5,404 research outputs found

    Generalized network-based dimensionality analysis

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    Network analysis opens new horizons for data analysis methods, as the results of ever-developing network science can be integrated into classical data analysis techniques. This paper presents the generalized version of network-based dimensionality reduction and analysis (NDA). The main contributions of this paper are as follows: (1) The proposed generalized dimensionality reduction and analysis (GNDA) method already handles low-dimensional high-sample-size (LDHSS) and high-dimensional and low-sample-size (HDLSS) at the same time. In addition, compared with existing methods, we show that only the proposed GNDA method adequately estimates the number of latent variables (LVs). (2) The proposed GNDA already considers any symmetric and nonsymmetric similarity functions between indicators (i.e., variables or observations) to specify LVs. (3) The proposed prefiltering and resolution parameters provide the hierarchical version of GNDA to check the robustness of LVs. The proposed GNDA method is compared with traditional dimensionality reduction methods on various simulated and real-world datasets

    Deep Learning Techniques for Electroencephalography Analysis

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    In this thesis we design deep learning techniques for training deep neural networks on electroencephalography (EEG) data and in particular on two problems, namely EEG-based motor imagery decoding and EEG-based affect recognition, addressing challenges associated with them. Regarding the problem of motor imagery (MI) decoding, we first consider the various kinds of domain shifts in the EEG signals, caused by inter-individual differences (e.g. brain anatomy, personality and cognitive profile). These domain shifts render multi-subject training a challenging task and impede robust cross-subject generalization. We build a two-stage model ensemble architecture and propose two objectives to train it, combining the strengths of curriculum learning and collaborative training. Our subject-independent experiments on the large datasets of Physionet and OpenBMI, verify the effectiveness of our approach. Next, we explore the utilization of the spatial covariance of EEG signals through alignment techniques, with the goal of learning domain-invariant representations. We introduce a Riemannian framework that concurrently performs covariance-based signal alignment and data augmentation, while training a convolutional neural network (CNN) on EEG time-series. Experiments on the BCI IV-2a dataset show that our method performs superiorly over traditional alignment, by inducing regularization to the weights of the CNN. We also study the problem of EEG-based affect recognition, inspired by works suggesting that emotions can be expressed in relative terms, i.e. through ordinal comparisons between different affective state levels. We propose treating data samples in a pairwise manner to infer the ordinal relation between their corresponding affective state labels, as an auxiliary training objective. We incorporate our objective in a deep network architecture which we jointly train on the tasks of sample-wise classification and pairwise ordinal ranking. We evaluate our method on the affective datasets of DEAP and SEED and obtain performance improvements over deep networks trained without the additional ranking objective

    Classical and quantum algorithms for scaling problems

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    This thesis is concerned with scaling problems, which have a plethora of connections to different areas of mathematics, physics and computer science. Although many structural aspects of these problems are understood by now, we only know how to solve them efficiently in special cases.We give new algorithms for non-commutative scaling problems with complexity guarantees that match the prior state of the art. To this end, we extend the well-known (self-concordance based) interior-point method (IPM) framework to Riemannian manifolds, motivated by its success in the commutative setting. Moreover, the IPM framework does not obviously suffer from the same obstructions to efficiency as previous methods. It also yields the first high-precision algorithms for other natural geometric problems in non-positive curvature.For the (commutative) problems of matrix scaling and balancing, we show that quantum algorithms can outperform the (already very efficient) state-of-the-art classical algorithms. Their time complexity can be sublinear in the input size; in certain parameter regimes they are also optimal, whereas in others we show no quantum speedup over the classical methods is possible. Along the way, we provide improvements over the long-standing state of the art for searching for all marked elements in a list, and computing the sum of a list of numbers.We identify a new application in the context of tensor networks for quantum many-body physics. We define a computable canonical form for uniform projected entangled pair states (as the solution to a scaling problem), circumventing previously known undecidability results. We also show, by characterizing the invariant polynomials, that the canonical form is determined by evaluating the tensor network contractions on networks of bounded size

    Learning recommender systems from biased user interactions

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    Recommender systems have been widely deployed to help users quickly find what they need from a collection of items. Predominant recommendation methods rely on supervised learning models to predict user ratings on items or the probabilities of users interacting with items. In addition, reinforcement learning models are crucial in improving long-term user engagement within recommender systems. In practice, both of these recommendation methods are commonly trained on logged user interactions and, therefore, subject to bias present in logged user interactions. This thesis concerns complex forms of bias in real-world user behaviors and aims to mitigate the effect of bias on reinforcement learning-based recommendation methods. The first part of the thesis consists of two research chapters, each dedicated to tackling a specific form of bias: dynamic selection bias and multifactorial bias. To mitigate the effect of dynamic selection bias and multifactorial bias, we propose a bias propensity estimation method for each. By incorporating the results from the bias propensity estimation methods, the widely used inverse propensity scoring-based debiasing method can be extended to correct for the corresponding bias. The second part of the thesis consists of two chapters that concern the effect of bias on reinforcement learning-based recommendation methods. Its first chapter focuses on mitigating the effect of bias on simulators, which enables the learning and evaluation of reinforcement learning-based recommendation methods. Its second chapter further explores different state encoders for reinforcement learning-based recommendation methods when learning and evaluating with the proposed debiased simulator

    The development of bioinformatics workflows to explore single-cell multi-omics data from T and B lymphocytes

