Search Results for author: Peng Tao

Found 8 papers, 5 papers with code

Brain-inspired Chaotic Graph Backpropagation for Large-scale Combinatorial Optimization

no code implementations13 Dec 2024 Peng Tao, Kazuyuki Aihara, Luonan Chen

To address this issue, inspired by possibly chaotic dynamics of real brain learning, we introduce a chaotic training algorithm, i. e. chaotic graph backpropagation (CGBP), which introduces a local loss function in GNN that makes the training process not only chaotic but also highly efficient.

Combinatorial Optimization Graph Neural Network

The need to implement FAIR principles in biomolecular simulations

no code implementations23 Jul 2024 Rommie Amaro, Johan Åqvist, Ivet Bahar, Federica Battistini, Adam Bellaiche, Daniel Beltran, Philip C. Biggin, Massimiliano Bonomi, Gregory R. Bowman, Richard Bryce, Giovanni Bussi, Paolo Carloni, David Case, Andrea Cavalli, Chie-En A. Chang, Thomas E. Cheatham III, Margaret S. Cheung, Cris Chipot, Lillian T. Chong, Preeti Choudhary, Gerardo Andres Cisneros, Cecilia Clementi, Rosana Collepardo-Guevara, Peter Coveney, Roberto Covino, T. Daniel Crawford, Matteo Dal Peraro, Bert de Groot, Lucie Delemotte, Marco De Vivo, Jonathan Essex, Franca Fraternali, Jiali Gao, Josep Lluís Gelpí, Francesco Luigi Gervasio, Fernando Danilo Gonzalez-Nilo, Helmut Grubmüller, Marina Guenza, Horacio V. Guzman, Sarah Harris, Teresa Head-Gordon, Rigoberto Hernandez, Adam Hospital, Niu Huang, Xuhui Huang, Gerhard Hummer, Javier Iglesias-Fernández, Jan H. Jensen, Shantenu Jha, Wanting Jiao, William L. Jorgensen, Shina Caroline Lynn Kamerlin, Syma Khalid, Charles Laughton, Michael Levitt, Vittorio Limongelli, Erik Lindahl, Kresten Lindorff-Larsen, Sharon Loverde, Magnus Lundborg, Yun Lyna Luo, Francisco Javier Luque, Charlotte I. Lynch, Alexander MacKerell, Alessandra Magistrato, Siewert J. Marrink, Hugh Martin, J. Andrew McCammon, Kenneth Merz, Vicent Moliner, Adrian Mulholland, Sohail Murad, Athi N. Naganathan, Shikha Nangia, Frank Noe, Agnes Noy, Julianna Oláh, Megan O'Mara, Mary Jo Ondrechen, José N. Onuchic, Alexey Onufriev, Silvia Osuna, Anna R. Panchenko, Sergio Pantano, Carol Parish, Michele Parrinello, Alberto Perez, Tomas Perez-Acle, Juan R. Perilla, B. Montgomery Pettitt, Adriana Pietropalo, Jean-Philip Piquemal, Adolfo Poma, Matej Praprotnik, Maria J. Ramos, Pengyu Ren, Nathalie Reuter, Adrian Roitberg, Edina Rosta, Carme Rovira, Benoit Roux, Ursula Röthlisberger, Karissa Y. Sanbonmatsu, Tamar Schlick, Alexey K. Shaytan, Carlos Simmerling, Jeremy C. Smith, Yuji Sugita, Katarzyna Świderek, Makoto Taiji, Peng Tao, D. Peter Tieleman, Irina G. Tikhonova, Julian Tirado-Rives, Inaki Tunón, Marc W. Van Der Kamp, David van der Spoel, Sameer Velankar, Gregory A. Voth, Rebecca Wade, Ariel Warshel, Valerie Vaissier Welborn, Stacey Wetmore, Travis J. Wheeler, Chung F. Wong, Lee-Wei Yang, Martin Zacharias, Modesto Orozco

This letter illustrates the opinion of the molecular dynamics (MD) community on the need to adopt a new FAIR paradigm for the use of molecular simulations.

PASSerRank: Prediction of Allosteric Sites with Learning to Rank

1 code implementation2 Feb 2023 Hao Tian, Sian Xiao, Xi Jiang, Peng Tao

One of the major challenges in allosteric drug research is the identification of allosteric sites.

Drug Discovery Learning-To-Rank +1

LAST: Latent Space Assisted Adaptive Sampling for Protein Trajectories

1 code implementation27 Apr 2022 Hao Tian, Xi Jiang, Sian Xiao, Hunter La Force, Eric C. Larson, Peng Tao

Based on this characteristic, we proposed a new adaptive sampling method, latent space assisted adaptive sampling for protein trajectories (LAST), to accelerate the exploration of protein conformational space.

Time Series Prediction by Multi-task GPR with Spatiotemporal Information Transformation

1 code implementation26 Apr 2022 Peng Tao, Xiaohu Hao, Jie Cheng, Luonan Chen

Making an accurate prediction of an unknown system only from a short-term time series is difficult due to the lack of sufficient information, especially in a multi-step-ahead manner.

GPR Prediction +2

Accurate ADMET Prediction with XGBoost

1 code implementation15 Apr 2022 Hao Tian, Rajas Ketkar, Peng Tao

The absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties are important in drug discovery as they define efficacy and safety.

Molecular Property Prediction Prediction +1

ivis Dimensionality Reduction Framework for Biomacromolecular Simulations

1 code implementation22 Apr 2020 Hao Tian, Peng Tao

Molecular dynamics (MD) simulations have been widely applied to study macromolecules including proteins.

Dimensionality Reduction

Residual-Recursion Autoencoder for Shape Illustration Images

no code implementations6 Feb 2020 Qianwei Zhou, Peng Tao, Xiaoxin Li, Sheng-Yong Chen, Fan Zhang, Haigen Hu

Shape illustration images (SIIs) are common and important in describing the cross-sections of industrial products.

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