Diffusion Models for Interferometric Satellite Aperture Radar

Probabilistic Diffusion Models (PDMs) have recently emerged as a very promising class of generative models, achieving high performance in natural image generation. However, their performance relative to non-natural images, like radar-based satellite data, remains largely unknown. Generating large amounts of synthetic (and especially labelled) satellite data is crucial to implement deep-learning approaches for the processing and analysis of (interferometric) satellite aperture radar data. Here, we leverage PDMs to generate several radar-based satellite image datasets. We show that PDMs succeed in generating images with complex and realistic structures, but that sampling time remains an issue. Indeed, accelerated sampling strategies, which work well on simple image datasets like MNIST, fail on our radar datasets. We provide a simple and versatile open-source https://github.com/thomaskerdreux/PDM_SAR_InSAR_generation to train, sample and evaluate PDMs using any dataset on a single GPU

High speed in-process defect detection in metal additive manufacturing

Additive manufacturing (AM) is defined as the process of joining materials to make objects from 3D model data, usually layer upon layer, as opposed to subtractive manufacturing technologies. This fabricating technique is also famously known as ‘3D printing’. Although its entire manufacturing chain is becoming more mature by improved pre-defined design, more accurate heat input and motion system and cleaner in-chamber atmosphere, there are still a number of influential factors that can have a negative impact on the manufacturing process that introduce ‘defects’, which will greatly lessen the density of the parts or even result in failure. For this reason, it is critical to be able to discover them effectively during the manufacturing process. This thesis aims to develop a methodology for the measurement and characterisation of surface texture of AM parts. Typically, optical metrology instruments including focus variation (FV) microscopy and fringe projection (FP) have been used to measure the surface texture of AM samples due to their suitability and reliability in the field of metrology. The thesis also develops optimum filtration methodology to characterise the AM surface by comparing different filters. In the recent decades, machine learning (ML) is presenting a high robustness and applicability in defect detection in comparison to the traditional digital image processing technique. In this thesis, several ML techniques have been investigated into in terms of their suitability for the research based on the processed data secured from the optical measuring instrument. A detailed defect review that collects the information in terms of the defects in LPBF process based on the related research of the global researchers is given. It provides the details about different types of defects and discusses the potential correlation between process parameters and generated defects. ML and AM are both research fields that have developed rapidly in recent decades. In particular, the combination of the two can effectively achieve the purpose of AM parameter optimisation, process control and defect detection. A review of the adaptability of ML to different types of data and its application in feature extraction to achieve in-line or offline defect detection is given. Specifically, it demonstrates how to select proper ML technique given various types of data and how to choose appropriate ML model depending on different forms of defect detection (defect classification and defect segmentation). For data acquisition, the parameters including the magnification of objective lens and illumination source of the optical instrument are optimised to provide accurate and reliable data. Then the surface is pre-processed and filtered with the discovered optimal filtration method. The applicability of different types of machine learning methods for defect detection is also investigated. Results show that principal component analysis may not be a suitable tool for classifying defects if using exclusively whereas convolutional neural network and U-Net (full convolutional network) have shown good performance in correctly classifying defects and segmenting defects from the measured surface. For future work, more measurement instruments which can potentially achieve efficient and accurate metrology can be considered being developed and used, and the variety of samples needs to be increased to provide more types of surface topographies. In addition, how to improve the applicability of PCA in defect classification for AM parts can be studied on and more values of hyperparameters and number of parameters of neural networks can be used to further improve the suitability of the model for the training data

