Andrew L. Ferguson

11 papers Journal 11

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	FlowBack: A Generalized Flow-Matching Approach for Biomolecular Backmapping. J. Chem. Inf. Model. Michael S. Jones, Smayan Khanna, Andrew L. Ferguson
2023	J	`jnl`	DiAMoNDBack: Diffusion-denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces. CoRR Michael S. Jones, Kirill Shmilovich, Andrew L. Ferguson
2023	J	`jnl`	GANs and Closures: Micro-Macro Consistency in Multiscale Modeling. Multiscale Model. Simul. Ellis R. Crabtree, Juan M. Bello-Rivas, Andrew L. Ferguson, Ioannis G. Kevrekidis
2022	J	`jnl`	GANs and Closures: Micro-Macro Consistency in Multiscale Modeling. CoRR Ellis R. Crabtree, Juan M. Bello-Rivas, Andrew L. Ferguson, Ioannis G. Kevrekidis
2020	J	`jnl`	Discovery of Self-Assembling π-Conjugated Peptides by Active Learning-Directed Coarse-Grained Molecular Simulation. CoRR Kirill Shmilovich, Rachael A. Mansbach, Hythem Sidky, Olivia E. Dunne, Sayak Subhra Panda, John D. Tovar, Andrew L. Ferguson
2019	J	`jnl`	Capabilities and Limitations of Time-lagged Autoencoders for Slow Mode Discovery in Dynamical Systems. CoRR Wei Chen, Hythem Sidky, Andrew L. Ferguson
2019	J	`jnl`	Nonlinear Discovery of Slow Molecular Modes using Hierarchical Dynamics Encoders. CoRR Wei Chen, Hythem Sidky, Andrew L. Ferguson
2018	J	`jnl`	Molecular enhanced sampling with autoencoders: On-the-fly collective variable discovery and accelerated free energy landscape exploration. J. Comput. Chem. Wei Chen, Andrew L. Ferguson
2017	J	`jnl`	BayesWHAM: A Bayesian approach for free energy estimation, reweighting, and uncertainty quantification in the weighted histogram analysis method. J. Comput. Chem. Andrew L. Ferguson
2016	J	`jnl`	Global graph matching using diffusion maps. Intell. Data Anal. Jingtian Hu, Andrew L. Ferguson
2014	J	`jnl`	The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by PLoS Comput. Biol. Jaclyn K. Mann, John P. Barton, Andrew L. Ferguson, Saleha Omarjee, Bruce D. Walker, Arup Chakraborty, Thumbi Ndung'u