Graph Priors, Optimal Transport, and Deep Learning in Biomedical Discovery

Recent advances in biomedical data collection allows the collection of massive datasets measuring thousands of features in thousands to millions of individual cells. This data has the potential to advance our understanding of biological mechanisms at a previously impossible resolution. However, there are few methods to understand data of this scale and type. While neural networks have made tremendous progress on supervised learning problems, there is still much work to be done in making them useful for discovery in data with more difficult to represent supervision. The flexibility and expressiveness of neural networks is sometimes a hindrance in these less supervised domains, as is the case when extracting knowledge from biomedical data. One type of prior knowledge that is more common in biological data comes in the form of geometric constraints. In this thesis, we aim to leverage this geometric knowledge to create scalable and interpretable models to understand this data. Encoding geometric priors into neural network and graph models allows us to characterize the models’ solutions as they relate to the fields of graph signal processing and optimal transport. These links allow us to understand and interpret this datatype. We divide this work into three sections. The first borrows concepts from graph signal processing to construct more interpretable and performant neural networks by constraining and structuring the architecture. The second borrows from the theory of optimal transport to perform anomaly detection and trajectory inference efficiently and with theoretical guarantees. The third examines how to compare distributions over an underlying manifold, which can be used to understand how different perturbations or conditions relate. For this we design an efficient approximation of optimal transport based on diffusion over a joint cell graph. Together, these works utilize our prior understanding of the data geometry to create more useful models of the data. We apply these methods to molecular graphs, images, single-cell sequencing, and health record data

Outlier-Robust Tensor Low-Rank Representation for Data Clustering

Low-rank tensor analysis has received widespread attention with many practical applications. However, the tensor data are often contaminated by outliers or sample-specific corruptions. How to recover the tensor data that are corrupted by outliers and perform data clustering remains a challenging problem. This paper develops an outlier-robust tensor low-rank representation (OR-TLRR) method for simultaneous outlier detection and tensor data clustering based on the tensor singular value decomposition (t-SVD) algebraic framework. It is motivated by the recently proposed tensor-tensor product induced by invertible linear transforms that satisfy certain conditions. For tensor observations with arbitrary outlier corruptions, OR-TLRR has provable performance guarantee for exactly recovering the row space of clean data and detecting outliers under mild conditions. Moreover, an extension of OR-TLRR is also proposed to handle the case when parts of the data are missing. Finally, extensive experimental results on both synthetic and real data demonstrate the effectiveness of the proposed algorithms.Comment: 12 pages, 1 figure; preprint of a journal pape

Generative-Discriminative Low Rank Decomposition for Medical Imaging Applications

In this thesis, we propose a method that can be used to extract biomarkers from medical images toward early diagnosis of abnormalities. Surge of demand for biomarkers and availability of medical images in the recent years call for accurate, repeatable, and interpretable approaches for extracting meaningful imaging features. However, extracting such information from medical images is a challenging task because the number of pixels (voxels) in a typical image is in order of millions while even a large sample-size in medical image dataset does not usually exceed a few hundred. Nevertheless, depending on the nature of an abnormality, only a parsimonious subset of voxels is typically relevant to the disease; therefore various notions of sparsity are exploited in this thesis to improve the generalization performance of the prediction task. We propose a novel discriminative dimensionality reduction method that yields good classification performance on various datasets without compromising the clinical interpretability of the results. This is achieved by combining the modelling strength of generative learning framework and the classification performance of discriminative learning paradigm. Clinical interpretability can be viewed as an additional measure of evaluation and is also helpful in designing methods that account for the clinical prior such as association of certain areas in a brain to a particular cognitive task or connectivity of some brain regions via neural fibres. We formulate our method as a large-scale optimization problem to solve a constrained matrix factorization. Finding an optimal solution of the large-scale matrix factorization renders off-the-shelf solver computationally prohibitive; therefore, we designed an efficient algorithm based on the proximal method to address the computational bottle-neck of the optimization problem. Our formulation is readily extended for different scenarios such as cases where a large cohort of subjects has uncertain or no class labels (semi-supervised learning) or a case where each subject has a battery of imaging channels (multi-channel), \etc. We show that by using various notions of sparsity as feasible sets of the optimization problem, we can encode different forms of prior knowledge ranging from brain parcellation to brain connectivity

