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Machine learning (ML) models have emerged as powerful tools for accelerating materials discovery and design by enabling accurate predictions of properties from compositional and structural data. These capabilities are vital for developing advanced technologies across fields such as energy, electronics, and biomedicine, potentially reducing the time and resources needed for new material exploration and promoting rapid innovation cycles. Recent efforts have focused on employing advanced ML algorithms, including deep learning-based graph neural networks, for property prediction. Additionally, ensemble models have proven to enhance the generalizability and robustness of ML and Deep Learning (DL). However, the use of such ensemble strategies in deep graph networks for material property prediction remains underexplored. Our research provides an in-depth evaluation of ensemble strategies in deep learning-based graph neural network, specifically targeting material property prediction tasks. By testing the Crystal Graph Convolutional Neural Network (CGCNN) and its multitask version, MT-CGCNN, we demonstrated that ensemble techniques, especially prediction averaging, substantially improve precision beyond traditional metrics for key properties like formation energy per atom $\left(\mathrm{\Delta }{E}^f\right)$, band gap $\left(E_g\right)$, density $\left(\rho \right)$, equivalent reaction energy per atom $\left(E_{\mathit{rxn,atom}}\right)$, energy per atom $\left(E_{\mathit{atom}}\right)$and atomic density $\left({\rho }_{\mathit{atom}}\right)$in 33,990 stable inorganic materials. These findings support the broader application of ensemble methods to enhance predictive accuracy in the field. 

Abstract Recent advances in genome sequencing and imputation technologies provide an exciting opportunity to comprehensively study the contribution of genetic variants to complex phenotypes. However, our ability to translate genetic discoveries into mechanistic insights remains limited at this point. In this paper, we propose an efficient knockoff-based method, GhostKnockoff, for genome-wide association studies (GWAS) that leads to improved power and ability to prioritize putative causal variants relative to conventional GWAS approaches. The method requires only Z-scores from conventional GWAS and hence can be easily applied to enhance existing and future studies. The method can also be applied to meta-analysis of multiple GWAS allowing for arbitrary sample overlap. We demonstrate its performance using empirical simulations and two applications: (1) a meta-analysis for Alzheimer’s disease comprising nine overlapping large-scale GWAS, whole-exome and whole-genome sequencing studies and (2) analysis of 1403 binary phenotypes from the UK Biobank data in 408,961 samples of European ancestry. Our results demonstrate that GhostKnockoff can identify putatively functional variants with weaker statistical effects that are missed by conventional association tests.