ACE: Explaining cluster from an adversarial perspective

A common workflow in single-cell RNA-seq analysis is to project the data to a latent space, cluster the cells in that space, and identify sets of marker genes that explain the differences among the discovered clusters. A primary drawback to this three-step procedure is that each step is carried out independently, thereby neglecting the effects of the nonlinear embedding and inter-gene dependencies on the selection of marker genes. Here we propose an integrated deep learning frame-work, Adversarial Clustering Explanation (ACE), that bundles all three steps into a single workflow. The method thus moves away from the notion of “marker genes” to instead identify a panel of explanatory genes. This panel may include genes that are not only enriched but also depleted relative to other cell types, as well as genes that exhibit differences between closely related cell types. Empirically, we demonstrate that ACE is able to identify gene panels that are both highly discriminative and nonredundant, and we demonstrate the applicability of ACE to an image recognition task.

On Deep Unsupervised Active Learning

Unsupervised active learning has attracted increasing attention in recent years, where its goal is to select representative samples in an unsupervised setting for human annotating. Most existing works are based on shallow linear models by assuming that each sample can be well approximated by the span (i.e., the set of all linear combinations) of certain selected samples, and then take these selected samples as representative ones to label. However, in practice, the data do not necessarily conform to linear models, and how to model nonlinearity of data often becomes the key point to success. In this paper, we present a novel Deep neural network framework for Unsupervised Active Learning, called DUAL. DUAL can explicitly learn a nonlinear embedding to map each input into a latent space through an encoder-decoder architecture, and introduce a selection block to select representative samples in the the learnt latent space. In the selection block, DUAL considers to simultaneously preserve the whole input patterns as well as the cluster structure of data. Extensive experiments are performed on six publicly available datasets, and experimental results clearly demonstrate the efficacy of our method, compared with state-of-the-arts.