A spatial-temporal topic model with sparse prior and RNN prior for bursty topic discovering in social networks

With the rapid growth of social network users, the social network has accumulated massive social network topics. However, due to the randomness of content, it becomes sparse and noisy, accompanied by many daily chats and meaningless topics, which brings challenges to bursty topics discovery. To deal with these problems, this paper proposes the spatial-temporal topic model with sparse prior and recurrent neural networks (RNN) prior for bursty topic discovering (ST-SRTM). The semantic relationship of words is learned through RNN to alleviate the sparsity. The spatial-temporal areas information is introduced to focus on bursty topics for further weakening the semantic sparsity of social network context. Besides, we introduced the “Spike and Slab” prior to decouple the sparseness and smoothness. Simultaneously, we realized the automatic discovery of social network bursts by introducing the burstiness of words as the prior and binary switching variables. We constructed multiple sets of comparative experiments to verify the performance of ST-SRTM by leveraging different evaluation indicators on real Sina Weibo data sets. The experimental results confirm the superiority of our ST-SRTM.

Who Is and Is Not "Average'"? Random Effects Selection with Spike-and-Slab Priors

Mixed effects models are often employed to study individual differences in psychological science. Such analyses commonly entail testing whether between-subject variability exists, but this is typically the extent of such analyses. We argue that researchers have much to gain by explicitly focusing on the individual in individual differences research. To this end, we propose the spike-and-slab prior distribution for random effect selection in (generalized) mixed-effects models as a means to gain a more nuanced perspective of individual differences. The prior for each random effect, or deviation away from the fixed effect, is a two-component mixture consisting of a point-mass 'spike' centered at zero and a diffuse 'slab' capturing non-zero values. Effectively, such an approach allows researchers to answer questions about each particular individual; specifically, "who is average?'" in the sense of deviating from an average effect, such as the population-averaged or common slope. We begin with an illustrative example, where the spike-and-slab formulation is used to select random intercepts in logistic regression. This demonstrates the utility of the proposed methodology in a simple setting while also highlighting its flexibility in fitting different kinds of models. We then extend the approach to random slopes that capture experimental effects. In two cognitive tasks, we show that despite there being little variability in the slopes, there were many individual differences in performance. Most notably, over 25% of the sample differed from the common slope in their experimental effect. We conclude with future directions for the presented methodology.

IntAPT: integrated assembly of phenotype-specific transcripts from multiple RNA-seq profiles

Motivation High-throughput RNA sequencing has revolutionized the scope and depth of transcriptome analysis. Accurate reconstruction of a phenotype-specific transcriptome is challenging due to the noise and variability of RNA-seq data. This requires computational identification of transcripts from multiple samples of the same phenotype, given the underlying consensus transcript structure. Results We present a Bayesian method, integrated assembly of phenotype-specific transcripts (IntAPT), that identifies phenotype-specific isoforms from multiple RNA-seq profiles. IntAPT features a novel two-layer Bayesian model to capture the presence of isoforms at the group layer and to quantify the abundance of isoforms at the sample layer. A spike-and-slab prior is used to model the isoform expression and to enforce the sparsity of expressed isoforms. Dependencies between the existence of isoforms and their expression are modeled explicitly to facilitate parameter estimation. Model parameters are estimated iteratively using Gibbs sampling to infer the joint posterior distribution, from which the presence and abundance of isoforms can reliably be determined. Studies using both simulations and real datasets show that IntAPT consistently outperforms existing methods for the IntAPT. Experimental results demonstrate that, despite sequencing errors, IntAPT exhibits a robust performance among multiple samples, resulting in notably improved identification of expressed isoforms of low abundance. Availability and implementation The IntAPT package is available at http://github.com/henryxushi/IntAPT. Supplementary information Supplementary data are available at Bioinformatics online.

A Sparse Topic Model for Bursty Topic Discovery in Social Networks

Bursty topic discovery aims to automatically identify bursty events and continuously keep track of known events. The existing methods focus on the topic model. However, the sparsity of short text brings the challenge to the traditional topic models because the words are too few to learn from the original corpus. To tackle this problem, we propose a Sparse Topic Model (STM) for bursty topic discovery. First, we distinguish the modeling between the bursty topic and the common topic to detect the change of the words in time and discover the bursty words. Second, we introduce “Spike and Slab” prior to decouple the sparsity and smoothness of a distribution. The bursty words are leveraged to achieve automatic discovery of the bursty topics. Finally, to evaluate the effectiveness of our proposed algorithm, we collect Sina weibo dataset to conduct various experiments. Both qualitative and quantitative evaluations demonstrate that the proposed STM algorithm outperforms favorably against several state-of-the-art methods

Borrowing of information across patient subgroups in a basket trial based on distributional discrepancy

Summary Basket trials have emerged as a new class of efficient approaches in oncology to evaluate a new treatment in several patient subgroups simultaneously. In this article, we extend the key ideas to disease areas outside of oncology, developing a robust Bayesian methodology for randomized, placebo-controlled basket trials with a continuous endpoint to enable borrowing of information across subtrials with similar treatment effects. After adjusting for covariates, information from a complementary subtrial can be represented into a commensurate prior for the parameter that underpins the subtrial under consideration. We propose using distributional discrepancy to characterize the commensurability between subtrials for appropriate borrowing of information through a spike-and-slab prior, which is placed on the prior precision factor. When the basket trial has at least three subtrials, commensurate priors for point-to-point borrowing are combined into a marginal predictive prior, according to the weights transformed from the pairwise discrepancy measures. In this way, only information from subtrial(s) with the most commensurate treatment effect is leveraged. The marginal predictive prior is updated to a robust posterior by the contemporary subtrial data to inform decision making. Operating characteristics of the proposed methodology are evaluated through simulations motivated by a real basket trial in chronic diseases. The proposed methodology has advantages compared to other selected Bayesian analysis models, for (i) identifying the most commensurate source of information and (ii) gauging the degree of borrowing from specific subtrials. Numerical results also suggest that our methodology can improve the precision of estimates and, potentially, the statistical power for hypothesis testing.