Multipole Graph Neural Operator for Parametric Partial Differential Equations

One of the main challenges in using deep learning-based methods for simulating physical systems and solving partial differential equations (PDEs) is formulating physics-based data in the desired structure for neural networks. Graph neural networks (GNNs) have gained popularity in this area since graphs offer a natural way of modeling particle interactions and provide a clear way of discretizing the continuum models. However, the graphs constructed for approximating such tasks usually ignore long-range interactions due to unfavorable scaling of the computational complexity with respect to the number of nodes. The errors due to these approximations scale with the discretization of the system, thereby not allowing for generalization under mesh-refinement. Inspired by the classical multipole methods, we propose a novel multi-level graph neural network framework that captures interaction at all ranges with only linear complexity. Our multi-level formulation is equivalent to recursively adding inducing points to the kernel matrix, unifying GNNs with multi-resolution matrix factorization of the kernel. Experiments confirm our multi-graph network learns discretization-invariant solution operators to PDEs and can be evaluated in linear time

Constructive Approximation and Learning by Greedy Algorithms

This thesis develops several kernel-based greedy algorithms for different machine learning problems and analyzes their theoretical and empirical properties. Greedy approaches have been extensively used in the past for tackling problems in combinatorial optimization where finding even a feasible solution can be a computationally hard problem (i.e., not solvable in polynomial time). A key feature of greedy algorithms is that a solution is constructed recursively from the smallest constituent parts. In each step of the constructive process a component is added to the partial solution from the previous step and, thus, the size of the optimization problem is reduced. The selected components are given by optimization problems that are simpler and easier to solve than the original problem. As such schemes are typically fast at constructing a solution they can be very effective on complex optimization problems where finding an optimal/good solution has a high computational cost. Moreover, greedy solutions are rather intuitive and the schemes themselves are simple to design and easy to implement. There is a large class of problems for which greedy schemes generate an optimal solution or a good approximation of the optimum. In the first part of the thesis, we develop two deterministic greedy algorithms for optimization problems in which a solution is given by a set of functions mapping an instance space to the space of reals. The first of the two approaches facilitates data understanding through interactive visualization by providing means for experts to incorporate their domain knowledge into otherwise static kernel principal component analysis. This is achieved by greedily constructing embedding directions that maximize the variance at data points (unexplained by the previously constructed embedding directions) while adhering to specified domain knowledge constraints. The second deterministic greedy approach is a supervised feature construction method capable of addressing the problem of kernel choice. The goal of the approach is to construct a feature representation for which a set of linear hypotheses is of sufficient capacity — large enough to contain a satisfactory solution to the considered problem and small enough to allow good generalization from a small number of training examples. The approach mimics functional gradient descent and constructs features by fitting squared error residuals. We show that the constructive process is consistent and provide conditions under which it converges to the optimal solution. In the second part of the thesis, we investigate two problems for which deterministic greedy schemes can fail to find an optimal solution or a good approximation of the optimum. This happens as a result of making a sequence of choices which take into account only the immediate reward without considering the consequences onto future decisions. To address this shortcoming of deterministic greedy schemes, we propose two efficient randomized greedy algorithms which are guaranteed to find effective solutions to the corresponding problems. In the first of the two approaches, we provide a mean to scale kernel methods to problems with millions of instances. An approach, frequently used in practice, for this type of problems is the Nyström method for low-rank approximation of kernel matrices. A crucial step in this method is the choice of landmarks which determine the quality of the approximation. We tackle this problem with a randomized greedy algorithm based on the K-means++ cluster seeding scheme and provide a theoretical and empirical study of its effectiveness. In the second problem for which a deterministic strategy can fail to find a good solution, the goal is to find a set of objects from a structured space that are likely to exhibit an unknown target property. This discrete optimization problem is of significant interest to cyclic discovery processes such as de novo drug design. We propose to address it with an adaptive Metropolis–Hastings approach that samples candidates from the posterior distribution of structures conditioned on them having the target property. The proposed constructive scheme defines a consistent random process and our empirical evaluation demonstrates its effectiveness across several different application domains

Multipole Graph Neural Operator for Parametric Partial Differential Equations

One of the main challenges in using deep learning-based methods for simulating physical systems and solving partial differential equations (PDEs) is formulating physics-based data in the desired structure for neural networks. Graph neural networks (GNNs) have gained popularity in this area since graphs offer a natural way of modeling particle interactions and provide a clear way of discretizing the continuum models. However, the graphs constructed for approximating such tasks usually ignore long-range interactions due to unfavorable scaling of the computational complexity with respect to the number of nodes. The errors due to these approximations scale with the discretization of the system, thereby not allowing for generalization under mesh-refinement. Inspired by the classical multipole methods, we purpose a novel multi-level graph neural network framework that captures interaction at all ranges with only linear complexity. Our multi-level formulation is equivalent to recursively adding inducing points to the kernel matrix, unifying GNNs with multi-resolution matrix factorization of the kernel. Experiments confirm our multi-graph network learns discretization-invariant solution operators to PDEs and can be evaluated in linear time

