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Deeptime: a Python library for machine learning dynamical models from
  time series data

Deeptime: a Python library for machine learning dynamical models from time series data

28 October 2021
Moritz Hoffmann
Martin K. Scherer
Tim Hempel
Andreas Mardt
Brian M. de Silva
B. Husic
Stefan Klus
Hao Wu
N. Kutz
Steven L. Brunton
Frank Noé
    AI4CE
ArXivPDFHTML

Papers citing "Deeptime: a Python library for machine learning dynamical models from time series data"

25 / 25 papers shown
Title
Addressing Challenges in Time Series Forecasting: A Comprehensive Comparison of Machine Learning Techniques
Addressing Challenges in Time Series Forecasting: A Comprehensive Comparison of Machine Learning Techniques
Seyedeh Azadeh Fallah Mortezanejad
Ruochen Wang
AI4TS
65
0
0
26 Mar 2025
Predicting the Energy Landscape of Stochastic Dynamical System via Physics-informed Self-supervised Learning
Predicting the Energy Landscape of Stochastic Dynamical System via Physics-informed Self-supervised Learning
Ruikun Li
Huandong Wang
Qingmin Liao
Yong Li
36
0
0
24 Feb 2025
Structure Language Models for Protein Conformation Generation
Structure Language Models for Protein Conformation Generation
Jiarui Lu
Xiaoyin Chen
Stephen Zhewen Lu
Chence Shi
Hongyu Guo
Yoshua Bengio
J. Tang
DiffM
25
2
0
24 Oct 2024
Optimizing adaptive sampling via Policy Ranking
Optimizing adaptive sampling via Policy Ranking
Hassan Nadeem
Diwakar Shukla
18
0
0
20 Oct 2024
Flow Matching for Optimal Reaction Coordinates of Biomolecular System
Flow Matching for Optimal Reaction Coordinates of Biomolecular System
Mingyuan Zhang
Zhicheng Zhang
Yong Wang
Hao Wu
22
1
0
30 Aug 2024
Force-Guided Bridge Matching for Full-Atom Time-Coarsened Dynamics of
  Peptides
Force-Guided Bridge Matching for Full-Atom Time-Coarsened Dynamics of Peptides
Ziyang Yu
Wenbing Huang
Yang Liu
OOD
AI4CE
19
1
0
27 Aug 2024
Protein Conformation Generation via Force-Guided SE(3) Diffusion Models
Protein Conformation Generation via Force-Guided SE(3) Diffusion Models
Yan Wang
Lihao Wang
Yuning Shen
Yiqun Wang
Huizhuo Yuan
Yue Wu
Quanquan Gu
DiffM
19
9
0
21 Mar 2024
Fusing Neural and Physical: Augment Protein Conformation Sampling with
  Tractable Simulations
Fusing Neural and Physical: Augment Protein Conformation Sampling with Tractable Simulations
Jiarui Lu
Zuobai Zhang
Bozitao Zhong
Chence Shi
Jian Tang
AI4CE
16
1
0
16 Feb 2024
Latent Representation and Simulation of Markov Processes via Time-Lagged
  Information Bottleneck
Latent Representation and Simulation of Markov Processes via Time-Lagged Information Bottleneck
Marco Federici
Patrick Forré
Ryota Tomioka
Bastiaan S. Veeling
8
3
0
13 Sep 2023
Reaction coordinate flows for model reduction of molecular kinetics
Reaction coordinate flows for model reduction of molecular kinetics
Hao Wu
Frank Noé
12
9
0
11 Sep 2023
Learning noise-induced transitions by multi-scaling reservoir computing
Learning noise-induced transitions by multi-scaling reservoir computing
Zequn Lin
Zhaofan Lu
Zengru Di
Ying Tang
17
4
0
11 Sep 2023
PyKoopman: A Python Package for Data-Driven Approximation of the Koopman
  Operator
PyKoopman: A Python Package for Data-Driven Approximation of the Koopman Operator
Shaowu Pan
E. Kaiser
Brian M. de Silva
J. Nathan Kutz
Steven L. Brunton
6
8
0
22 Jun 2023
