Uniform Manifold Approximation and Projection (UMAP) and its Variants: Tutorial and Survey

Uniform Manifold Approximation and Projection (UMAP) is one of the state-of-the-art methods for dimensionality reduction and data visualization. This is a tutorial and survey paper on UMAP and its variants. We start with UMAP algorithm where we explain probabilities of neighborhood in the input and embedding spaces, optimization of cost function, training algorithm, derivation of gradients, and supervised and semi-supervised embedding by UMAP. Then, we introduce the theory behind UMAP by algebraic topology and category theory. Then, we introduce UMAP as a neighbor embedding method and compare it with t-SNE and LargeVis algorithms. We discuss negative sampling and repulsive forces in UMAPs cost function. DensMAP is then explained for density-preserving embedding. We then introduce parametric UMAP for embedding by deep learning and progressive UMAP for streaming and out-of-sample data embedding.

Johnson-Lindenstrauss Lemma, Linear and Nonlinear Random Projections, Random Fourier Features, and Random Kitchen Sinks: Tutorial and Survey

This is a tutorial and survey paper on the Johnson-Lindenstrauss (JL) lemma and linear and nonlinear random projections. We start with linear random projection and then justify its correctness by JL lemma and its proof. Then, sparse random projections with $ell_1$ norm and interpolation norm are introduced. Two main applications of random projection, which are low-rank matrix approximation and approximate nearest neighbor search by random projection onto hypercube, are explained. Random Fourier Features (RFF) and Random Kitchen Sinks (RKS) are explained as methods for nonlinear random projection. Some other methods for nonlinear random projection, including extreme learning machine, randomly weighted neural networks, and ensemble of random projections, are also introduced.

Restricted Boltzmann Machine and Deep Belief Network: Tutorial and Survey

This is a tutorial and survey paper on Boltzmann Machine (BM), Restricted Boltzmann Machine (RBM), and Deep Belief Network (DBN). We start with the required background on probabilistic graphical models, Markov random field, Gibbs sampling, statistical physics, Ising model, and the Hopfield network. Then, we introduce the structures of BM and RBM. The conditional distributions of visible and hidden variables, Gibbs sampling in RBM for generating variables, training BM and RBM by maximum likelihood estimation, and contrastive divergence are explained. Then, we discuss different possible discrete and continuous distributions for the variables. We introduce conditional RBM and how it is trained. Finally, we explain deep belief network as a stack of RBM models. This paper on Boltzmann machines can be useful in various fields including data science, statistics, neural computation, and statistical physics.

Unified Framework for Spectral Dimensionality Reduction, Maximum Variance Unfolding, and Kernel Learning By Semidefinite Programming: Tutorial and Survey

This is a tutorial and survey paper on unification of spectral dimensionality reduction methods, kernel learning by Semidefinite Programming (SDP), Maximum Variance Unfolding (MVU) or Semidefinite Embedding (SDE), and its variants. We first explain how the spectral dimensionality reduction methods can be unified as kernel Principal Component Analysis (PCA) with different kernels. This unification can be interpreted as eigenfunction learning or representation of kernel in terms of distance matrix. Then, since the spectral methods are unified as kernel PCA, we say let us learn the best kernel for unfolding the manifold of data to its maximum variance. We first briefly introduce kernel learning by SDP for the transduction task. Then, we explain MVU in detail. Vario

Legendre Deep Neural Network (LDNN) and its application for approximation of nonlinear Volterra Fredholm Hammerstein integral equations

Various phenomena in biology, physics, and engineering are modeled by differential equations. These differential equations including partial differential equations and ordinary differential equations can be converted and represented as integral equations. In particular, Volterra Fredholm Hammerstein integral equations are the main type of these integral equations and researchers are interested in investigating and solving these equations. In this paper, we propose Legendre Deep Neural Network (LDNN) for solving nonlinear Volterra Fredholm Hammerstein integral equations (VFHIEs). LDNN utilizes Legendre orthogonal polynomials as activation functions of the Deep structure. We present how LDNN can be used to solve nonlinear VFHIEs. We show using the Gaussian quadrature collocation method in combination with LDNN results in a novel numerical solution for nonlinear VFHIEs. Several examples are given to verify the performance and accuracy of LDNN.

Reproducing Kernel Hilbert Space, Mercers Theorem, Eigenfunctions, Nystrom Method, and Use of Kernels in Machine Learning: Tutorial and Survey

This is a tutorial and survey paper on kernels, kernel methods, and related fields. We start with reviewing the history of kernels in functional analysis and machine learning. Then, Mercer kernel, Hilbert and Banach spaces, Reproducing Kernel Hilbert Space (RKHS), Mercers theorem and its proof, frequently used kernels, kernel construction from distance metric, important classes of kernels (including bounded, integrally positive definite, universal, stationary, and characteristic kernels), kernel centering and normalization, and eigenfunctions are explained in detail. Then, we introduce types of use of kernels in machine learning including kernel methods (such as kernel support vector machines), kernel learning by semi-definite programming, Hilbert-Schmidt independence criterion, maximum mean discrepancy, kernel mean embedding, and kernel dimensionality reduction. We also cover rank and factorization of kernel matrix as well as the approximation of eigenfunctions and kernels using the Nystr{o}m method. This paper can be useful for various fields of science including machine learning, dimensionality reduction, functional analysis in mathematics, and mathematical physics in quantum mechanics.

Laplacian-Based Dimensionality Reduction Including Spectral Clustering, Laplacian Eigenmap, Locality Preserving Projection, Graph Embedding, and Diffusion Map: Tutorial and Survey

This is a tutorial and survey paper for nonlinear dimensionality and feature extraction methods which are based on the Laplacian of graph of data. We first introduce adjacency matrix, definition of Laplacian matrix, and the interpretation of Laplacian. Then, we cover the cuts of graph and spectral clustering which applies clustering in a subspace of data. Different optimization variants of Laplacian eigenmap and its out-of-sample extension are explained. Thereafter, we introduce the locality preserving projection and its kernel variant as linear special cases of Laplacian eigenmap. Versions of graph embedding are then explained which are generaliz

Symbolically Solving Partial Differential Equations using Deep Learning

We describe a neural-based method for generating exact or approximate solutions to differential equations in the form of mathematical expressions. Unlike other neural methods, our system returns symbolic expressions that can be interpreted directly. Our method uses a neural architecture for learning mathematical expressions to optimize a customizable objective, and is scalable, compact, and easily adaptable for a variety of tasks and configurations. The system has been shown to effectively find exact or approximate symbolic solutions to various differential equations with applications in natural sciences. In this work, we highlight how our method applies to partial differential equations over multiple variables and more complex boundary and initial value conditions.

A Neuro-Symbolic Method for Solving Differential and Functional Equations

When neural networks are used to solve differential equations, they usually produce solutions in the form of black-box functions that are not directly mathematically interpretable. We introduce a method for generating symbolic expressions to solve differential equations while leveraging deep learning training methods. Unlike existing methods, our system does not require learning a language model over symbolic mathematics, making it scalable, compact, and easily adaptable for a variety of tasks and configurations. As part of the method, we propose a novel neural architecture for learning mathematical expressions to optimize a customizable objective. The system is designed to always return a valid symbolic formula, generating a useful approximation when an exact analytic solution to a differential equation is not or cannot be found. We demonstrate through examples how our method can be applied on a number of differential equations, often obtaining symbolic approximations that are useful or insightful. Furthermore, we show how the system can be effortlessly generalized to find symbolic solutions to other mathematical tasks, including integration and functional equations.