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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.

This paper develops a notion of geometric quantiles on Hadamard spaces, also known as global non-positive curvature spaces. After providing some definitions and basic properties, including scaled isometry equivariance and a necessary condition on the gradient of the quantile loss function at quantiles on Hadamard manifolds, we investigate asymptotic properties of sample quantiles on Hadamard manifolds, such as strong consistency and joint asymptotic normality. We provide a detailed description of how to compute quantiles using a gradient descent algorithm in hyperbolic space and, in particular, an explicit formula for the gradient of the quantile loss function, along with experiments using simulated and real single-cell RNA sequencing data.

To plan and optimize energy storage demands that account for Li-ion battery aging dynamics, techniques need to be developed to diagnose battery internal states accurately and rapidly. This study seeks to reduce the computational resources needed to determine a battery's internal states by replacing physics-based Li-ion battery models -- such as the single-particle model (SPM) and the pseudo-2D (P2D) model -- with a physics-informed neural network (PINN) surrogate. The surrogate model makes high-throughput techniques, such as Bayesian calibration, tractable to determine battery internal parameters from voltage responses. This manuscript is the first of a two-part series that introduces PINN surrogates of Li-ion battery models for parameter inference (i.e., state-of-health diagnostics). In this first part, a method is presented for constructing a PINN surrogate of the SPM. A multi-fidelity hierarchical training, where several neural nets are trained with multiple physics-loss fidelities is shown to significantly improve the surrogate accuracy when only training on the governing equation residuals. The implementation is made available in a companion repository (//github.com/NREL/pinnstripes). The techniques used to develop a PINN surrogate of the SPM are extended in Part II for the PINN surrogate for the P2D battery model, and explore the Bayesian calibration capabilities of both surrogates.

Despite numerous years of research into the merits and trade-offs of various model selection criteria, obtaining robust results that elucidate the behavior of cross-validation remains a challenging endeavor. In this paper, we highlight the inherent limitations of cross-validation when employed to discern the structure of a Gaussian graphical model. We provide finite-sample bounds on the probability that the Lasso estimator for the neighborhood of a node within a Gaussian graphical model, optimized using a prediction oracle, misidentifies the neighborhood. Our results pertain to both undirected and directed acyclic graphs, encompassing general, sparse covariance structures. To support our theoretical findings, we conduct an empirical investigation of this inconsistency by contrasting our outcomes with other commonly used information criteria through an extensive simulation study. Given that many algorithms designed to learn the structure of graphical models require hyperparameter selection, the precise calibration of this hyperparameter is paramount for accurately estimating the inherent structure. Consequently, our observations shed light on this widely recognized practical challenge.

We prove the convergence of meshfree method for solving the elliptic Monge-Ampere equation with Dirichlet boundary on the bounded domain. L2 error is obtained based on the kernel-based trial spaces generated by the compactly supported radial basis functions. We obtain the convergence result when the testing discretization is finer than the trial discretization. The convergence rate depend on the regularity of the solution, the smoothness of the computing domain, and the approximation of scaled kernel-based spaces. The presented convergence theory covers a wide range of kernel-based trial spaces including stationary approximation and non-stationary approximation. An extension to non-Dirichlet boundary condition is in a forthcoming paper.

signSGD is popular in nonconvex optimization due to its communication efficiency. Yet, existing analyses of signSGD rely on assuming that data are sampled with replacement in each iteration, contradicting the practical implementation where data are randomly reshuffled and sequentially fed into the algorithm. We bridge this gap by proving the first convergence result of signSGD with random reshuffling (SignRR) for nonconvex optimization. Given the dataset size $n$, the number of epochs of data passes $T$, and the variance bound of a stochastic gradient $\sigma^2$, we show that SignRR has the same convergence rate $O(\log(nT)/\sqrt{nT} + \|\sigma\|_1)$ as signSGD \citep{bernstein2018signsgd}. We then present SignRVR and SignRVM, which leverage variance-reduced gradients and momentum updates respectively, both converging at $O(\log (nT)/\sqrt{nT} + \log (nT)\sqrt{n}/\sqrt{T})$. In contrast with the analysis of signSGD, our results do not require an extremely large batch size in each iteration to be of the same order as the total number of iterations \citep{bernstein2018signsgd} or the signs of stochastic and true gradients match element-wise with a minimum probability of 1/2 \citep{safaryan2021stochastic}. We also extend our algorithms to cases where data are distributed across different machines, yielding dist-SignRVR and dist-SignRVM, both converging at $O(\log (n_0T)/\sqrt{n_0T} + \log (n_0T)\sqrt{n_0}/\sqrt{T})$, where $n_0$ is the dataset size of a single machine. We back up our theoretical findings through experiments on simulated and real-world problems, verifying that randomly reshuffled sign methods match or surpass existing baselines.

Online speech recognition, where the model only accesses context to the left, is an important and challenging use case for ASR systems. In this work, we investigate augmenting neural encoders for online ASR by incorporating structured state-space sequence models (S4), a family of models that provide a parameter-efficient way of accessing arbitrarily long left context. We performed systematic ablation studies to compare variants of S4 models and propose two novel approaches that combine them with convolutions. We found that the most effective design is to stack a small S4 using real-valued recurrent weights with a local convolution, allowing them to work complementarily. Our best model achieves WERs of 4.01%/8.53% on test sets from Librispeech, outperforming Conformers with extensively tuned convolution.

Accurately forecasting the direction of financial returns poses a formidable challenge, given the inherent unpredictability of financial time series. The task becomes even more arduous when applied to cryptocurrency returns, given the chaotic and intricately complex nature of crypto markets. In this study, we present a novel prediction algorithm using limit order book (LOB) data rooted in the Hawkes model, a category of point processes. Coupled with a continuous output error (COE) model, our approach offers a precise forecast of return signs by leveraging predictions of future financial interactions. Capitalizing on the non-uniformly sampled structure of the original time series, our strategy surpasses benchmark models in both prediction accuracy and cumulative profit when implemented in a trading environment. The efficacy of our approach is validated through Monte Carlo simulations across 50 scenarios. The research draws on LOB measurements from a centralized cryptocurrency exchange where the stablecoin Tether is exchanged against the U.S. dollar.

Hashing has been widely used in approximate nearest search for large-scale database retrieval for its computation and storage efficiency. Deep hashing, which devises convolutional neural network architecture to exploit and extract the semantic information or feature of images, has received increasing attention recently. In this survey, several deep supervised hashing methods for image retrieval are evaluated and I conclude three main different directions for deep supervised hashing methods. Several comments are made at the end. Moreover, to break through the bottleneck of the existing hashing methods, I propose a Shadow Recurrent Hashing(SRH) method as a try. Specifically, I devise a CNN architecture to extract the semantic features of images and design a loss function to encourage similar images projected close. To this end, I propose a concept: shadow of the CNN output. During optimization process, the CNN output and its shadow are guiding each other so as to achieve the optimal solution as much as possible. Several experiments on dataset CIFAR-10 show the satisfying performance of SRH.

Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.