D6.1: Technologies and Tools for Lexical Acquisition

This report describes the technologies and tools to be used for Lexical Acquisition in PANACEA. It includes descriptions of existing technologies and tools which can be built on and improved within PANACEA, as well as of new technologies and tools to be developed and integrated in PANACEA platform. The report also specifies the Lexical Resources to be produced. Four main areas of lexical acquisition are included: Subcategorization frames (SCFs), Selectional Preferences (SPs), Lexical-semantic Classes (LCs), for both nouns and verbs, and Multi-Word Expressions (MWEs)

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

Getting More out of Biomedical Documents with GATE's Full Lifecycle Open Source Text Analytics.

This software article describes the GATE family of open source text analysis tools and processes. GATE is one of the most widely used systems of its type with yearly download rates of tens of thousands and many active users in both academic and industrial contexts. In this paper we report three examples of GATE-based systems operating in the life sciences and in medicine. First, in genome-wide association studies which have contributed to discovery of a head and neck cancer mutation association. Second, medical records analysis which has significantly increased the statistical power of treatment/ outcome models in the UK’s largest psychiatric patient cohort. Third, richer constructs in drug-related searching. We also explore the ways in which the GATE family supports the various stages of the lifecycle present in our examples. We conclude that the deployment of text mining for document abstraction or rich search and navigation is best thought of as a process, and that with the right computational tools and data collection strategies this process can be made defined and repeatable. The GATE research programme is now 20 years old and has grown from its roots as a specialist development tool for text processing to become a rather comprehensive ecosystem, bringing together software developers, language engineers and research staff from diverse fields. GATE now has a strong claim to cover a uniquely wide range of the lifecycle of text analysis systems. It forms a focal point for the integration and reuse of advances that have been made by many people (the majority outside of the authors’ own group) who work in text processing for biomedicine and other areas. GATE is available online ,1. under GNU open source licences and runs on all major operating systems. Support is available from an active user and developer community and also on a commercial basis

Statistical parsing of noun phrase structure

Noun phrases (NPs) are a crucial part of natural language, exhibiting in many cases an extremely complex structure. However, NP structure is largely ignored by the statistical parsing field, as the most widely-used corpus is not annotated with it. This lack of gold-standard data has restricted all previous efforts to parse NPs, making it impossible to perform the supervised experiments that have achieved high performance in so many Natural Language Processing (NLP) tasks. We comprehensively solve this problem by manually annotating NP structure for the entire Wall Street Journal section of the Penn Treebank. The inter-annotator agreement scores that we attain refute the belief that the task is too difficult, and demonstrate that consistent NP annotation is possible. Our gold-standard NP data is now available and will be useful for all parsers. We present three statistical methods for parsing NP structure. Firstly, we apply the Collins (2003) model, and find that its recovery of NP structure is significantly worse than its overall performance. Through much experimentation, we determine that this is not a result of the special base-NP model used by the parser, but primarily caused by a lack of lexical information. Secondly, we construct a wide-coverage, large-scale NP Bracketing system, applying a supervised model to achieve excellent results. Our Penn Treebank data set, which is orders of magnitude larger than those used previously, makes this possible for the first time. We then implement and experiment with a wide variety of features in order to determine an optimal model. Having achieved this, we use the NP Bracketing system to reanalyse NPs outputted by the Collins (2003) parser. Our post-processor outperforms this state-of-the-art parser. For our third model, we convert the NP data to CCGbank (Hockenmaier and Steedman, 2007), a corpus that uses the Combinatory Categorial Grammar (CCG) formalism. We experiment with a CCG parser and again, implement features that improve performance. We also evaluate the CCG parser against the Briscoe and Carroll (2006) reannotation of DepBank (King et al., 2003), another corpus that annotates NP structure. This supplies further evidence that parser performance is increased by improving the representation of NP structure. Finally, the error analysis we carry out on the CCG data shows that again, a lack of lexicalisation causes difficulties for the parser. We find that NPs are particularly reliant on this lexical information, due to their exceptional productivity and the reduced explicitness present in modifier sequences. Our results show that NP parsing is a significantly harder task than parsing in general. This thesis comprehensively analyses the NP parsing task. Our contributions allow wide-coverage, large-scale NP parsers to be constructed for the first time, and motivate further NP parsing research for the future. The results of our work can provide significant benefits for many NLP tasks, as the crucial information contained in NP structure is now available for all downstream systems

