Fan Zhong

Xiaoqiong Xia, Chaoyu Zhu, Yuqi Shan et al.

Accurate and robust drug response prediction is of utmost importance in precision medicine. Although many models have been developed to utilize the representations of drugs and cancer cell lines for predicting cancer drug responses (CDR), their performances can be improved by addressing issues such as insufficient data modality, suboptimal fusion algorithms, and poor generalizability for novel drugs or cell lines. We introduce TransCDR, which uses transfer learning to learn drug representations and fuses multi-modality features of drugs and cell lines by a self-attention mechanism, to predict the IC50 values or sensitive states of drugs on cell lines. We are the first to systematically evaluate the generalization of the CDR prediction model to novel (i.e., never-before-seen) compound scaffolds and cell line clusters. TransCDR shows better generalizability than 8 state-of-the-art models. TransCDR outperforms its 5 variants that train drug encoders (i.e., RNN and AttentiveFP) from scratch under various scenarios. The most critical contributors among multiple drug notations and omics profiles are Extended Connectivity Fingerprint and genetic mutation. Additionally, the attention-based fusion module further enhances the predictive performance of TransCDR. TransCDR, trained on the GDSC dataset, demonstrates strong predictive performance on the external testing set CCLE. It is also utilized to predict missing CDRs on GDSC. Moreover, we investigate the biological mechanisms underlying drug response by classifying 7,675 patients from TCGA into drug-sensitive or drug-resistant groups, followed by a Gene Set Enrichment Analysis. TransCDR emerges as a potent tool with significant potential in drug response prediction. The source code and data can be accessed at https://github.com/XiaoqiongXia/TransCDR.

Jichao Zhang, Yezhi Shu, Songhua Xu et al.

Recent Image-to-Image Translation algorithms have achieved significant progress in neural style transfer and image attribute manipulation tasks. However, existing approaches require exhaustively labelling training data, which is labor demanding, difficult to scale up, and hard to migrate into new domains. To overcome such a key limitation, we propose Sparsely Grouped Generative Adversarial Networks (SG-GAN) as a novel approach that can translate images on sparsely grouped datasets where only a few samples for training are labelled. Using a novel one-input multi-output architecture, SG-GAN is well-suited for tackling sparsely grouped learning and multi-task learning. The proposed model can translate images among multiple groups using only a single commonly trained model. To experimentally validate advantages of the new model, we apply the proposed method to tackle a series of attribute manipulation tasks for facial images. Experimental results demonstrate that SG-GAN can generate image translation results of comparable quality with baselines methods on adequately labelled datasets and results of superior quality on sparsely grouped datasets. The official implementation is publicly available:https://github.com/zhangqianhui/Sparsely-Grouped-GAN.