The Role of Riemannian Manifolds in Computer Vision: From Coding to Deep Metric Learning

A diverse number of tasks in computer vision and machine learning enjoy from representations of data that are compact yet discriminative, informative and robust to critical measurements. Two notable representations are offered by Region Covariance Descriptors (RCovD) and linear subspaces which are naturally analyzed through the manifold of Symmetric Positive Definite (SPD) matrices and the Grassmann manifold, respectively, two widely used types of Riemannian manifolds in computer vision. As our first objective, we examine image and video-based recognition applications where the local descriptors have the aforementioned Riemannian structures, namely the SPD or linear subspace structure. Initially, we provide a solution to compute Riemannian version of the conventional Vector of Locally aggregated Descriptors (VLAD), using geodesic distance of the underlying manifold as the nearness measure. Next, by having a closer look at the resulting codes, we formulate a new concept which we name Local Difference Vectors (LDV). LDVs enable us to elegantly expand our Riemannian coding techniques to any arbitrary metric as well as provide intrinsic solutions to Riemannian sparse coding and its variants when local structured descriptors are considered. We then turn our attention to two special types of covariance descriptors namely infinite-dimensional RCovDs and rank-deficient covariance matrices for which the underlying Riemannian structure, i.e. the manifold of SPD matrices is out of reach to great extent. %Generally speaking, infinite-dimensional RCovDs offer better discriminatory power over their low-dimensional counterparts. To overcome this difficulty, we propose to approximate the infinite-dimensional RCovDs by making use of two feature mappings, namely random Fourier features and the Nystrom method. As for the rank-deficient covariance matrices, unlike most existing approaches that employ inference tools by predefined regularizers, we derive positive definite kernels that can be decomposed into the kernels on the cone of SPD matrices and kernels on the Grassmann manifolds and show their effectiveness for image set classification task. Furthermore, inspired by attractive properties of Riemannian optimization techniques, we extend the recently introduced Keep It Simple and Straightforward MEtric learning (KISSME) method to the scenarios where input data is non-linearly distributed. To this end, we make use of the infinite dimensional covariance matrices and propose techniques towards projecting on the positive cone in a Reproducing Kernel Hilbert Space (RKHS). We also address the sensitivity issue of the KISSME to the input dimensionality. The KISSME algorithm is greatly dependent on Principal Component Analysis (PCA) as a preprocessing step which can lead to difficulties, especially when the dimensionality is not meticulously set. To address this issue, based on the KISSME algorithm, we develop a Riemannian framework to jointly learn a mapping performing dimensionality reduction and a metric in the induced space. Lastly, in line with the recent trend in metric learning, we devise end-to-end learning of a generic deep network for metric learning using our derivation

Large Scale Kernel Methods for Fun and Profit

Kernel methods are among the most flexible classes of machine learning models with strong theoretical guarantees. Wide classes of functions can be approximated arbitrarily well with kernels, while fast convergence and learning rates have been formally shown to hold. Exact kernel methods are known to scale poorly with increasing dataset size, and we believe that one of the factors limiting their usage in modern machine learning is the lack of scalable and easy to use algorithms and software. The main goal of this thesis is to study kernel methods from the point of view of efficient learning, with particular emphasis on large-scale data, but also on low-latency training, and user efficiency. We improve the state-of-the-art for scaling kernel solvers to datasets with billions of points using the Falkon algorithm, which combines random projections with fast optimization. Running it on GPUs, we show how to fully utilize available computing power for training kernel machines. To boost the ease-of-use of approximate kernel solvers, we propose an algorithm for automated hyperparameter tuning. By minimizing a penalized loss function, a model can be learned together with its hyperparameters, reducing the time needed for user-driven experimentation. In the setting of multi-class learning, we show that – under stringent but realistic assumptions on the separation between classes – a wide set of algorithms needs much fewer data points than in the more general setting (without assumptions on class separation) to reach the same accuracy. The first part of the thesis develops a framework for efficient and scalable kernel machines. This raises the question of whether our approaches can be used successfully in real-world applications, especially compared to alternatives based on deep learning which are often deemed hard to beat. The second part aims to investigate this question on two main applications, chosen because of the paramount importance of having an efficient algorithm. First, we consider the problem of instance segmentation of images taken from the iCub robot. Here Falkon is used as part of a larger pipeline, but the efficiency afforded by our solver is essential to ensure smooth human-robot interactions. In the second instance, we consider time-series forecasting of wind speed, analysing the relevance of different physical variables on the predictions themselves. We investigate different schemes to adapt i.i.d. learning to the time-series setting. Overall, this work aims to demonstrate, through novel algorithms and examples, that kernel methods are up to computationally demanding tasks, and that there are concrete applications in which their use is warranted and more efficient than that of other, more complex, and less theoretically grounded models

