A primer on correlation-based dimension reduction methods for multi-omics analysis

The continuing advances of omic technologies mean that it is now more tangible to measure the numerous features collectively reflecting the molecular properties of a sample. When multiple omic methods are used, statistical and computational approaches can exploit these large, connected profiles. Multi-omics is the integration of different omic data sources from the same biological sample. In this review, we focus on correlation-based dimension reduction approaches for single omic datasets, followed by methods for pairs of omics datasets, before detailing further techniques for three or more omic datasets. We also briefly detail network methods when three or more omic datasets are available and which complement correlation-oriented tools. To aid readers new to this area, these are all linked to relevant R packages that can implement these procedures. Finally, we discuss scenarios of experimental design and present road maps that simplify the selection of appropriate analysis methods. This review will guide researchers navigate the emerging methods for multi-omics and help them integrate diverse omic datasets appropriately and embrace the opportunity of population multi-omics.Comment: 30 pages, 2 figures, 6 table

Tensor Decompositions for Signal Processing Applications From Two-way to Multiway Component Analysis

The widespread use of multi-sensor technology and the emergence of big datasets has highlighted the limitations of standard flat-view matrix models and the necessity to move towards more versatile data analysis tools. We show that higher-order tensors (i.e., multiway arrays) enable such a fundamental paradigm shift towards models that are essentially polynomial and whose uniqueness, unlike the matrix methods, is guaranteed under verymild and natural conditions. Benefiting fromthe power ofmultilinear algebra as theirmathematical backbone, data analysis techniques using tensor decompositions are shown to have great flexibility in the choice of constraints that match data properties, and to find more general latent components in the data than matrix-based methods. A comprehensive introduction to tensor decompositions is provided from a signal processing perspective, starting from the algebraic foundations, via basic Canonical Polyadic and Tucker models, through to advanced cause-effect and multi-view data analysis schemes. We show that tensor decompositions enable natural generalizations of some commonly used signal processing paradigms, such as canonical correlation and subspace techniques, signal separation, linear regression, feature extraction and classification. We also cover computational aspects, and point out how ideas from compressed sensing and scientific computing may be used for addressing the otherwise unmanageable storage and manipulation problems associated with big datasets. The concepts are supported by illustrative real world case studies illuminating the benefits of the tensor framework, as efficient and promising tools for modern signal processing, data analysis and machine learning applications; these benefits also extend to vector/matrix data through tensorization. Keywords: ICA, NMF, CPD, Tucker decomposition, HOSVD, tensor networks, Tensor Train

Enhancing Deep Learning Models through Tensorization: A Comprehensive Survey and Framework

The burgeoning growth of public domain data and the increasing complexity of deep learning model architectures have underscored the need for more efficient data representation and analysis techniques. This paper is motivated by the work of (Helal, 2023) and aims to present a comprehensive overview of tensorization. This transformative approach bridges the gap between the inherently multidimensional nature of data and the simplified 2-dimensional matrices commonly used in linear algebra-based machine learning algorithms. This paper explores the steps involved in tensorization, multidimensional data sources, various multiway analysis methods employed, and the benefits of these approaches. A small example of Blind Source Separation (BSS) is presented comparing 2-dimensional algorithms and a multiway algorithm in Python. Results indicate that multiway analysis is more expressive. Contrary to the intuition of the dimensionality curse, utilising multidimensional datasets in their native form and applying multiway analysis methods grounded in multilinear algebra reveal a profound capacity to capture intricate interrelationships among various dimensions while, surprisingly, reducing the number of model parameters and accelerating processing. A survey of the multi-away analysis methods and integration with various Deep Neural Networks models is presented using case studies in different application domains.Comment: 34 pages, 8 figures, 4 table

FML: Face Model Learning from Videos

Monocular image-based 3D reconstruction of faces is a long-standing problem in computer vision. Since image data is a 2D projection of a 3D face, the resulting depth ambiguity makes the problem ill-posed. Most existing methods rely on data-driven priors that are built from limited 3D face scans. In contrast, we propose multi-frame video-based self-supervised training of a deep network that (i) learns a face identity model both in shape and appearance while (ii) jointly learning to reconstruct 3D faces. Our face model is learned using only corpora of in-the-wild video clips collected from the Internet. This virtually endless source of training data enables learning of a highly general 3D face model. In order to achieve this, we propose a novel multi-frame consistency loss that ensures consistent shape and appearance across multiple frames of a subject's face, thus minimizing depth ambiguity. At test time we can use an arbitrary number of frames, so that we can perform both monocular as well as multi-frame reconstruction.Comment: CVPR 2019 (Oral). Video: https://www.youtube.com/watch?v=SG2BwxCw0lQ, Project Page: https://gvv.mpi-inf.mpg.de/projects/FML19

Tensor Networks for Dimensionality Reduction and Large-Scale Optimizations. Part 2 Applications and Future Perspectives

Part 2 of this monograph builds on the introduction to tensor networks and their operations presented in Part 1. It focuses on tensor network models for super-compressed higher-order representation of data/parameters and related cost functions, while providing an outline of their applications in machine learning and data analytics. A particular emphasis is on the tensor train (TT) and Hierarchical Tucker (HT) decompositions, and their physically meaningful interpretations which reflect the scalability of the tensor network approach. Through a graphical approach, we also elucidate how, by virtue of the underlying low-rank tensor approximations and sophisticated contractions of core tensors, tensor networks have the ability to perform distributed computations on otherwise prohibitively large volumes of data/parameters, thereby alleviating or even eliminating the curse of dimensionality. The usefulness of this concept is illustrated over a number of applied areas, including generalized regression and classification (support tensor machines, canonical correlation analysis, higher order partial least squares), generalized eigenvalue decomposition, Riemannian optimization, and in the optimization of deep neural networks. Part 1 and Part 2 of this work can be used either as stand-alone separate texts, or indeed as a conjoint comprehensive review of the exciting field of low-rank tensor networks and tensor decompositions.Comment: 232 page

