Search Results for author: Wujie Wang

Found 7 papers, 7 papers with code

Forces are not Enough: Benchmark and Critical Evaluation for Machine Learning Force Fields with Molecular Simulations

1 code implementation13 Oct 2022 Xiang Fu, Zhenghao Wu, Wujie Wang, Tian Xie, Sinan Keten, Rafael Gomez-Bombarelli, Tommi Jaakkola

We benchmark a collection of state-of-the-art (SOTA) ML FF models and illustrate, in particular, how the commonly benchmarked force accuracy is not well aligned with relevant simulation metrics.

Learning Pair Potentials using Differentiable Simulations

1 code implementation16 Sep 2022 Wujie Wang, Zhenghao Wu, Rafael Gómez-Bombarelli

We show that our methods can be used to simultaneously fit potentials for simulations at different compositions and temperatures to improve the transferability of the learned potentials.

Generative Coarse-Graining of Molecular Conformations

1 code implementation28 Jan 2022 Wujie Wang, Minkai Xu, Chen Cai, Benjamin Kurt Miller, Tess Smidt, Yusu Wang, Jian Tang, Rafael Gómez-Bombarelli

Coarse-graining (CG) of molecular simulations simplifies the particle representation by grouping selected atoms into pseudo-beads and drastically accelerates simulation.

An End-to-End Framework for Molecular Conformation Generation via Bilevel Programming

1 code implementation15 May 2021 Minkai Xu, Wujie Wang, Shitong Luo, Chence Shi, Yoshua Bengio, Rafael Gomez-Bombarelli, Jian Tang

Specifically, the molecular graph is first encoded in a latent space, and then the 3D structures are generated by solving a principled bilevel optimization program.

Bilevel Optimization

Temperature-transferable coarse-graining of ionic liquids with dual graph convolutional neural networks

2 code implementations28 Jul 2020 Jurgis Ruza, Wujie Wang, Daniel Schwalbe-Koda, Simon Axelrod, William H. Harris, Rafael Gomez-Bombarelli

The potential of mean force is expressed as two jointly-trained neural network interatomic potentials that learn the coupled short-range and the many-body long range molecular interactions.

Computational Physics Materials Science

Differentiable Molecular Simulations for Control and Learning

2 code implementations ICLR Workshop DeepDiffEq 2019 Wujie Wang, Simon Axelrod, Rafael Gómez-Bombarelli

From the perspective of engineering, one wishes to control the Hamiltonian to achieve desired simulation outcomes and structures, as in self-assembly and optical control, to then realize systems with the desired Hamiltonian in the lab.

Coarse-Graining Auto-Encoders for Molecular Dynamics

1 code implementation6 Dec 2018 Wujie Wang, Rafael Gómez-Bombarelli

Autograin is trained to learn the optimal mapping between all-atom and reduced representation, using the reconstruction loss to facilitate the learning of coarse-grained variables.

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