An Unsupervised Approach to Modelling Visual Data

For very large visual datasets, producing expert ground-truth data for training supervised algorithms can represent a substantial human effort. In these situations there is scope for the use of unsupervised approaches that can model collections of images and automatically summarise their content. The primary motivation for this thesis comes from the problem of labelling large visual datasets of the seafloor obtained by an Autonomous Underwater Vehicle (AUV) for ecological analysis. It is expensive to label this data, as taxonomical experts for the specific region are required, whereas automatically generated summaries can be used to focus the efforts of experts, and inform decisions on additional sampling. The contributions in this thesis arise from modelling this visual data in entirely unsupervised ways to obtain comprehensive visual summaries. Firstly, popular unsupervised image feature learning approaches are adapted to work with large datasets and unsupervised clustering algorithms. Next, using Bayesian models the performance of rudimentary scene clustering is boosted by sharing clusters between multiple related datasets, such as regular photo albums or AUV surveys. These Bayesian scene clustering models are extended to simultaneously cluster sub-image segments to form unsupervised notions of “objects” within scenes. The frequency distribution of these objects within scenes is used as the scene descriptor for simultaneous scene clustering. Finally, this simultaneous clustering model is extended to make use of whole image descriptors, which encode rudimentary spatial information, as well as object frequency distributions to describe scenes. This is achieved by unifying the previously presented Bayesian clustering models, and in so doing rectifies some of their weaknesses and limitations. Hence, the final contribution of this thesis is a practical unsupervised algorithm for modelling images from the super-pixel to album levels, and is applicable to large datasets

Sparse Modeling for Image and Vision Processing

In recent years, a large amount of multi-disciplinary research has been conducted on sparse models and their applications. In statistics and machine learning, the sparsity principle is used to perform model selection---that is, automatically selecting a simple model among a large collection of them. In signal processing, sparse coding consists of representing data with linear combinations of a few dictionary elements. Subsequently, the corresponding tools have been widely adopted by several scientific communities such as neuroscience, bioinformatics, or computer vision. The goal of this monograph is to offer a self-contained view of sparse modeling for visual recognition and image processing. More specifically, we focus on applications where the dictionary is learned and adapted to data, yielding a compact representation that has been successful in various contexts.Comment: 205 pages, to appear in Foundations and Trends in Computer Graphics and Visio

Advanced Computational Methods for Oncological Image Analysis

[Cancer is the second most common cause of death worldwide and encompasses highly variable clinical and biological scenarios. Some of the current clinical challenges are (i) early diagnosis of the disease and (ii) precision medicine, which allows for treatments targeted to specific clinical cases. The ultimate goal is to optimize the clinical workflow by combining accurate diagnosis with the most suitable therapies. Toward this, large-scale machine learning research can define associations among clinical, imaging, and multi-omics studies, making it possible to provide reliable diagnostic and prognostic biomarkers for precision oncology. Such reliable computer-assisted methods (i.e., artificial intelligence) together with clinicians’ unique knowledge can be used to properly handle typical issues in evaluation/quantification procedures (i.e., operator dependence and time-consuming tasks). These technical advances can significantly improve result repeatability in disease diagnosis and guide toward appropriate cancer care. Indeed, the need to apply machine learning and computational intelligence techniques has steadily increased to effectively perform image processing operations—such as segmentation, co-registration, classification, and dimensionality reduction—and multi-omics data integration.

Efficient Learning Machines

Computer scienc

Using contour information and segmentation for object registration, modeling and retrieval

This thesis considers different aspects of the utilization of contour information and syntactic and semantic image segmentation for object registration, modeling and retrieval in the context of content-based indexing and retrieval in large collections of images. Target applications include retrieval in collections of closed silhouettes, holistic w ord recognition in handwritten historical manuscripts and shape registration. Also, the thesis explores the feasibility of contour-based syntactic features for improving the correspondence of the output of bottom-up segmentation to semantic objects present in the scene and discusses the feasibility of different strategies for image analysis utilizing contour information, e.g. segmentation driven by visual features versus segmentation driven by shape models or semi-automatic in selected application scenarios. There are three contributions in this thesis. The first contribution considers structure analysis based on the shape and spatial configuration of image regions (socalled syntactic visual features) and their utilization for automatic image segmentation. The second contribution is the study of novel shape features, matching algorithms and similarity measures. Various applications of the proposed solutions are presented throughout the thesis providing the basis for the third contribution which is a discussion of the feasibility of different recognition strategies utilizing contour information. In each case, the performance and generality of the proposed approach has been analyzed based on extensive rigorous experimentation using as large as possible test collections

Hidden Markov Models

Hidden Markov Models (HMMs), although known for decades, have made a big career nowadays and are still in state of development. This book presents theoretical issues and a variety of HMMs applications in speech recognition and synthesis, medicine, neurosciences, computational biology, bioinformatics, seismology, environment protection and engineering. I hope that the reader will find this book useful and helpful for their own research

Diffeomorphic Transformations for Time Series Analysis: An Efficient Approach to Nonlinear Warping

