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Variational Bayesian posterior inference often requires simplifying approximations such as mean-field parametrisation to ensure tractability. However, prior work has associated the variational mean-field approximation for Bayesian neural networks with underfitting in the case of small datasets or large model sizes. In this work, we show that invariances in the likelihood function of over-parametrised models contribute to this phenomenon because these invariances complicate the structure of the posterior by introducing discrete and/or continuous modes which cannot be well approximated by Gaussian mean-field distributions. In particular, we show that the mean-field approximation has an additional gap in the evidence lower bound compared to a purpose-built posterior that takes into account the known invariances. Importantly, this invariance gap is not constant; it vanishes as the approximation reverts to the prior. We proceed by first considering translation invariances in a linear model with a single data point in detail. We show that, while the true posterior can be constructed from a mean-field parametrisation, this is achieved only if the objective function takes into account the invariance gap. Then, we transfer our analysis of the linear model to neural networks. Our analysis provides a framework for future work to explore solutions to the invariance problem.

The scheduled launch of the LISA Mission in the next decade has called attention to the gravitational self-force problem. Despite an extensive body of theoretical work, long-time numerical computations of gravitational waves from extreme-mass-ratio-inspirals remain challenging. This work proposes a class of numerical evolution schemes suitable to this problem based on Hermite integration. Their most important feature is time-reversal symmetry and unconditional stability, which enables these methods to preserve symplectic structure, energy, momentum and other Noether charges over long time periods. We apply Noether's theorem to the master fields of black hole perturbation theory on a hyperboloidal slice of Schwarzschild spacetime to show that there exist constants of evolution that numerical simulations must preserve. We demonstrate that time-symmetric integration schemes based on a 2-point Taylor expansion (such as Hermite integration) numerically conserve these quantities, unlike schemes based on a 1-point Taylor expansion (such as Runge-Kutta). This makes time-symmetric schemes ideal for long-time EMRI simulations.

Context: Automated software defect prediction (SDP) methods are increasingly applied, often with the use of machine learning (ML) techniques. Yet, the existing ML-based approaches require manually extracted features, which are cumbersome, time consuming and hardly capture the semantic information reported in bug reporting tools. Deep learning (DL) techniques provide practitioners with the opportunities to automatically extract and learn from more complex and high-dimensional data. Objective: The purpose of this study is to systematically identify, analyze, summarize, and synthesize the current state of the utilization of DL algorithms for SDP in the literature. Method: We systematically selected a pool of 102 peer-reviewed studies and then conducted a quantitative and qualitative analysis using the data extracted from these studies. Results: Main highlights include: (1) most studies applied supervised DL; (2) two third of the studies used metrics as an input to DL algorithms; (3) Convolutional Neural Network is the most frequently used DL algorithm. Conclusion: Based on our findings, we propose to (1) develop more comprehensive DL approaches that automatically capture the needed features; (2) use diverse software artifacts other than source code; (3) adopt data augmentation techniques to tackle the class imbalance problem; (4) publish replication packages.

Producing statistics that respect the privacy of the samples while still maintaining their accuracy is an important topic of research. We study minimax lower bounds when the class of estimators is restricted to the differentially private ones. In particular, we show that characterizing the power of a distributional test under differential privacy can be done by solving a transport problem. With specific coupling constructions, this observation allows us to derivate Le Cam-type and Fano-type inequalities for both regular definitions of differential privacy and for divergence-based ones (based on Renyi divergence). We then proceed to illustrate our results on three simple, fully worked out examples. In particular, we show that the problem class has a huge importance on the provable degradation of utility due to privacy. For some problems, privacy leads to a provable degradation only when the rate of the privacy parameters is small enough whereas for other problem, the degradation systematically occurs under much looser hypotheses on the privacy parametters. Finally, we show that the known privacy guarantees of DP-SGLD, a private convex solver, when used to perform maximum likelihood, leads to an algorithm that is near-minimax optimal in both the sample size and the privacy tuning parameters of the problem for a broad class of parametric estimation procedures that includes exponential families.

This paper investigates the competitiveness of semi-implicit Runge-Kutta (RK) and spectral deferred correction (SDC) time-integration methods up to order six for incompressible Navier-Stokes problems in conjunction with a high-order discontinuous Galerkin method for space discretization. It is proposed to harness the implicit and explicit RK parts as a partitioned scheme, which provides a natural basis for the underlying projection scheme and yields a straight-forward approach for accommodating nonlinear viscosity. Numerical experiments on laminar flow, variable viscosity and transition to turbulence are carried out to assess accuracy, convergence and computational efficiency. Although the methods of order 3 or higher are susceptible to order reduction due to time-dependent boundary conditions, two third-order RK methods are identified that perform well in all test cases and clearly surpass all second-order schemes including the popular extrapolated backward difference method. The considered SDC methods are more accurate than the RK methods, but become competitive only for relative errors smaller than ca $10^{-5}$.

