42 research outputs found

    Computational techniques to interpret the neural code underlying complex cognitive processes

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    Advances in large-scale neural recording technology have significantly improved the capacity to further elucidate the neural code underlying complex cognitive processes. This thesis aimed to investigate two research questions in rodent models. First, what is the role of the hippocampus in memory and specifically what is the underlying neural code that contributes to spatial memory and navigational decision-making. Second, how is social cognition represented in the medial prefrontal cortex at the level of individual neurons. To start, the thesis begins by investigating memory and social cognition in the context of healthy and diseased states that use non-invasive methods (i.e. fMRI and animal behavioural studies). The main body of the thesis then shifts to developing our fundamental understanding of the neural mechanisms underpinning these cognitive processes by applying computational techniques to ana lyse stable large-scale neural recordings. To achieve this, tailored calcium imaging and behaviour preprocessing computational pipelines were developed and optimised for use in social interaction and spatial navigation experimental analysis. In parallel, a review was conducted on methods for multivariate/neural population analysis. A comparison of multiple neural manifold learning (NML) algorithms identified that non linear algorithms such as UMAP are more adaptable across datasets of varying noise and behavioural complexity. Furthermore, the review visualises how NML can be applied to disease states in the brain and introduces the secondary analyses that can be used to enhance or characterise a neural manifold. Lastly, the preprocessing and analytical pipelines were combined to investigate the neural mechanisms in volved in social cognition and spatial memory. The social cognition study explored how neural firing in the medial Prefrontal cortex changed as a function of the social dominance paradigm, the "Tube Test". The univariate analysis identified an ensemble of behavioural-tuned neurons that fire preferentially during specific behaviours such as "pushing" or "retreating" for the animal’s own behaviour and/or the competitor’s behaviour. Furthermore, in dominant animals, the neural population exhibited greater average firing than that of subordinate animals. Next, to investigate spatial memory, a spatial recency task was used, where rats learnt to navigate towards one of three reward locations and then recall the rewarded location of the session. During the task, over 1000 neurons were recorded from the hippocampal CA1 region for five rats over multiple sessions. Multivariate analysis revealed that the sequence of neurons encoding an animal’s spatial position leading up to a rewarded location was also active in the decision period before the animal navigates to the rewarded location. The result posits that prospective replay of neural sequences in the hippocampal CA1 region could provide a mechanism by which decision-making is supported

    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

    Behavior quantification as the missing link between fields: Tools for digital psychiatry and their role in the future of neurobiology

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    The great behavioral heterogeneity observed between individuals with the same psychiatric disorder and even within one individual over time complicates both clinical practice and biomedical research. However, modern technologies are an exciting opportunity to improve behavioral characterization. Existing psychiatry methods that are qualitative or unscalable, such as patient surveys or clinical interviews, can now be collected at a greater capacity and analyzed to produce new quantitative measures. Furthermore, recent capabilities for continuous collection of passive sensor streams, such as phone GPS or smartwatch accelerometer, open avenues of novel questioning that were previously entirely unrealistic. Their temporally dense nature enables a cohesive study of real-time neural and behavioral signals. To develop comprehensive neurobiological models of psychiatric disease, it will be critical to first develop strong methods for behavioral quantification. There is huge potential in what can theoretically be captured by current technologies, but this in itself presents a large computational challenge -- one that will necessitate new data processing tools, new machine learning techniques, and ultimately a shift in how interdisciplinary work is conducted. In my thesis, I detail research projects that take different perspectives on digital psychiatry, subsequently tying ideas together with a concluding discussion on the future of the field. I also provide software infrastructure where relevant, with extensive documentation. Major contributions include scientific arguments and proof of concept results for daily free-form audio journals as an underappreciated psychiatry research datatype, as well as novel stability theorems and pilot empirical success for a proposed multi-area recurrent neural network architecture.Comment: PhD thesis cop

    Friction, Vibration and Dynamic Properties of Transmission System under Wear Progression

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    This reprint focuses on wear and fatigue analysis, the dynamic properties of coating surfaces in transmission systems, and non-destructive condition monitoring for the health management of transmission systems. Transmission systems play a vital role in various types of industrial structure, including wind turbines, vehicles, mining and material-handling equipment, offshore vessels, and aircrafts. Surface wear is an inevitable phenomenon during the service life of transmission systems (such as on gearboxes, bearings, and shafts), and wear propagation can reduce the durability of the contact coating surface. As a result, the performance of the transmission system can degrade significantly, which can cause sudden shutdown of the whole system and lead to unexpected economic loss and accidents. Therefore, to ensure adequate health management of the transmission system, it is necessary to investigate the friction, vibration, and dynamic properties of its contact coating surface and monitor its operating conditions

    Machine Learning Methods with Noisy, Incomplete or Small Datasets

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    In many machine learning applications, available datasets are sometimes incomplete, noisy or affected by artifacts. In supervised scenarios, it could happen that label information has low quality, which might include unbalanced training sets, noisy labels and other problems. Moreover, in practice, it is very common that available data samples are not enough to derive useful supervised or unsupervised classifiers. All these issues are commonly referred to as the low-quality data problem. This book collects novel contributions on machine learning methods for low-quality datasets, to contribute to the dissemination of new ideas to solve this challenging problem, and to provide clear examples of application in real scenarios