The proliferation and ubiquity of temporal data across many disciplines has sparked interest for similarity, classification and clustering methods specifically designed to handle time series data. A core issue when dealing with time series is determining their pairwise similarity, i.e., the degree to which a given time series resembles another. Traditional distance measures such as the Euclidean are not well-suited due to the time-dependent nature of the data. Elastic metrics such as dynamic time warping (DTW) offer a promising approach, but are limited by their computational complexity, non-differentiability and sensitivity to noise and outliers. This thesis proposes novel elastic alignment methods that use parametric \& diffeomorphic warping transformations as a means of overcoming the shortcomings of DTW-based metrics. The proposed method is differentiable \& invertible, well-suited for deep learning architectures, robust to noise and outliers, computationally efficient, and is expressive and flexible enough to capture complex patterns. Furthermore, a closed-form solution was developed for the gradient of these diffeomorphic transformations, which allows an efficient search in the parameter space, leading to better solutions at convergence. Leveraging the benefits of these closed-form diffeomorphic transformations, this thesis proposes a suite of advancements that include: (a) an enhanced temporal transformer network for time series alignment and averaging, (b) a deep-learning based time series classification model to simultaneously align and classify signals with high accuracy, (c) an incremental time series clustering algorithm that is warping-invariant, scalable and can operate under limited computational and time resources, and finally, (d) a normalizing flow model that enhances the flexibility of affine transformations in coupling and autoregressive layers.Comment: PhD Thesis, defended at the University of Navarra on July 17, 2023. 277 pages, 8 chapters, 1 appendi

Characterising Exoplanet Atmospheres using Traditional Methods and Supervised Machine Learning

Since the discovery of the first extrasolar planets over 25 years ago, the field of exoplanet research has exploded. Today we have over 4000 confirmed exoplanets, with a wide variety of sizes, orbital separations, and host stars. The characterisation of this diverse population of objects has led to exciting discoveries about the conditions of alien worlds. Future technological advances are expected to provide an abundance of exoplanet spectra with a higher precision and sensitivity than ever before. This calls for a parallel advancement in the accuracy and speed of atmospheric models to interpret this influx of data. In this thesis, my work on atmospheric retrievals is presented. Starting with traditional techniques, my first thesis paper applies a Bayesian retrieval in combination with an analytical atmospheric model to the Hubble transmission spectra of 38 different exoplanets. My second paper considers the theoretical model of the sodium doublet, and the effect of dropping the assumption of local-thermodynamic equilibrium. From here, I went on to develop a method that uses supervised machine learning to improve the speed and efficiency of the retrieval. This method was explained and tested in a collaborative paper with machine learning experts in Bern. The machine learning retrieval is then applied in several follow-up studies, covering a range of different scenarios. One of these was my final thesis paper, which further extends the new retrieval to high-resolution spectra using the cross-correlation function. In addition to my own papers, I have contributed to a number of studies led by collaborators by running retrievals, assisting other students, and participating in scientific discussions. I have also worked on several observing proposals, both for high-resolution ground-based observatories and for the upcoming James Webb Space Telescope. I plan to continue my work on exoplanet characterisation and machine learning in the future, using the technique to combine high- and low-resolution spectra to gain further insight into the atmospheres of these distant planets. The speed and efficiency of machine learning will also allow for statistical studies of exoplanets as the quantity of atmospheric spectra from new and upcoming telescopes escalates. Not only will these studies teach us about the conditions and potential habitability of exoplanets, but they will also answer questions about planet formation, diverse chemical processes, and the uniqueness of our solar system

Advanced receivers for distributed cooperation in mobile ad hoc networks

Mobile ad hoc networks (MANETs) are rapidly deployable wireless communications systems, operating with minimal coordination in order to avoid spectral efficiency losses caused by overhead. Cooperative transmission schemes are attractive for MANETs, but the distributed nature of such protocols comes with an increased level of interference, whose impact is further amplified by the need to push the limits of energy and spectral efficiency. Hence, the impact of interference has to be mitigated through with the use PHY layer signal processing algorithms with reasonable computational complexity. Recent advances in iterative digital receiver design techniques exploit approximate Bayesian inference and derivative message passing techniques to improve the capabilities of well-established turbo detectors. In particular, expectation propagation (EP) is a flexible technique which offers attractive complexity-performance trade-offs in situations where conventional belief propagation is limited by computational complexity. Moreover, thanks to emerging techniques in deep learning, such iterative structures are cast into deep detection networks, where learning the algorithmic hyper-parameters further improves receiver performance. In this thesis, EP-based finite-impulse response decision feedback equalizers are designed, and they achieve significant improvements, especially in high spectral efficiency applications, over more conventional turbo-equalization techniques, while having the advantage of being asymptotically predictable. A framework for designing frequency-domain EP-based receivers is proposed, in order to obtain detection architectures with low computational complexity. This framework is theoretically and numerically analysed with a focus on channel equalization, and then it is also extended to handle detection for time-varying channels and multiple-antenna systems. The design of multiple-user detectors and the impact of channel estimation are also explored to understand the capabilities and limits of this framework. Finally, a finite-length performance prediction method is presented for carrying out link abstraction for the EP-based frequency domain equalizer. The impact of accurate physical layer modelling is evaluated in the context of cooperative broadcasting in tactical MANETs, thanks to a flexible MAC-level simulato