle the vocabulary mismatch problem. Also, determining which similarity measures to use and how to effectively combine them in alignment systems are challenges that have persisted in this area. In this work, we introduce a random forest classifier approach for ontology alignment which relies on word embedding to discover semantic similarities between concepts. Specifically, we combine string-based and semantic similarity measures to form feature vectors that are used by the classifier model to determine when concepts match. By harnessing background knowledge and relying on minimal information from the ontologies, our approach can deal with knowledge-light ontological resources. It also eliminates the need for learning the aggregation weights of multiple similarity measures. Our experiments using Ontology Alignment Evaluation Initiative (OAEI) dataset and real-world ontologies highlight the utility of our approach and show that it can outperform state-of-the-art alignment systems

N-gram-based statistical machine translation versus syntax augmented machine translation: comparison and system combination

In this paper we compare and contrast two approaches to Machine Translation (MT): the CMU-UKA Syntax Augmented Machine Translation system (SAMT) and UPC-TALP N-gram-based Statistical Machine Translation (SMT). SAMT is a hierarchical syntax-driven translation system underlain by a phrase-based model and a target part parse tree. In N-gram-based SMT, the translation process is based on bilingual units related to word-to-word alignment and statistical modeling of the bilingual context following a maximumentropy framework. We provide a stepby- step comparison of the systems and report results in terms of automatic evaluation metrics and required computational resources for a smaller Arabic-to-English translation task (1.5M tokens in the training corpus). Human error analysis clarifies advantages and disadvantages of the systems under consideration. Finally, we combine the output of both systems to yield significant improvements in translation quality.Postprint (published version

SAD-based Italian Forced Alignment Strategies

Abstract. The Evalita 2011 contest proposed two forced alignment tasks, word and phone segmentation, and two modalities, "open" and "closed". A system for each combination of task and modality has been proposed and submitted for evaluation. Direct use of silence/activity detection in forced alignment has been tested. Positive effects were shown in the acoustic model training step, especially when dealing with long pauses. Exploitation of multiple forced alignment systems through a voting procedure has also been tested

Tracking relevant alignment characteristics for machine translation

In most statistical machine translation (SMT) systems, bilingual segments are extracted via word alignment. In this paper we compare alignments tuned directly according to alignment F-score and BLEU score in order to investigate the alignment characteristics that are helpful in translation. We report results for two different SMT systems (a phrase-based and an n-gram-based system) on Chinese to English IWSLT data, and Spanish to English European Parliament data. We give alignment hints to improve BLEU score, depending on the SMT system used and the type of corpus

Source-side context-informed hypothesis alignment for combining outputs from machine translation systems

This paper presents a new hypothesis alignment method for combining outputs of multiple machine translation (MT) systems. Traditional hypothesis alignment algorithms such as TER, HMM and IHMM do not directly utilise the context information of the source side but rather address the alignment issues via the output data itself. In this paper, a source-side context-informed (SSCI) hypothesis alignment method is proposed to carry out the word alignment and word reordering issues. First of all, the source–target word alignment links are produced as the hidden variables by exporting source phrase spans during the translation decoding process. Secondly, a mapping strategy and normalisation model are employed to acquire the 1- to-1 alignment links and build the confusion network (CN). The source-side context-based method outperforms the state-of-the-art TERbased alignment model in our experiments on the WMT09 English-to-French and NIST Chinese-to-English data sets respectively. Experimental results demonstrate that our proposed approach scores consistently among the best results across different data and language pair conditions

Measuring Semantic Textual Similarity and Automatic Answer Assessment in Dialogue Based Tutoring Systems

This dissertation presents methods and resources proposed to improve onmeasuring semantic textual similarity and their applications in student responseunderstanding in dialogue based Intelligent Tutoring Systems. In order to predict the extent of similarity between given pair of sentences,we have proposed machine learning models using dozens of features, such as thescores calculated using optimal multi-level alignment, vector based compositionalsemantics, and machine translation evaluation methods. Furthermore, we haveproposed models towards adding an interpretation layer on top of similaritymeasurement systems. Our models on predicting and interpreting the semanticsimilarity have been the top performing systems in SemEval (a premier venue for thesemantic evaluation) for the last three years. The correlations between our models\u27predictions and the human judgments were above 0.80 for several datasets while ourmodels being very robust than many other top performing systems. Moreover, wehave proposed Bayesian. We have also proposed a novel Neural Network based word representationmapping approach which allows us to map the vector based representation of a wordfound in one model to the another model where the word representation is missing,effectively pooling together the vocabularies and corresponding representationsacross models. Our experiments show that the model coverage increased by few toseveral times depending on which model\u27s vocabulary is taken as a reference. Also,the transformed representations were well correlated to the native target modelvectors showing that the mapped representations can be used with condence tosubstitute the missing word representations in the target model. models to adapt similarity models across domains. Furthermore, we have proposed methods to improve open-ended answersassessment in dialogue based tutoring systems which is very challenging because ofthe variations in student answers which often are not self contained and need thecontextual information (e.g., dialogue history) in order to better assess theircorrectness. In that, we have proposed Probabilistic Soft Logic (PSL) modelsaugmenting semantic similarity information with other knowledge. To detect intra- and inter-sentential negation scope and focus in tutorialdialogs, we have developed Conditional Random Fields (CRF) models. The resultsindicate that our approach is very effective in detecting negation scope and focus intutorial dialogue context and can be further developed to augment the naturallanguage understanding systems. Additionally, we created resources (datasets, models, and tools) for fosteringresearch in semantic similarity and student response understanding inconversational tutoring systems

Example-based controlled translation

The first research on integrating controlled language data in an Example-Based Machine Translation (EBMT) system was published in [Gough & Way, 2003]. We improve on their sub-sentential alignment algorithm to populate the system’s databases with more than six times as many potentially useful fragments. Together with two simple novel improvements—correcting mistranslations in the lexicon, and allowing multiple translations in the lexicon—translation quality improves considerably when target language translations are constrained. We also develop the first EBMT system which attempts to filter the source language data using controlled language specifications. We provide detailed automatic and human evaluations of a number of experiments carried out to test the quality of the system. We observe that our system outperforms Logomedia in a number of tests. Finally, despite conflicting results from different automatic evaluation metrics, we observe a preference for controlling the source data rather than the target translations