Georgios Kontonatsios

Topic detection using paragraph vectors to support active learning in systematic reviews

Graphical abstract

Using a Random Forest Classifier to Compile Bilingual Dictionaries of Technical Terms from Comparable Corpora

We describe a machine learning approach, a Random Forest (RF) classifier, that is used to automatically compile bilingual dictionaries of technical terms from comparable corpora. We evaluate the RF classifier against a popular term alignment method, namely context vectors, and we report an improvement of the translation accuracy. As an application, we use the automatically extracted dictionary in combination with a trained Statistical Machine Translation (SMT) system to more accurately translate unknown terms. The dictionary extraction method described in this paper is freely available 1 .

Text Mining the History of Medicine.

Historical text archives constitute a rich and diverse source of information, which is becoming increasingly readily accessible, due to large-scale digitisation efforts. However, it can be difficult for researchers to explore and search such large volumes of data in an efficient manner. Text mining (TM) methods can help, through their ability to recognise various types of semantic information automatically, e.g., instances of concepts (places, medical conditions, drugs, etc.), synonyms/variant forms of concepts, and relationships holding between concepts (which drugs are used to treat which medical conditions, etc.). TM analysis allows search systems to incorporate functionality such as automatic suggestions of synonyms of user-entered query terms, exploration of different concepts mentioned within search results or isolation of documents in which concepts are related in specific ways. However, applying TM methods to historical text can be challenging, according to differences and evolutions in vocabulary, terminology, language structure and style, compared to more modern text. In this article, we present our efforts to overcome the various challenges faced in the semantic analysis of published historical medical text dating back to the mid 19th century. Firstly, we used evidence from diverse historical medical documents from different periods to develop new resources that provide accounts of the multiple, evolving ways in which concepts, their variants and relationships amongst them may be expressed. These resources were employed to support the development of a modular processing pipeline of TM tools for the robust detection of semantic information in historical medical documents with varying characteristics. We applied the pipeline to two large-scale medical document archives covering wide temporal ranges as the basis for the development of a publicly accessible semantically-oriented search system. The novel resources are available for research purposes, while the processing pipeline and its modules may be used and configured within the Argo TM platform.

Supporting Systematic Reviews Using LDA-based Document Representations

BackgroundIdentifying relevant studies for inclusion in a systematic review (i.e. screening) is a complex, laborious and expensive task. Recently, a number of studies has shown that the use of machine learning and text mining methods to automatically identify relevant studies has the potential to drastically decrease the workload involved in the screening phase. The vast majority of these machine learning methods exploit the same underlying principle, i.e. a study is modelled as a bag-of-words (BOW).MethodsWe explore the use of topic modelling methods to derive a more informative representation of studies. We apply Latent Dirichlet allocation (LDA), an unsupervised topic modelling approach, to automatically identify topics in a collection of studies. We then represent each study as a distribution of LDA topics. Additionally, we enrich topics derived using LDA with multi-word terms identified by using an automatic term recognition (ATR) tool. For evaluation purposes, we carry out automatic identification of relevant studies using support vector machine (SVM)-based classifiers that employ both our novel topic-based representation and the BOW representation.ResultsOur results show that the SVM classifier is able to identify a greater number of relevant studies when using the LDA representation than the BOW representation. These observations hold for two systematic reviews of the clinical domain and three reviews of the social science domain.ConclusionsA topic-based feature representation of documents outperforms the BOW representation when applied to the task of automatic citation screening. The proposed term-enriched topics are more informative and less ambiguous to systematic reviewers.

Combining String and Context Similarity for Bilingual Term Alignment from Comparable Corpora

Automatically compiling bilingual dictionaries of technical terms from comparable corpora is a challenging problem, yet with many potential applications. In this paper, we exploit two independent observations about term translations: (a) terms are often formed by corresponding sub-lexical units across languages and (b) a term and its translation tend to appear in similar lexical context. Based on the first observation, we develop a new character n-gram compositional method, a logistic regression classifier, for learning a string similarity measure of term translations. According to the second observation, we use an existing context-based approach. For evaluation, we investigate the performance of compositional and context-based methods on: (a) similar and unrelated languages, (b) corpora of different degree of comparability and (c) the translation of frequent and rare terms. Finally, we combine the two translation clues, namely string and contextual similarity, in a linear model and we show substantial improvements over the two translation signals.

