One essential problem in quantifying the collective behaviors of molecular systems lies in the accurate construction of free energy surfaces (FESs). The main challenges arise from the prevalence of energy barriers and the high dimensionality. Existing approaches are often based on sophisticated enhanced sampling methods to establish efficient exploration of the full-phase space. On the other hand, the collection of optimal sample points for the numerical approximation of FESs remains largely under-explored, where the discretization error could become dominant for systems with a large number of collective variables (CVs). We propose a consensus sampling-based approach by reformulating the construction as a minimax problem which simultaneously optimizes the function representation and the training set. In particular, the maximization step establishes a stochastic interacting particle system to achieve the adaptive sampling of the max-residue regime by modulating the exploitation of the Laplace approximation of the current loss function and the exploration of the uncharted phase space; the minimization step updates the FES approximation with the new training set. By iteratively solving the minimax problem, the present method essentially achieves an adversarial learning of the FESs with unified tasks for both phase space exploration and posterior error-enhanced sampling. We demonstrate the method by constructing the FESs of molecular systems with a number of CVs up to 30.
相關內容
We study the complexity (that is, the weight of the multiplication table) of the elliptic normal bases introduced by Couveignes and Lercier. We give an upper bound on the complexity of these elliptic normal bases, and we analyze the weight of some special vectors related to the multiplication table of those bases. This analysis leads us to some perspectives on the search for low complexity normal bases from elliptic periods.
We establish finite-sample guarantees for efficient proper learning of bounded-degree polytrees, a rich class of high-dimensional probability distributions and a subclass of Bayesian networks, a widely-studied type of graphical model. Recently, Bhattacharyya et al. (2021) obtained finite-sample guarantees for recovering tree-structured Bayesian networks, i.e., 1-polytrees. We extend their results by providing an efficient algorithm which learns $d$-polytrees in polynomial time and sample complexity for any bounded $d$ when the underlying undirected graph (skeleton) is known. We complement our algorithm with an information-theoretic sample complexity lower bound, showing that the dependence on the dimension and target accuracy parameters are nearly tight.
We study the existence and uniqueness of Lp-bounded mild solutions for a class ofsemilinear stochastic evolutions equations driven by a real L\'evy processes withoutGaussian component not square integrable for instance the stable process through atruncation method by separating the big and small jumps together with the classicaland simple Banach fixed point theorem ; under local Lipschitz, Holder, linear growthconditions on the coefficients.
This paper introduces a new series of methods which combine modal decomposition algorithms, such as singular value decomposition and high-order singular value decomposition, and deep learning architectures to repair, enhance, and increase the quality and precision of numerical and experimental data. A combination of two- and three-dimensional, numerical and experimental dasasets are used to demonstrate the reconstruction capacity of the presented methods, showing that these methods can be used to reconstruct any type of dataset, showing outstanding results when applied to highly complex data, which is noisy. The combination of benefits of these techniques results in a series of data-driven methods which are capable of repairing and/or enhancing the resolution of a dataset by identifying the underlying physics that define the data, which is incomplete or under-resolved, filtering any existing noise. These methods and the Python codes are included in the first release of ModelFLOWs-app.
We study propositional proof systems with inference rules that formalize restricted versions of the ability to make assumptions that hold without loss of generality, commonly used informally to shorten proofs. Each system we study is built on resolution. They are called BC${}^-$, RAT${}^-$, SBC${}^-$, and GER${}^-$, denoting respectively blocked clauses, resolution asymmetric tautologies, set-blocked clauses, and generalized extended resolution - all "without new variables." They may be viewed as weak versions of extended resolution (ER) since they are defined by first generalizing the extension rule and then taking away the ability to introduce new variables. Except for SBC${}^-$, they are known to be strictly between resolution and extended resolution. Several separations between these systems were proved earlier by exploiting the fact that they effectively simulate ER. We answer the questions left open: We prove exponential lower bounds for SBC${}^-$ proofs of a binary encoding of the pigeonhole principle, which separates ER from SBC${}^-$. Using this new separation, we prove that both RAT${}^-$ and GER${}^-$ are exponentially separated from SBC${}^-$. This completes the picture of their relative strengths.
