9,525 research outputs found

    Exploring missing heritability in neurodevelopmental disorders:Learning from regulatory elements

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    In this thesis, I aimed to solve part of the missing heritability in neurodevelopmental disorders, using computational approaches. Next to the investigations of a novel epilepsy syndrome and investigations aiming to elucidate the regulation of the gene involved, I investigated and prioritized genomic sequences that have implications in gene regulation during the developmental stages of human brain, with the goal to create an atlas of high confidence non-coding regulatory elements that future studies can assess for genetic variants in genetically unexplained individuals suffering from neurodevelopmental disorders that are of suspected genetic origin

    Graduate Catalog of Studies, 2023-2024

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    Applications of Deep Learning Models in Financial Forecasting

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    In financial markets, deep learning techniques sparked a revolution, reshaping conventional approaches and amplifying predictive capabilities. This thesis explored the applications of deep learning models to unravel insights and methodologies aimed at advancing financial forecasting. The crux of the research problem lies in the applications of predictive models within financial domains, characterised by high volatility and uncertainty. This thesis investigated the application of advanced deep-learning methodologies in the context of financial forecasting, addressing the challenges posed by the dynamic nature of financial markets. These challenges were tackled by exploring a range of techniques, including convolutional neural networks (CNNs), long short-term memory networks (LSTMs), autoencoders (AEs), and variational autoencoders (VAEs), along with approaches such as encoding financial time series into images. Through analysis, methodologies such as transfer learning, convolutional neural networks, long short-term memory networks, generative modelling, and image encoding of time series data were examined. These methodologies collectively offered a comprehensive toolkit for extracting meaningful insights from financial data. The present work investigated the practicality of a deep learning CNN-LSTM model within the Directional Change framework to predict significant DC events—a task crucial for timely decisionmaking in financial markets. Furthermore, the potential of autoencoders and variational autoencoders to enhance financial forecasting accuracy and remove noise from financial time series data was explored. Leveraging their capacity within financial time series, these models offered promising avenues for improved data representation and subsequent forecasting. To further contribute to financial prediction capabilities, a deep multi-model was developed that harnessed the power of pre-trained computer vision models. This innovative approach aimed to predict the VVIX, utilising the cross-disciplinary synergy between computer vision and financial forecasting. By integrating knowledge from these domains, novel insights into the prediction of market volatility were provided

    A survey on vulnerability of federated learning: A learning algorithm perspective

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    Federated Learning (FL) has emerged as a powerful paradigm for training Machine Learning (ML), particularly Deep Learning (DL) models on multiple devices or servers while maintaining data localized at owners’ sites. Without centralizing data, FL holds promise for scenarios where data integrity, privacy and security and are critical. However, this decentralized training process also opens up new avenues for opponents to launch unique attacks, where it has been becoming an urgent need to understand the vulnerabilities and corresponding defense mechanisms from a learning algorithm perspective. This review paper takes a comprehensive look at malicious attacks against FL, categorizing them from new perspectives on attack origins and targets, and providing insights into their methodology and impact. In this survey, we focus on threat models targeting the learning process of FL systems. Based on the source and target of the attack, we categorize existing threat models into four types, Data to Model (D2M), Model to Data (M2D), Model to Model (M2M) and composite attacks. For each attack type, we discuss the defense strategies proposed, highlighting their effectiveness, assumptions and potential areas for improvement. Defense strategies have evolved from using a singular metric to excluding malicious clients, to employing a multifaceted approach examining client models at various phases. In this survey paper, our research indicates that the to-learn data, the learning gradients, and the learned model at different stages all can be manipulated to initiate malicious attacks that range from undermining model performance, reconstructing private local data, and to inserting backdoors. We have also seen these threat are becoming more insidious. While earlier studies typically amplified malicious gradients, recent endeavors subtly alter the least significant weights in local models to bypass defense measures. This literature review provides a holistic understanding of the current FL threat landscape and highlights the importance of developing robust, efficient, and privacy-preserving defenses to ensure the safe and trusted adoption of FL in real-world applications. The categorized bibliography can be found at: https://github.com/Rand2AI/Awesome-Vulnerability-of-Federated-Learning

    On the Generation of Realistic and Robust Counterfactual Explanations for Algorithmic Recourse