Towards PACE-CAD Systems

Despite phenomenal advancements in the availability of medical image datasets and the development of modern classification algorithms, Computer-Aided Diagnosis (CAD) has had limited practical exposure in the real-world clinical workflow. This is primarily because of the inherently demanding and sensitive nature of medical diagnosis that can have far-reaching and serious repercussions in case of misdiagnosis. In this work, a paradigm called PACE (Pragmatic, Accurate, Confident, & Explainable) is presented as a set of some of must-have features for any CAD. Diagnosis of glaucoma using Retinal Fundus Images (RFIs) is taken as the primary use case for development of various methods that may enrich an ordinary CAD system with PACE. However, depending on specific requirements for different methods, other application areas in ophthalmology and dermatology have also been explored. Pragmatic CAD systems refer to a solution that can perform reliably in day-to-day clinical setup. In this research two, of possibly many, aspects of a pragmatic CAD are addressed. Firstly, observing that the existing medical image datasets are small and not representative of images taken in the real-world, a large RFI dataset for glaucoma detection is curated and published. Secondly, realising that a salient attribute of a reliable and pragmatic CAD is its ability to perform in a range of clinically relevant scenarios, classification of 622 unique cutaneous diseases in one of the largest publicly available datasets of skin lesions is successfully performed. Accuracy is one of the most essential metrics of any CAD system's performance. Domain knowledge relevant to three types of diseases, namely glaucoma, Diabetic Retinopathy (DR), and skin lesions, is industriously utilised in an attempt to improve the accuracy. For glaucoma, a two-stage framework for automatic Optic Disc (OD) localisation and glaucoma detection is developed, which marked new state-of-the-art for glaucoma detection and OD localisation. To identify DR, a model is proposed that combines coarse-grained classifiers with fine-grained classifiers and grades the disease in four stages with respect to severity. Lastly, different methods of modelling and incorporating metadata are also examined and their effect on a model's classification performance is studied. Confidence in diagnosing a disease is equally important as the diagnosis itself. One of the biggest reasons hampering the successful deployment of CAD in the real-world is that medical diagnosis cannot be readily decided based on an algorithm's output. Therefore, a hybrid CNN architecture is proposed with the convolutional feature extractor trained using point estimates and a dense classifier trained using Bayesian estimates. Evaluation on 13 publicly available datasets shows the superiority of this method in terms of classification accuracy and also provides an estimate of uncertainty for every prediction. Explainability of AI-driven algorithms has become a legal requirement after Europe’s General Data Protection Regulations came into effect. This research presents a framework for easy-to-understand textual explanations of skin lesion diagnosis. The framework is called ExAID (Explainable AI for Dermatology) and relies upon two fundamental modules. The first module uses any deep skin lesion classifier and performs detailed analysis on its latent space to map human-understandable disease-related concepts to the latent representation learnt by the deep model. The second module proposes Concept Localisation Maps, which extend Concept Activation Vectors by locating significant regions corresponding to a learned concept in the latent space of a trained image classifier. This thesis probes many viable solutions to equip a CAD system with PACE. However, it is noted that some of these methods require specific attributes in datasets and, therefore, not all methods may be applied on a single dataset. Regardless, this work anticipates that consolidating PACE into a CAD system can not only increase the confidence of medical practitioners in such tools but also serve as a stepping stone for the further development of AI-driven technologies in healthcare

Recommended Implementation of Quantitative Susceptibility Mapping for Clinical Research in The Brain: A Consensus of the ISMRM Electro-Magnetic Tissue Properties Study Group

This article provides recommendations for implementing quantitative susceptibility mapping (QSM) for clinical brain research. It is a consensus of the ISMRM Electro-Magnetic Tissue Properties Study Group. While QSM technical development continues to advance rapidly, the current QSM methods have been demonstrated to be repeatable and reproducible for generating quantitative tissue magnetic susceptibility maps in the brain. However, the many QSM approaches available give rise to the need in the neuroimaging community for guidelines on implementation. This article describes relevant considerations and provides specific implementation recommendations for all steps in QSM data acquisition, processing, analysis, and presentation in scientific publications. We recommend that data be acquired using a monopolar 3D multi-echo GRE sequence, that phase images be saved and exported in DICOM format and unwrapped using an exact unwrapping approach. Multi-echo images should be combined before background removal, and a brain mask created using a brain extraction tool with the incorporation of phase-quality-based masking. Background fields should be removed within the brain mask using a technique based on SHARP or PDF, and the optimization approach to dipole inversion should be employed with a sparsity-based regularization. Susceptibility values should be measured relative to a specified reference, including the common reference region of whole brain as a region of interest in the analysis, and QSM results should be reported with - as a minimum - the acquisition and processing specifications listed in the last section of the article. These recommendations should facilitate clinical QSM research and lead to increased harmonization in data acquisition, analysis, and reporting

