Stochastic Variational Inference-Based Parallel and Online Supervised Topic Model for Large-Scale Text Processing

Topic modeling is a mainstream and effective technology to deal with text data, with wide applications in text analysis, natural language, personalized recommendation, computer vision, etc. Among all the known topic models, supervised Latent Dirichlet Allocation （sLDA） is acknowledged as a popular and competitive supervised topic model. How- ever, the gradual increase of the scale of datasets makes sLDA more and more inefficient and time-consuming, and limits its applications in a very narrow range. To solve it, a parallel online sLDA, named PO-sLDA （Parallel and Online sLDA）, is proposed in this study. It uses the stochastic variational inference as the learning method to make the training procedure more rapid and efficient, and a parallel computing mechanism implemented via the MapReduce framework is proposed to promote the capacity of cloud computing and big data processing. The online training capacity supported by PO-sLDA expands the application scope of this approach, making it instrumental for real-life applications with high real-time demand. The validation using two datasets with different sizes shows that the proposed approach has the comparative accuracy as the sLDA and can efficiently accelerate the training procedure. Moreover, its good convergence and online training capacity make it lucrative for the large-scale text data analyzing and processing.

Towards precise reconstruction of gene regulatory networks by data integration

Background： More and more high-throughput datasets are available from multiple levels of measuring gene regulations. The reverse engineering of gene regulatory networks from these data offers a valuable research paradigm to decipher regulatory mechanisms. So far, numerous methods have been developed for reconstructing gene regulatory networks. Results： In this paper, we provide a review of bioinformatics methods for inferring gene regulatory network from omics data. To achieve the precision reconstruction of gene regulatory networks, an intuitive alternative is to integrate these available resources in a rational framework. We also provide computational perspectives in the endeavors of inferring gene regulatory networks from heterogeneous data. We highlight the importance of multi-omics data integration with prior knowledge in gene regulatory network inferences. Conclusions： We provide computational perspectives of inferring gene regulatory networks from multiple omics data and present theoretical analyses of existing challenges and possible solutions. We emphasize on prior knowledge and data integration in network inferences owing to their abilities of identifying regulatory causality.