Sentence representation with manifold learning for biomedical texts

Extraction of microRNA-target interaction sentences from biomedical literature by deep learning approach

MicroRNA (miRNA)-target interaction (MTI) plays a substantial role in various cell activities, molecular regulations and physiological processes. Published biomedical literature is the carrier of high-confidence MTI knowledge. However, digging out this knowledge in an efficient manner from large-scale published articles remains challenging. To address this issue, we were motivated to construct a deep learning-based model. We applied the pre-trained language models to biomedical text to obtain the representation, and subsequently fed them into a deep neural network with gate mechanism layers and a fully connected layer for the extraction of MTI information sentences. Performances of the proposed models were evaluated using two datasets constructed on the basis of text data obtained from miRTarBase. The validation and test results revealed that incorporating both PubMedBERT and SciBERT for sentence level encoding with the long short-term memory (LSTM)-based deep neural network can yield an outstanding performance, with both F1 and accuracy being higher than 80% on validation data and test data. Additionally, the proposed deep learning method outperformed the following machine learning methods: random forest, support vector machine, logistic regression and bidirectional LSTM. This work would greatly facilitate studies on MTI analysis and regulations. It is anticipated that this work can assist in large-scale screening of miRNAs, thereby revealing their functional roles in various diseases, which is important for the development of highly specific drugs with fewer side effects. Source code and corpus are publicly available at https://github.com/qi29.

CharAs-CBert: Character Assist Construction-Bert Sentence Representation Improving Sentiment Classification

In the process of semantic capture, traditional sentence representation methods tend to lose a lot of global and contextual semantics and ignore the internal structure information of words in sentences. To address these limitations, we propose a sentence representation method for character-assisted construction-Bert (CharAs-CBert) to improve the accuracy of sentiment text classification. First, based on the construction, a more effective construction vector is generated to distinguish the basic morphology of the sentence and reduce the ambiguity of the same word in different sentences. At the same time, it aims to strengthen the representation of salient words and effectively capture contextual semantics. Second, character feature vectors are introduced to explore the internal structure information of sentences and improve the representation ability of local and global semantics. Then, to make the sentence representation have better stability and robustness, character information, word information, and construction vectors are combined and used together for sentence representation. Finally, the evaluation and verification are carried out on various open-source baseline data such as ACL-14 and SemEval 2014 to demonstrate the validity and reliability of sentence representation, namely, the F1 and ACC are 87.54% and 92.88% on ACL14, respectively.

Text Similarity Measurement Method and Application of Online Medical Community Based on Density Peak Clustering

Text similarity measurement is a link between basic research such as text modeling and upper-level application research of text potential information. In order to improve the accuracy of text similarity measurement, this paper proposes a semantic similarity calculation method integrating word2vec model and TF-IDF, and applies it to the density peak clustering of Chinese text data consulted by patients in online medical community. Experimental results show that the proposed similarity measurement method is superior to the traditional method. Furthermore, the study is among the first to apply the density peak clustering algorithm to online medical community, which offers a reference for how to find out user demands from medical text data in the big data environment.