Search for: All records

Designing and generating new data under targeted properties has been attracting various critical applications such as molecule design, image editing and speech synthesis. Traditional hand-crafted approaches heavily rely on expertise experience and intensive human efforts, yet still suffer from the insufficiency of scientific knowledge and low throughput to support effective and efficient data generation. Recently, the advancement of deep learning has created the opportunity for expressive methods to learn the underlying representation and properties of data. Such capability provides new ways of determining the mutual relationship between the structural patterns and functional properties of the data and leveraging such relationships to generate structural data, given the desired properties. This article is a systematic review that explains this promising research area, commonly known as controllable deep data generation. First, the article raises the potential challenges and provides preliminaries. Then the article formally defines controllable deep data generation, proposes a taxonomy on various techniques and summarizes the evaluation metrics in this specific domain. After that, the article introduces exciting applications of controllable deep data generation, experimentally analyzes and compares existing works. Finally, this article highlights the promising future directions of controllable deep data generation and identifies five potential challenges. 

Abstract A major question in systems biology is how to identify the core gene regulatory circuit that governs the decision-making of a biological process. Here, we develop a computational platform, named NetAct, for constructing core transcription factor regulatory networks using both transcriptomics data and literature-based transcription factor-target databases. NetAct robustly infers regulators’ activity using target expression, constructs networks based on transcriptional activity, and integrates mathematical modeling for validation. Our in silico benchmark test shows that NetAct outperforms existing algorithms in inferring transcriptional activity and gene networks. We illustrate the application of NetAct to model networks driving TGF-β-induced epithelial-mesenchymal transition and macrophage polarization.