The aim of this paper is to present our approach (IxaMed) in the PharmacoNER 2019 task. The task consists of identifying chemical, drug, and gene/protein mentions from clinical case studies written in Spanish. The evaluation of the task is divided in two scenarios: one corresponding to the detection of named entities and one corresponding to the indexation of named entities that have been previously identified. In order to identify named entities we have made use of a Bi-LSTM with a CRF on top in combination with different types of word embeddings. We have achieved our best result (86.81 F-Score) combining pretrained word embeddings of Wikipedia and Electronic Health Records (50M words) with contextual string embeddings of Wikipedia and Electronic Health Records. On the other hand, for the indexation of the named entities we have used the Levenshtein distance obtaining a 85.34 F-Score as our best result.

Discourse information is crucial for a better understanding of the text structure and it is also necessary to describe which part of an opinionated text is more relevant or to decide how a text span can change the polarity (strengthen or weaken) of other span by means of coherence relations. This work presents the first results on the annotation of the Basque Opinion Corpus using Rhetorical Structure Theory (RST). Our evaluation results and analysis show us the main avenues to improve on a future annotation process. We have also extracted the subjectivity of several rhetorical relations and the results show the effect of sentiment words in relations and the influence of each relation in the semantic orientation value.

In this work, we have analyzed the effects of negation on the semantic orientation in Basque. The analysis shows that negation markers can strengthen, weaken or have no effect on sentiment orientation of a word or a group of words. Using the Constraint Grammar formalism, we have designed and evaluated a set of linguistic rules to formalize these three phenomena. The results show that two phenomena, strengthening and no change, have been identified accurately and the third one, weakening, with acceptable results.

The goal of this paper is to examine the impact of simple feature engineering mechanisms before applying more sophisticated techniques to the task of medical NER. Sometimes papers using scientifically sound techniques present raw baselines that could be improved adding simple and cheap features. This work focuses on entity recognition for the clinical domain for three languages: English, Swedish and Spanish. The task is tackled using simple features, starting from the window size, capitalization, prefixes, and moving to POS and semantic tags. This work demonstrates that a simple initial step of feature engineering can improve the baseline results significantly. Hence, the contributions of this paper are: first, a short list of guidelines well supported with experimental results on three languages and, second, a detailed description of the relevance of these features for medical NER.

Electronic health records show great variability since the same concept is often expressed with different terms, either scientific latin forms, common or lay variants and even vernacular naming. Deep learning enables distributional representation of terms in a vector-space, and therefore, related terms tend to be close in the vector space. Accordingly, embedding words through these vectors opens the way towards accounting for semantic relatedness through classical algebraic operations. In this work we propose a simple though efficient unsupervised characterization of Adverse Drug Reactions (ADRs). This approach exploits the embedding representation of the terms involved in candidate ADR events, that is, drug-disease entity pairs. In brief, the ADRs are represented as vectors that link the drug with the disease in their context through a recursive additive model. We discovered that a low-dimensional representation that makes use of the modulus and argument of the embedded representation of the ADR event shows correlation with the manually annotated class. Thus, it can be derived that this characterization results in to be beneficial for further classification tasks as predictive features.

This paper presents a robust parsing system for unrestricted Basque texts. It analyzes a sentence in two stages: a unification-based parser builds basic syntactic units such as NPs, PPs, and sentential complements, while a finite-state parser performs syntactic disambiguation and filtering of the results. The system has been applied to the acquisition of verbal subcategorization information, obtaining 66% recall and 87% precision in the determination of verb subcategorization instances. This information will be later incorporated to the parser, in order to improve its performance.