This review explores the use of machine learning in discovering collective variables for biomolecular dynamics.
problem Understanding the conformational dynamics and molecular recognition in biomolecules.
method Statistical analysis of high-dimensional spatiotemporal data generated from molecular dynamics simulations.
result Machine learning algorithms can be used to discover abstract collective variables that describe biomolecular dynamics.
Method learns dynamics of slow variables from stochastic data.
problem Modeling unknown multiscale stochastic systems with limited data.
method Data-driven approach to learn effective dynamics from bursts of observation data.
result Generative model accurately captures effective dynamics of slow variables.
This work extends identifiability analysis to sequential latent variable models, focusing on Switching Dynamical Systems.
problem Identifying latent variables in sequential data models.
method Proved identifiability of Markov Switching Models and established conditions for Switching Dynamical Systems.
result Identifiability of latent variables and non-linear mappings in Switching Dynamical Systems up to affine transformations.
Improved robust latent variable estimation for neural dynamics.
problem Inconsistent results due to noise and nonlinearity in existing models.
method Probabilistic approach to latent variable estimation in decomposed models.
result More accurate latent variable inference in nonlinear systems with diverse noise conditions.
New method models complex dynamics using a base variable.
problem Modeling complex high-frequency dynamics from time series.
method Constructing a joint model with a base variable and a target variable.
result Successfully models chaotic behavior and reconstructs statistical properties.
Study identifies latent variables and models from spacecraft data.
problem Learning reliable models from spacecraft data with complex relationships.
method Inductive bias inspired by controllable canonical forms for sparse, input-dependent latent variables.
result Identifies latent variables up to scaling and determines dynamic models up to transformations for linear and affine systems.
Paper tackles dynamic behavior of variable topology mechanisms, presenting new transition conditions.
problem Dynamic behavior of mechanisms with changing kinematic topology.
method Presented new transition conditions for variable topology mechanisms using projected motion equations and Voronets equations.
result Results show the dynamic behavior of joint locking in 3R and 6DOF mechanisms.
Proposes a new signal model for high-dimensional, small-sample-size data.
problem Signal detection in high-dimensional, small-sample-size datasets.
method Intrinsic signal model based on dynamical system assumption.
result Taguchi method effectively detects signals in the proposed model.
Optimally explores dynamical systems with varying properties using context inference.
problem Learning dynamics models for systems with varying properties.
method Formulates dynamics models as stochastic processes conditioned on a latent context variable inferred from system transitions. Uses probabilistic formulation to compute optimal action sequences for exploration.
result Demonstrates effectiveness of the method on non-linear toy-problems and reinforcement learning environments.
A new model captures variability in time series data.
problem Capturing high variability in time series data.
method Temporal latent variables and dynamic weight modifications.
result Demonstrated efficacy on various sequential data.
ISOKANN learns collective variables and effective dynamics for metastable transitions.
problem Understanding metastable transitions in complex molecular systems.
method Integrates Koopman operators with neural networks to extract CVs and effective dynamics.
result Reconstructs coarse-grained kinetics and reproduces transition times across barriers.
Model infers latent variables in sparse coding models using Langevin dynamics.
problem Sampling posterior distribution in sparse coding models.
method Langevin dynamics for inference and simultaneous learning of parameters.
result Langevin dynamics efficiently sample from 'L0 sparse' posterior distribution.
New CGMD model predicts non-equilibrium processes better than existing methods.
problem Inconsistency in conditional distribution of unresolved variables.
method Time-lagged independent component analysis to minimize entropy contribution of unresolved variables.
result The model's generalization ability for non-equilibrium processes is significantly improved.
Framework learns image dynamics between time steps using latent variables.
problem Challenges in capturing evolving image patterns and temporal information.
method Estimates intermediary image stages using a physical latent variable model.
result Demonstrates robustness and effectiveness in geoscientific imagery.
A new method combines predictors and their lags using supervised PCA for dynamic forecasting.
problem Dynamic forecasting with many predictors.
method Supervised PCA with re-scaling and penalized methods.
result The method outperforms traditional PCA and diffusion-index approaches in prediction.
