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Stochastic Gradient Descent (SGD) algorithms are widely used in optimizing neural networks, with Random Reshuffling (RR) and Single Shuffle (SS) being popular choices for cycling through random or single permutations of the training data. However, the convergence properties of these algorithms in the non-convex case are not fully understood. Existing results suggest that, in realistic training scenarios where the number of epochs is smaller than the training set size, RR may perform worse than SGD. In this paper, we analyze a general SGD algorithm that allows for arbitrary data orderings and show improved convergence rates for non-convex functions. Specifically, our analysis reveals that SGD with random and single shuffling is always faster or at least as good as classical SGD with replacement, regardless of the number of iterations. Overall, our study highlights the benefits of using SGD with random/single shuffling and provides new insights into its convergence properties for non-convex optimization.

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The starting point for much of multivariate analysis (MVA) is an $n\times p$ data matrix whose $n$ rows represent observations and whose $p$ columns represent variables. Some multivariate data sets, however, may be best conceptualized not as $n$ discrete $p$-variate observations, but as $p$ curves or functions defined on a common time interval. We introduce a framework for extending techniques of multivariate analysis to such settings. The proposed framework rests on the assumption that the curves can be represented as linear combinations of basis functions such as B-splines. This is formally identical to the Ramsay-Silverman representation of functional data; but whereas functional data analysis extends MVA to the case of observations that are curves rather than vectors -- heuristically, $n\times p$ data with $p$ infinite -- we are instead concerned with what happens when $n$ is infinite. We describe how to translate the classical MVA methods of covariance and correlation estimation, principal component analysis, Fisher's linear discriminant analysis, and $k$-means clustering to the continuous-time setting. We illustrate the methods with a novel perspective on a well-known Canadian weather data set, and with applications to neurobiological and environmetric data. The methods are implemented in the publicly available R package \texttt{ctmva}.

The linear bandit problem has been studied for many years in both stochastic and adversarial settings. Designing an algorithm that can optimize the environment without knowing the loss type attracts lots of interest. \citet{LeeLWZ021} propose an algorithm that actively detects the loss type and then switches between different algorithms specially designed for specific settings. However, such an approach requires meticulous designs to perform well in all environments. Follow-the-regularized-leader (FTRL) is another type of popular algorithm that can adapt to different environments. This algorithm is of simple design and the regret bounds are shown to be optimal in traditional multi-armed bandit problems compared with the detect-switch type. Designing an FTRL-type algorithm for linear bandits is an important question that has been open for a long time. In this paper, we prove that the FTRL algorithm with a negative entropy regularizer can achieve the best-of-three-world results for the linear bandit problem. Our regret bounds achieve the same or nearly the same order as the previous detect-switch type algorithm but with a much simpler algorithmic design.

Current statistical methods in differential proteomics analysis generally leave aside several challenges, such as missing values, correlations between peptide intensities and uncertainty quantification. Moreover, they provide point estimates, such as the mean intensity for a given peptide or protein in a given condition. The decision of whether an analyte should be considered as differential is then based on comparing the p-value to a significance threshold, usually 5%. In the state-of-the-art limma approach, a hierarchical model is used to deduce the posterior distribution of the variance estimator for each analyte. The expectation of this distribution is then used as a moderated estimation of variance and is injected directly into the expression of the t-statistic. However, instead of merely relying on the moderated estimates, we could provide more powerful and intuitive results by leveraging a fully Bayesian approach and hence allow the quantification of uncertainty. The present work introduces this idea by taking advantage of standard results from Bayesian inference with conjugate priors in hierarchical models to derive a methodology tailored to handle multiple imputation contexts. Furthermore, we aim to tackle a more general problem of multivariate differential analysis, to account for possible inter-peptide correlations. By defining a hierarchical model with prior distributions on both mean and variance parameters, we achieve a global quantification of uncertainty for differential analysis. The inference is thus performed by computing the posterior distribution for the difference in mean peptide intensities between two experimental conditions. In contrast to more flexible models that can be achieved with hierarchical structures, our choice of conjugate priors maintains analytical expressions for direct sampling from posterior distributions without requiring expensive MCMC methods.

The main bottleneck in designing efficient dynamic algorithms is the unknown nature of the update sequence. In particular, there are some problems, like 3-vertex connectivity, planar digraph all pairs shortest paths, and others, where the separation in runtime between the best partially dynamic solutions and the best fully dynamic solutions is polynomial, sometimes even exponential. In this paper, we formulate the predicted-deletion dynamic model, motivated by a recent line of empirical work about predicting edge updates in dynamic graphs. In this model, edges are inserted and deleted online, and when an edge is inserted, it is accompanied by a "prediction" of its deletion time. This models real world settings where services may have access to historical data or other information about an input and can subsequently use such information make predictions about user behavior. The model is also of theoretical interest, as it interpolates between the partially dynamic and fully dynamic settings, and provides a natural extension of the algorithms with predictions paradigm to the dynamic setting. We give a novel framework for this model that "lifts" partially dynamic algorithms into the fully dynamic setting with little overhead. We use our framework to obtain improved efficiency bounds over the state-of-the-art dynamic algorithms for a variety of problems. In particular, we design algorithms that have amortized update time that scales with a partially dynamic algorithm, with high probability, when the predictions are of high quality. On the flip side, our algorithms do no worse than existing fully-dynamic algorithms when the predictions are of low quality. Furthermore, our algorithms exhibit a graceful trade-off between the two cases. Thus, we are able to take advantage of ML predictions asymptotically "for free.''

