Biomedical Information Extraction from scientific literature presents two unique and nontrivial challenges. First, compared with general natural language texts, sentences from scientific papers usually possess wider contexts between knowledge elements. Moreover, comprehending the fine-grained scientific entities and events urgently requires domain-specific background knowledge. In this paper, we propose a novel biomedical Information Extraction (IE) model to tackle these two challenges and extract scientific entities and events from English research papers. We perform Abstract Meaning Representation (AMR) to compress the wide context to uncover a clear semantic structure for each complex sentence. Besides, we construct the sentence-level knowledge graph from an external knowledge base and use it to enrich the AMR graph to improve the model's understanding of complex scientific concepts. We use an edge-conditioned graph attention network to encode the knowledgeenriched AMR graph for biomedical IE tasks. Experiments on the GENIA 2011 dataset show that the AMR and external knowledge have contributed 1.8% and 3.0% absolute F-score gains respectively. In order to evaluate the impact of our approach on real-world problems that involve topic-specific fine-grained knowledge elements, we have also created a new ontology and annotated corpus for entity and event extraction for the COVID-19 scientific literature, which can serve as a new benchmark for the biomedical IE community. 1

This paper proposes using a Bidirectional LSTM-CRF model in order to identify the tense and aspect of verbs. The information that this classifier outputs can be useful for ordering events and can provide a pre-processing step to improve efficiency of annotating this type of information. This neural network architecture has been successfully employed for other sequential labeling tasks, and we show that it significantly outperforms the rule-based tool TMV-annotator on the Propbank I dataset.

This paper describes the evolution of the Prop-Bank approach to semantic role labeling over the last two decades. During this time the Prop-Bank frame files have been expanded to include non-verbal predicates such as adjectives, prepositions and multi-word expressions. The number of domains, genres and languages that have been PropBanked has also expanded greatly, creating an opportunity for much more challenging and robust testing of the generalization capabilities of PropBank semantic role labeling systems. We also describe the substantial effort that has gone into ensuring the consistency and reliability of the various annotated datasets and resources, to better support the training and evaluation of such systems.

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