Deploying and sharing U-Compare workflows as web services

BackgroundU-Compare is a text mining platform that allows the construction, evaluation and comparison of text mining workflows. U-Compare contains a large library of components that are tuned to the biomedical domain. Users can rapidly develop biomedical text mining workflows by mixing and matching U-Compare’s components. Workflows developed using U-Compare can be exported and sent to other users who, in turn, can import and re-use them. However, the resulting workflows are standalone applications, i.e., software tools that run and are accessible only via a local machine, and that can only be run with the U-Compare platform.ResultsWe address the above issues by extending U-Compare to convert standalone workflows into web services automatically, via a two-click process. The resulting web services can be registered on a central server and made publicly available. Alternatively, users can make web services available on their own servers, after installing the web application framework, which is part of the extension to U-Compare. We have performed a user-oriented evaluation of the proposed extension, by asking users who have tested the enhanced functionality of U-Compare to complete questionnaires that assess its functionality, reliability, usability, efficiency and maintainability. The results obtained reveal that the new functionality is well received by users.ConclusionsThe web services produced by U-Compare are built on top of open standards, i.e., REST and SOAP protocols, and therefore, they are decoupled from the underlying platform. Exported workflows can be integrated with any application that supports these open standards. We demonstrate how the newly extended U-Compare enhances the cross-platform interoperability of workflows, by seamlessly importing a number of text mining workflow web services exported from U-Compare into Taverna, i.e., a generic scientific workflow construction platform.

Constructing a biodiversity terminological inventory

The increasing growth of literature in biodiversity presents challenges to users who need to discover pertinent information in an efficient and timely manner. In response, text mining techniques offer solutions by facilitating the automated discovery of knowledge from large textual data. An important step in text mining is the recognition of concepts via their linguistic realisation, i.e., terms. However, a given concept may be referred to in text using various synonyms or term variants, making search systems likely to overlook documents mentioning less known variants, which are albeit relevant to a query term. Domain-specific terminological resources, which include term variants, synonyms and related terms, are thus important in supporting semantic search over large textual archives. This article describes the use of text mining methods for the automatic construction of a large-scale biodiversity term inventory. The inventory consists of names of species, amongst which naming variations are prevalent. We apply a number of distributional semantic techniques on all of the titles in the Biodiversity Heritage Library, to compute semantic similarity between species names and support the automated construction of the resource. With the construction of our biodiversity term inventory, we demonstrate that distributional semantic models are able to identify semantically similar names that are not yet recorded in existing taxonomies. Such methods can thus be used to update existing taxonomies semi-automatically by deriving semantically related taxonomic names from a text corpus and allowing expert curators to validate them. We also evaluate our inventory as a means to improve search by facilitating automatic query expansion. Specifically, we developed a visual search interface that suggests semantically related species names, which are available in our inventory but not always in other repositories, to incorporate into the search query. An assessment of the interface by domain experts reveals that our query expansion based on related names is useful for increasing the number of relevant documents retrieved. Its exploitation can benefit both users and developers of search engines and text mining applications.

A Cross-Lingual Similarity Measure for Detecting Biomedical Term Translations

Bilingual dictionaries for technical terms such as biomedical terms are an important resource for machine translation systems as well as for humans who would like to understand a concept described in a foreign language. Often a biomedical term is first proposed in English and later it is manually translated to other languages. Despite the fact that there are large monolingual lexicons of biomedical terms, only a fraction of those term lexicons are translated to other languages. Manually compiling large-scale bilingual dictionaries for technical domains is a challenging task because it is difficult to find a sufficiently large number of bilingual experts. We propose a cross-lingual similarity measure for detecting most similar translation candidates for a biomedical term specified in one language (source) from another language (target). Specifically, a biomedical term in a language is represented using two types of features: (a) intrinsic features that consist of character n-grams extracted from the term under consideration, and (b) extrinsic features that consist of unigrams and bigrams extracted from the contextual windows surrounding the term under consideration. We propose a cross-lingual similarity measure using each of those feature types. First, to reduce the dimensionality of the feature space in each language, we propose prototype vector projection (PVP)—a non-negative lower-dimensional vector projection method. Second, we propose a method to learn a mapping between the feature spaces in the source and target language using partial least squares regression (PLSR). The proposed method requires only a small number of training instances to learn a cross-lingual similarity measure. The proposed PVP method outperforms popular dimensionality reduction methods such as the singular value decomposition (SVD) and non-negative matrix factorization (NMF) in a nearest neighbor prediction task. Moreover, our experimental results covering several language pairs such as English–French, English–Spanish, English–Greek, and English–Japanese show that the proposed method outperforms several other feature projection methods in biomedical term translation prediction tasks.

A semi-supervised approach using label propagation to support citation screening

Graphical abstract

Facilitating the analysis of discourse phenomena in an interoperable NLP platform

The analysis of discourse phenomena is essential in many natural language processing (NLP) applications. The growing diversity of available corpora and NLP tools brings a multitude of representation formats. In order to alleviate the problem of incompatible formats when constructing complex text mining pipelines, the Unstructured Information Management Architecture (UIMA) provides a standard means of communication between tools and resources. U-Compare, a text mining workflow construction platform based on UIMA, further enhances interoperability through a shared system of data types, allowing free combination of compliant components into workflows. Although U-Compare and its type system already support syntactic and semantic analyses, support for the analysis of discourse phenomena was previously lacking. In response, we have extended the U-Compare type system with new discourse-level types. We illustrate processing and visualisation of discourse information in U-Compare by providing several new deserialisation components for corpora containing discourse annotations. The new U-Compare is downloadable from http://nactem.ac.uk/ucompare.