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Conventional correlated topic models are able to capture correlation structure among latent topics by replacing the Dirichlet prior with the logistic normal distribution. Word embeddings have been proven to be able to capture semantic regularities in language. Therefore, the semantic relatedness and correlations between words can be directly calculated in the word embedding space, for example, via cosine values. In this paper, we propose a novel correlated topic model using word embeddings. The proposed model enables us to exploit the additional word-level correlation information in word embeddings and directly model topic correlation in the continuous word embedding space. In the model, words in documents are replaced with meaningful word embeddings, topics are modeled as multivariate Gaussian distributions over the word embeddings and topic correlations are learned among the continuous Gaussian topics. A Gibbs sampling solution with data augmentation is given to perform inference. We evaluate our model on the 20 Newsgroups dataset and the Reuters-21578 dataset qualitatively and quantitatively. The experimental results show the effectiveness of our proposed model.

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Motivation MEDLINE is the primary bibliographic database maintained by National Library of Medicine (NLM). MEDLINE citations are indexed with Medical Subject Headings (MeSH), which is a controlled vocabulary curated by the NLM experts. This greatly facilitates the applications of biomedical research and knowledge discovery. Currently, MeSH indexing is manually performed by human experts. To reduce the time and monetary cost associated with manual annotation, many automatic MeSH indexing systems have been proposed to assist manual annotation, including DeepMeSH and NLM’s official model Medical Text Indexer (MTI). However, the existing models usually rely on the intermediate results of other models and suffer from efficiency issues. We propose an end-to-end framework, MeSHProbeNet (formerly named as xgx), which utilizes deep learning and self-attentive MeSH probes to index MeSH terms. Each MeSH probe enables the model to extract one specific aspect of biomedical knowledge from an input article, thus comprehensive biomedical information can be extracted with different MeSH probes and interpretability can be achieved at word level. MeSH terms are finally recommended with a unified classifier, making MeSHProbeNet both time efficient and space efficient. Results MeSHProbeNet won the first place in the latest batch of Task A in the 2018 BioASQ challenge. The result on the last test set of the challenge is reported in this paper. Compared with other state-of-the-art models, such as MTI and DeepMeSH, MeSHProbeNet achieves the highest scores in all the F-measures, including Example Based F-Measure, Macro F-Measure, Micro F-Measure, Hierarchical F-Measure and Lowest Common Ancestor F-measure. We also intuitively show how MeSHProbeNet is able to extract comprehensive biomedical knowledge from an input article.

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