Learned SVD: solving inverse problems via hybrid autoencoding

Our world is full of physics-driven data where effective mappings between data manifolds are desired. There is an increasing demand for understanding combined model-based and data-driven methods. We propose a nonlinear, learned singular value decomposition (L-SVD), which combines autoencoders that simultaneously learn and connect latent codes for desired signals and given measurements. We provide a convergence analysis for a specifically structured L-SVD that acts as a regularisation method. In a more general setting, we investigate the topic of model reduction via data dimensionality reduction to obtain a regularised inversion. We present a promising direction for solving inverse problems in cases where the underlying physics are not fully understood or have very complex behaviour. We show that the building blocks of learned inversion maps can be obtained automatically, with improved performance upon classical methods and better interpretability than black-box methods

Deep learning cardiac motion analysis for human survival prediction

Motion analysis is used in computer vision to understand the behaviour of moving objects in sequences of images. Optimising the interpretation of dynamic biological systems requires accurate and precise motion tracking as well as efficient representations of high-dimensional motion trajectories so that these can be used for prediction tasks. Here we use image sequences of the heart, acquired using cardiac magnetic resonance imaging, to create time-resolved three-dimensional segmentations using a fully convolutional network trained on anatomical shape priors. This dense motion model formed the input to a supervised denoising autoencoder (4Dsurvival), which is a hybrid network consisting of an autoencoder that learns a task-specific latent code representation trained on observed outcome data, yielding a latent representation optimised for survival prediction. To handle right-censored survival outcomes, our network used a Cox partial likelihood loss function. In a study of 302 patients the predictive accuracy (quantified by Harrell's C-index) was significantly higher (p < .0001) for our model C=0.73 (95$\%$ CI: 0.68 - 0.78) than the human benchmark of C=0.59 (95$\%$ CI: 0.53 - 0.65). This work demonstrates how a complex computer vision task using high-dimensional medical image data can efficiently predict human survival

Generalised Gaussian Process Latent Variable Models (GPLVM) with Stochastic Variational Inference

Gaussian process latent variable models (GPLVM) are a flexible and non-linear approach to dimensionality reduction, extending classical Gaussian processes to an unsupervised learning context. The Bayesian incarnation of the GPLVM Titsias and Lawrence, 2010] uses a variational framework, where the posterior over latent variables is approximated by a well-behaved variational family, a factorized Gaussian yielding a tractable lower bound. However, the non-factories ability of the lower bound prevents truly scalable inference. In this work, we study the doubly stochastic formulation of the Bayesian GPLVM model amenable with minibatch training. We show how this framework is compatible with different latent variable formulations and perform experiments to compare a suite of models. Further, we demonstrate how we can train in the presence of massively missing data and obtain high-fidelity reconstructions. We demonstrate the model's performance by benchmarking against the canonical sparse GPLVM for high-dimensional data examples.Comment: AISTATS 202

ICAM: Interpretable Classification via Disentangled Representations and Feature Attribution Mapping

Feature attribution (FA), or the assignment of class-relevance to different locations in an image, is important for many classification problems but is particularly crucial within the neuroscience domain, where accurate mechanistic models of behaviours, or disease, require knowledge of all features discriminative of a trait. At the same time, predicting class relevance from brain images is challenging as phenotypes are typically heterogeneous, and changes occur against a background of significant natural variation. Here, we present a novel framework for creating class specific FA maps through image-to-image translation. We propose the use of a VAE-GAN to explicitly disentangle class relevance from background features for improved interpretability properties, which results in meaningful FA maps. We validate our method on 2D and 3D brain image datasets of dementia (ADNI dataset), ageing (UK Biobank), and (simulated) lesion detection. We show that FA maps generated by our method outperform baseline FA methods when validated against ground truth. More significantly, our approach is the first to use latent space sampling to support exploration of phenotype variation. Our code will be available online at https://github.com/CherBass/ICAM.Comment: Submitted to NeurIPS 2020: Neural Information Processing Systems. Keywords: interpretable, classification, feature attribution, domain translation, variational autoencoder, generative adversarial network, neuroimagin

