We present a neural architecture for containment relation identification between medical events and/or temporal expressions. We experiment on a corpus of deidentified clinical notes in English from the Mayo Clinic, namely the THYME corpus. Our model achieves an F-measure of 0.613 and outperforms the best result reported on this corpus to date.

SemEval 2016 Task 12 addresses temporal reasoning in the clinical domain. In this paper, we present our participation for relation extraction based on gold standard entities (subtasks DR and CR). We used a supervised approach comparing plain lexical features to word embeddings for temporal relation identification, and obtained above-median scores.

In this paper we present our participation to SemEval 2017 Task 12. We used a neural network based approach for entity and temporal relation extraction, and experimented with two domain adaptation strategies. We achieved competitive performance for both tasks.

In this paper, we present a method for temporal relation extraction from clinical narratives in French and in English. We experiment on two comparable corpora, the MERLOT corpus for French and the THYME corpus for English, and show that a common approach can be used for both languages.

Many applications in biomedical natural language processing rely on sequence tagging as an initial step to perform more complex analysis. To support text analysis in the biomedical domain, we introduce Yet Another SEquence Tagger (YASET), an open-source multi purpose sequence tagger that implements state-ofthe-art deep learning algorithms for sequence tagging. Herein, we evaluate YASET on partof-speech tagging and named entity recognition in a variety of text genres including articles from the biomedical literature in English and clinical narratives in French. To further characterize performance, we report distributions over 30 runs and different sizes of training datasets. YASET provides stateof-the-art performance on the CoNLL 2003 NER dataset (F1=0.87), MEDPOST corpus (F1=0.97), MERLoT corpus (F1=0.99) and NCBI disease corpus (F1=0.81). We believe that YASET is a versatile and efficient tool that can be used for sequence tagging in biomedical and clinical texts.