Linguistic knowledge-based vocabularies for Neural Machine Translation

This article has been published in a revised form in Natural Language Engineering https://doi.org/10.1017/S1351324920000364. This version is free to view and download for private research and study only. Not for re-distribution, re-sale or use in derivative works. © Cambridge University PressNeural Networks applied to Machine Translation need a finite vocabulary to express textual information as a sequence of discrete tokens. The currently dominant subword vocabularies exploit statistically-discovered common parts of words to achieve the flexibility of character-based vocabularies without delegating the whole learning of word formation to the neural network. However, they trade this for the inability to apply word-level token associations, which limits their use in semantically-rich areas and prevents some transfer learning approaches e.g. cross-lingual pretrained embeddings, and reduces their interpretability. In this work, we propose new hybrid linguistically-grounded vocabulary definition strategies that keep both the advantages of subword vocabularies and the word-level associations, enabling neural networks to profit from the derived benefits. We test the proposed approaches in both morphologically rich and poor languages, showing that, for the former, the quality in the translation of out-of-domain texts is improved with respect to a strong subword baseline.This work is partially supported by Lucy Software / United Language Group (ULG) and the Catalan Agency for Management of University and Research Grants (AGAUR) through an Industrial PhD Grant. This work is also supported in part by the Spanish Ministerio de Economa y Competitividad, the European Regional Development Fund and the Agencia Estatal de Investigacin, through the postdoctoral senior grant Ramn y Cajal, contract TEC2015-69266-P (MINECO/FEDER,EU) and contract PCIN-2017-079 (AEI/MINECO).Peer ReviewedPostprint (author's final draft

Surfing the modeling of pos taggers in low-resource scenarios

The recent trend toward the application of deep structured techniques has revealed the limits of huge models in natural language processing. This has reawakened the interest in traditional machine learning algorithms, which have proved still to be competitive in certain contexts, particularly in low-resource settings. In parallel, model selection has become an essential task to boost performance at reasonable cost, even more so when we talk about processes involving domains where the training and/or computational resources are scarce. Against this backdrop, we evaluate the early estimation of learning curves as a practical mechanism for selecting the most appropriate model in scenarios characterized by the use of non-deep learners in resource-lean settings. On the basis of a formal approximation model previously evaluated under conditions of wide availability of training and validation resources, we study the reliability of such an approach in a different and much more demanding operational environment. Using as a case study the generation of pos taggers for Galician, a language belonging to the Western Ibero-Romance group, the experimental results are consistent with our expectations.Ministerio de Ciencia e Innovación | Ref. PID2020-113230RB-C21Ministerio de Ciencia e Innovación | Ref. PID2020-113230RB-C22Xunta de Galicia | Ref. ED431C 2020/1

Data and systems for medication-related text classification and concept normalization from Twitter: insights from the Social Media Mining for Health (SMM4H)-2017 shared task

Objective: We executed the Social Media Mining for Health (SMM4H) 2017 shared tasks to enable the community-driven development and large-scale evaluation of automatic text processing methods for the classification and normalization of health-related text from social media. An additional objective was to publicly release manually annotated data.Materials and Methods: We organized 3 independent subtasks: automatic classification of self-reports of 1) adverse drug reactions (ADRs) and 2) medication consumption, from medication-mentioning tweets, and 3) normalization of ADR expressions. Training data consisted of 15 717 annotated tweets for (1), 10 260 for (2), and 6650 ADR phrases and identifiers for (3); and exhibited typical properties of social-media-based health-related texts. Systems were evaluated using 9961, 7513, and 2500 instances for the 3 subtasks, respectively. We evaluated performances of classes of methods and ensembles of system combinations following the shared tasks.Results: Among 55 system runs, the best system scores for the 3 subtasks were 0.435 (ADR class F1-score) for subtask-1, 0.693 (micro-averaged F1-score over two classes) for subtask-2, and 88.5% (accuracy) for subtask-3. Ensembles of system combinations obtained best scores of 0.476, 0.702, and 88.7%, outperforming individual systems.Discussion: Among individual systems, support vector machines and convolutional neural networks showed high performance. Performance gains achieved by ensembles of system combinations suggest that such strategies may be suitable for operational systems relying on difficult text classification tasks (eg, subtask-1).Conclusions: Data imbalance and lack of context remain challenges for natural language processing of social media text. Annotated data from the shared task have been made available as reference standards for future studies (http://dx.doi.org/10.17632/rxwfb3tysd.1).</div