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Accurate prediction of the kinetic sequence of physicochemical states using generative artificial intelligence.

作者信息

Bera Palash, Mondal Jagannath

机构信息

Tata Institute of Fundamental Research Hyderabad Telangana 500046 India

出版信息

Chem Sci. 2025 Apr 10. doi: 10.1039/d5sc00108k.


DOI:10.1039/d5sc00108k
PMID:40271036
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12012632/
Abstract

Capturing the time evolution and predicting kinetic sequences of states of physicochemical systems present significant challenges due to the precision and computational effort required. In this study, we demonstrate that 'Generative Pre-trained Transformer (GPT)', an artificial intelligence model renowned for machine translation and natural language processing, can be effectively adapted to predict the dynamical state-to-state transition kinetics of biologically relevant physicochemical systems. Specifically, by using sequences of time-discretized states from Molecular Dynamics (MD) simulation trajectories akin to the vocabulary corpus of a language, we show that a GPT-based model can learn the complex syntactic and semantic relationships within the trajectory. This enables GPT to predict kinetically accurate sequences of states for a diverse set of biomolecules of varying complexity, at a much quicker pace than traditional MD simulations and with a better efficiency than other baseline time-series prediction approaches. More significantly, the approach is found to be equally adept at forecasting the time evolution of out-of-equilibrium active systems that do not maintain detailed balance. An analysis of the mechanism inherent in GPT reveals the crucial role of the 'self-attention mechanism' in capturing the long-range correlations necessary for accurate state-to-state transition predictions. Together, our results highlight generative artificial intelligence's ability to generate kinetic sequences of states of physicochemical systems with statistical precision.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d8a/12093490/af61bb50063c/d5sc00108k-f9.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d8a/12093490/d635c6cc883a/d5sc00108k-f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d8a/12093490/9bd4a92d9421/d5sc00108k-f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d8a/12093490/bbbf83a4c8d3/d5sc00108k-f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d8a/12093490/5570e67f30d0/d5sc00108k-f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d8a/12093490/e38073bfe96c/d5sc00108k-f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d8a/12093490/40782c85aa79/d5sc00108k-f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d8a/12093490/9bd0bfb675c6/d5sc00108k-f7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d8a/12093490/d54bb1881cac/d5sc00108k-f8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d8a/12093490/af61bb50063c/d5sc00108k-f9.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d8a/12093490/d635c6cc883a/d5sc00108k-f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d8a/12093490/9bd4a92d9421/d5sc00108k-f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d8a/12093490/bbbf83a4c8d3/d5sc00108k-f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d8a/12093490/5570e67f30d0/d5sc00108k-f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d8a/12093490/e38073bfe96c/d5sc00108k-f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d8a/12093490/40782c85aa79/d5sc00108k-f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d8a/12093490/9bd0bfb675c6/d5sc00108k-f7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d8a/12093490/d54bb1881cac/d5sc00108k-f8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d8a/12093490/af61bb50063c/d5sc00108k-f9.jpg

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本文引用的文献

[1]
Machine learning unravels inherent structural patterns in Escherichia coli Hi-C matrices and predicts chromosome dynamics.

Nucleic Acids Res. 2024-10-14

[2]
Enhanced Sampling with Machine Learning.

Annu Rev Phys Chem. 2024-6

[3]
Interplay of cell motility and self-secreted extracellular polymeric substance induced depletion effects on spatial patterning in a growing microbial colony.

Soft Matter. 2023-11-1

[4]
A deep encoder-decoder framework for identifying distinct ligand binding pathways.

J Chem Phys. 2023-5-21

[5]
Conformational Plasticity in α-Synuclein and How Crowded Environment Modulates It.

J Phys Chem B. 2023-5-11

[6]
A mechanistic understanding of microcolony morphogenesis: coexistence of mobile and sessile aggregates.

Soft Matter. 2023-2-1

[7]
Path sampling of recurrent neural networks by incorporating known physics.

Nat Commun. 2022-11-24

[8]
From data to noise to data for mixing physics across temperatures with generative artificial intelligence.

Proc Natl Acad Sci U S A. 2022-8-9

[9]
A deep autoencoder framework for discovery of metastable ensembles in biomacromolecules.

J Chem Phys. 2021-9-21

[10]
Mechanistic underpinning of cell aspect ratio-dependent emergent collective motions in swarming bacteria.

Soft Matter. 2021-8-21

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