Confronting the data deluge: How artificial intelligence can be used in the study of plant stress

• Published in: Computational and structural biotechnology journal Vol. 23; pp. 3454 - 3466
• Main Authors: Koh, Eugene, Sunil, Rohan Shawn, Lam, Hilbert Yuen In, Mutwil, Marek
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.12.2024; Research Network of Computational and Structural Biotechnology; Elsevier
• Subjects: Artificial intelligence; Large language models; Large-scale data; Plant stress resilience; Review; Plant stress resilience; Large-scale data; Large language models; Artificial intelligence
• ISSN: 2001-0370; 2001-0370
• DOI: 10.1016/j.csbj.2024.09.010

The advent of the genomics era enabled the generation of high-throughput data and computational methods that serve as powerful hypothesis-generating tools to understand the genomic and gene functional basis of plant stress resilience. The proliferation of experimental and analytical methods used in biology has resulted in a situation where plentiful data exists, but the volume and heterogeneity of this data has made analysis a significant challenge. Current advanced deep-learning models have displayed an unprecedented level of comprehension and problem-solving ability, and have been used to predict gene structure, function and expression based on DNA or protein sequence, and prominently also their use in high-throughput phenomics in agriculture. However, the application of deep-learning models to understand gene regulatory and signalling behaviour is still in its infancy. We discuss in this review the availability of data resources and bioinformatic tools, and several applications of these advanced ML/AI models in the context of plant stress response, and demonstrate the use of a publicly available LLM (ChatGPT) to derive a knowledge graph of various experimental and computational methods used in the study of plant stress. We hope this will stimulate further interest in collaboration between computer scientists, computational biologists and plant scientists to distil the deluge of genomic, transcriptomic, proteomic, metabolomic and phenomic data into meaningful knowledge that can be used for the benefit of humanity. [Display omitted]