Semantic transference for enriching multilingual biomedical knowledge resources

Biomedical knowledge resources (KRs) are mainly expressed in English, and many applications using them suffer from the scarcity of knowledge in non- English languages. The goal of the present work is to take maximum profit from existing multilingual biomedical KRs lexicons to enrich their non-English counterparts. We propose to combine different automatic methods to gener- ate pair-wise language alignments. More specifically, we use two well-known translation methods (GIZA++ and Moses), and we propose a new ad-hoc method specially devised for multilingual KRs. Then, resulting alignments are used to transfer semantics between KRs across their languages. Transfer- ence quality is ensured by checking the semantic coherence of the generated alignments. Experiments have been carried out over the Spanish, French and German UMLS Metathesaurus counterparts. As a result, the enriched Span- ish KR can grow up to 1,514,217 concepts (originally 286,659), the French KR up to 1,104,968 concepts (originally 83,119), and the German KR up to 1,136,020 concepts (originally 86,842)

In no uncertain terms : a dataset for monolingual and multilingual automatic term extraction from comparable corpora

Automatic term extraction is a productive field of research within natural language processing, but it still faces significant obstacles regarding datasets and evaluation, which require manual term annotation. This is an arduous task, made even more difficult by the lack of a clear distinction between terms and general language, which results in low inter-annotator agreement. There is a large need for well-documented, manually validated datasets, especially in the rising field of multilingual term extraction from comparable corpora, which presents a unique new set of challenges. In this paper, a new approach is presented for both monolingual and multilingual term annotation in comparable corpora. The detailed guidelines with different term labels, the domain- and language-independent methodology and the large volumes annotated in three different languages and four different domains make this a rich resource. The resulting datasets are not just suited for evaluation purposes but can also serve as a general source of information about terms and even as training data for supervised methods. Moreover, the gold standard for multilingual term extraction from comparable corpora contains information about term variants and translation equivalents, which allows an in-depth, nuanced evaluation

Impact of translation on biomedical information extraction from real-life clinical notes

The objective of our study is to determine whether using English tools to extract and normalize French medical concepts on translations provides comparable performance to French models trained on a set of annotated French clinical notes. We compare two methods: a method involving French language models and a method involving English language models. For the native French method, the Named Entity Recognition (NER) and normalization steps are performed separately. For the translated English method, after the first translation step, we compare a two-step method and a terminology-oriented method that performs extraction and normalization at the same time. We used French, English and bilingual annotated datasets to evaluate all steps (NER, normalization and translation) of our algorithms. Concerning the results, the native French method performs better than the translated English one with a global f1 score of 0.51 [0.47;0.55] against 0.39 [0.34;0.44] and 0.38 [0.36;0.40] for the two English methods tested. In conclusion, despite the recent improvement of the translation models, there is a significant performance difference between the two approaches in favor of the native French method which is more efficient on French medical texts, even with few annotated documents.Comment: 26 pages, 2 figures, 5 table

Foundation, Implementation and Evaluation of the MorphoSaurus System: Subword Indexing, Lexical Learning and Word Sense Disambiguation for Medical Cross-Language Information Retrieval

Im medizinischen Alltag, zu welchem viel Dokumentations- und Recherchearbeit gehört, ist mittlerweile der überwiegende Teil textuell kodierter Information elektronisch verfügbar. Hiermit kommt der Entwicklung leistungsfähiger Methoden zur effizienten Recherche eine vorrangige Bedeutung zu. Bewertet man die Nützlichkeit gängiger Textretrievalsysteme aus dem Blickwinkel der medizinischen Fachsprache, dann mangelt es ihnen an morphologischer Funktionalität (Flexion, Derivation und Komposition), lexikalisch-semantischer Funktionalität und der Fähigkeit zu einer sprachübergreifenden Analyse großer Dokumentenbestände. In der vorliegenden Promotionsschrift werden die theoretischen Grundlagen des MorphoSaurus-Systems (ein Akronym für Morphem-Thesaurus) behandelt. Dessen methodischer Kern stellt ein um Morpheme der medizinischen Fach- und Laiensprache gruppierter Thesaurus dar, dessen Einträge mittels semantischer Relationen sprachübergreifend verknüpft sind. Darauf aufbauend wird ein Verfahren vorgestellt, welches (komplexe) Wörter in Morpheme segmentiert, die durch sprachunabhängige, konzeptklassenartige Symbole ersetzt werden. Die resultierende Repräsentation ist die Basis für das sprachübergreifende, morphemorientierte Textretrieval. Neben der Kerntechnologie wird eine Methode zur automatischen Akquise von Lexikoneinträgen vorgestellt, wodurch bestehende Morphemlexika um weitere Sprachen ergänzt werden. Die Berücksichtigung sprachübergreifender Phänomene führt im Anschluss zu einem neuartigen Verfahren zur Auflösung von semantischen Ambiguitäten. Die Leistungsfähigkeit des morphemorientierten Textretrievals wird im Rahmen umfangreicher, standardisierter Evaluationen empirisch getestet und gängigen Herangehensweisen gegenübergestellt

Romanian Language Technology — a view from an academic perspective

The article reports on research and developments pursued by the Research Institute for Artificial Intelligence "Mihai Draganescu" of the Romanian Academy in order to narrow the gaps identified by the deep analysis on the European languages made by Meta-Net white papers and published by Springer in 2012. Except English, all the European languages needed significant research and development in order to reach an adequate technological level, in line with the expectations and requirements of the knowledge society

