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)

Event Extraction: A Survey

Extracting the reported events from text is one of the key research themes in natural language processing. This process includes several tasks such as event detection, argument extraction, role labeling. As one of the most important topics in natural language processing and natural language understanding, the applications of event extraction spans across a wide range of domains such as newswire, biomedical domain, history and humanity, and cyber security. This report presents a comprehensive survey for event detection from textual documents. In this report, we provide the task definition, the evaluation method, as well as the benchmark datasets and a taxonomy of methodologies for event extraction. We also present our vision of future research direction in event detection.Comment: 20 page

Towards new information resources for public health: From WordNet to MedicalWordNet

In the last two decades, WORDNET has evolved as the most comprehensive computational lexicon of general English. In this article, we discuss its potential for supporting the creation of an entirely new kind of information resource for public health, viz. MEDICAL WORDNET. This resource is not to be conceived merely as a lexical extension of the original WORDNET to medical terminology; indeed, there is already a considerable degree of overlap between WORDNET and the vocabulary of medicine. Instead, we propose a new type of repository, consisting of three large collections of (1) medically relevant word forms, structured along the lines of the existing Princeton WORDNET; (2) medically validated propositions, referred to here as medical facts, which will constitute what we shall call MEDICAL FACTNET; and (3) propositions reflecting laypersons’ medical beliefs, which will constitute what we shall call the MEDICAL BELIEFNET. We introduce a methodology for setting up the MEDICAL WORDNET. We then turn to the discussion of research challenges that have to be met in order to build this new type of information resource

Clinical Natural Language Processing in languages other than English: opportunities and challenges

Background: Natural language processing applied to clinical text or aimed at a clinical outcome has been thriving in recent years. This paper offers the first broad overview of clinical Natural Language Processing (NLP) for languages other than English. Recent studies are summarized to offer insights and outline opportunities in this area. Main Body We envision three groups of intended readers: (1) NLP researchers leveraging experience gained in other languages, (2) NLP researchers faced with establishing clinical text processing in a language other than English, and (3) clinical informatics researchers and practitioners looking for resources in their languages in order to apply NLP techniques and tools to clinical practice and/or investigation. We review work in clinical NLP in languages other than English. We classify these studies into three groups: (i) studies describing the development of new NLP systems or components de novo, (ii) studies describing the adaptation of NLP architectures developed for English to another language, and (iii) studies focusing on a particular clinical application. Conclusion: We show the advantages and drawbacks of each method, and highlight the appropriate application context. Finally, we identify major challenges and opportunities that will affect the impact of NLP on clinical practice and public health studies in a context that encompasses English as well as other languages

Adaptation of machine translation for multilingual information retrieval in the medical domain

Objective. We investigate machine translation (MT) of user search queries in the context of cross-lingual information retrieval (IR) in the medical domain. The main focus is on techniques to adapt MT to increase translation quality; however, we also explore MT adaptation to improve eectiveness of cross-lingual IR. Methods and Data. Our MT system is Moses, a state-of-the-art phrase-based statistical machine translation system. The IR system is based on the BM25 retrieval model implemented in the Lucene search engine. The MT techniques employed in this work include in-domain training and tuning, intelligent training data selection, optimization of phrase table configuration, compound splitting, and exploiting synonyms as translation variants. The IR methods include morphological normalization and using multiple translation variants for query expansion. The experiments are performed and thoroughly evaluated on three language pairs: Czech–English, German–English, and French–English. MT quality is evaluated on data sets created within the Khresmoi project and IR eectiveness is tested on the CLEF eHealth 2013 data sets. Results. The search query translation results achieved in our experiments are outstanding – our systems outperform not only our strong baselines, but also Google Translate and Microsoft Bing Translator in direct comparison carried out on all the language pairs. The baseline BLEU scores increased from 26.59 to 41.45 for Czech–English, from 23.03 to 40.82 for German–English, and from 32.67 to 40.82 for French–English. This is a 55% improvement on average. In terms of the IR performance on this particular test collection, a significant improvement over the baseline is achieved only for French–English. For Czech–English and German–English, the increased MT quality does not lead to better IR results. Conclusions. Most of the MT techniques employed in our experiments improve MT of medical search queries. Especially the intelligent training data selection proves to be very successful for domain adaptation of MT. Certain improvements are also obtained from German compound splitting on the source language side. Translation quality, however, does not appear to correlate with the IR performance – better translation does not necessarily yield better retrieval. We discuss in detail the contribution of the individual techniques and state-of-the-art features and provide future research directions

Building End-to-End Neural Machine Translation Systems for Crisis Scenarios: The Case of COVID-19

