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A Variational Approach to London Dispersion Interactions without Density Distortion.

ABSTRACT: We introduce a class of variational wave functions that captures the long-range interaction between neutral systems (atoms and molecules) without changing the diagonal of the density matrix of each monomer. The corresponding energy optimization yields explicit expressions for the dispersion coefficients in terms of the ground-state pair densities of the isolated systems, providing a clean theoretical framework to build new approximations in several contexts. As the individual monomer densities are kept fixed, we can also unambiguously assess the effect of the density distortion on London dispersion interactions; for example, we obtain virtually exact dispersion coefficients between two hydrogen atoms up to C₁₀ and relative errors below 0.2% in other simple cases.

SUBMITTER: Kooi DP

PROVIDER: S-EPMC6452420 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

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A Variational Approach to London Dispersion Interactions without Density Distortion.

Kooi Derk P DP Gori-Giorgi Paola P

The journal of physical chemistry letters 20190320 7

We introduce a class of variational wave functions that captures the long-range interaction between neutral systems (atoms and molecules) without changing the diagonal of the density matrix of each monomer. The corresponding energy optimization yields explicit expressions for the dispersion coefficients in terms of the ground-state pair densities of the isolated systems, providing a clean theoretical framework to build new approximations in several contexts. As the individual monomer densities a ...[more]

PMID: 30865464

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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

A Variational Approach to London Dispersion Interactions without Density Distortion.

Publications

A Variational Approach to London Dispersion Interactions without Density Distortion.

Similar Datasets

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