Deep generative modelling of the imaged human brain

Human-machine symbiosis is a very promising opportunity for the field of neurology given that the interpretation of the imaged human brain is a trivial feat for neither entity. However, before machine learning systems can be used in real world clinical situations, many issues with automated analysis must first be solved. In this thesis I aim to address what I consider the three biggest hurdles to the adoption of automated machine learning interpretative systems. For each issue, I will first elucidate the reader on its importance given the overarching narratives of both neurology and machine learning, and then showcase my proposed solutions to these issues through the use of deep generative models of the imaged human brain. First, I start by addressing what is an uncontroversial and universal sign of intelligence: the ability to extrapolate knowledge to unseen cases. Human neuroradiologists have studied the anatomy of the healthy brain and can therefore, with some success, identify most pathologies present on an imaged brain, even without having ever been previously exposed to them. Current discriminative machine learning systems require vast amounts of labelled data in order to accurately identify diseases. In this first part I provide a generative framework that permits machine learning models to more efficiently leverage unlabelled data for better diagnoses with either none or small amounts of labels. Secondly, I address a major ethical concern in medicine: equitable evaluation of all patients, regardless of demographics or other identifying characteristics. This is, unfortunately, something that even human practitioners fail at, making the matter ever more pressing: unaddressed biases in data will become biases in the models. To address this concern I suggest a framework through which a generative model synthesises demographically counterfactual brain imaging to successfully reduce the proliferation of demographic biases in discriminative models. Finally, I tackle the challenge of spatial anatomical inference, a task at the centre of the field of lesion-deficit mapping, which given brain lesions and associated cognitive deficits attempts to discover the true functional anatomy of the brain. I provide a new Bayesian generative framework and implementation that allows for greatly improved results on this challenge, hopefully, paving part of the road towards a greater and more complete understanding of the human brain

Survey of Image Processing Techniques for Brain Pathology Diagnosis: Challenges and Opportunities

In recent years, a number of new products introduced to the global market combine intelligent robotics, artificial intelligence and smart interfaces to provide powerful tools to support professional decision making. However, while brain disease diagnosis from the brain scan images is supported by imaging robotics, the data analysis to form a medical diagnosis is performed solely by highly trained medical professionals. Recent advances in medical imaging techniques, artificial intelligence, machine learning and computer vision present new opportunities to build intelligent decision support tools to aid the diagnostic process, increase the disease detection accuracy, reduce error, automate the monitoring of patient's recovery, and discover new knowledge about the disease cause and its treatment. This article introduces the topic of medical diagnosis of brain diseases from the MRI based images. We describe existing, multi-modal imaging techniques of the brain's soft tissue and describe in detail how are the resulting images are analyzed by a radiologist to form a diagnosis. Several comparisons between the best results of classifying natural scenes and medical image analysis illustrate the challenges of applying existing image processing techniques to the medical image analysis domain. The survey of medical image processing methods also identified several knowledge gaps, the need for automation of image processing analysis, and the identification of the brain structures in the medical images that differentiate healthy tissue from a pathology. This survey is grounded in the cases of brain tumor analysis and the traumatic brain injury diagnoses, as these two case studies illustrate the vastly different approaches needed to define, extract, and synthesize meaningful information from multiple MRI image sets for a diagnosis. Finally, the article summarizes artificial intelligence frameworks that are built as multi-stage, hybrid, hierarchical information processing work-flows and the benefits of applying these models for medical diagnosis to build intelligent physician's aids with knowledge transparency, expert knowledge embedding, and increased analytical quality

On Improving Generalization of CNN-Based Image Classification with Delineation Maps Using the CORF Push-Pull Inhibition Operator

Deployed image classification pipelines are typically dependent on the images captured in real-world environments. This means that images might be affected by different sources of perturbations (e.g. sensor noise in low-light environments). The main challenge arises by the fact that image quality directly impacts the reliability and consistency of classification tasks. This challenge has, hence, attracted wide interest within the computer vision communities. We propose a transformation step that attempts to enhance the generalization ability of CNN models in the presence of unseen noise in the test set. Concretely, the delineation maps of given images are determined using the CORF push-pull inhibition operator. Such an operation transforms an input image into a space that is more robust to noise before being processed by a CNN. We evaluated our approach on the Fashion MNIST data set with an AlexNet model. It turned out that the proposed CORF-augmented pipeline achieved comparable results on noise-free images to those of a conventional AlexNet classification model without CORF delineation maps, but it consistently achieved significantly superior performance on test images perturbed with different levels of Gaussian and uniform noise