Advancing the search for gravitational waves using machine learning

Over 100 years ago Einstein formulated his now famous theory of General Relativity. In his theory he lays out a set of equations which lead to the beginning of a brand-new astronomical field, Gravitational wave (GW) astronomy. The LIGO-Virgo-KAGRA Collaboration (LVK)’s aim is the detection of GW events from some of the most violent and cataclysmic events in the known universe. The LVK detectors are composed of large-scale Michelson Morley interferometers which are able to detect GWs from a range of sources including: binary black holes (BBHs), binary neutron stars (BNSs), neutron star black holes (NSBHs), supernovae and stochastic GWs. Although these GW events release an incredible amount of energy, the amplitudes of the GWs from such events are also incredibly small. The LVK uses sophisticated techniques such as matched filtering and Bayesian inference in order to both detect and infer source parameters from GW events. Although optimal under many circumstances, these standard methods are computationally expensive to use. Given that the expected number of GW detections by the LVK will be of order 100s in the coming years, there is an urgent need for less computationally expensive detection and parameter inference techniques. A possible solution to reducing the computational expense of such techniques is the exciting field of machine learning (ML). In the first chapter of this thesis, GWs are introduced and it is explained how GWs are detected by the LVK. The sources of GWs are given, as well as methodologies for detecting various source types, such as matched filtering. In addition to GW signal detection techniques, the methods for estimating the parameters of detected GW signals is described (i.e. Bayesian inference). In the second chapter several machine learning algorithms are introduced including: perceptrons, convolutional neural networks (CNNs), autoencoders (AEs), variational autoencoders (VAEs) and conditional variational autoencoders (CVAEs). Practical advice on training/data augmentation techniques is also provided to the reader. In the third chapter, a survey on several ML techniques applied a variety of GW problems are shown. In this thesis, various ML and statistical techniques were deployed such as CVAEs and CNNs in two first-of-their-kind proof-of-principle studies. In the fourth chapter it is described how a CNN may be used to match the sensitivity of matched filtering, the standard technique used by the LVK for detecting GWs. It was shown how a CNN may be trained using simulated BBH waveforms buried in Gaussian noise and signals with Gaussian noise alone. Results of the CNN classification predictions were compared to results from matched filtering given the same testing data as the CNN. In the results it was demonstrated through receiver operating characteristics and efficiency curves that the ML approach is able to achieve the same levels of sensitivity as that of matched filtering. It is also shown that the CNN approach is able to generate predictions in low-latency. Given approximately 25000 GW time series, the CNN is able to produce classification predictions for all 25000 in 1s. In the fifth and sixth chapters, it is shown how CVAEs may be used in order to perform Bayesian inference. A CVAE was trained using simulated BBH waveforms in Gaussian noise, as well as the source parameter values of those waveforms. When testing, the CVAE is only supplied the BBH waveform and is able to produce samples from the Bayesian posterior. Results were compared to that of several standard Bayesian samplers used by the LVK including: Dynesty, ptemcee, emcee, and CPnest. It is shown that when properly trained the CVAE method is able to produce Bayesian posteriors which are consistent with other Bayesian samplers. Results are quantified using a variety of figures of merit such as probability-probability (p-p) plots in order to check the 1-dimensional marginalised posteriors from all approaches are self-consistent with the frequentist perspective. The Jensen—Shannon (JS)-divergence was also employed in order to compute the similarity of different posterior distributions from one another, as well as other figures of merit. It was also demonstrated that the CVAE model was able to produce posteriors with 8000 samples in under a second, representing a 6 order of magnitude increase in performance over traditional sampling methods

