This work presents the first large-scale biomedical Spanish language models trained from scratch, using large biomedical corpora consisting of a total of 1.1B tokens and an EHR corpus of 95M tokens. We compared them against general-domain and other domain-specific models for Spanish on three clinical NER tasks. As main results, our models are superior across the NER tasks, rendering them more convenient for clinical NLP applications. Furthermore, our findings indicate that when enough data is available, pre-training from scratch is better than continual pre-training when tested on clinical tasks, raising an exciting research question about which approach is optimal. Our models and fine-tuning scripts are publicly available at HuggingFace and GitHub.

Nested Named Entity Recognition (NER) is an information extraction task that aims to identify entities that may be nested within other entity mentions. Despite the availability of several corpora with nested entities in the Spanish clinical domain, most previous work has overlooked them due to the lack of models and a clear annotation scheme for dealing with the task. To fill this gap, this paper provides an empirical study of straightforward methods for tackling the nested NER task on two Spanish clinical datasets, Clinical Trials, and the Chilean Waiting List. We assess the advantages and limitations of two sequence labeling approaches; one based on Multiple LSTM-CRF architectures and another on Joint labeling models. To better understand the differences between these models, we compute task-specific metrics that adequately measure the ability of models to detect nested entities and perform a fine-grained comparison across models. Our experimental results show that employing domain-specific language models trained from scratch significantly improves the performance obtained with strong domain-specific and general-domain baselines, achieving state-of-the-art results in both datasets. Specifically, we obtained F1 scores of 89.21 and 83.16 in Clinical Trials and the Chilean Waiting List, respectively. Interestingly enough, we observe that the task-specific metrics and analysis properly reflect the limitations of the models when recognizing nested entities. Finally, we perform a case study on an aggregated NER dataset created from several clinical corpora in Spanish. We highlight how entity length and the simultaneous recognition of inner and outer entities are the most critical variables for the nested NER task.

Recently, multilingual question answering became a crucial research topic, and it is receiving increased interest in the NLP community. However, the unavailability of large-scale datasets makes it challenging to train multilingual QA systems with performance comparable to the English ones. In this work, we develop the Translate Align Retrieve (TAR) method to automatically translate the Stanford Question Answering Dataset (SQuAD) v1.1 to Spanish. We then used this dataset to train Spanish QA systems by fine-tuning a Multilingual-BERT model. Finally, we evaluated our QA models with the recently proposed MLQA and XQuAD benchmarks for cross-lingual Extractive QA. Experimental results show that our models outperform the previous Multilingual-BERT baselines achieving the new state-of-the-art values of 68.1 F1 on the Spanish MLQA corpus and 77.6 F1 on the Spanish XQuAD corpus. The resulting, synthetically generated SQuAD-es v1.1 corpora, with almost 100% of data contained in the original English version, to the best of our knowledge, is the first large-scale QA training resource for Spanish.

In this work, we give a description of the TALP-UPC systems submitted for the WMT19 Biomedical Translation Task. Our proposed strategy is NMT model-independent and relies only on one ingredient, a biomedical terminology list. We first extracted such a terminology list by labelling biomedical words in our training dataset using the BabelNet API. Then, we designed a data preparation strategy to insert the terms information at a token level. Finally, we trained the Transformer model with this terms-informed data. Our best-submitted system ranked 2nd and 3rd for Spanish-English and English-Spanish translation directions, respectively.