    International Conference on Mathematical Analysis and Applications in Science and Engineering – Book of Extended Abstracts

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    The present volume on Mathematical Analysis and Applications in Science and Engineering - Book of Extended Abstracts of the ICMASC’2022 collects the extended abstracts of the talks presented at the International Conference on Mathematical Analysis and Applications in Science and Engineering – ICMA2SC'22 that took place at the beautiful city of Porto, Portugal, in June 27th-June 29th 2022 (3 days). Its aim was to bring together researchers in every discipline of applied mathematics, science, engineering, industry, and technology, to discuss the development of new mathematical models, theories, and applications that contribute to the advancement of scientific knowledge and practice. Authors proposed research in topics including partial and ordinary differential equations, integer and fractional order equations, linear algebra, numerical analysis, operations research, discrete mathematics, optimization, control, probability, computational mathematics, amongst others. The conference was designed to maximize the involvement of all participants and will present the state-of- the-art research and the latest achievements.info:eu-repo/semantics/publishedVersio

    Data Visualization, Dimensionality Reduction, and Data Alignment via Manifold Learning

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    The high dimensionality of modern data introduces significant challenges in descriptive and exploratory data analysis. These challenges gave rise to extensive work on dimensionality reduction and manifold learning aiming to provide low dimensional representations that preserve or uncover intrinsic patterns and structures in the data. In this thesis, we expand the current literature in manifold learning developing two methods called DIG (Dynamical Information Geometry) and GRAE (Geometry Regularized Autoencoders). DIG is a method capable of finding low-dimensional representations of high-frequency multivariate time series data, especially suited for visualization. GRAE is a general framework which splices the well-established machinery from kernel manifold learning methods to recover a sensitive geometry, alongside the parametric structure of autoencoders. Manifold learning can also be useful to study data collected from different measurement instruments, conditions, or protocols of the same underlying system. In such cases the data is acquired in a multi-domain representation. The last two Chapters of this thesis are devoted to two new methods capable of aligning multi-domain data, leveraging their geometric structure alongside limited common information. First, we present DTA (Diffusion Transport Alignment), a semi-supervised manifold alignment method that exploits prior one-to-one correspondence knowledge between distinct data views and finds an aligned common representation. And finally, we introduce MALI (Manifold Alignment with Label Information). Here we drop the one-to-one prior correspondences assumption, since in many scenarios such information can not be provided, either due to the nature of the experimental design, or it becomes extremely costly. Instead, MALI only needs side-information in the form of discrete labels/classes present in both domains

    Sense and Respond

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    Over the past century, the manufacturing industry has undergone a number of paradigm shifts: from the Ford assembly line (1900s) and its focus on efficiency to the Toyota production system (1960s) and its focus on effectiveness and JIDOKA; from flexible manufacturing (1980s) to reconfigurable manufacturing (1990s) (both following the trend of mass customization); and from agent-based manufacturing (2000s) to cloud manufacturing (2010s) (both deploying the value stream complexity into the material and information flow, respectively). The next natural evolutionary step is to provide value by creating industrial cyber-physical assets with human-like intelligence. This will only be possible by further integrating strategic smart sensor technology into the manufacturing cyber-physical value creating processes in which industrial equipment is monitored and controlled for analyzing compression, temperature, moisture, vibrations, and performance. For instance, in the new wave of the ‘Industrial Internet of Things’ (IIoT), smart sensors will enable the development of new applications by interconnecting software, machines, and humans throughout the manufacturing process, thus enabling suppliers and manufacturers to rapidly respond to changing standards. This reprint of “Sense and Respond” aims to cover recent developments in the field of industrial applications, especially smart sensor technologies that increase the productivity, quality, reliability, and safety of industrial cyber-physical value-creating processes

    Graph Neural Networks on SPD Manifolds for Motor Imagery Classification: A Perspective from the Time-Frequency Analysis

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    Motor imagery (MI) classification is one of the most widely-concern research topics in Electroencephalography (EEG)-based brain-computer interfaces (BCIs) with extensive industry value. The MI-EEG classifiers' tendency has changed fundamentally over the past twenty years, while classifiers' performance is gradually increasing. In particular, owing to the need for characterizing signals' non-Euclidean inherence, the first geometric deep learning (GDL) framework, Tensor-CSPNet, has recently emerged in the BCI study. In essence, Tensor-CSPNet is a deep learning-based classifier on the second-order statistics of EEGs. In contrast to the first-order statistics, using these second-order statistics is the classical treatment of EEG signals, and the discriminative information contained in these second-order statistics is adequate for MI-EEG classification. In this study, we present another GDL classifier for MI-EEG classification called Graph-CSPNet, using graph-based techniques to simultaneously characterize the EEG signals in both the time and frequency domains. It is realized from the perspective of the time-frequency analysis that profoundly influences signal processing and BCI studies. Contrary to Tensor-CSPNet, the architecture of Graph-CSPNet is further simplified with more flexibility to cope with variable time-frequency resolution for signal segmentation to capture the localized fluctuations. In the experiments, Graph-CSPNet is evaluated on subject-specific scenarios from two well-used MI-EEG datasets and produces near-optimal classification accuracies.Comment: 16 pages, 5 figures, 9 Tables; This work has been submitted to the IEEE for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessibl
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