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    The adaptive immune response is responsible for recognising, containing and eliminating viral infection, and protecting from further reinfection. This antigen-specific response is driven by T and B cells, which recognise antigenic epitopes via highly specific heterodimeric surface receptors, termed T-cell receptors (TCRs) and B cell receptors (BCRs). The theoretical diversity of the receptor repertoire that can be generated via homologous recombination of V, D and J genes is large enough (>1015 unique sequences) that virtually any antigen can be recognised. However, only a subset of these are generated within the human body, and how they succeed in specifically recognising any pathogen(s) and distinguishing these from self-proteins remains largely unresolved. The recent advances in applying single-cell genomics technologies to simultaneously measure the clonality, surface phenotype and transcriptomic signature of pathogen- specific immune cells have significantly improved understanding of these questions. Single-cell multi-omics permits the accurate identification of clonally expanded populations, their differentiation trajectories, the level of immune receptor repertoire diversity involved in the response and the phenotypic and molecular heterogeneity. This thesis aims to develop a bioinformatic workflow utilising single-cell multi-omics data to explore, quantify and predict the clonal and transcriptomic signatures of the human T-cell response during and following viral infection. In the first aim, a web application, VDJView, was developed to facilitate the simultaneous analysis and visualisation of clonal, transcriptomic and clinical metadata of T and B cell multi-omics data. The application permits non-bioinformaticians to perform quality control and common analyses of single-cell genomics data integrated with other metadata, thus permitting the identification of biologically and clinically relevant parameters. The second aim pertains to analysing the functional, molecular and immune receptor profiles of CD8+ T cells in the acute phase of primary hepatitis C virus (HCV) infection. This analysis identified a novel population of progenitors of exhausted T cells, and lineage tracing revealed distinct trajectories with multiple fates and evolutionary plasticity. Furthermore, it was observed that high-magnitude IFN-Îł CD8+ T-cell response is associated with the increased probability of viral escape and chronic infection. Finally, in the third aim, a novel analysis is presented based on the topological characteristics of a network generated on pathogen-specific, paired-chain, CD8+ TCRs. This analysis revealed how some cross-reactivity between TCRs can be explained via the sequence similarity between TCRs and that this property is not uniformly distributed across all pathogen-specific TCR repertoires. Strong correlations between the topological properties of the network and the biological properties of the TCR sequences were identified and highlighted. The suite of workflows and methods presented in this thesis are designed to be adaptable to various T and B cell multi-omic datasets. The associated analyses contribute to understanding the role of T and B cells in the adaptive immune response to viral-infection and cancer

    LIPIcs, Volume 251, ITCS 2023, Complete Volume

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    LIPIcs, Volume 251, ITCS 2023, Complete Volum

    Machine learning applications in search algorithms for gravitational waves from compact binary mergers

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    Gravitational waves from compact binary mergers are now routinely observed by Earth-bound detectors. These observations enable exciting new science, as they have opened a new window to the Universe. However, extracting gravitational-wave signals from the noisy detector data is a challenging problem. The most sensitive search algorithms for compact binary mergers use matched filtering, an algorithm that compares the data with a set of expected template signals. As detectors are upgraded and more sophisticated signal models become available, the number of required templates will increase, which can make some sources computationally prohibitive to search for. The computational cost is of particular concern when low-latency alerts should be issued to maximize the time for electromagnetic follow-up observations. One potential solution to reduce computational requirements that has started to be explored in the last decade is machine learning. However, different proposed deep learning searches target varying parameter spaces and use metrics that are not always comparable to existing literature. Consequently, a clear picture of the capabilities of machine learning searches has been sorely missing. In this thesis, we closely examine the sensitivity of various deep learning gravitational-wave search algorithms and introduce new methods to detect signals from binary black hole and binary neutron star mergers at previously untested statistical confidence levels. By using the sensitive distance as our core metric, we allow for a direct comparison of our algorithms to state-of-the-art search pipelines. As part of this thesis, we organized a global mock data challenge to create a benchmark for machine learning search algorithms targeting compact binaries. This way, the tools developed in this thesis are made available to the greater community by publishing them as open source software. Our studies show that, depending on the parameter space, deep learning gravitational-wave search algorithms are already competitive with current production search pipelines. We also find that strategies developed for traditional searches can be effectively adapted to their machine learning counterparts. In regions where matched filtering becomes computationally expensive, available deep learning algorithms are also limited in their capability. We find reduced sensitivity to long duration signals compared to the excellent results for short-duration binary black hole signals

    Neural Architecture Search for Image Segmentation and Classification

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    Deep learning (DL) is a class of machine learning algorithms that relies on deep neural networks (DNNs) for computations. Unlike traditional machine learning algorithms, DL can learn from raw data directly and effectively. Hence, DL has been successfully applied to tackle many real-world problems. When applying DL to a given problem, the primary task is designing the optimum DNN. This task relies heavily on human expertise, is time-consuming, and requires many trial-and-error experiments. This thesis aims to automate the laborious task of designing the optimum DNN by exploring the neural architecture search (NAS) approach. Here, we propose two new NAS algorithms for two real-world problems: pedestrian lane detection for assistive navigation and hyperspectral image segmentation for biosecurity scanning. Additionally, we also introduce a new dataset-agnostic predictor of neural network performance, which can be used to speed-up NAS algorithms that require the evaluation of candidate DNNs
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