Keyphrase annotation task aims to retrieve the most representative phrases that express the essential gist of documents. In reality, some phrases that best summarize documents are often absent from the original text, which motivates researchers to develop generation methods, being able to create phrases. Existing generation approaches usually adopt the encoder-decoder framework for sequence generation. However, the widely-used recurrent neural network might fail to capture long-range dependencies among items. In addition, intuitively, as keyphrases are likely to correlate with topical words, some methods propose to introduce topic models into keyphrase generation. But they hardly leverage the global information of topics. In view of this, we employ the Transformer architecture with the pre-trained BERT model as the encoder-decoder framework for keyphrase generation. BERT and Transformer are demonstrated to be effective for many text mining tasks. But they have not been extensively studied for keyphrase generation. Furthermore, we propose a topic attention mechanism to utilize the corpus-level topic information globally for keyphrase generation. Specifically, we propose BertTKG, a keyphrase generation method that uses a contextualized neural topic model for corpus-level topic representation learning, and then enhances the document representations learned by pre-trained language model for better keyphrase decoding. Extensive experiments conducted on three public datasets manifest the superiority of BertTKG.

SUMMARY: Molecular-similarity searches based on two-dimensional (2D) fingerprint and three-dimensional (3D) shape represent two widely used ligand-based virtual screening (VS) methods in computer-aided drug design. 2D fingerprint-based VS utilizes the binary fragment information on a known ligand, whereas 3D shape-based VS takes advantage of geometric information for predefined features from a 3D conformation. Given their different advantages, it would be desirable to hybridize 2D fingerprint and 3D shape molecular-similarity approaches in drug discovery. Here, we presented a general hybrid molecular-similarity protocol, referred to as HybridSim, obtained by combining the 2D fingerprint- and 3D shape-based similarity search methods and evaluated its performance on 595,036 actives and decoys for 40 pharmaceutically relevant targets available in the Directory of Useful Decoys Enhanced (DUD-E). Our results showed that HybridSim significantly improved the overall performance in 40 VS projects as compared with using only 2D fingerprint and 3D shape methods. Furthermore, HybridSim-VS, the first online platform using the proposed HybridSim method coupled with 17,839,945 screenable and purchasable compounds, was developed to provide large-scale and proficient VS capabilities to experts and nonexperts in the field. AVAILABILITY AND IMPLEMENTATION: HybridSim-VS web server is freely available at http://www.rcidm.org/HybridSim-VS/. CONTACT: [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.