Generative-Discriminitive Basis Learning for Medical Imaging

This paper presents a novel dimensionality reduction method for classification in medical imaging. The goal is to transform very high-dimensional input (typically, millions of voxels) to a low-dimensional representation (small number of constructed features) that preserves discriminative signal and is clinically interpretable. We formulate the task as a constrained optimization problem that combines generative and discriminative objectives and show how to extend it to the semisupervised learning (SSL) setting. We propose a novel largescale algorithm to solve the resulting optimization problem. In the fully supervised case, we demonstrate accuracy rates that are better than or comparable to state-of-the-art algorithms on several datasets while producing a representation of the group difference that is consistent with prior clinical reports. Effectiveness of the proposed algorithm for SSL is evaluated with both benchmark and medical imaging datasets. In the benchmark datasets, the results are better than or comparable to the state-of-the-art methods for SSL. For evaluation of the SSL setting in medical datasets, we use images of subjects with Mild Cognitive Impairment (MCI), which is believed to be a precursor to Alzheimer’s disease (AD), as unlabeled data. AD subjects and Normal Control (NC) subjects are used as labeled data, and we try to predict conversion from MCI to AD on follow-up. The semi-supervised extension of this method not only improves the generalization accuracy for the labeled data (AD/NC) slightly but is also able to predict subjects which are likely to converge to AD

Recovering Structured Low-rank Operators Using Nuclear Norms

This work considers the problem of recovering matrices and operators from limited and/or noisy observations. Whereas matrices result from summing tensor products of vectors, operators result from summing tensor products of matrices. These constructions lead to viewing both matrices and operators as the sum of "simple" rank-1 factors. A popular line of work in this direction is low-rank matrix recovery, i.e., using linear measurements of a matrix to reconstruct it as the sum of few rank-1 factors. Rank minimization problems are hard in general, and a popular approach to avoid them is convex relaxation. Using the trace norm as a surrogate for rank, the low-rank matrix recovery problem becomes convex. While the trace norm has received much attention in the literature, other convexifications are possible. This thesis focuses on the class of nuclear norms—a class that includes the trace norm itself. Much as the trace norm is a convex surrogate for the matrix rank, other nuclear norms provide convex complexity measures for additional matrix structure. Namely, nuclear norms measure the structure of the factors used to construct the matrix. Transitioning to the operator framework allows for novel uses of nuclear norms in recovering these structured matrices. In particular, this thesis shows how to lift structured matrix factorization problems to rank-1 operator recovery problems. This new viewpoint allows nuclear norms to measure richer types of structures present in matrix factorizations. This work also includes a Python software package to model and solve structured operator recovery problems. Systematic numerical experiments in operator denoising demonstrate the effectiveness of nuclear norms in recovering structured operators. In particular, choosing a specific nuclear norm that corresponds to the underlying factor structure of the operator improves the performance of the recovery procedures when compared, for instance, to the trace norm. Applications in hyperspectral imaging and self-calibration demonstrate the additional flexibility gained by utilizing operator (as opposed to matrix) factorization models.</p

Recent Advances in Embedded Computing, Intelligence and Applications

The latest proliferation of Internet of Things deployments and edge computing combined with artificial intelligence has led to new exciting application scenarios, where embedded digital devices are essential enablers. Moreover, new powerful and efficient devices are appearing to cope with workloads formerly reserved for the cloud, such as deep learning. These devices allow processing close to where data are generated, avoiding bottlenecks due to communication limitations. The efficient integration of hardware, software and artificial intelligence capabilities deployed in real sensing contexts empowers the edge intelligence paradigm, which will ultimately contribute to the fostering of the offloading processing functionalities to the edge. In this Special Issue, researchers have contributed nine peer-reviewed papers covering a wide range of topics in the area of edge intelligence. Among them are hardware-accelerated implementations of deep neural networks, IoT platforms for extreme edge computing, neuro-evolvable and neuromorphic machine learning, and embedded recommender systems

Seamless Multimodal Biometrics for Continuous Personalised Wellbeing Monitoring

Artificially intelligent perception is increasingly present in the lives of every one of us. Vehicles are no exception, (...) In the near future, pattern recognition will have an even stronger role in vehicles, as self-driving cars will require automated ways to understand what is happening around (and within) them and act accordingly. (...) This doctoral work focused on advancing in-vehicle sensing through the research of novel computer vision and pattern recognition methodologies for both biometrics and wellbeing monitoring. The main focus has been on electrocardiogram (ECG) biometrics, a trait well-known for its potential for seamless driver monitoring. Major efforts were devoted to achieving improved performance in identification and identity verification in off-the-person scenarios, well-known for increased noise and variability. Here, end-to-end deep learning ECG biometric solutions were proposed and important topics were addressed such as cross-database and long-term performance, waveform relevance through explainability, and interlead conversion. Face biometrics, a natural complement to the ECG in seamless unconstrained scenarios, was also studied in this work. The open challenges of masked face recognition and interpretability in biometrics were tackled in an effort to evolve towards algorithms that are more transparent, trustworthy, and robust to significant occlusions. Within the topic of wellbeing monitoring, improved solutions to multimodal emotion recognition in groups of people and activity/violence recognition in in-vehicle scenarios were proposed. At last, we also proposed a novel way to learn template security within end-to-end models, dismissing additional separate encryption processes, and a self-supervised learning approach tailored to sequential data, in order to ensure data security and optimal performance. (...)Comment: Doctoral thesis presented and approved on the 21st of December 2022 to the University of Port