The European Language Resources and Technologies Forum: Shaping the Future of the Multilingual Digital Europe

Proceedings of the 1st FLaReNet Forum on the European Language Resources and Technologies, held in Vienna, at the Austrian Academy of Science, on 12-13 February 2009

D-TERMINE : data-driven term extraction methodologies investigated

Automatic term extraction is a task in the field of natural language processing that aims to automatically identify terminology in collections of specialised, domain-specific texts. Terminology is defined as domain-specific vocabulary and consists of both single-word terms (e.g., corpus in the field of linguistics, referring to a large collection of texts) and multi-word terms (e.g., automatic term extraction). Terminology is a crucial part of specialised communication since terms can concisely express very specific and essential information. Therefore, quickly and automatically identifying terms is useful in a wide range of contexts. Automatic term extraction can be used by language professionals to find which terms are used in a domain and how, based on a relevant corpus. It is also useful for other tasks in natural language processing, including machine translation. One of the main difficulties with term extraction, both manual and automatic, is the vague boundary between general language and terminology. When different people identify terms in the same text, it will invariably produce different results. Consequently, creating manually annotated datasets for term extraction is a costly, time- and effort- consuming task. This can hinder research on automatic term extraction, which requires gold standard data for evaluation, preferably even in multiple languages and domains, since terms are language- and domain-dependent. Moreover, supervised machine learning methodologies rely on annotated training data to automatically deduce the characteristics of terms, so this knowledge can be used to detect terms in other corpora as well. Consequently, the first part of this PhD project was dedicated to the construction and validation of a new dataset for automatic term extraction, called ACTER – Annotated Corpora for Term Extraction Research. Terms and Named Entities were manually identified with four different labels in twelve specialised corpora. The dataset contains corpora in three languages and four domains, leading to a total of more than 100k annotations, made over almost 600k tokens. It was made publicly available during a shared task we organised, in which five international teams competed to automatically extract terms from the same test data. This illustrated how ACTER can contribute towards advancing the state-of-the-art. It also revealed that there is still a lot of room for improvement, with moderate scores even for the best teams. Therefore, the second part of this dissertation was devoted to researching how supervised machine learning techniques might contribute. The traditional, hybrid approach to automatic term extraction relies on a combination of linguistic and statistical clues to detect terms. An initial list of unique candidate terms is extracted based on linguistic information (e.g., part-of-speech patterns) and this list is filtered based on statistical metrics that use frequencies to measure whether a candidate term might be relevant. The result is a ranked list of candidate terms. HAMLET – Hybrid, Adaptable Machine Learning Approach to Extract Terminology – was developed based on this traditional approach and applies machine learning to efficiently combine more information than could be used with a rule-based approach. This makes HAMLET less susceptible to typical issues like low recall on rare terms. While domain and language have a large impact on results, robust performance was reached even without domain- specific training data, and HAMLET compared favourably to a state-of-the-art rule-based system. Building on these findings, the third and final part of the project was dedicated to investigating methodologies that are even further removed from the traditional approach. Instead of starting from an initial list of unique candidate terms, potential terms were labelled immediately in the running text, in their original context. Two sequential labelling approaches were developed, evaluated and compared: a feature- based conditional random fields classifier, and a recurrent neural network with word embeddings. The latter outperformed the feature-based approach and was compared to HAMLET as well, obtaining comparable and even better results. In conclusion, this research resulted in an extensive, reusable dataset and three distinct new methodologies for automatic term extraction. The elaborate evaluations went beyond reporting scores and revealed the strengths and weaknesses of the different approaches. This identified challenges for future research, since some terms, especially ambiguous ones, remain problematic for all systems. However, overall, results were promising and the approaches were complementary, revealing great potential for new methodologies that combine multiple strategies

Corpus compilation and development of a machine translation system for translating clinical reports between Basque and Spanish

140 p. (eusk.) 136 p. (eng.)Tesi honetan txosten klinikoak euskararen eta gazteleraren artean itzultzen laguntzeko garatutako itzultzaile automatikoak deskribatzen dira. Txosten klinikoak euskaraz idatz daitezen sustatzeko helburuarekin, euskaratik gaztelerara itzultzeko sistemaren garapena lehenetsi da.Gure hurbilpena datuetan oinarritutakoa izan da, horretarako txosten klinikoak euskararen eta gazteleraren artean itzultzeko lagungarriak izan zitezkeen corpusak bilduz. Domeinu klinikoan terminologia aberatsa izanik, hauek ere kontuan hartu dira corpusak biltzerakoan .Tesian zehar sistema desberdinak garatu dira, horietako gehienak Itzultzaile Automatiko Neuronalak izanik. Bestalde, Itzultzaile Automatiko Estatistikoak eta Erregeletan Oinarritutako Itzultzaile Automatikoak atzeranzko itzulpena egiteko ere erabili dira.Garatutako sistemen kalitatea neurtzeaz gain, atzeranzko itzulpen bidez sortutako corpusen aniztasun lexikala ere neurtu da, eta sistema batzuk garatzeko datuen hautespena ere aplikatu da.Diseinatutako aurrerapenak nazioarteko testuinguruan kokatzeko, proposaturiko metodoak alemanetik ingelesera, eta ingelesaren eta gazteleraren artean itzultzeko ere probatu dira