Comparisons of frequency distributions often invoke the concept of shift to describe directional changes in properties such as the mean. In the present study, we sought to define shift as a property in and of itself. Specifically, we define distributional shift (DS) as the concentration of frequencies away from the discrete class having the greatest value (e.g., the right-most bin of a histogram). We derive a measure of DS using the normalized sum of exponentiated cumulative frequencies. We then define relative distributional shift (RDS) as the difference in DS between two distributions, revealing the magnitude and direction by which one distribution is concentrated to lesser or greater discrete classes relative to another. We find that RDS is highly related to popular measures that, while based on the comparison of frequency distributions, do not explicitly consider shift. While RDS provides a useful complement to other comparative measures, DS allows shift to be quantified as a property of individual distributions, similar in concept to a statistical moment.
Dynamical systems across the sciences, from electrical circuits to ecological networks, undergo qualitative and often catastrophic changes in behavior, called bifurcations, when their underlying parameters cross a threshold. Existing methods predict oncoming catastrophes in individual systems but are primarily time-series-based and struggle both to categorize qualitative dynamical regimes across diverse systems and to generalize to real data. To address this challenge, we propose a data-driven, physically-informed deep-learning framework for classifying dynamical regimes and characterizing bifurcation boundaries based on the extraction of topologically invariant features. We focus on the paradigmatic case of the supercritical Hopf bifurcation, which is used to model periodic dynamics across a wide range of applications. Our convolutional attention method is trained with data augmentations that encourage the learning of topological invariants which can be used to detect bifurcation boundaries in unseen systems and to design models of biological systems like oscillatory gene regulatory networks. We further demonstrate our method's use in analyzing real data by recovering distinct proliferation and differentiation dynamics along pancreatic endocrinogenesis trajectory in gene expression space based on single-cell data. Our method provides valuable insights into the qualitative, long-term behavior of a wide range of dynamical systems, and can detect bifurcations or catastrophic transitions in large-scale physical and biological systems.
We generalize the Poisson limit theorem to binary functions of random objects whose law is invariant under the action of an amenable group. Examples include stationary random fields, exchangeable sequences, and exchangeable graphs. A celebrated result of E. Lindenstrauss shows that normalized sums over certain increasing subsets of such groups approximate expectations. Our results clarify that the corresponding unnormalized sums of binary statistics are asymptotically Poisson, provided suitable mixing conditions hold. They extend further to randomly subsampled sums and also show that strict invariance of the distribution is not needed if the requisite mixing condition defined by the group holds. We illustrate the results with applications to random fields, Cayley graphs, and Poisson processes on groups.
We study discretizations of fractional fully nonlinear equations by powers of discrete Laplacians. Our problems are parabolic and of order $\sigma\in(0,2)$ since they involve fractional Laplace operators $(-\Delta)^{\sigma/2}$. They arise e.g.~in control and game theory as dynamic programming equations, and solutions are non-smooth in general and should be interpreted as viscosity solutions. Our approximations are realized as finite-difference quadrature approximations and are 2nd order accurate for all values of $\sigma$. The accuracy of previous approximations depend on $\sigma$ and are worse when $\sigma$ is close to $2$. We show that the schemes are monotone, consistent, $L^\infty$-stable, and convergent using a priori estimates, viscosity solutions theory, and the method of half-relaxed limits. We present several numerical examples.
The structured $\varepsilon$-stability radius is introduced as a quantity to assess the robustness of transient bounds of solutions to linear differential equations under structured perturbations of the matrix. This applies to general linear structures such as complex or real matrices with a given sparsity pattern or with restricted range and corange, or special classes such as Toeplitz matrices. The notion conceptually combines unstructured and structured pseudospectra in a joint pseudospectrum, allowing for the use of resolvent bounds as with unstructured pseudospectra and for structured perturbations as with structured pseudospectra. We propose and study an algorithm for computing the structured $\varepsilon$-stability radius. This algorithm solves eigenvalue optimization problems via suitably discretized rank-1 matrix differential equations that originate from a gradient system. The proposed algorithm has essentially the same computational cost as the known rank-1 algorithms for computing unstructured and structured stability radii. Numerical experiments illustrate the behavior of the algorithm.
小貼士
登錄享
相關主題
注冊地址： 北京市海淀區羊坊店路18號2幢3層301-191