Pantomimic Gestures for Human-Robot Interaction

This work introduces a pantomimic gesture interface, which classifies human hand gestures using unmanned aerial vehicle (UAV) behaviour recordings as training data. We argue that pantomimic gestures are more intuitive than iconic gestures and show that a pantomimic gesture recognition strategy using micro UAV behaviour recordings can be more robust than one trained directly using hand gestures. Hand gestures are isolated by applying a maximum information criterion, with features extracted using principal component analysis (PCA) and compared using a nearest neighbour classifier. These features are biased in that they are better suited to classifying certain behaviours. We show how a Bayesian update step accounting for the geometry of training features compensates for this, resulting in fairer classification results, and introduce a weighted voting system to aid in sequence labelling.This is the author accepted manuscript. The final version is available from IEEE via http://dx.doi.org/10.1109/TRO.2015.247595

Residual Tensor Train: A Quantum-inspired Approach for Learning Multiple Multilinear Correlations

States of quantum many-body systems are defined in a high-dimensional Hilbert space, where rich and complex interactions among subsystems can be modelled. In machine learning, complex multiple multilinear correlations may also exist within input features. In this paper, we present a quantum-inspired multilinear model, named Residual Tensor Train (ResTT), to capture the multiple multilinear correlations of features, from low to high orders, within a single model. ResTT is able to build a robust decision boundary in a high-dimensional space for solving fitting and classification tasks. In particular, we prove that the fully-connected layer and the Volterra series can be taken as special cases of ResTT. Furthermore, we derive the rule for weight initialization that stabilizes the training of ResTT based on a mean-field analysis. We prove that such a rule is much more relaxed than that of TT, which means ResTT can easily address the vanishing and exploding gradient problem that exists in the existing TT models. Numerical experiments demonstrate that ResTT outperforms the state-of-the-art tensor network and benchmark deep learning models on MNIST and Fashion-MNIST datasets. Moreover, ResTT achieves better performance than other statistical methods on two practical examples with limited data which are known to have complex feature interactions.Comment: 12 pages, 6 figure

Tensor Networks for Dimensionality Reduction and Large-Scale Optimizations. Part 2 Applications and Future Perspectives

Part 2 of this monograph builds on the introduction to tensor networks and their operations presented in Part 1. It focuses on tensor network models for super-compressed higher-order representation of data/parameters and related cost functions, while providing an outline of their applications in machine learning and data analytics. A particular emphasis is on the tensor train (TT) and Hierarchical Tucker (HT) decompositions, and their physically meaningful interpretations which reflect the scalability of the tensor network approach. Through a graphical approach, we also elucidate how, by virtue of the underlying low-rank tensor approximations and sophisticated contractions of core tensors, tensor networks have the ability to perform distributed computations on otherwise prohibitively large volumes of data/parameters, thereby alleviating or even eliminating the curse of dimensionality. The usefulness of this concept is illustrated over a number of applied areas, including generalized regression and classification (support tensor machines, canonical correlation analysis, higher order partial least squares), generalized eigenvalue decomposition, Riemannian optimization, and in the optimization of deep neural networks. Part 1 and Part 2 of this work can be used either as stand-alone separate texts, or indeed as a conjoint comprehensive review of the exciting field of low-rank tensor networks and tensor decompositions.Comment: 232 page

Latent variable regression and applications to planetary seismic instrumentation

The work presented in this thesis is framed by the concept of latent variables, a modern data analytics approach. A latent variable represents an extracted component from a dataset which is not directly measured. The concept is first applied to combat the problem of ill-posed regression through the promising method of partial least squares (PLS). In this context the latent variables within a data matrix are extracted through an iterative algorithm based on cross-covariance as an optimisation criterion. This work first extends the PLS algorithm, using adaptive and recursive techniques, for online, non-stationary data applications. The standard PLS algorithm is further generalised for complex-, quaternion- and tensor-valued data. In doing so it is shown that the multidimensional algebras facilitate physically meaningful representations, demonstrated through smart-grid frequency estimation and image-classification tasks. The second part of the thesis uses this knowledge to inform a performance analysis of the MEMS microseismometer implemented for the InSight mission to Mars. This is given in terms of the sensor's intrinsic self-noise, the estimation of which is achieved from experimental data with a colocated instrument. The standard coherence and proposed delta noise estimators are analysed with respect to practical issues. The implementation of algorithms for the alignment, calibration and post-processing of the data then enabled a definitive self-noise estimate, validated from data acquired in ultra-quiet, deep-space environment. A method for the decorrelation of the microseismometer's output from its thermal response is proposed. To do so a novel sensor fusion approach based on the Kalman filter is developed for a full-band transfer-function correction, in contrast to the traditional ill-posed frequency division method. This algorithm was applied to experimental data which determined the thermal model coefficients while validating the sensor's performance at tidal frequencies 1E-5Hz and in extreme environments at -65C. This thesis, therefore, provides a definitive view of the latent variables perspective. This is achieved through the general algorithms developed for regression with multidimensional data and the bespoke application to seismic instrumentation.Open Acces