In this paper, we propose an online convex optimization method with two different levels of adaptivity. On a higher level, our method is agnostic to the specific type and curvature of the loss functions, while at a lower level, it can exploit the niceness of the environments and attain problem-dependent guarantees. To be specific, we obtain $\mathcal{O}(\ln V_T)$, $\mathcal{O}(d \ln V_T)$ and $\hat{\mathcal{O}}(\sqrt{V_T})$ regret bounds for strongly convex, exp-concave and convex loss functions, respectively, where $d$ is the dimension, $V_T$ denotes problem-dependent gradient variations and $\hat{\mathcal{O}}(\cdot)$-notation omits logarithmic factors on $V_T$. Our result finds broad implications and applications. It not only safeguards the worst-case guarantees, but also implies the small-loss bounds in analysis directly. Besides, it draws deep connections with adversarial/stochastic convex optimization and game theory, further validating its practical potential. Our method is based on a multi-layer online ensemble incorporating novel ingredients, including carefully-designed optimism for unifying diverse function types and cascaded corrections for algorithmic stability. Remarkably, despite its multi-layer structure, our algorithm necessitates only one gradient query per round, making it favorable when the gradient evaluation is time-consuming. This is facilitated by a novel regret decomposition equipped with customized surrogate losses.

Randomized trials balance all covariates on average and provide the gold standard for estimating treatment effects. Chance imbalances nevertheless exist more or less in realized treatment allocations and intrigue an important question: what should we do in case the treatment groups differ with respect to some important baseline characteristics? A common strategy is to conduct a {\it preliminary test} of the balance of baseline covariates after randomization, and invoke covariate adjustment for subsequent inference if and only if the realized allocation fails some prespecified criterion. Although such practice is intuitive and popular among practitioners, the existing literature has so far only evaluated its properties under strong parametric model assumptions in theory and simulation, yielding results of limited generality. To fill this gap, we examine two strategies for conducting preliminary test-based covariate adjustment by regression, and evaluate the validity and efficiency of the resulting inferences from the randomization-based perspective. As it turns out, the preliminary-test estimator based on the analysis of covariance can be even less efficient than the unadjusted difference in means, and risks anticonservative confidence intervals based on normal approximation even with the robust standard error. The preliminary-test estimator based on the fully interacted specification is on the other hand less efficient than its counterpart under the {\it always-adjust} strategy, and yields overconservative confidence intervals based on normal approximation. Based on theory and simulation, we echo the existing literature and do not recommend the preliminary-test procedure for covariate adjustment in randomized trials.

We study the bias of Stochastic Gradient Descent (SGD) to learn low-rank weight matrices when training deep ReLU neural networks. Our results show that training neural networks with mini-batch SGD and weight decay causes a bias towards rank minimization over the weight matrices. Specifically, we show, both theoretically and empirically, that this bias is more pronounced when using smaller batch sizes, higher learning rates, or increased weight decay. Additionally, we predict and observe empirically that weight decay is necessary to achieve this bias. In addition, we show that in the presence of intermediate neural collapse, the learned weights are particularly low-rank. Unlike previous literature, our analysis does not rely on assumptions about the data, convergence, or optimality of the weight matrices. Furthermore, it applies to a wide range of neural network architectures of any width or depth. Finally, we empirically investigate the connection between this bias and generalization, finding that it has a marginal effect on generalization.

Gaussian process (GP) regression is a Bayesian nonparametric method for regression and interpolation, offering a principled way of quantifying the uncertainties of predicted function values. For the quantified uncertainties to be well-calibrated, however, the covariance kernel of the GP prior has to be carefully selected. In this paper, we theoretically compare two methods for choosing the kernel in GP regression: cross-validation and maximum likelihood estimation. Focusing on the scale-parameter estimation of a Brownian motion kernel in the noiseless setting, we prove that cross-validation can yield asymptotically well-calibrated credible intervals for a broader class of ground-truth functions than maximum likelihood estimation, suggesting an advantage of the former over the latter.

Hypothesis transfer learning (HTL) contrasts domain adaptation by allowing for a previous task leverage, named the source, into a new one, the target, without requiring access to the source data. Indeed, HTL relies only on a hypothesis learnt from such source data, relieving the hurdle of expansive data storage and providing great practical benefits. Hence, HTL is highly beneficial for real-world applications relying on big data. The analysis of such a method from a theoretical perspective faces multiple challenges, particularly in classification tasks. This paper deals with this problem by studying the learning theory of HTL through algorithmic stability, an attractive theoretical framework for machine learning algorithms analysis. In particular, we are interested in the statistical behaviour of the regularized empirical risk minimizers in the case of binary classification. Our stability analysis provides learning guarantees under mild assumptions. Consequently, we derive several complexity-free generalization bounds for essential statistical quantities like the training error, the excess risk and cross-validation estimates. These refined bounds allow understanding the benefits of transfer learning and comparing the behaviour of standard losses in different scenarios, leading to valuable insights for practitioners.

Continuous space species distribution models (SDMs) have a long-standing history as a valuable tool in ecological statistical analysis. Geostatistical and preferential models are both common models in ecology. Geostatistical models are employed when the process under study is independent of the sampling locations, while preferential models are employed when sampling locations are dependent on the process under study. But, what if we have both types of data collectd over the same process? Can we combine them? If so, how should we combine them? This study investigated the suitability of both geostatistical and preferential models, as well as a mixture model that accounts for the different sampling schemes. Results suggest that in general the preferential and mixture models have satisfactory and close results in most cases, while the geostatistical models presents systematically worse estimates at higher spatial complexity, smaller number of samples and lower proportion of completely random samples.

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