In this note, we study the dynamics and associated zeta functions of conformally compact manifolds with variable negative sectional curvatures. We begin with a discussion of a larger class of manifolds known as convex co-compact manifolds with variable negative curvature. Applying results from dynamics on these spaces,…
A hybrid model for Bayesian optimization handles mixed variables using MCTS for categorical and GP for continuous.
problem Optimizing functions with mixed variable types (continuous, integer, categorical).
method Merges MCTS for categorical and GP for continuous variables, integrates UCTS search strategy, and dynamically selects kernels.
result Hybrid models outperform traditional methods in Bayesian optimization.
Two Bayesian optimization methods tackle dynamic design spaces with mixed variables.
problem Optimizing complex systems with varying numbers and types of variables and constraints.
method Two Bayesian optimization approaches: budget allocation and kernel function.
result Both methods converge faster and more consistently than standard approaches.
Representation learning over graph structured data has been mostly studied in static graph settings while efforts for modeling dynamic graphs are still scant. In this paper, we develop a novel hierarchical variational model that introduces additional latent random variables to jointly model the hidden states of a graph…
Study optimal adjustment sets for causal policies with hidden variables.
problem Estimating dynamic treatment regimes with hidden variables.
method Developed criteria for graphs without hidden variables to compare estimators, extended to dynamic policies and hidden variables.
result Existence and computation of optimal minimal and globally optimal adjustment sets.
A new method reduces high-dimensional state space for dynamic choice models.
problem Estimation of dynamic discrete choice models is computationally intensive and infeasible in high-dimensional settings.
method Recursive partitioning algorithm to reduce dimensionality of high-dimensional state space.
result Our method reduces estimation bias and makes estimation feasible.
A new algorithm uses IVs to learn optimal policies from observational data.
problem Learning optimal policies from unobserved variable confounded data.
method IV-aided Value Iteration (IVVI) algorithm based on conditional moment restrictions.
result First provably efficient algorithm for instrument-aided offline RL.
New metric improves latent dynamics inference from neural data.
problem Limitations of co-smoothing in predicting latent dynamics.
method Few-shot co-smoothing to assess latent dynamics.
result High co-smoothing models often have extraneous dynamics, which few-shot co-smoothing detects.
Study analyzes Bayesian inference algorithms using dynamical functional approach.
problem Analysis of approximate inference algorithms for large Gaussian latent variable models.
method Dynamical functional approach to model nontrivial dependencies and obtain exact effective stochastic process.
result Closed-form expressions for the rate of convergence are derived and validated.
This paper examines how Higher-Order Langevin Dynamics reduces memorization in diffusion models.
problem Memorization of training samples in diffusion models, violating copyright and privacy.
method Introduces Higher-Order Langevin Dynamics (HOLD) to regularize diffusion model trajectories.
result The dynamics of the data variable in HOLD are governed by a low-pass-filtered version of the learned score function, with smoothness increasing with model order.
Neural population activity often exhibits rich variability and temporal structure. This variability is thought to arise from single-neuron stochasticity, neural dynamics on short time-scales, as well as from modulations of neural firing properties on long time-scales, often referred to as "non-stationarity". To better …
For recurrent neural networks trained on time series with target and exogenous variables, in addition to accurate prediction, it is also desired to provide interpretable insights into the data. In this paper, we explore the structure of LSTM recurrent neural networks to learn variable-wise hidden states, with the aim t…
Paper defends diffusion models from membership inference attacks using Langevin dynamics.
problem Defending diffusion models against membership inference attacks.
method Uses critically-damped higher-order Langevin dynamics with auxiliary variables.
result Demonstrates improved resistance to membership inference attacks through theoretical investigation and validation.
Network analysis improves stock return forecasting.
problem Improving stock return forecasting using network properties.
method Network analysis of stock return correlations, using individual and global properties of stocks.
result 50% improvement in R2 score for long-term stock returns forecasting, 3% for short-term.
AR model forecasts partially observed dynamical time series by estimating evolution function and imputing missing variables.
problem Forecasting dynamical time series with missing variables.
method Autoregressive with slack time series (ARS) model.
result ARS model forecasts future time series with time-invariant and linear assumptions.
Fourier Neural Operators accurately predict dynamics of high-dimensional ionic models.
problem Approximating stiff, multiscale ionic models using neural networks.
method Fourier Neural Operators for learning dynamics of high-dimensional ionic models.
result Fourier Neural Operators can accurately predict dynamics of high-dimensional ionic models.
A new method selects variables efficiently for fast and accurate dynamic system identification.
problem Efficiently selecting variables for scalable Gaussian processes.
method Forward variable selection using Karhunen-Loève decomposition and Gibbs sampling.
result Method yields competitive accuracies and inference times for dynamic systems.
