This study uses persistent homology to analyze complex transitional networks from time series data.
problem Lack of effective tools to summarize complex topology in transitional networks.
method Persistent homology from topological data analysis applied to coarse-grained state-space networks (CGSSN).
result CGSSN improves dynamic state detection and noise robustness compared to other methods.
Temporal coarse-graining of multi-sector default count data generates effective correlation matrices and rank copulas.
problem Explaining the difference in default dependence between monthly and annual aggregation.
method Dynamic low-rank state-space model with AR(1) latent credit-state factors.
result Effective correlation matrices and rank copulas are generated from monthly default count data.
Machine learning generates coarse-grained force fields for molecular dynamics.
problem Creating thermodynamically consistent coarse-grained models for larger systems.
method Hybrid architecture using graph neural networks to learn molecular features.
result Framework reproduces thermodynamics for small biomolecular systems.
Dynamical systems with large state-spaces are often expensive to thoroughly explore experimentally. Coarse-graining methods aim to define simpler systems which are more amenable to analysis and exploration; most current methods, however, focus on a priori state aggregation based on similarities in transition rates, whi…
The paper tackles physical constraints in probabilistic machine learning for CG models of high-dimensional systems.
problem Introducing physical constraints in probabilistic machine learning objectives for coarse-graining dynamical systems.
method Formulating coarse-graining process using probabilistic state-space model and accounting for constraints as virtual observables.
result Probabilistic inference tools can identify coarse-grained variables without needing a fine-to-coarse projection or time-derivatives.
The paper develops a physics-aware method for modeling multiscale dynamics with reduced data.
problem Discovering effective, lower-dimensional models for high-dimensional dynamical systems.
method Probabilistic deep neural networks incorporating physical constraints.
result The method reduces the need for extensive multiscale simulations (Small Data regime).
The combination of high-dimensionality and disparity of time scales encountered in many problems in computational physics has motivated the development of coarse-grained (CG) models. In this paper, we advocate the paradigm of data-driven discovery for extract- ing governing equations by employing fine-scale simulation …
GDML learns effective CG models from all-atom data.
problem Learning effective coarse-grained force fields efficiently.
method Ensemble learning with stratified sampling and GDML.
result GDML yields smaller free energy error than neural networks.
Graph neural network predicts optimal coarse-grained mapping operators.
problem Optimal coarse-grained mapping operators selection for molecular dynamics simulations.
method Graph Neural Network (DSGPM) trained on expert-annotated data.
result DSGPM outperforms state-of-the-art methods in graph segmentation.
This paper models default data to capture dynamic dependence across sectors.
problem Static models fail to explain monthly default dependence.
method Dynamic low-rank state-space model for monthly multi-sector default-count data.
result Effective correlation matrices and copulas are induced from monthly data.
Generative model learns spin-glass dynamics and properties.
problem Complex behavior of many-body systems in statistical physics and computer science.
method Self-supervised learning with normalizing flows.
result Key physical and computational properties of spin-glasses are learned.
Sparsity helps reduce the computational complexity of deep neural networks by skipping zeros. Taking advantage of sparsity is listed as a high priority in next generation DNN accelerators such as TPU. The structure of sparsity, i.e., the granularity of pruning, affects the efficiency of hardware accelerator design as w…
Tensor network architecture for classification and regression using wavelet transformations.
problem Efficiently performing classification and regression tasks on complex data.
method Tensor network layers based on MERA and MPS, with adaptive fine-graining.
result Adaptive fine-graining improves model performance without loss in accuracy.
MLP residual networks implement a selective coarse-graining procedure governed by the spectral structure of the input distribution.
problem Understanding the coarse-graining procedure in MLP residual networks
method Analyzing a pure MLP residual stack on synthetic Markov chain sequences
result MLP residual networks implement a selective coarse-graining procedure governed by the spectral structure of the input distribution
Extracts coarse-grained PDEs from microscopic simulations.
problem Discovering effective PDEs for macro-scale processes from microscopic data.
method Combining neural networks with equation-free numerics and data-driven approaches.
result Efficiently discovers macro-scale PDEs from microscopic simulations.
