Machine Learning for Robust Understanding of Scene Materials in Hyperspectral Images

The major challenges in hyperspectral (HS) imaging and data analysis are expensive sensors, high dimensionality of the signal, limited ground truth, and spectral variability. This dissertation develops and analyzes machine learning based methods to address these problems. In the first part, we examine one of the most important HS data analysis tasks-vegetation parameter estimation. We present two Gaussian processes based approaches for improving the accuracy of vegetation parameter retrieval when ground truth is limited and/or spectral variability is high. The first is the adoption of covariance functions based on well-established metrics, such as, spectral angle and spectral correlation, which are known to be better measures of similarity for spectral data. The second is the joint modeling of related vegetation parameters by multitask Gaussian processes so that the prediction accuracy of the vegetation parameter of interest can be improved with the aid of related vegetation parameters for which a larger set of ground truth is available. The efficacy of the proposed methods is demonstrated by comparing them against state-of-the art approaches on three real-world HS datasets and one synthetic dataset. In the second part, we demonstrate how Bayesian optimization can be applied to jointly tune the different components of hyperspectral data analysis frameworks for better performance. Experimental validation on the spatial-spectral classification framework consisting of a classifier and a Markov random field is provided. In the third part, we investigate whether high dimensional HS spectra can be reconstructed from low dimensional multispectral (MS) signals, that can be obtained from much cheaper, lower spectral resolution sensors. A novel end-to-end convolutional residual neural network architecture is proposed that can simultaneously optimize both the MS bands and the transformation to reconstruct HS spectra from MS signals by analyzing a large quantity of HS data. The learned band can be implemented in sensor hardware and the learned transformation can be incorporated in the data processing pipeline to build a low-cost hyperspectral data collection system. Using a diverse set of real-world datasets, we show how the proposed approach of optimizing MS bands along with the transformation rather than just optimizing the transformation with fixed bands, as proposed by previous studies, can drastically increase the reconstruction accuracy. Additionally, we also investigate the prospects of using reconstructed HS spectra for land cover classification

Bayesian image restoration and bacteria detection in optical endomicroscopy

Optical microscopy systems can be used to obtain high-resolution microscopic images of tissue cultures and ex vivo tissue samples. This imaging technique can be translated for in vivo, in situ applications by using optical fibres and miniature optics. Fibred optical endomicroscopy (OEM) can enable optical biopsy in organs inaccessible by any other imaging systems, and hence can provide rapid and accurate diagnosis in a short time. The raw data the system produce is difficult to interpret as it is modulated by a fibre bundle pattern, producing what is called the “honeycomb effect”. Moreover, the data is further degraded due to the fibre core cross coupling problem. On the other hand, there is an unmet clinical need for automatic tools that can help the clinicians to detect fluorescently labelled bacteria in distal lung images. The aim of this thesis is to develop advanced image processing algorithms that can address the above mentioned problems. First, we provide a statistical model for the fibre core cross coupling problem and the sparse sampling by imaging fibre bundles (honeycomb artefact), which are formulated here as a restoration problem for the first time in the literature. We then introduce a non-linear interpolation method, based on Gaussian processes regression, in order to recover an interpretable scene from the deconvolved data. Second, we develop two bacteria detection algorithms, each of which provides different characteristics. The first approach considers joint formulation to the sparse coding and anomaly detection problems. The anomalies here are considered as candidate bacteria, which are annotated with the help of a trained clinician. Although this approach provides good detection performance and outperforms existing methods in the literature, the user has to carefully tune some crucial model parameters. Hence, we propose a more adaptive approach, for which a Bayesian framework is adopted. This approach not only outperforms the proposed supervised approach and existing methods in the literature but also provides computation time that competes with optimization-based methods

Bayesian Dictionary Learning for Single and Coupled Feature Spaces

Over-complete bases offer the flexibility to represent much wider range of signals with more elementary basis atoms than signal dimension. The use of over-complete dictionaries for sparse representation has been a new trend recently and has increasingly become recognized as providing high performance for applications such as denoise, image super-resolution, inpaiting, compression, blind source separation and linear unmixing. This dissertation studies the dictionary learning for single or coupled feature spaces and its application in image restoration tasks. A Bayesian strategy using a beta process prior is applied to solve both problems. Firstly, we illustrate how to generalize the existing beta process dictionary learning method (BP) to learn dictionary for single feature space. The advantage of this approach is that the number of dictionary atoms and their relative importance may be inferred non-parametrically. Next, we propose a new beta process joint dictionary learning method (BP-JDL) for coupled feature spaces, where the learned dictionaries also reflect the relationship between the two spaces. Compared to previous couple feature spaces dictionary learning algorithms, our algorithm not only provides dictionaries that customized to each feature space, but also adds more consistent and accurate mapping between the two feature spaces. This is due to the unique property of the beta process model that the sparse representation can be decomposed to values and dictionary atom indicators. The proposed algorithm is able to learn sparse representations that correspond to the same dictionary atoms with the same sparsity but different values in coupled feature spaces, thus bringing consistent and accurate mapping between coupled feature spaces. Two applications, single image super-resolution and inverse halftoning, are chosen to evaluate the performance of the proposed Bayesian approach. In both cases, the Bayesian approach, either for single feature space or coupled feature spaces, outperforms state-of-the-art methods in comparative domains

Hyperspectral and Multispectral Image Fusion Using the Conditional Denoising Diffusion Probabilistic Model

Hyperspectral images (HSI) have a large amount of spectral information reflecting the characteristics of matter, while their spatial resolution is low due to the limitations of imaging technology. Complementary to this are multispectral images (MSI), e.g., RGB images, with high spatial resolution but insufficient spectral bands. Hyperspectral and multispectral image fusion is a technique for acquiring ideal images that have both high spatial and high spectral resolution cost-effectively. Many existing HSI and MSI fusion algorithms rely on known imaging degradation models, which are often not available in practice. In this paper, we propose a deep fusion method based on the conditional denoising diffusion probabilistic model, called DDPM-Fus. Specifically, the DDPM-Fus contains the forward diffusion process which gradually adds Gaussian noise to the high spatial resolution HSI (HrHSI) and another reverse denoising process which learns to predict the desired HrHSI from its noisy version conditioning on the corresponding high spatial resolution MSI (HrMSI) and low spatial resolution HSI (LrHSI). Once the training is completes, the proposed DDPM-Fus implements the reverse process on the test HrMSI and LrHSI to generate the fused HrHSI. Experiments conducted on one indoor and two remote sensing datasets show the superiority of the proposed model when compared with other advanced deep learningbased fusion methods. The codes of this work will be opensourced at this address: https://github.com/shuaikaishi/DDPMFus for reproducibility