Unsupervised Learning from Shollow to Deep

Machine learning plays a pivotal role in most state-of-the-art systems in many application research domains. With the rising of deep learning, massive labeled data become the solution of feature learning, which enables the model to learn automatically. Unfortunately, the trained deep learning model is hard to adapt to other datasets without fine-tuning, and the applicability of machine learning methods is limited by the amount of available labeled data. Therefore, the aim of this thesis is to alleviate the limitations of supervised learning by exploring algorithms to learn good internal representations, and invariant feature hierarchies from unlabelled data. Firstly, we extend the traditional dictionary learning and sparse coding algorithms onto hierarchical image representations in a principled way. To achieve dictionary atoms capture additional information from extended receptive fields and attain improved descriptive capacity, we present a two-pass multi-resolution cascade framework for dictionary learning and sparse coding. This cascade method allows collaborative reconstructions at different resolutions using only the same dimensional dictionary atoms. The jointly learned dictionary comprises atoms that adapt to the information available at the coarsest layer, where the support of atoms reaches a maximum range, and the residual images, where the supplementary details refine progressively a reconstruction objective. Our method generates flexible and accurate representations using only a small number of coefficients, and is efficient in computation. In the following work, we propose to incorporate the traditional self-expressiveness property into deep learning to explore better representation for subspace clustering. This architecture is built upon deep auto-encoders, which non-linearly map the input data into a latent space. Our key idea is to introduce a novel self-expressive layer between the encoder and the decoder to mimic the ``self-expressiveness'' property that has proven effective in traditional subspace clustering. Being differentiable, our new self-expressive layer provides a simple but effective way to learn pairwise affinities between all data points through a standard back-propagation procedure. Being nonlinear, our neural-network based method is able to cluster data points having complex (often nonlinear) structures. However, Subspace clustering algorithms are notorious for their scalability issues because building and processing large affinity matrices are demanding. We propose two methods to tackle this problem. One method is based on $k$-Subspace Clustering, where we introduce a method that simultaneously learns an embedding space along subspaces within it to minimize a notion of reconstruction error, thus addressing the problem of subspace clustering in an end-to-end learning paradigm. This in turn frees us from the need of having an affinity matrix to perform clustering. The other way starts from using a feed forward network to replace the spectral clustering and learn the affinities of each data from "self-expressive" layer. We introduce the Neural Collaborative Subspace Clustering, where it benefits from a classifier which determines whether a pair of points lies on the same subspace under supervision of "self-expressive" layer. Essential to our model is the construction of two affinity matrices, one from the classifier and the other from a notion of subspace self-expressiveness, to supervise training in a collaborative scheme. In summary, we make constributions on how to perform the unsupervised learning in several tasks in this thesis. It starts from traditional sparse coding and dictionary learning perspective in low-level vision. Then, we exploit how to incorporate unsupervised learning in convolutional neural networks without label information and make subspace clustering to large scale dataset. Furthermore, we also extend the clustering on dense prediction task (saliency detection)

ROBUST DEEP LEARNING METHODS FOR SOLVING INVERSE PROBLEMS IN MEDICAL IMAGING

The medical imaging field has a long history of incorporating machine learning algorithms to address inverse problems in image acquisition and analysis. With the impressive successes of deep neural networks on natural images, we seek to answer the obvious question: do these successes also transfer to the medical image domain? The answer may seem straightforward on the surface. Tasks like image-to-image transformation, segmentation, detection, etc., have direct applications for medical images. For example, metal artifact reduction for Computed Tomography (CT) and reconstruction from undersampled k-space signal for Magnetic Resonance (MR) imaging can be formulated as an image-to-image transformation; lesion/tumor detection and segmentation are obvious applications for higher level vision tasks. While these tasks may be similar in formulation, many practical constraints and requirements exist in solving these tasks for medical images. Patient data is highly sensitive and usually only accessible from individual institutions. This creates constraints on the available groundtruth, dataset size, and computational resources in these institutions to train performant models. Due to the mission-critical nature in healthcare applications, requirements such as performance robustness and speed are also stringent. As such, the big-data, dense-computation, supervised learning paradigm in mainstream deep learning is often insufficient to address these situations. In this dissertation, we investigate ways to benefit from the powerful representational capacity of deep neural networks while still satisfying the above-mentioned constraints and requirements. The first part of this dissertation focuses on adapting supervised learning to account for variations such as different medical image modality, image quality, architecture designs, tasks, etc. The second part of this dissertation focuses on improving model robustness on unseen data through domain adaptation, which ameliorates performance degradation due to distribution shifts. The last part of this dissertation focuses on self-supervised learning and learning from synthetic data with a focus in tomographic imaging; this is essential in many situations where the desired groundtruth may not be accessible

Deep Learning and Quantum-computing Based Optimization in Medical Imaging and Power Dispatcing

