Ke Deng

Xiaofei Xu, Ke Deng, Fei Hu et al.

Many words have evolved in meaning as a result of cultural and social change. Understanding such changes is crucial for modelling language and cultural evolution. Low-dimensional embedding methods have shown promise in detecting words' meaning change by encoding them into dense vectors. However, when exploring semantic change of words over time, these methods require the alignment of word embeddings across different time periods. This process is computationally expensive, prohibitively time consuming and suffering from contextual variability. In this paper, we propose a new and scalable method for encoding words from different time periods into one dense vector space. This can greatly improve performance when it comes to identifying words that have changed in meaning over time. We evaluated our method on dataset from Google Books N-gram. Our method outperformed three other popular methods in terms of the number of words correctly identified to have changed in meaning. Additionally, we provide an intuitive visualization of the semantic evolution of some words extracted by our method

Zhe Sun, Ting Wang, Ke Deng et al.

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.