Deep Learning Methods for Human Activity Recognition using Wearables

Wearable sensors provide an infrastructure-less multi-modal sensing method. Current trends point to a pervasive integration of wearables into our lives with these devices providing the basis for wellness and healthcare applications across rehabilitation, caring for a growing older population, and improving human performance. Fundamental to these applications is our ability to automatically and accurately recognise human activities from often tiny sensors embedded in wearables. In this dissertation, we consider the problem of human activity recognition (HAR) using multi-channel time-series data captured by wearable sensors. Our collective know-how regarding the solution of HAR problems with wearables has progressed immensely through the use of deep learning paradigms. Nevertheless, this field still faces unique methodological challenges. As such, this dissertation focuses on developing end-to-end deep learning frameworks to promote HAR application opportunities using wearable sensor technologies and to mitigate specific associated challenges. In our efforts, the investigated problems cover a diverse range of HAR challenges and spans from fully supervised to unsupervised problem domains. In order to enhance automatic feature extraction from multi-channel time-series data for HAR, the problem of learning enriched and highly discriminative activity feature representations with deep neural networks is considered. Accordingly, novel end-to-end network elements are designed which: (a) exploit the latent relationships between multi-channel sensor modalities and specific activities, (b) employ effective regularisation through data-agnostic augmentation for multi-modal sensor data streams, and (c) incorporate optimization objectives to encourage minimal intra-class representation differences, while maximising inter-class differences to achieve more discriminative features. In order to promote new opportunities in HAR with emerging battery-less sensing platforms, the problem of learning from irregularly sampled and temporally sparse readings captured by passive sensing modalities is considered. For the first time, an efficient set-based deep learning framework is developed to address the problem. This framework is able to learn directly from the generated data, bypassing the need for the conventional interpolation pre-processing stage. In order to address the multi-class window problem and create potential solutions for the challenging task of concurrent human activity recognition, the problem of enabling simultaneous prediction of multiple activities for sensory segments is considered. As such, the flexibility provided by the emerging set learning concepts is further leveraged to introduce a novel formulation of HAR. This formulation treats HAR as a set prediction problem and elegantly caters for segments carrying sensor data from multiple activities. To address this set prediction problem, a unified deep HAR architecture is designed that: (a) incorporates a set objective to learn mappings from raw input sensory segments to target activity sets, and (b) precedes the supervised learning phase with unsupervised parameter pre-training to exploit unlabelled data for better generalisation performance. In order to leverage the easily accessible unlabelled activity data-streams to serve downstream classification tasks, the problem of unsupervised representation learning from multi-channel time-series data is considered. For the first time, a novel recurrent generative adversarial (GAN) framework is developed that explores the GAN’s latent feature space to extract highly discriminating activity features in an unsupervised fashion. The superiority of the learned representations is substantiated by their ability to outperform the de facto unsupervised approaches based on autoencoder frameworks. At the same time, they rival the recognition performance of fully supervised trained models on downstream classification benchmarks. In recognition of the scarcity of large-scale annotated sensor datasets and the tediousness of collecting additional labelled data in this domain, the hitherto unexplored problem of end-to-end clustering of human activities from unlabelled wearable data is considered. To address this problem, a first study is presented for the purpose of developing a stand-alone deep learning paradigm to discover semantically meaningful clusters of human actions. In particular, the paradigm is intended to: (a) leverage the inherently sequential nature of sensory data, (b) exploit self-supervision from reconstruction and future prediction tasks, and (c) incorporate clustering-oriented objectives to promote the formation of highly discriminative activity clusters. The systematic investigations in this study create new opportunities for HAR to learn human activities using unlabelled data that can be conveniently and cheaply collected from wearables.Thesis (Ph.D.) -- University of Adelaide, School of Computer Science, 202

ICAM-reg: Interpretable Classification and Regression with Feature Attribution for Mapping Neurological Phenotypes in Individual Scans

Feature attribution (FA), or the assignment of class-relevance to different locations in an image, is important for many classification and regression problems but is particularly crucial within the neuroscience domain, where accurate mechanistic models of behaviours, or disease, require knowledge of all features discriminative of a trait. At the same time, predicting class relevance from brain images is challenging as phenotypes are typically heterogeneous, and changes occur against a background of significant natural variation. Here, we present an extension of the ICAM framework for creating prediction specific FA maps through image-to-image translation