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.…
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48 results for “coarse-grained model”
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.
Ensemble Learning of Coarse-Grained Molecular Dynamics Force Fields with a Kernel Approachphysics.comp-ph
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.
Data coarse graining can improve model performancecond-mat.stat-mech
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.
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.
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.
Coarse-Graining Auto-Encoders for Molecular Dynamicsphysics.chem-ph
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…
Embedded-physics machine learning for coarse-graining and collective variable discovery without datacs.LG
We present a novel learning framework that consistently embeds underlying physics while bypassing a significant drawback of most modern, data-driven coarse-grained approaches in the context of molecular dynamics (MD), i.e., the availability of big data. The generation of a sufficiently large training dataset poses a co…
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.
Coarse graining correlation matrices according to macrostructures: Financial markets as a paradigmq-fin.ST
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-Probability Paths Generates Effective Default Correlationq-fin.ST
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.
Refining Coarse-grained Spatial Data using Auxiliary Spatial Data Sets with Various Granularitiesstat.ML
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…
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.
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.
Temporal Coarse-Graining of Latent Default-Probability Paths Generates Effective Default Correlationq-fin.ST
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.
Predictive Coarse-Grainingstat.ML
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…
Operator Forces For Coarse-Grained Molecular Dynamicsphysics.chem-ph
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.
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…
Incorporating physical constraints in a deep probabilistic machine learning framework for coarse-graining dynamical systemsphysics.comp-ph
Data-based discovery of effective, coarse-grained (CG) models of high-dimensional dynamical systems presents a unique challenge in computational physics and particularly in the context of multiscale problems. The present paper offers a data-based, probablistic perspective that enables the quantification of predictive u…
We introduce a hierarchical architecture for video understanding that exploits the structure of real world actions by capturing targets at different levels of granularity. We design the model such that it first learns simpler coarse-grained tasks, and then moves on to learn more fine-grained targets. The model is train…
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.
We present an algorithm for supervised learning using tensor networks, employing a step of preprocessing the data by coarse-graining through a sequence of wavelet transformations. We represent these transformations as a set of tensor network layers identical to those in a multi-scale entanglement renormalization ansatz…
We discuss a Bayesian formulation to coarse-graining (CG) of PDEs where the coefficients (e.g. material parameters) exhibit random, fine scale variability. The direct solution to such problems requires grids that are small enough to resolve this fine scale variability which unavoidably requires the repeated solution of…
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…
When Big Data Fails! Relative success of adaptive agents using coarse-grained information to compete for limited resourcesphysics.soc-ph
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…
Temporal Coarse-Graining of Multi-Sector Default Count Data Generates Posterior-Implied Copulasq-fin.RM
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.
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…
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 …
Coarse-graining and Self-similarity of Price Fluctuationscond-mat.stat-mech
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…
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.
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.
On the generalization ability of coarse-grained molecular dynamics models for non-equilibrium processesphysics.comp-ph
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.
Introduce a thermodynamically informed, temperature-transferable MLCG framework for proteins.
problem Temperature transferability of MLCG models for proteins.
method Explicit decomposition of CG potential into energetic and entropic components.
result Reproduces temperature-dependent quantities like heat capacity.
Investment strategy due to the minimization of portfolio noise level by observations of coarse-grained entropycond-mat.stat-mech
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…
Physics-aware, deep probabilistic modeling of multiscale dynamics in the Small Data regimephysics.comp-ph
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).
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
Reduced models derived from agent-based systems using Koopman theory.
problem Time-consuming simulations of large agent-based systems.
method Koopman operator theory applied to simulation data.
result Derived reduced models match known analytical results.
The paper reduces the complexity of financial market correlation matrices to a 2x2 matrix.
problem Reducing the complexity of financial market correlation matrices for easier analysis.
method Sectorial coarse graining followed by averaging over blocks of stocks.
result Averaging over blocks of stocks results in a reduced matrix with specific properties.
Coarse-Graining Hamiltonian Systems Using WSINDyphysics.comp-ph
WSINDy identifies reduced Hamiltonian systems from particle interactions.
problem Coarse-graining Hamiltonian dynamics with approximate symmetries.
method WSINDy algorithm applied to Hamiltonian systems with timescale separation.
result WSINDy successfully identifies reduced Hamiltonian systems from noisy data.
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…
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.
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 …
Statistical (machine learning) tools for equation discovery require large amounts of data that are typically computer generated rather than experimentally observed. Multiscale modeling and stochastic simulations are two areas where learning on simulated data can lead to such discovery. In both, the data are generated w…
The paper develops a framework for abstracting causal models using category theory.
problem Difficulties in changing the variables used to describe a system, especially from fine-grained to coarse-grained.
method Introduces a category of interventional causal models and uses enriched category theory to prove compositionality properties.
result Compositionality of model transformations is established, with bounded errors for each step.
We propose a method based on finite mixture models for classifying a set of observations into number of different categories. In order to demonstrate the method, we show how the component densities for the mixture model can be derived by using the maximum entropy method in conjunction with conservation of Pythagorean m…
The ubiquitous deployment of monitoring devices in urban flow monitoring systems induces a significant cost for maintenance and operation. A technique is required to reduce the number of deployed devices, while preventing the degeneration of data accuracy and granularity. In this paper, we present an approach for infer…
Improved investment performance with fine-grained LLM tasks.
problem Abstract financial trading systems often overlook real-world workflow intricacies, leading to degraded performance.
method Proposes a multi-agent LLM trading framework that decomposes investment analysis into fine-grained tasks.
result Fine-grained task decomposition significantly improves risk-adjusted returns compared to coarse-grained designs.
Neural Coarse-Graining: Extracting slowly-varying latent degrees of freedom with neural networkscs.AI
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…