Biomedical event extraction is a crucial task in order to automatically extract information from the increasingly growing body of biomedical literature. Despite advances in the methods in recent years, most event extraction systems are still evaluated in-domain and on complete event structures only. This makes it hard to determine the performance of intermediate stages of the task, such as edge detection, across different corpora. Motivated by these limitations, we present the first cross-domain study of edge detection for biomedical event extraction. We analyze differences between five existing gold standard corpora, create a standardized benchmark corpus, and provide a strong baseline model for edge detection. Experiments show a large drop in performance when the baseline is applied on out-of-domain data, confirming the need for domain adaptation methods for the task. To encourage research efforts in this direction, we make both the data and the baseline available to the research community: https://www.cosbi.eu/cfx/9985.
Lexical normalization is the task of translating non-standard social media data to a standard form. Previous work has shown that this is beneficial for many downstream tasks in multiple languages. However, for Italian, there is no benchmark available for lexical normalization, despite the presence of many benchmarks for other tasks involving social media data. In this paper, we discuss the creation of a lexical normalization dataset for Italian. After two rounds of annotation, a Cohen’s kappa score of 78.64 is obtained. During this process, we also analyze the inter-annotator agreement for this task, which is only rarely done on datasets for lexical normalization,and when it is reported, the analysis usually remains shallow. Furthermore, we utilize this dataset to train a lexical normalization model and show that it can be used to improve dependency parsing of social media data. All annotated data and the code to reproduce the results are available at: http://bitbucket.org/robvanderg/normit.
Deep neural networks excel at learning from labeled data and achieve state-of-the-art results on a wide array of Natural Language Processing tasks. In contrast, learning from unlabeled data, especially under domain shift, remains a challenge. Motivated by the latest advances, in this survey we review neural unsupervised domain adaptation techniques which do not require labeled target domain data. This is a more challenging yet a more widely applicable setup. We outline methods, from early traditional non-neural methods to pre-trained model transfer. We also revisit the notion of domain, and we uncover a bias in the type of Natural Language Processing tasks which received most attention. Lastly, we outline future directions, particularly the broader need for out-of-distribution generalization of future NLP.
We introduce Biomedical Event Extraction as Sequence Labeling (BeeSL), a joint end-to-end neural information extraction model. BeeSL recasts the task as sequence labeling, taking advantage of a multi-label aware encoding strategy and jointly modeling the intermediate tasks via multi-task learning. BeeSL is fast, accurate, end-to-end, and unlike current methods does not require any external knowledge base or preprocessing tools. BeeSL outperforms the current best system (Li et al., 2019) on the Genia 2011 benchmark by 1.57% absolute F1 score reaching 60.22% F1, establishing a new state of the art for the task. Importantly, we also provide first results on biomedical event extraction without gold entity information. Empirical results show that BeeSL’s speed and accuracy makes it a viable approach for large-scale real-world scenarios.