1. Abrupt environmental changes can lead to evolutionary shifts in not only mean (optimal value), but also variance of descendants in trait evolution. There are some methods to detect shifts in optimal value but few studies consider shifts in variance. 2. We use a multi-optima and multi-variance OU process model to describe the trait evolution process with shifts in both optimal value and variance and provide analysis of how the covariance between species changes when shifts in variance occur along the path. 3. We propose a new method to detect the shifts in both variance and optimal values based on minimizing the loss function with L1 penalty. We implement our method in a new R package, ShiVa (Detection of evolutionary shifts in variance). 4. We conduct simulations to compare our method with the two methods considering only shifts in optimal values (l1ou; PhylogeneticEM). Our method shows strength in predictive ability and includes far fewer false positive shifts in optimal value compared to other methods when shifts in variance actually exist. When there are only shifts in optimal value, our method performs similarly to other methods. We applied our method to the cordylid data, ShiVa outperformed l1ou and phyloEM, exhibiting the highest log-likelihood and lowest BIC.
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Non-Hermitian topological phases can produce some remarkable properties, compared with their Hermitian counterpart, such as the breakdown of conventional bulk-boundary correspondence and the non-Hermitian topological edge mode. Here, we introduce several algorithms with multi-layer perceptron (MLP), and convolutional neural network (CNN) in the field of deep learning, to predict the winding of eigenvalues non-Hermitian Hamiltonians. Subsequently, we use the smallest module of the periodic circuit as one unit to construct high-dimensional circuit data features. Further, we use the Dense Convolutional Network (DenseNet), a type of convolutional neural network that utilizes dense connections between layers to design a non-Hermitian topolectrical Chern circuit, as the DenseNet algorithm is more suitable for processing high-dimensional data. Our results demonstrate the effectiveness of the deep learning network in capturing the global topological characteristics of a non-Hermitian system based on training data.
By interpreting planar polynomial curves as complex-valued functions of a real parameter, an inner product, norm, metric function, and the notion of orthogonality may be defined for such curves. This approach is applied to the complex pre-image polynomials that generate planar Pythagorean-hodograph (PH) curves, to facilitate the implementation of bounded modifications of them that preserve their PH nature. The problems of bounded modifications under the constraint of fixed curve end points and end tangent directions, and of increasing the arc length of a PH curve by a prescribed amount, are also addressed.
The broad class of multivariate unified skew-normal (SUN) distributions has been recently shown to possess fundamental conjugacy properties. When used as priors for the vector of parameters in general probit, tobit, and multinomial probit models, these distributions yield posteriors that still belong to the SUN family. Although such a core result has led to important advancements in Bayesian inference and computation, its applicability beyond likelihoods associated with fully-observed, discretized, or censored realizations from multivariate Gaussian models remains yet unexplored. This article covers such an important gap by proving that the wider family of multivariate unified skew-elliptical (SUE) distributions, which extends SUNs to more general perturbations of elliptical densities, guarantees conjugacy for broader classes of models, beyond those relying on fully-observed, discretized or censored Gaussians. Such a result leverages the closure under linear combinations, conditioning and marginalization of SUE to prove that such a family is conjugate to the likelihood induced by general multivariate regression models for fully-observed, censored or dichotomized realizations from skew-elliptical distributions. This advancement substantially enlarges the set of models that enable conjugate Bayesian inference to general formulations arising from elliptical and skew-elliptical families, including the multivariate Student's t and skew-t, among others.
Sine-skewed circular distributions are identifiable and have easily-computable trigonometric moments and a simple random number generation algorithm, whereas they are known to have relatively low levels of asymmetry. This study proposes a new family of circular distributions that can be skewed more significantly than that of existing models. It is shown that a subfamily of the proposed distributions is identifiable with respect to parameters and all distributions in the subfamily have explicit trigonometric moments and a simple random number generation algorithm. The maximum likelihood estimation for model parameters is considered and its finite sample performances are investigated by numerical simulations. Some real data applications are illustrated for practical purposes.
Covariance and Hessian matrices have been analyzed separately in the literature for classification problems. However, integrating these matrices has the potential to enhance their combined power in improving classification performance. We present a novel approach that combines the eigenanalysis of a covariance matrix evaluated on a training set with a Hessian matrix evaluated on a deep learning model to achieve optimal class separability in binary classification tasks. Our approach is substantiated by formal proofs that establish its capability to maximize between-class mean distance and minimize within-class variances. By projecting data into the combined space of the most relevant eigendirections from both matrices, we achieve optimal class separability as per the linear discriminant analysis (LDA) criteria. Empirical validation across neural and health datasets consistently supports our theoretical framework and demonstrates that our method outperforms established methods. Our method stands out by addressing both LDA criteria, unlike PCA and the Hessian method, which predominantly emphasize one criterion each. This comprehensive approach captures intricate patterns and relationships, enhancing classification performance. Furthermore, through the utilization of both LDA criteria, our method outperforms LDA itself by leveraging higher-dimensional feature spaces, in accordance with Cover's theorem, which favors linear separability in higher dimensions. Our method also surpasses kernel-based methods and manifold learning techniques in performance. Additionally, our approach sheds light on complex DNN decision-making, rendering them comprehensible within a 2D space.