Str2Str: A Score-based Framework for Zero-shot Protein Conformation
  Sampling
Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling
Jiarui Lu
Bozitao Zhong
Zuobai Zhang
Jian Tang
14
24
0
05 Jun 2023
Implicit Transfer Operator Learning: Multiple Time-Resolution Surrogates
  for Molecular Dynamics
Implicit Transfer Operator Learning: Multiple Time-Resolution Surrogates for Molecular Dynamics
M. Schreiner
Ole Winther
Simon Olsson
OOD
AI4CE
27
13
0
29 May 2023
SimbaML: Connecting Mechanistic Models and Machine Learning with
  Augmented Data
SimbaML: Connecting Mechanistic Models and Machine Learning with Augmented Data
Maixmilian Kleissl
Lukas Drews
Benedict Heyder
Julian Zabbarov
Pascal Iversen
Simon Witzke
B. Renard
Katharina Baum
AI4CE
9
3
0
08 Apr 2023
Internal-Coordinate Density Modelling of Protein Structure: Covariance
  Matters
Internal-Coordinate Density Modelling of Protein Structure: Covariance Matters
Marloes Arts
J. Frellsen
Wouter Boomsma
21
0
0
27 Feb 2023
Two for One: Diffusion Models and Force Fields for Coarse-Grained
  Molecular Dynamics
Two for One: Diffusion Models and Force Fields for Coarse-Grained Molecular Dynamics
Marloes Arts
Victor Garcia Satorras
Chin-Wei Huang
Daniel Zuegner
Marco Federici
C. Clementi
Frank Noé
Robert Pinsler
Rianne van den Berg
DiffM
9
85
0
01 Feb 2023
Koopman-theoretic Approach for Identification of Exogenous Anomalies in
  Nonstationary Time-series Data
Koopman-theoretic Approach for Identification of Exogenous Anomalies in Nonstationary Time-series Data
Alex Troy Mallen
Christoph Keller
J. Nathan Kutz
AI4TS
11
0
0
18 Sep 2022
Building Robust Machine Learning Models for Small Chemical Science Data:
  The Case of Shear Viscosity
Building Robust Machine Learning Models for Small Chemical Science Data: The Case of Shear Viscosity
Nikhil V. S. Avula
S. K. Veesam
Sudarshan Behera
S. Balasubramanian
19
8
0
23 Aug 2022
Thermodynamics-inspired Explanations of Artificial Intelligence
Thermodynamics-inspired Explanations of Artificial Intelligence
S. Mehdi
P. Tiwary
AI4CE
8
15
0
27 Jun 2022
GraphVAMPNet, using graph neural networks and variational approach to
  markov processes for dynamical modeling of biomolecules
GraphVAMPNet, using graph neural networks and variational approach to markov processes for dynamical modeling of biomolecules
Mahdi Ghorbani
Samarjeet Prasad
Jeffery B. Klauda
B. Brooks
GNN
14
30
0
12 Jan 2022
The Past as a Stochastic Process
The Past as a Stochastic Process
David Wolpert
M. Price
Stefani A. Crabtree
Timothy A. Kohler
Jürgen Jost
James C. Evans
P. Stadler
Hajime Shimao
M. Laubichler
AI4TS
11
0
0
11 Dec 2021
Collective variable discovery in the age of machine learning: reality,
  hype and everything in between
Collective variable discovery in the age of machine learning: reality, hype and everything in between
S. Bhakat
AI4CE
14
24
0
06 Dec 2021
Time-lagged autoencoders: Deep learning of slow collective variables for
  molecular kinetics
Time-lagged autoencoders: Deep learning of slow collective variables for molecular kinetics
C. Wehmeyer
Frank Noé
AI4CE
BDL
106
355
0
30 Oct 2017
Estimation and uncertainty of reversible Markov models
Estimation and uncertainty of reversible Markov models
Benjamin Trendelkamp-Schroer
Hao Wu
Fabian Paul
Frank Noé
68
129
0
19 Jul 2015
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