Motivation: Single cell transcriptome sequencing (scRNA-Seq) has become a revolutionary tool to study cellular and molecular processes at single cell resolution. Among existing technologies, the recently developed droplet-based platform enables efficient parallel processing of thousands of single cells with direct counting of transcript copies using Unique Molecular Identifier (UMI). Despite the technology advances, statistical methods and computational tools are still lacking for analyzing droplet-based scRNA-Seq data. Particularly, model-based approaches for clustering large-scale single cell transcriptomic data are still under-explored. Methods: We developed DIMM-SC, a Dirichlet Mixture Model for clustering droplet-based Single Cell transcriptomic data. This approach explicitly models UMI count data from scRNA-Seq experiments and characterizes variations across different cell clusters via a Dirichlet mixture prior. An expectation-maximization algorithm is used for parameter inference. Results: We performed comprehensive simulations to evaluate DIMM-SC and compared it with existing clustering methods such as K-means, CellTree and Seurat. In addition, we analyzed public scRNA-Seq datasets with known cluster labels and in-house scRNA-Seq datasets from a study of systemic sclerosis with prior biological knowledge to benchmark and validate DIMM-SC. Both simulation studies and real data applications demonstrated that overall, DIMM-SC achieves substantially improved clustering accuracy and much lower clustering variability compared to other existing clustering methods. More importantly, as a model-based approach, DIMM-SC is able to quantify the clustering uncertainty for each single cell, facilitating rigorous statistical inference and biological interpretations, which are typically unavailable from existing clustering methods.

Opinion target extraction is a fundamental task in opinion mining. In recent years, neural network based supervised learning methods have achieved competitive performance on this task. However, as with any supervised learning method, neural network based methods for this task cannot work well when the training data comes from a different domain than the test data. On the other hand, some rule-based unsupervised methods have shown to be robust when applied to different domains. In this work, we use rule-based unsupervised methods to create auxiliary labels and use neural network models to learn a hidden representation that works well for different domains. When this hidden representation is used for opinion target extraction, we find that it can outperform a number of strong baselines with a large margin.

As the rapid growth of online social media attracts a large number of Internet users, the large volume of content generated by these users also provides us with an opportunity to study the lexical variation of people of different ages. In this paper, we present a latent variable model that jointly models the lexical content of tweets and Twitter users’ ages. Our model inherently assumes that a topic has not only a word distribution but also an age distribution. We propose a Gibbs-EM algorithm to perform inference on our model. Empirical evaluation shows that our model can learn meaningful age-specific topics such as “school” for teenagers and “health” for older people. Our model can also be used for age prediction and performs better than a number of baseline methods.

Collective classification has been intensively studied due to its impact in many important applications, such as web mining, bioinformatics and citation analysis. Collective classification approaches exploit the dependencies of a group of linked objects whose class labels are correlated and need to be predicted simultaneously. In this paper, we focus on studying the collective classification problem in heterogeneous networks, which involves multiple types of data objects interconnected by multiple types of links. Intuitively, two objects are correlated if they are linked by many paths in the network. However, most existing approaches measure the dependencies among objects through directly links or indirect links without considering the different semantic meanings behind different paths. In this paper, we study the collective classification problem taht is defined among the same type of objects in heterogenous networks. Moreover, by considering different linkage paths in the network, one can capture the subtlety of different types of dependencies among objects. We introduce the concept of meta-path based dependencies among objects, where a meta path is a path consisting a certain sequence of linke types. We show that the quality of collective classification results strongly depends upon the meta paths used. To accommodate the large network size, a novel solution, called HCC (meta-path based Heterogenous Collective Classification), is developed to effectively assign labels to a group of instances that are interconnected through different meta-paths. The proposed HCC model can capture different types of dependencies among objects with respect to different meta paths. Empirical studies on real-world networks demonstrate that effectiveness of the proposed meta path-based collective classification approach.