Julien Fauqueur


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Learning Informative Representations of Biomedical Relations with Latent Variable Models
Harshil Shah | Julien Fauqueur
Proceedings of SustaiNLP: Workshop on Simple and Efficient Natural Language Processing

Extracting biomedical relations from large corpora of scientific documents is a challenging natural language processing task. Existing approaches usually focus on identifying a relation either in a single sentence (mention-level) or across an entire corpus (pair-level). In both cases, recent methods have achieved strong results by learning a point estimate to represent the relation; this is then used as the input to a relation classifier. However, the relation expressed in text between a pair of biomedical entities is often more complex than can be captured by a point estimate. To address this issue, we propose a latent variable model with an arbitrarily flexible distribution to represent the relation between an entity pair. Additionally, our model provides a unified architecture for both mention-level and pair-level relation extraction. We demonstrate that our model achieves results competitive with strong baselines for both tasks while having fewer parameters and being significantly faster to train. We make our code publicly available.


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Constructing large scale biomedical knowledge bases from scratch with rapid annotation of interpretable patterns
Julien Fauqueur | Ashok Thillaisundaram | Theodosia Togia
Proceedings of the 18th BioNLP Workshop and Shared Task

Knowledge base construction is crucial for summarising, understanding and inferring relationships between biomedical entities. However, for many practical applications such as drug discovery, the scarcity of relevant facts (e.g. gene X is therapeutic target for disease Y) severely limits a domain expert’s ability to create a usable knowledge base, either directly or by training a relation extraction model. In this paper, we present a simple and effective method of extracting new facts with a pre-specified binary relationship type from the biomedical literature, without requiring any training data or hand-crafted rules. Our system discovers, ranks and presents the most salient patterns to domain experts in an interpretable form. By marking patterns as compatible with the desired relationship type, experts indirectly batch-annotate candidate pairs whose relationship is expressed with such patterns in the literature. Even with a complete absence of seed data, experts are able to discover thousands of high-quality pairs with the desired relationship within minutes. When a small number of relevant pairs do exist - even when their relationship is more general (e.g. gene X is biologically associated with disease Y) than the relationship of interest - our system leverages them in order to i) learn a better ranking of the patterns to be annotated or ii) generate weakly labelled pairs in a fully automated manner. We evaluate our method both intrinsically and via a downstream knowledge base completion task, and show that it is an effective way of constructing knowledge bases when few or no relevant facts are already available.