Η Μηχανική Μετάφραση είναι ένα σημαντικό κομμάτι της Επεξεργασίας Φυσικής Γλώσσας, καθώς στοχεύει στην γρήγορη και αυτόματη μετάφραση διαφόρων ειδών κειμένων. Τα τελευταία χρόνια, η επικράτηση της Νευρωνικής Μηχανικής Μετάφρασης και η δημιουργία μεγάλων παράλληλων συλλογών κειμένων έχει οδηγήσει σε σημαντική βελτίωση της ποιότητας μετάφρασης. Ωστόσο, τα μεταφραστικά μοντέλα δεν είναι απαραιτήτως κατάλληλα για όλους τους τομείς κειμένων κι αυτό έχει οδηγήσει σε διάφορες έρευνες σχετικές με την προσαρμογή υπαρχόντων συστημάτων Μηχανικής Μετάφρασης σε διάφορους γνωστικούς τομείς κειμένων, δηλ. στο πώς να βελτιωθεί καλύτερα η ποιότητα μετάφρασης για μία συγκεκριμένη θεματική ή είδος κειμένων. Η Μηχανική Μετάφραση για Καταστάσεις Κρίσεων είναι μία ιδιαίτερη εφαρμογή της εξειδίκευσης συστημάτων σε θεματικούς τομείς, η οποία ασχολείται με την γρήγορη εξειδίκευση ενός υπάρχοντος συστήματος Μηχανικής Μετάφρασης για μία κατάσταση κρίσης, καθώς η ενσωμάτωση ενός τέτοιου συστήματος σε μία υποδομή ταχείας απόκρισης μπορεί να επιταχύνει την παροχή βοήθειας και την λήψη αποφάσεων. Η πανδημία του COVID-19 αποδείχτηκε μία κρίση μεγάλης διάρκειας και διεθνούς χαρακτήρα στην οποία παρουσιάστηκαν μεγάλα κενά στην διαφανή, έγκαιρη και αποτελεσματική επικοινωνία με το κοινό, ενώ σημαδεύτηκε από παραπληροφόρηση, θεωρίες συνομωσίας και σημαντικούς περιορισμούς στην ελευθερία του Τύπου. Περαιτέρω έρευνα στο πεδίο της Μηχανικής Μετάφρασης για Καταστάσεις Κρίσεων θα μπορούσε να συνδράμει σημαντικά στην αντιμετώπιση παρόμοιων μελλοντικών κρίσεων. Η παρούσα διπλωματική εργασία εστιάζει στην περίπτωση της πανδημίας του COVID-19 και στην μετάφραση αγγλικών κειμένων στα ελληνικά, ενώ επίσης κατασκευάζονται δύο εξειδικευμένα πολυγλωσσικά παράλληλα σώματα κειμένων. Το ένα σχετίζεται με τον COVID-19 και το άλλο προέρχεται από περιλήψεις ακαδημαϊκών εργασιών και διατριβών. Στην αρχή περιγράφουμε την διαδικασία συλλογής καινούριων παράλληλων σωμάτων κειμένων για συγκεκριμένους τομείς και την δημιουργία συνθετικών δεδομένων. Αυτά τα δεδομένα συνδυάζονται με υπάρχοντα παράλληλα δεδομένα ώστε να εξειδικεύσουν ένα υπάρχον σύστημα για τον COVID-19. Η διαδικασία αυτή περιλαμβάνει επίσης το φιλτράρισμα, την προεπεξεργασία και την επιλογή κατάλληλων δεδομένων, τα οποία παρουσιάζονται αναλυτικώς. Έπειτα, κάνουμε πειράματα πάνω σε διαφορετικές στρατηγικές εξειδίκευσης υπαρχόντων συστημάτων Μηχανικής Μετάφρασης για μία προσομοιωμένη κατάσταση κρίσης όπου τα σχετικά δεδομένα αυξάνονται με την πάροδο του χρόνου. Μας ενδιαφέρει επίσης το φαινόμενο “catastrophic forgetting” στο οποίο παρουσιάζεται μείωση της ποιότητας μετάφρασης σε κείμενα γενικού περιεχομένου. Τέλος, κατασκευάζουμε ένα ολοκληρωμένο σύστημα Νευρωνικής Μηχανικής Μετάφρασης το οποίο είναι εξειδικευμένο στην μετάφραση αγγλικών κειμένων σχετικά με τον COVID-19 στα ελληνικά. Αξιολογούμε διεξοδικά την απόδοσή του σε διαφορετικά είδη κειμένων ώστε να βρούμε τα δυνατά και αδύνατα σημεία του, κάνοντας χρήση οκτώ εξειδικευμένων δοκιμασιών (εκ των οποίων τα τέσσερα δημιουργήθηκαν για την παρούσα διπλωματική) και άλλων διαθέσιμων μοντέλων και υπηρεσιών μετάφρασης.Machine Translation is a crucial task of Natural Language Processing, as it aims to provide a fast and automatic way of translating various types of texts. In recent years, the emergence of Neural Machine Translation and the compilation of large-scale parallel corpora have led to significant improvements in translation quality. However, translation models are not necessarily suited for all domains and, thus, there has been significant research on domain adaptation of Neural Machine Translation Systems, i.e., on how to best improve the translation quality of an existing system for a specific topic or genre. Crisis Machine Translation is a special case of Domain Adaptation which is concerned with the rapid adaptation of an existing Machine Translation system for a crisis scenario, as the integration of such a system in a rapid response infrastructure can accelerate the speed of decision making and relief provision. The COVID-19 pandemic proved to be a prolonged and global crisis with large gaps in transparent, timely, and effective communication; it was also marked by misinformation, conspiracy theories, and significant restrictions on press freedom. Further research on Crisis Machine Translation could play an important role in better responding to future similar crises. In this thesis, we focus on the case of the COVID-19 pandemic and the English-Greek translation direction, while we also create two domain-specific multilingual parallel corpora; one which is related to COVID-19 and one which has been gathered from the abstracts of academic theses and dissertations. First, we describe the methodologies of acquiring new domain-specific parallel corpora and generating synthetic data which are combined with existing parallel data so as to adapt an existing system to the domain of COVID-19. This process includes data filtering, pre-processing, and selection pipelines, which are also described in detail. Afterwards, we conduct experiments on different fine-tuning strategies for a simulated crisis scenario in which varying amounts of related data become available as time progresses. We are also concerned with the phenomenon of “catastrophic forgetting”, i.e., the degradation of system performance on general texts. Lastly, we construct an end-to-end Neural Machine Translation system which is specialized in translating COVID-19 related English texts into Greek. In order to assess its performance across different domains and determine its strengths and weaknesses, we conduct an extended evaluation with eight test sets (half of them have been specifically created for this thesis) and other publicly available models and commercial translation services