Atomistic or ab-initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time- and length-scales accessible with such computationally expensive simulations is the definition of coarse-grained molecular models.…
Data coarse graining improves model performance by filtering out less relevant features.
problem Lossy data transformations lose information but can improve model generalization.
method Data coarse graining schemes that systematically discard features based on relevance to the learning task.
result A 'high-pass' scheme helps models generalize better by filtering out less relevant features.
New framework embeds physics in coarse-grained models without big data.
problem Lack of big data and computational demand in data-driven coarse-graining.
method Proposes a novel objective based on reverse Kullback-Leibler divergence that incorporates physics in the form of force fields.
result Generative coarse-grained model predicts atomistic configurations and reveals physicochemical CVs.
Molecular dynamics simulations provide theoretical insight into the microscopic behavior of materials in condensed phase and, as a predictive tool, enable computational design of new compounds. However, because of the large temporal and spatial scales involved in thermodynamic and kinetic phenomena in materials, atomis…
Financial markets analyzed by reducing correlation matrix complexity.
problem Understanding complex financial market correlations.
method Coarse graining Pearson correlation matrices into Guhr matrices by market sectors.
result Significant reduction in the number of relevant variables.
Temporal coarse-graining of latent default paths explains effective correlation in corporate defaults.
problem Understanding effective default correlation in corporate defaults.
method Temporal coarse-graining of latent default-probability paths, applied to corporate default-count data.
result Temporal coarse-graining provides a scale-consistent baseline that improves identifiability and reduces over-allocation of long-horizon fluctuations.
CG-BGs combine flow-based models with PMFs to sample large systems efficiently.
problem Sampling equilibrium molecular configurations from the Boltzmann distribution is challenging.
method Coarse-grained Boltzmann Generators (CG-BGs) use flow-based models and learned PMFs for efficient sampling.
result CG-BGs provide a practical route for sampling larger molecular systems efficiently.
Although there has been a rapid development of practical applications, theoretical explanations of deep learning are in their infancy. Deep learning performs a sophisticated coarse graining. Since coarse graining is a key ingredient of the renormalization group (RG), RG may provide a useful theoretical framework direct…
DiAMoNDBack models protein backmapping from coarse-grained Cα traces.
problem Restoring all-atom details from coarse-grained protein representations.
method Autoregressive denoising diffusion model for residue-by-residue backmapping.
result Achieves state-of-the-art reconstruction performance in diverse applications.
Framework preserves emergent physics in non-equilibrium systems from particle trajectories.
problem Linking short spatiotemporal scales to emergent bulk physics in multiscale systems.
method Metriplectic bracket formalism for structure-preserving coarse-graining.
result Preservation of thermodynamic laws and conservation in machine-learned dynamics.
Temporal aggregation reveals latent default correlation from monthly data.
problem Understanding effective default correlation from monthly default data.
method Temporal coarse-graining of latent default-probability paths.
result Temporal coarse-graining improves identifiability and reduces over-allocation of long-horizon fluctuations.
New method uses normalizing flows to improve force fields for coarse-grained molecular dynamics.
problem Lack of reference atomistic forces makes force matching infeasible for MLCG force fields.
method Introduces noise-based kernels adapted to low-data regimes using normalizing flows.
result Flow-based kernels reduce local distortions while preserving global accuracy.
A new method learns state and proposal dynamics in state-space models using neural networks.
problem Inference in non-linear state-space models.
method StateMixNN method using neural networks for proposal and transition distributions.
result Significantly improved recovery of hidden state, especially in highly non-linear scenarios.
LSS learns molecular trajectories from MD data.
problem Limited integration time steps in MD simulations.
method Three deep learning networks for slow collective variables, dynamics, and configuration reconstruction.
result Generates ultra-long synthetic folding trajectories.
Predicts cryptocurrency prices with deep state-space model.
problem Predicting day-ahead crypto-currency prices.
method Proposes a deep state-space model combining state-space formulation and deep neural networks.
result The deep state-space model outperforms state-of-the-art and classical methods in accuracy.
We propose a probabilistic model for refining coarse-grained spatial data by utilizing auxiliary spatial data sets. Existing methods require that the spatial granularities of the auxiliary data sets are the same as the desired granularity of target data. The proposed model can effectively make use of auxiliary data set…
The paper analyzes variational autoencoders for state space models with risk bounds.
problem Analyzing the risk associated with variational autoencoders for state space models.
method Backward factorization of variational distributions to analyze excess risk, providing oracle inequalities and upper bounds.
result Explicit upper bounds on variational estimation error for state space models under strong mixing assumptions.
