Chun Ye

Yueming Yin, Haifeng Hu, Zhen Yang et al.

Computational discovery of ideal lead compounds is a critical process for modern drug discovery. It comprises multiple stages: hit screening, molecular property prediction, and molecule optimization. Current efforts are disparate, involving the establishment of models for each stage, followed by multi-stage multi-model integration. However, this is non-ideal, as clumsy integration of incompatible models increases research overheads, and may even reduce success rates in drug discovery. Facilitating compatibilities requires establishing inherent model consistencies across lead discovery stages. Towards that effect, we propose an open deep graph learning (DGL) based pipeline: generative adversarial feature subspace enhancement (GAFSE), which first unifies the modeling of these stages into one learning framework. GAFSE also offers standardized modular design and streamlined interfaces for future expansions and community support. GAFSE combines adversarial/generative learning, graph attention network, graph reconstruction network, and optimizes the classification/regression loss, adversarial/generative loss, and reconstruction loss simultaneously. Convergence analysis theoretically guarantees model generalization performance. Exhaustive benchmarking demonstrates that the GAFSE pipeline achieves excellent performance across almost all lead discovery stages, while also providing valuable model interpretability. Hence, we believe this tool will enhance the efficiency and productivity of drug discovery researchers.

Bryan He, Matthew Thomson, Meena Subramaniam et al.

Single-cell RNA sequencing (scRNA-seq) has the potential to provide powerful, high-resolution signatures to inform disease prognosis and precision medicine. This paper takes an important first step towards this goal by developing an interpretable machine learning algorithm, CloudPred, to predict individuals' disease phenotypes from their scRNA-seq data. Predicting phenotype from scRNA-seq is challenging for standard machine learning methods -- the number of cells measured can vary by orders of magnitude across individuals and the cell populations are also highly heterogeneous. Typical analysis creates pseudo-bulk samples which are biased toward prior annotations and also lose the single cell resolution. CloudPred addresses these challenges via a novel end-to-end differentiable learning algorithm which is coupled with a biologically informed mixture of cell types model. CloudPred automatically infers the cell subpopulation that are salient for the phenotype without prior annotations. We developed a systematic simulation platform to evaluate the performance of CloudPred and several alternative methods we propose, and find that CloudPred outperforms the alternative methods across several settings. We further validated CloudPred on a real scRNA-seq dataset of 142 lupus patients and controls. CloudPred achieves AUROC of 0.98 while identifying a specific subpopulation of CD4 T cells whose presence is highly indicative of lupus. CloudPred is a powerful new framework to predict clinical phenotypes from scRNA-seq data and to identify relevant cells.

Laura Deming, Sasha Targ, Nate Sauder et al.

Each human genome is a 3 billion base pair set of encoding instructions. Decoding the genome using deep learning fundamentally differs from most tasks, as we do not know the full structure of the data and therefore cannot design architectures to suit it. As such, architectures that fit the structure of genomics should be learned not prescribed. Here, we develop a novel search algorithm, applicable across domains, that discovers an optimal architecture which simultaneously learns general genomic patterns and identifies the most important sequence motifs in predicting functional genomic outcomes. The architectures we find using this algorithm succeed at using only RNA expression data to predict gene regulatory structure, learn human-interpretable visualizations of key sequence motifs, and surpass state-of-the-art results on benchmark genomics challenges.