兵庫県立大学大学院202

Scientific Workflow Integration For Services Computing

In recent years, significant scientific advances are increasingly achieved through complex scientific processes. As the exponential growth in computing technologies and scientific data, a scientific workflow may comprise a large number of heterogeneous scientific services and applications, provided by different organizations. These services, applications, and their associated data are usually distributed across heterogeneous computing environments. The integration and management of such scientific workflows are pushing the limits of current workflow technology. This dissertation presents an integrated solution to composing, scheduling, executing and developing scientific workflows and scientific workflow management systems. To provide a foundation for workflow composition, scheduling, execution and management, we propose the first reference architecture for scientific workflow management systems. The reference architecture not only provides a high-level organization of subsystems and their interactions in a workflow system, but also provides a basis for comparison between different systems and a guidance for the architectural design of an SWFMS in a specific scientific domain. To integrate heterogeneous services and applications and enable them composed to workflows, we propose a task template model which not only provides an appropriate abstraction of heterogeneous services and applications, but also encapsulates the composition and mapping of shims and functional task components within a task interface. Our proposed task specification language (TSL) not only integrates heterogeneous services and applications into uniform workflow tasks, but also provides a solution to address both TYPE-I and TYPE-II shimming problems in composing scientific workflows. To schedule scientific workflows in emerging services computing environments, we propose two workflow scheduling algorithms, the SHEFT algorithm and the SCPOR algorithm, to prioritize tasks in a workflow, map tasks onto suitable resources and order the execution of tasks on the assigned resources, so that the workflow makespan can be minimized. Our extensive experiments have shown that our proposed algorithms not only outperform other algorithms for large-scale, data-intensive and compute intensive workflows, but also allow the assigned resources elastically change on demand of the size of workflows. To execute workflows on distributed computing environments, we propose a task run model to model the run-time behaviors of tasks. The proposed task run description language (TRDL) enables the execution of task instances constructed from heterogeneous services and applications. We also develop an SOA based task management subsystem to manage all task templates, task instances and task runs for the invocation and execution of various heterogeneous task components. Finally, our developed SOA based workflow management system, the VIEW system, and a VIEW based workflow application system, the FiberFlow system, validate our architectures, models, languages, and algorithms

Psychology as Philosophy, Philosophy as Psychology--Articles and Reviews 2006-2019

Since philosophical problems are the result of our innate psychology, or as Wittgenstein put it, due to the lack of perspicuity of language, they run throughout human discourse and behavior, so there is endless need for philosophical analysis, not only in the ‘human sciences’ of philosophy, sociology, anthropology, political science, psychology, history, literature, religion, etc., but in the ‘hard sciences’ of physics, mathematics, and biology. It is universal to mix the language game questions with the real scientific ones as to what the empirical facts are. Scientism is ever-present and Wittgenstein, arguably the greatest intuitive psychologist of all time, has laid it before us long ago, beginning with the Blue and Brown Books in the early 1930’s. Language is programmed in our genes and is involved in nearly all our social behavior. Philosophy in the strict sense (i.e., academic philosophy), is as Wittgenstein showed us, the study of the way language is used (language games) and I regard it as the descriptive psychology of higher order thought (i.e., pretty much everything involving language which is often called System 2 or slow thinking). However, as I hope I have shown in my writings over the last decade, nonlinguistic behavior or System 1 or fast thinking is also described with language and this leads to endless confusion which I have tried to clarify here and which is summarized in the tables that I present. It is my contention that the table of intentionality (rationality, mind, thought, language, personality etc.) that features prominently here describes more or less accurately, or at least serves as an heuristic for, how we think and behave, and so it encompasses not merely philosophy and psychology, but everything else (history, literature, mathematics, politics etc.). Note especially that intentionality and rationality as I (along with Searle, Wittgenstein and others) view it, includes both conscious deliberative linguistic System 2 and unconscious automated prelinguistic System 1 actions or reflexes. I provide a critical survey of some of the major findings of two of the most eminent students of behavior of modern times, Ludwig Wittgenstein and John Searle, on the logical structure of intentionality (mind, language, behavior), taking as my starting point Wittgenstein’s fundamental discovery –that all truly ‘philosophical’ problems are the same—confusions about how to use language in a particular context, and so all solutions are the same—looking at how language can be used in the context at issue so that its truth conditions (Conditions of Satisfaction or COS) are clear. The basic problem is that one can say anything, but one cannot mean (state clear COS for) any arbitrary utterance and meaning is only possible in a very specific context. I analyze various writings by and about them from the modern perspective of the two systems of thought (popularized as ‘thinking fast, thinking slow’), employing a new table of intentionality and new dual systems nomenclature. I show that this is a powerful heuristic for describing behavior with critical reviews of the writings of a wide variety of behavioral scientists (i.e., everyone). The first group of articles attempt to give some insight into how we behave that is reasonably free of theoretical delusions. In the next three groups I comment on three of the principal delusions preventing a sustainable world— technology, religion and politics (cooperative groups). People believe that society can be saved by them, so I provide some suggestions in the rest of the book as to why this is unlikely via short articles and reviews of recent books by well-known writers