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    This recent widespread deployment of machine learning algorithms presents many new challenges. Machine learning algorithms are usually opaque and can be particularly difficult to interpret. When humans are involved, algorithmic and automated decisions can negatively impact people’s lives. Therefore, end users would like to be insured against potential harm. One popular way to achieve this is to provide end users access to algorithmic recourse, which gives end users negatively affected by algorithmic decisions the opportunity to reverse unfavorable decisions, e.g., from a loan denial to a loan acceptance. In this thesis, we design recourse algorithms to meet various end user needs. First, we propose methods for the generation of realistic recourses. We use generative models to suggest recourses likely to occur under the data distribution. To this end, we shift the recourse action from the input space to the generative model’s latent space, allowing to generate counterfactuals that lie in regions with data support. Second, we observe that small changes applied to the recourses prescribed to end users likely invalidate the suggested recourse after being nosily implemented in practice. Motivated by this observation, we design methods for the generation of robust recourses and for assessing the robustness of recourse algorithms to data deletion requests. Third, the lack of a commonly used code-base for counterfactual explanation and algorithmic recourse algorithms and the vast array of evaluation measures in literature make it difficult to compare the per formance of different algorithms. To solve this problem, we provide an open source benchmarking library that streamlines the evaluation process and can be used for benchmarking, rapidly developing new methods, and setting up new experiments. In summary, our work contributes to a more reliable interaction of end users and machine learned models by covering fundamental aspects of the recourse process and suggests new solutions towards generating realistic and robust counterfactual explanations for algorithmic recourse

    A survey on vulnerability of federated learning: A learning algorithm perspective

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    Federated Learning (FL) has emerged as a powerful paradigm for training Machine Learning (ML), particularly Deep Learning (DL) models on multiple devices or servers while maintaining data localized at owners’ sites. Without centralizing data, FL holds promise for scenarios where data integrity, privacy and security and are critical. However, this decentralized training process also opens up new avenues for opponents to launch unique attacks, where it has been becoming an urgent need to understand the vulnerabilities and corresponding defense mechanisms from a learning algorithm perspective. This review paper takes a comprehensive look at malicious attacks against FL, categorizing them from new perspectives on attack origins and targets, and providing insights into their methodology and impact. In this survey, we focus on threat models targeting the learning process of FL systems. Based on the source and target of the attack, we categorize existing threat models into four types, Data to Model (D2M), Model to Data (M2D), Model to Model (M2M) and composite attacks. For each attack type, we discuss the defense strategies proposed, highlighting their effectiveness, assumptions and potential areas for improvement. Defense strategies have evolved from using a singular metric to excluding malicious clients, to employing a multifaceted approach examining client models at various phases. In this survey paper, our research indicates that the to-learn data, the learning gradients, and the learned model at different stages all can be manipulated to initiate malicious attacks that range from undermining model performance, reconstructing private local data, and to inserting backdoors. We have also seen these threat are becoming more insidious. While earlier studies typically amplified malicious gradients, recent endeavors subtly alter the least significant weights in local models to bypass defense measures. This literature review provides a holistic understanding of the current FL threat landscape and highlights the importance of developing robust, efficient, and privacy-preserving defenses to ensure the safe and trusted adoption of FL in real-world applications. The categorized bibliography can be found at: https://github.com/Rand2AI/Awesome-Vulnerability-of-Federated-Learning

    Content-aware frame interpolation (CAFI): deep learning-based temporal super-resolution for fast bioimaging

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    The development of high-resolution microscopes has made it possible to investigate cellular processes in 3D and over time. However, observing fast cellular dynamics remains challenging because of photobleaching and phototoxicity. Here we report the implementation of two content-aware frame interpolation (CAFI) deep learning networks, Zooming SlowMo and Depth-Aware Video Frame Interpolation, that are highly suited for accurately predicting images in between image pairs, therefore improving the temporal resolution of image series post-acquisition. We show that CAFI is capable of understanding the motion context of biological structures and can perform better than standard interpolation methods. We benchmark CAFI’s performance on 12 different datasets, obtained from four different microscopy modalities, and demonstrate its capabilities for single-particle tracking and nuclear segmentation. CAFI potentially allows for reduced light exposure and phototoxicity on the sample for improved long-term live-cell imaging. The models and the training and testing data are available via the ZeroCostDL4Mic platform

    Graduate Catalog of Studies, 2023-2024

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    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
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