We present a loss function for neural networks that encompasses an idea of trivial versus non-trivial predictions, such that the network jointly determines its own prediction goals and learns to satisfy them. This permits the network to choose sub-sets of a problem which are most amenable to its abilities to focus on s…
Cellular regulatory dynamics is driven by large and intricate networks of interactions at the molecular scale, whose sheer size obfuscates understanding. In light of limited experimental data, many parameters of such dynamics are unknown, and thus models built on the detailed, mechanistic viewpoint overfit and are not …
We propose a new approach for analyzing price fluctuations in their strongly correlated regime ranging from minutes to months. This is done by employing a self-similarity assumption for the magnitude of coarse-grained price fluctuation or volatility. The existence of a Cramer function, the characteristic function for s…
Weakly-supervised learning is a paradigm for alleviating the scarcity of labeled data by leveraging lower-quality but larger-scale supervision signals. While existing work mainly focuses on utilizing a certain type of weak supervision, we present a probabilistic framework, learning from indirect observations, for learn…
Novel graph network learns hierarchical network structure.
problem Lack of information in hierarchical network topology.
method Hierarchical clustering for multiscale decomposition, graph convolutional layers.
result Competitive performance on citation network benchmark.
New method for efficient probabilistic deep state-space models.
problem Efficient inference for probabilistic deep state-space models.
method Deterministic inference algorithm for ProDSSM with neural network weights.
result Superior balance between predictive performance and computational budget.
Gaussian state space models have been used for decades as generative models of sequential data. They admit an intuitive probabilistic interpretation, have a simple functional form, and enjoy widespread adoption. We introduce a unified algorithm to efficiently learn a broad class of linear and non-linear state space mod…
Survey of weak form's role in equation learning, parameter estimation, and coarse graining.
problem Noise robustness, accuracy, and computational efficiency in weak form applications.
method Survey and recent developments in weak form versions of equation learning, parameter estimation, and coarse graining.
result Surprising noise robustness, accuracy, and computational efficiency in weak form applications.
This paper reviews deep learning methods for state space models.
problem Analyzing temporal dynamics in dynamical systems.
method Selective review of deep neural network approaches for state space models.
result Unified perspective on discrete and continuous time SSMs.
A new machine-learned CG model predicts protein structures efficiently.
problem Developing a universal, computationally efficient protein simulation model.
method Combining deep learning with all-atom protein simulations to create a transferable CG force field.
result The model predicts protein structures, intermediates, and fluctuations efficiently.
Improved CG force-field learning from all-atom data.
problem Training accurate coarse-grained models from all-atom simulations is challenging.
method Optimized force mapping to improve statistical efficiency of force-field learning.
result Substantially improved CG force-fields can be learned from the same simulation data.
The automated construction of coarse-grained models represents a pivotal component in computer simulation of physical systems and is a key enabler in various analysis and design tasks related to uncertainty quantification. Pertinent methods are severely inhibited by the high-dimension of the parametric input and the li…
We propose a data-driven, coarse-graining formulation in the context of equilibrium statistical mechanics. In contrast to existing techniques which are based on a fine-to-coarse map, we adopt the opposite strategy by prescribing a probabilistic coarse-to-fine map. This corresponds to a directed probabilistic model wher…
This work studies learning dynamics in SSMs, linking them to deep linear networks.
problem Lack of theoretical understanding of SSMs, especially in deep state spaces.
method Analyzes learning dynamics of linear SSMs, focusing on frequency domain, and establishes links to deep linear networks.
result Analytical solutions for SSM learning dynamics under mild assumptions, linking to deep linear networks.
The recent trend for acquiring big data assumes that possessing quantitatively more and qualitatively finer data necessarily provides an advantage that may be critical in competitive situations. Using a model complex adaptive system where agents compete for a limited resource using information coarse-grained to differe…
Using a recently developed method of noise level estimation that makes use of properties of the coarse grained-entropy we have analyzed the noise level for the Dow Jones index and a few stocks from the New York Stock Exchange. We have found that the noise level ranges from 40 to 80 percent of the signal variance. The c…