The adaptive processing of structured data is a long-standing research topic in machine learning that investigates how to automatically learn a mapping from a structured input to outputs of various nature. Recently, there has been an increasing interest in the adaptive processing of graphs, which led to the development of different neural network-based methodologies. In this thesis, we take a different route and develop a Bayesian Deep Learning framework for graph learning. The dissertation begins with a review of the principles over which most of the methods in the field are built, followed by a study on graph classification reproducibility issues. We then proceed to bridge the basic ideas of deep learning for graphs with the Bayesian world, by building our deep architectures in an incremental fashion. This framework allows us to consider graphs with discrete and continuous edge features, producing unsupervised embeddings rich enough to reach the state of the art on several classification tasks. Our approach is also amenable to a Bayesian nonparametric extension that automatizes the choice of almost all model's hyper-parameters. Two real-world applications demonstrate the efficacy of deep learning for graphs. The first concerns the prediction of information-theoretic quantities for molecular simulations with supervised neural models. After that, we exploit our Bayesian models to solve a malware-classification task while being robust to intra-procedural code obfuscation techniques. We conclude the dissertation with an attempt to blend the best of the neural and Bayesian worlds together. The resulting hybrid model is able to predict multimodal distributions conditioned on input graphs, with the consequent ability to model stochasticity and uncertainty better than most works. Overall, we aim to provide a Bayesian perspective into the articulated research field of deep learning for graphs.

This book develops an effective theory approach to understanding deep neural networks of practical relevance. Beginning from a first-principles component-level picture of networks, we explain how to determine an accurate description of the output of trained networks by solving layer-to-layer iteration equations and nonlinear learning dynamics. A main result is that the predictions of networks are described by nearly-Gaussian distributions, with the depth-to-width aspect ratio of the network controlling the deviations from the infinite-width Gaussian description. We explain how these effectively-deep networks learn nontrivial representations from training and more broadly analyze the mechanism of representation learning for nonlinear models. From a nearly-kernel-methods perspective, we find that the dependence of such models' predictions on the underlying learning algorithm can be expressed in a simple and universal way. To obtain these results, we develop the notion of representation group flow (RG flow) to characterize the propagation of signals through the network. By tuning networks to criticality, we give a practical solution to the exploding and vanishing gradient problem. We further explain how RG flow leads to near-universal behavior and lets us categorize networks built from different activation functions into universality classes. Altogether, we show that the depth-to-width ratio governs the effective model complexity of the ensemble of trained networks. By using information-theoretic techniques, we estimate the optimal aspect ratio at which we expect the network to be practically most useful and show how residual connections can be used to push this scale to arbitrary depths. With these tools, we can learn in detail about the inductive bias of architectures, hyperparameters, and optimizers.

Deep learning is usually described as an experiment-driven field under continuous criticizes of lacking theoretical foundations. This problem has been partially fixed by a large volume of literature which has so far not been well organized. This paper reviews and organizes the recent advances in deep learning theory. The literature is categorized in six groups: (1) complexity and capacity-based approaches for analyzing the generalizability of deep learning; (2) stochastic differential equations and their dynamic systems for modelling stochastic gradient descent and its variants, which characterize the optimization and generalization of deep learning, partially inspired by Bayesian inference; (3) the geometrical structures of the loss landscape that drives the trajectories of the dynamic systems; (4) the roles of over-parameterization of deep neural networks from both positive and negative perspectives; (5) theoretical foundations of several special structures in network architectures; and (6) the increasingly intensive concerns in ethics and security and their relationships with generalizability.

Over the past few years, we have seen fundamental breakthroughs in core problems in machine learning, largely driven by advances in deep neural networks. At the same time, the amount of data collected in a wide array of scientific domains is dramatically increasing in both size and complexity. Taken together, this suggests many exciting opportunities for deep learning applications in scientific settings. But a significant challenge to this is simply knowing where to start. The sheer breadth and diversity of different deep learning techniques makes it difficult to determine what scientific problems might be most amenable to these methods, or which specific combination of methods might offer the most promising first approach. In this survey, we focus on addressing this central issue, providing an overview of many widely used deep learning models, spanning visual, sequential and graph structured data, associated tasks and different training methods, along with techniques to use deep learning with less data and better interpret these complex models --- two central considerations for many scientific use cases. We also include overviews of the full design process, implementation tips, and links to a plethora of tutorials, research summaries and open-sourced deep learning pipelines and pretrained models, developed by the community. We hope that this survey will help accelerate the use of deep learning across different scientific domains.

When and why can a neural network be successfully trained? This article provides an overview of optimization algorithms and theory for training neural networks. First, we discuss the issue of gradient explosion/vanishing and the more general issue of undesirable spectrum, and then discuss practical solutions including careful initialization and normalization methods. Second, we review generic optimization methods used in training neural networks, such as SGD, adaptive gradient methods and distributed methods, and theoretical results for these algorithms. Third, we review existing research on the global issues of neural network training, including results on bad local minima, mode connectivity, lottery ticket hypothesis and infinite-width analysis.