BACKGROUND: In this study, we investigated the efficacy of current state-of-the-art neural sentence embedding models for semantic similarity estimation of sentences from biomedical literature. We trained different neural embedding models on 1.7 million articles from the PubMed Open Access dataset, and evaluated them based on a biomedical benchmark set containing 100 sentence pairs annotated by human experts and a smaller contradiction subset derived from the original benchmark set. RESULTS: With a Pearson correlation of 0.819, our best unsupervised model based on the Paragraph Vector Distributed Memory algorithm outperforms previous state-of-the-art results achieved on the BIOSSES biomedical benchmark set. Moreover, our proposed supervised model that combines different string-based similarity metrics with a neural embedding model surpasses previous ontology-dependent supervised state-of-the-art approaches in terms of Pearson's r (r=0.871) on the biomedical benchmark set. In contrast to the promising results for the original benchmark, we found our best models' performance on the smaller contradiction subset to be poor. CONCLUSIONS: In this study we highlighted the value of neural network-based models for semantic similarity estimation in the biomedical domain by showing that they can keep up with and even surpass previous state-of-the-art approaches for semantic similarity estimation that depend on the availability of laboriously curated ontologies when evaluated on a biomedical benchmark set. Capturing contradictions and negations in biomedical sentences, however, emerged as an essential area for further work.
Motivation: The amount of information available in textual format is rapidly increasing in the biomedical domain. Therefore, natural language processing (NLP) applications are becoming increasingly important to facilitate the retrieval and analysis of these data. Computing the semantic similarity between sentences is an important component in many NLP tasks including text retrieval and summarization. A number of approaches have been proposed for semantic sentence similarity estimation for generic English. However, our experiments showed that such approaches do not effectively cover biomedical knowledge and produce poor results for biomedical text. Methods: We propose several approaches for sentence-level semantic similarity computation in the biomedical domain, including string similarity measures and measures based on the distributed vector representations of sentences learned in an unsupervised manner from a large biomedical corpus. In addition, ontology-based approaches are presented that utilize general and domain-specific ontologies. Finally, a supervised regression based model is developed that effectively combines the different similarity computation metrics. A benchmark data set consisting of 100 sentence pairs from the biomedical literature is manually annotated by five human experts and used for evaluating the proposed methods. Results: The experiments showed that the supervised semantic sentence similarity computation approach obtained the best performance (0.836 correlation with gold standard human annotations) and improved over the state-of-the-art domain-independent systems up to 42.6% in terms of the Pearson correlation metric.
Sentence embeddings have become an essential part of today's natural language processing (NLP) systems, especially together advanced deep learning methods. Although pre-trained sentence encoders are available in the general domain, none exists for biomedical texts to date. In this work, we introduce BioSentVec: the first open set of sentence embeddings trained with over 30 million documents from both scholarly articles in PubMed and clinical notes in the MIMIC-III Clinical Database. We evaluate BioSentVec embeddings in two sentence pair similarity tasks in different text genres. Our benchmarking results demonstrate that the BioSentVec embeddings can better capture sentence semantics compared to the other competitive alternatives and achieve state-of-the-art performance in both tasks. We expect BioSentVec to facilitate the research and development in biomedical text mining and to complement the existing resources in biomedical word embeddings. BioSentVec is publicly available at https://github.com/ncbi-nlp/BioSentVec