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An effective implementation of enhanced sampling algorithms for molecular dynamics simulations requires a priori knowledge of the approximate reaction coordinate describing the relevant mechanisms in the system. Here we demonstrate how the…

Biological Physics · Physics 2021-12-22 Shams Mehdi , Dedi Wang , Shashank Pant , Pratyush Tiwary

Markov state models (MSMs) are valuable for studying dynamics of protein conformational changes via statistical analysis of molecular dynamics (MD) simulations. In MSMs, the complex configuration space is coarse-grained into conformational…

Biological Physics · Physics 2024-06-11 Dedi Wang , Yunrui Qiu , Eric Beyerle , Xuhui Huang , Pratyush Tiwary

Molecular dynamics simulations offer detailed insights into atomic motions but face timescale limitations. Enhanced sampling methods have addressed these challenges but even with machine learning, they often rely on pre-selected…

Machine Learning · Computer Science 2024-09-19 Ziyue Zou , Dedi Wang , Pratyush Tiwary

Generative modeling becomes increasingly data-intensive in high-dimensional spaces. In molecular science, where data collection is expensive and important events are rare, compression to lower-dimensional manifolds is especially important…

Machine Learning · Computer Science 2025-10-14 Richard John , Yunrui Qiu , Lukas Herron , Pratyush Tiwary

When examining dynamics occurring at non-zero temperatures, both energy and entropy must be taken into account while describing activated barrier crossing events. Furthermore, good reaction coordinates need to be constructed to describe…

Chemical Physics · Physics 2022-03-16 E. R. Beyerle , Shams Mehdi , Pratyush Tiwary

Identifying the dynamical state variables of a system from high-dimensional observations is a central problem across physical sciences. The challenge is that the state variables are not directly observable and must be inferred from raw…

Data Analysis, Statistics and Probability · Physics 2026-04-28 K. Michael Martini , Eslam Abdelaleem , Paarth Gulati , Ilya Nemenman

Reinforcement Learning (RL) has recently achieved remarkable success in robotic control. However, most works in RL operate in simulated environments where privileged knowledge (e.g., dynamics, surroundings, terrains) is readily available.…

Machine Learning · Computer Science 2024-10-15 Haoran He , Peilin Wu , Chenjia Bai , Hang Lai , Lingxiao Wang , Ling Pan , Xiaolin Hu , Weinan Zhang

We investigate crystal nucleation in supersaturated colloid suspensions using enhanced molecular dynamics simulations augmented with machine learning techniques. The simulations reveal that crystallization in the model colloidal system…

Soft Condensed Matter · Physics 2024-04-30 Vanessa J. Meraz , Ziyue Zou , Pratyush Tiwary

Markov processes are widely used mathematical models for describing dynamic systems in various fields. However, accurately simulating large-scale systems at long time scales is computationally expensive due to the short time steps required…

Machine Learning · Computer Science 2024-01-29 Marco Federici , Patrick Forré , Ryota Tomioka , Bastiaan S. Veeling

Deep reinforcement learning (DRL) agents are often sensitive to visual changes that were unseen in their training environments. To address this problem, we leverage the sequential nature of RL to learn robust representations that encode…

Artificial Intelligence · Computer Science 2022-07-15 Jiameng Fan , Wenchao Li

Effective adaptation to distribution shifts in training data is pivotal for sustaining robustness in neural networks, especially when removing specific biases or outdated information, a process known as machine unlearning. Traditional…

Machine Learning · Computer Science 2024-05-24 Ling Han , Hao Huang , Dustin Scheinost , Mary-Anne Hartley , María Rodríguez Martínez

The Information Bottleneck (IB) principle offers an information-theoretic framework for analyzing the training process of deep neural networks (DNNs). Its essence lies in tracking the dynamics of two mutual information (MI) values: between…

Machine Learning · Computer Science 2024-05-10 Ivan Butakov , Alexander Tolmachev , Sofia Malanchuk , Anna Neopryatnaya , Alexey Frolov , Kirill Andreev

Several self-supervised representation learning methods have been proposed for reinforcement learning (RL) with rich observations. For real-world applications of RL, recovering underlying latent states is crucial, particularly when sensory…

The fruits of science are relationships made comprehensible, often by way of approximation. While deep learning is an extremely powerful way to find relationships in data, its use in science has been hindered by the difficulty of…

Machine Learning · Computer Science 2022-04-18 Kieran A. Murphy , Dani S. Bassett

In the Information Bottleneck (IB), when tuning the relative strength between compression and prediction terms, how do the two terms behave, and what's their relationship with the dataset and the learned representation? In this paper, we…

Machine Learning · Computer Science 2020-01-08 Tailin Wu , Ian Fischer

Learning effective joint embedding for cross-modal data has always been a focus in the field of multimodal machine learning. We argue that during multimodal fusion, the generated multimodal embedding may be redundant, and the discriminative…

Machine Learning · Computer Science 2022-12-06 Sijie Mai , Ying Zeng , Haifeng Hu

Deep learning has become the most powerful machine learning tool in the last decade. However, how to efficiently train deep neural networks remains to be thoroughly solved. The widely used minibatch stochastic gradient descent (SGD) still…

Machine Learning · Computer Science 2021-05-18 Xinyu Peng , Jiawei Zhang , Fei-Yue Wang , Li Li

Multimodal data has significantly advanced recommendation systems by integrating diverse information sources to model user preferences and item characteristics. However, these systems often struggle with redundant and irrelevant…

Information Retrieval · Computer Science 2025-09-25 Hui Wang , Jinghui Qin , Wushao Wen , Qingling Li , Shanshan Zhong , Zhongzhan Huang

Deep reinforcement learning has recently shown many impressive successes. However, one major obstacle towards applying such methods to real-world problems is their lack of data-efficiency. To this end, we propose the Bottleneck Simulator: a…

Machine Learning · Computer Science 2018-07-13 Iulian Vlad Serban , Chinnadhurai Sankar , Michael Pieper , Joelle Pineau , Yoshua Bengio

The information bottleneck principle is an elegant and useful approach to representation learning. In this paper, we investigate the problem of representation learning in the context of reinforcement learning using the information…

Machine Learning · Computer Science 2019-11-14 Pei Yingjun , Hou Xinwen
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