It is well-known that one can construct solutions to the nonlocal Cahn-Hilliard equation with singular potentials via Yosida approximation with parameter $\lambda \to 0$. The usual method is based on compactness arguments and does not provide any rate of convergence. Here, we fill the gap and we obtain an explicit convergence rate $\sqrt{\lambda}$. The proof is based on the theory of maximal monotone operators and an observation that the nonlocal operator is of Hilbert-Schmidt type. Our estimate can provide convergence result for the Galerkin methods where the parameter $\lambda$ could be linked to the discretization parameters, yielding appropriate error estimates.
Motivated by the important statistical role of sparsity, the paper uncovers four reparametrizations for covariance matrices in which sparsity is associated with conditional independence graphs in a notional Gaussian model. The intimate relationship between the Iwasawa decomposition of the general linear group and the open cone of positive definite matrices allows a unifying perspective. Specifically, the positive definite cone can be reconstructed without loss or redundancy from the exponential map applied to four Lie subalgebras determined by the Iwasawa decomposition of the general linear group. This accords geometric interpretations to the reparametrizations and the corresponding notion of sparsity. Conditions that ensure legitimacy of the reparametrizations for statistical models are identified. While the focus of this work is on understanding population-level structure, there are strong methodological implications. In particular, since the population-level sparsity manifests in a vector space, imposition of sparsity on relevant sample quantities produces a covariance estimate that respects the positive definite cone constraint.
We present an information-theoretic lower bound for the problem of parameter estimation with time-uniform coverage guarantees. Via a new a reduction to sequential testing, we obtain stronger lower bounds that capture the hardness of the time-uniform setting. In the case of location model estimation, logistic regression, and exponential family models, our $\Omega(\sqrt{n^{-1}\log \log n})$ lower bound is sharp to within constant factors in typical settings.
Since its introduction in 2011, the partial information decomposition (PID) has triggered an explosion of interest in the field of multivariate information theory and the study of emergent, higher-order ("synergistic") interactions in complex systems. Despite its power, however, the PID has a number of limitations that restrict its general applicability: it scales poorly with system size and the standard approach to decomposition hinges on a definition of "redundancy", leaving synergy only vaguely defined as "that information not redundant." Other heuristic measures, such as the O-information, have been introduced, although these measures typically only provided a summary statistic of redundancy/synergy dominance, rather than direct insight into the synergy itself. To address this issue, we present an alternative decomposition that is synergy-first, scales much more gracefully than the PID, and has a straightforward interpretation. Our approach defines synergy as that information in a set that would be lost following the minimally invasive perturbation on any single element. By generalizing this idea to sets of elements, we construct a totally ordered "backbone" of partial synergy atoms that sweeps systems scales. Our approach starts with entropy, but can be generalized to the Kullback-Leibler divergence, and by extension, to the total correlation and the single-target mutual information. Finally, we show that this approach can be used to decompose higher-order interactions beyond just information theory: we demonstrate this by showing how synergistic combinations of pairwise edges in a complex network supports signal communicability and global integration. We conclude by discussing how this perspective on synergistic structure (information-based or otherwise) can deepen our understanding of part-whole relationships in complex systems.
We determine the computational power of isometric tensor network states (isoTNS), a variational ansatz originally developed to numerically find and compute properties of gapped ground states and topological states in two dimensions. By mapping 2D isoTNS to 1+1D unitary quantum circuits, we find that computing local expectation values in isoTNS is $\textsf{BQP}$-complete. We then introduce injective isoTNS, which are those isoTNS that are the unique ground states of frustration-free Hamiltonians, and which are characterized by an injectivity parameter $\delta\in(0,1/D]$, where $D$ is the bond dimension of the isoTNS. We show that injectivity necessarily adds depolarizing noise to the circuit at a rate $\eta=\delta^2D^2$. We show that weakly injective isoTNS (small $\delta$) are still $\textsf{BQP}$-complete, but that there exists an efficient classical algorithm to compute local expectation values in strongly injective isoTNS ($\eta\geq0.41$). Sampling from isoTNS corresponds to monitored quantum dynamics and we exhibit a family of isoTNS that undergo a phase transition from a hard regime to an easy phase where the monitored circuit can be sampled efficiently. Our results can be used to design provable algorithms to contract isoTNS. Our mapping between ground states of certain frustration-free Hamiltonians to open circuit dynamics in one dimension fewer may be of independent interest.
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