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

Automatic medical term generation for a low-resource language: translation of SNOMED CT into Basque

211 p. (eusk.) 148 p. (eng.)Tesi-lan honetan, terminoak automatikoki euskaratzeko sistemak garatu eta ebaluatu ditugu. Horretarako,SNOMED CT, terminologia kliniko zabala barnebiltzen duen ontologia hartu dugu abiapuntutzat, etaEuSnomed deritzon sistema garatu dugu horren euskaratzea kudeatzeko. EuSnomedek lau urratsekoalgoritmoa inplementatzen du terminoen euskarazko ordainak lortzeko: Lehenengo urratsak baliabidelexikalak erabiltzen ditu SNOMED CTren terminoei euskarazko ordainak zuzenean esleitzeko. Besteakbeste, Euskalterm banku terminologikoa, Zientzia eta Teknologiaren Hiztegi Entziklopedikoa, eta GizaAnatomiako Atlasa erabili ditugu. Bigarren urratserako, ingelesezko termino neoklasikoak euskaratzekoNeoTerm sistema garatu dugu. Sistema horrek, afixu neoklasikoen baliokidetzak eta transliterazio erregelakerabiltzen ditu euskarazko ordainak sortzeko. Hirugarrenerako, ingelesezko termino konplexuak euskaratzendituen KabiTerm sistema garatu dugu. KabiTermek termino konplexuetan agertzen diren habiaratutakoterminoen egiturak erabiltzen ditu euskarazko egiturak sortzeko, eta horrela termino konplexuakosatzeko. Azken urratsean, erregeletan oinarritzen den Matxin itzultzaile automatikoa osasun-zientziendomeinura egokitu dugu, MatxinMed sortuz. Horretarako Matxin domeinura egokitzeko prestatu dugu,eta besteak beste, hiztegia zabaldu diogu osasun-zientzietako testuak itzuli ahal izateko. Garatutako lauurratsak ebaluatuak izan dira metodo ezberdinak erabiliz. Alde batetik, aditu talde txiki batekin egin dugulehenengo bi urratsen ebaluazioa, eta bestetik, osasun-zientzietako euskal komunitateari esker egin dugunMedbaluatoia kanpainaren baitan azkeneko bi urratsetako sistemen ebaluazioa egin da

Approaches towards a Lexical Web: the role of Interoperability

After highlighting some of the major dimensions that are relevant for Language Resources (LR) and contribute to their infrastructural role, I underline some priority areas of concern today with respect to implementing an open Language Infrastructure, and specifically what we could call a ?Lexical Web?. My objective is to show that it is imperative to define an underlying global strategy behind the set of initiatives which are/can be launched in Europe and world-wide, and that it is necessary an allembracing vision and a cooperation among different communities to achieve more coherent and useful results. I end up mentioning two new European initiatives that in this direction and promise to be influential in shaping the future of the LR area

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