Machine learning for the automation and optimisation of optical coordinate measurement

Camera based methods for optical coordinate metrology are growing in popularity due to their non-contact probing technique, fast data acquisition time, high point density and high surface coverage. However, these optical approaches are often highly user dependent, have high dependence on accurate system characterisation, and can be slow in processing the raw data acquired during measurement. Machine learning approaches have the potential to remedy the shortcomings of such optical coordinate measurement systems. The aim of this thesis is to remove dependence on the user entirely by enabling full automation and optimisation of optical coordinate measurements for the first time. A novel software pipeline is proposed, built, and evaluated which will enable automated and optimised measurements to be conducted. No such automated and optimised system for performing optical coordinate measurements currently exists. The pipeline can be roughly summarised as follows: intelligent characterisation -> view planning -> object pose estimation -> automated data acquisition -> optimised reconstruction. Several novel methods were developed in order to enable the embodiment of this pipeline. Chapter 4 presents an intelligent camera characterisation (the process of determining a mathematical model of the optical system) is performed using a hybrid approach wherein an EfficientNet convolutional neural network provides sub-pixel corrections to feature locations provided by the popular OpenCV library. The proposed characterisation scheme is shown to robustly refine the characterisation result as quantified by a 50 % reduction in the mean residual magnitude. The camera characterisation is performed before measurements are performed and the results are fed as an input to the pipeline. Chapter 5 presents a novel genetic optimisation approach is presented to create an imaging strategy, ie. the positions from which data should be captured relative to part’s specific geometry. This approach exploits the computer aided design (CAD) data of a given part, ensuring any measurement is optimal given a specific target geometry. This view planning approach is shown to give reconstructions with closer agreement to tactile coordinate measurement machine (CMM) results from 18 images compared to unoptimised measurements using 60 images. This view planning algorithm assumes the part is perfectly placed in the centre of the measurement volume so is first adjusted for an arbitrary placement of the part before being used for data acquistion. Chapter 6 presents a generative model for the creation of surface texture data is presented, allowing the generation of synthetic butt realistic datasets for the training of statistical models. The surface texture generated by the proposed model is shown to be quantitatively representative of real focus variation microscope measurements. The model developed in this chapter is used to produce large synthetic but realistic datasets for the training of further statistical models. Chapter 7 presents an autonomous background removal approach is proposed which removes superfluous data from images captured during a measurement. Using images processed by this algorithm to reconstruct a 3D measurement of an object is shown to be effective in reducing data processing times and improving measurement results. Use the proposed background removal on images before reconstruction are shown to benefit from up to a 41 % reduction in data processing times, a reduction in superfluous background points of up to 98 %, an increase in point density on the object surface of up to 10 %, and an improved agreement with CMM as measured by both a reduction in outliers and reduction in the standard deviation of point to mesh distances of up to 51 microns. The background removal algorithm is used to both improve the final reconstruction and within stereo pose estimation. Finally, in Chapter 8, two methods (one monocular and one stereo) for establishing the initial pose of the part to be measured relative to the measurement volume are presented. This is an important step to enabling automation as it allows the user to place the object at an arbitrary location in the measurement volume and for the pipeline to adjust the imaging strategy to account for this placement, enabling the optimised view plan to be carried out without the need for special part fixturing. It is shown that the monocular method can locate a part to within an average of 13 mm and the stereo method can locate apart to within an average of 0.44 mm as evaluated on 240 test images. Pose estimation is used to provide a correction to the view plan for an arbitrary part placement without the need for specialised fixturing or fiducial marking. This pipeline enables an inexperienced user to place a part anywhere in the measurement volume of a system and, from the part’s associated CAD data, the system will perform an optimal measurement without the need for any user input. Each new method which was developed as part of this pipeline has been validated against real experimental data from current measurement systems and shown to be effective. In future work given in Section 9.1, a possible hardware integration of the methods developed in this thesis is presented. Although the creation of this hardware is beyond the scope of this thesis