Dataset Information

Explore Protein Conformational Space With Variational Autoencoder.

ABSTRACT: Molecular dynamics (MD) simulations have been actively used in the study of protein structure and function. However, extensive sampling in the protein conformational space requires large computational resources and takes a prohibitive amount of time. In this study, we demonstrated that variational autoencoders (VAEs), a type of deep learning model, can be employed to explore the conformational space of a protein through MD simulations. VAEs are shown to be superior to autoencoders (AEs) through a benchmark study, with low deviation between the training and decoded conformations. Moreover, we show that the learned latent space in the VAE can be used to generate unsampled protein conformations. Additional simulations starting from these generated conformations accelerated the sampling process and explored hidden spaces in the conformational landscape.

SUBMITTER: Tian H

PROVIDER: S-EPMC8633506 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Publications

Explore Protein Conformational Space With Variational Autoencoder.

Tian Hao H Jiang Xi X Trozzi Francesco F Xiao Sian S Larson Eric C EC Tao Peng P

Frontiers in molecular biosciences 20211112

Molecular dynamics (MD) simulations have been actively used in the study of protein structure and function. However, extensive sampling in the protein conformational space requires large computational resources and takes a prohibitive amount of time. In this study, we demonstrated that variational autoencoders (VAEs), a type of deep learning model, can be employed to explore the conformational space of a protein through MD simulations. VAEs are shown to be superior to autoencoders (AEs) through ...[more]

PMID: 34869602

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Project description:BackgroundMultiple studies have shown the utility of transcriptome-wide RNA-seq profiles as features for machine learning-based prediction of response to chemotherapy in cancer. While tumor transcriptome profiles are publicly available for thousands of tumors for many cancer types, a relatively modest number of tumor profiles are clinically annotated for response to chemotherapy. The paucity of labeled examples and the high dimension of the feature data limit performance for predicting therapeutic response using fully-supervised classification methods. Recently, multiple studies have established the utility of a deep neural network approach, the variational autoencoder (VAE), for generating meaningful latent features from original data. Here, we report the first study of a semi-supervised approach using VAE-encoded tumor transcriptome features and regularized gradient boosted decision trees (XGBoost) to predict chemotherapy drug response for five cancer types: colon, pancreatic, bladder, breast, and sarcoma.ResultsWe found: (1) VAE-encoding of the tumor transcriptome preserves the cancer type identity of the tumor, suggesting preservation of biologically relevant information; and (2) as a feature-set for supervised classification to predict response-to-chemotherapy, the unsupervised VAE encoding of the tumor's gene expression profile leads to better area under the receiver operating characteristic curve and area under the precision-recall curve classification performance than the original gene expression profile or the PCA principal components or the ICA components of the gene expression profile, in four out of five cancer types that we tested.ConclusionsGiven high-dimensional "omics" data, the VAE is a powerful tool for obtaining a nonlinear low-dimensional embedding; it yields features that retain biological patterns that distinguish between different types of cancer and that enable more accurate tumor transcriptome-based prediction of response to chemotherapy than would be possible using the original data or their principal components.

Dataset Information

Explore Protein Conformational Space With Variational Autoencoder.

Publications

Explore Protein Conformational Space With Variational Autoencoder.

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