A self-training interpretable cell type annotation framework using specific marker gene.

Motivation: Recent advances in sequencing technology provide opportunities to study biological processes at a higher resolution. Cell type annotation is an important step in scRNA-seq analysis, which often relies on established marker genes. However, most of the previous methods divide the identification of cell types into two stages, clustering and assignment, whose performances are susceptible to the clustering algorithm, and the marker information cannot effectively guide the clustering process.

Comprehensive single-cell RNA-seq analysis using deep interpretable generative modeling guided by biological hierarchy knowledge.

Recent advances in microfluidics and sequencing technologies allow researchers to explore cellular heterogeneity at single-cell resolution. In recent years, deep learning frameworks, such as generative models, have brought great changes to the analysis of transcriptomic data. Nevertheless, relying on the potential space of these generative models alone is insufficient to generate biological explanations.

A Drug Combination Prediction Framework Based on Graph Convolutional Network and Heterogeneous Information.

Combination therapy, which can improve therapeutic efficacy and reduce side effects, plays an important role in the treatment of complex diseases. Yet, a large number of possible combinations among candidate compounds limits our ability to identify effective combinations. Though many studies have focused on predicting potential drug combinations, the existing methods are not entirely satisfactory in terms of performance and scalability.

TADC: A Topic-Aware Dynamic Convolutional Neural Network for Aspect Extraction.

Aspect extraction is one of the key tasks in fine-grained sentiment analysis. This task aims to identify explicit opinion targets from user-generated documents. Currently, the mainstream methods for aspect extraction are built on recurrent neural networks (RNNs), which are difficult to parallelize.

TACN: A Topical Adversarial Capsule Network for textual network embedding.

Combining topological information and attributed information of nodes in networks effectively is a valuable task in network embedding. Nevertheless, many prior network embedding methods regarded attributed information of nodes as simple attribute sets or ignored them totally. In some scenarios, the hidden information contained in vertex attributes are essential to network embedding.

Fast Supervised Topic Models for Short Text Emotion Detection.

With the development of social network platforms, discussion forums, and question answering websites, a huge number of short messages that typically contain a few words for an individual document are posted by online users. In these short messages, emotions are frequently embedded for communicating opinions, expressing friendship, and promoting influence. It is quite valuable to detect emotions from short messages, but the corresponding task suffers from the sparsity of feature space.

Affective topic model for social emotion detection.

The rapid development of social media services has been a great boon for the communication of emotions through blogs, microblogs/tweets, instant-messaging tools, news portals, and so forth. This paper is concerned with the detection of emotions evoked in a reader by social media. Compared to classical sentiment analysis conducted from the writer's perspective, analysis from the reader's perspective can be more meaningful when applied to social media.

Community-aware user profile enrichment in folksonomy.

In the era of big data, collaborative tagging (a.k.a.