Gaussian Process Optimization with Adaptive Sketching: Scalable and No Regret

Gaussian processes (GP) are a well studied Bayesian approach for the optimization of black-box functions. Despite their effectiveness in simple problems, GP-based algorithms hardly scale to high-dimensional functions, as their per-iteration time and space cost is at least quadratic in the number of dimensions $d$ and iterations $t$. Given a set of $A$ alternatives to choose from, the overall runtime $O(t^3A)$ is prohibitive. In this paper we introduce BKB (budgeted kernelized bandit), a new approximate GP algorithm for optimization under bandit feedback that achieves near-optimal regret (and hence near-optimal convergence rate) with near-constant per-iteration complexity and remarkably no assumption on the input space or covariance of the GP. We combine a kernelized linear bandit algorithm (GP-UCB) with randomized matrix sketching based on leverage score sampling, and we prove that randomly sampling inducing points based on their posterior variance gives an accurate low-rank approximation of the GP, preserving variance estimates and confidence intervals. As a consequence, BKB does not suffer from variance starvation, an important problem faced by many previous sparse GP approximations. Moreover, we show that our procedure selects at most $\tilde{O}(d_{eff})$ points, where $d_{eff}$ is the effective dimension of the explored space, which is typically much smaller than both $d$ and $t$. This greatly reduces the dimensionality of the problem, thus leading to a $O(TAd_{eff}^2)$ runtime and $O(A d_{eff})$ space complexity.Comment: Accepted at COLT 2019. Corrected typos and improved comparison with existing method

Principal Component Analysis

This book is aimed at raising awareness of researchers, scientists and engineers on the benefits of Principal Component Analysis (PCA) in data analysis. In this book, the reader will find the applications of PCA in fields such as image processing, biometric, face recognition and speech processing. It also includes the core concepts and the state-of-the-art methods in data analysis and feature extraction

Multi-view Subspace Learning for Large-Scale Multi-Modal Data Analysis

Dimensionality reduction methods play a big role within the modern machine learning techniques, and subspace learning is one of the common approaches to it. Although various methods have been proposed over the past years, many of them suffer from limitations related to the unimodality assumptions on the data and low speed in the cases of high-dimensional data (in linear formulations) or large datasets (in kernel-based formulations). In this work, several methods for overcoming these limitations are proposed. In this thesis, the problem of the large-scale multi-modal data analysis for single- and multi-view data is discussed, and several extensions for Subclass Discriminant Analysis (SDA) are proposed. First, a Spectral Regression Subclass Discriminant Analysis method relying on the Graph Embedding-based formulation of SDA is proposed as a way to reduce the training time, and it is shown how the solution can be obtained efficiently, therefore reducing the computational requirements. Secondly, a novel multi-view formulation for Subclass Discriminant Analysis is proposed, allowing to extend it to data coming from multiple views. Besides, a speed-up approach for the multi-view formulation that allows reducing the computational requirements of the method is proposed. Linear and nonlinear kernel-based formulations are proposed for all the extensions. Experiments are performed on nine single-view and nine multi-view datasets and the accuracy and speed of the proposed extensions are evaluated. Experimentally it is shown that the proposed approaches result in a significant reduction of the training time while providing competitive performance, as compared to other subspace-learning based methods

A machine learning approach to the unsupervised segmentation of mitochondria in subcellular electron microscopy data

Recent advances in cellular and subcellular microscopy demonstrated its potential towards unravelling the mechanisms of various diseases at the molecular level. The biggest challenge in both human- and computer-based visual analysis of micrographs is the variety of nanostructures and mitochondrial morphologies. The state-of-the-art is, however, dominated by supervised manual data annotation and early attempts to automate the segmentation process were based on supervised machine learning techniques which require large datasets for training. Given a minimal number of training sequences or none at all, unsupervised machine learning formulations, such as spectral dimensionality reduction, are known to be superior in detecting salient image structures. This thesis presents three major contributions developed around the spectral clustering framework which is proven to capture perceptual organization features. Firstly, we approach the problem of mitochondria localization. We propose a novel grouping method for the extracted line segments which describes the normal mitochondrial morphology. Experimental findings show that the clusters obtained successfully model the inner mitochondrial membrane folding and therefore can be used as markers for the subsequent segmentation approaches. Secondly, we developed an unsupervised mitochondria segmentation framework. This method follows the evolutional ability of human vision to extrapolate salient membrane structures in a micrograph. Furthermore, we designed robust non-parametric similarity models according to Gestaltic laws of visual segregation. Experiments demonstrate that such models automatically adapt to the statistical structure of the biological domain and return optimal performance in pixel classification tasks under the wide variety of distributional assumptions. The last major contribution addresses the computational complexity of spectral clustering. Here, we introduced a new anticorrelation-based spectral clustering formulation with the objective to improve both: speed and quality of segmentation. The experimental findings showed the applicability of our dimensionality reduction algorithm to very large scale problems as well as asymmetric, dense and non-Euclidean datasets