Paper proposes a fast method for learning deep latent variable models.
problem Learning deep generative models with hierarchical latent variables.
method Noise initialized short run MCMC with variational optimization of step size.
result The method outperforms VAE in reconstruction and synthesis quality.
A novel Bayesian method for dynamic sparsity in Gaussian dynamic linear regression.
problem Variable selection and shrinkage in time-varying regression models.
method Time-varying sparsity via Markov switching priors for coefficients' variances, extending spike-and-slab priors.
result Induces smoothness or shrinkage towards zero at each time point, leading to improved model performance.
Develops methods to identify and estimate causal effects with instrumental variables.
problem Causal inference with confounded treatment assignment and unobserved variables.
method General nonparametric causal framework, debiased machine learning, semiparametric theory.
result Consistent and asymptotically normal estimators for average treatment effect.
We propose an efficient inference method for switching nonlinear dynamical systems. The key idea is to learn an inference network which can be used as a proposal distribution for the continuous latent variables, while performing exact marginalization of the discrete latent variables. This allows us to use the reparamet…
A new method uses higher-order Langevin dynamics with critical damping for better generative modeling.
problem Improving generative models using Langevin dynamics with auxiliary variables.
method Introducing higher-order Langevin dynamics with critical damping, providing closed-form solutions.
result Improved generative models with better performance as measured by FID metric.
Dimensionality reduction is ubiquitous in analysis of complex dynamics. The conventional dimensionality reduction techniques, however, focus on reproducing the underlying configuration space, rather than the dynamics itself. The constructed low-dimensional space does not provide complete and accurate description of the…
Extends integrability to cosymplectic manifolds.
problem Integrability of Hamiltonian systems on cosymplectic manifolds.
method Extended Arnold-Liouville and noncommutative integrability to cosymplectic manifolds, proved a variant of non-commutative integrability for specific fields, constructed action-angle variables.
result Variant of non-commutative integrability for evaluation and Reeb vector fields on cosymplectic manifolds.
Langevin autoencoders improve deep latent variable models with efficient posterior sampling.
problem Efficient posterior sampling in deep latent variable models using MCMC.
method Amortized Langevin dynamics (ALD) replaces datapoint-wise sampling with encoder updates.
result ALD is valid as an MCMC algorithm with the target posterior as a stationary distribution.
We introduce the variational filtering EM algorithm, a simple, general-purpose method for performing variational inference in dynamical latent variable models using information from only past and present variables, i.e. filtering. The algorithm is derived from the variational objective in the filtering setting and cons…
New model captures state-dependent variability in partially observed systems.
problem Structured stochasticity not captured by constant-variance models.
method State-coupled stochastic volatility framework with particle expectation-maximization.
result Model consistently reduces recovery bias under partial observation.
The Dynamical Gaussian Process Latent Variable Models provide an elegant non-parametric framework for learning the low dimensional representations of the high-dimensional time-series. Real world observational studies, however, are often ill-conditioned: the observations can be noisy, not assuming the luxury of relative…
Framework LiLY recovers latent causal variables from time-series data under distribution shifts.
problem Learning and correcting models under unknown distribution shifts in time-series data.
method LiLY framework that recovers latent causal variables and identifies their relations from temporal data under different distribution shifts.
result The framework reliably identifies time-delayed latent causal influences from observed variables under different distribution changes.
We propose a dynamic network model where two mechanisms control the probability of a link between two nodes: (i) the existence or absence of this link in the past, and (ii) node-specific latent variables (dynamic fitnesses) describing the propensity of each node to create links. Assuming a Markov dynamics for both mech…
New model preserves symmetry in multivariate time series, improving performance.
problem Implicit ordering in MTS models violates inherent exchangeability.
method Permutation-equivariant 2D state space model with canonical architecture.
result Eliminates sequential dependency chains and simplifies stability analysis.
We propose a new approach for properly analyzing stochastic time series by mapping the dynamics of time series fluctuations onto a suitable nonequilibrium surface-growth problem. In this framework, the fluctuation sampling time interval plays the role of time variable, whereas the physical time is treated as the analog…
In this paper we develop a general conceptual approach to the problem of existence of action-angle variables for dynamical systems, which establishes and uses the fundamental conservation property of associated torus actions: anything which is preserved by the system is also preserved by the associated torus actions. T…