2,834 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

    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

    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

    Documenting Knowledge Graph Embedding and Link Prediction using Knowledge Graphs

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    In recent years, sub-symbolic learning, i.e., Knowledge Graph Embedding (KGE) incorporated with Knowledge Graphs (KGs) has gained significant attention in various downstream tasks (e.g., Link Prediction (LP)). These techniques learn a latent vector representation of KG's semantical structure to infer missing links. Nonetheless, the KGE models remain a black box, and the decision-making process behind them is not clear. Thus, the trustability and reliability of the model's outcomes have been challenged. While many state-of-the-art approaches provide data-driven frameworks to address these issues, they do not always provide a complete understanding, and the interpretations are not machine-readable. That is why, in this work, we extend a hybrid interpretable framework, InterpretME, in the field of the KGE models, especially for translation distance models, which include TransE, TransH, TransR, and TransD. The experimental evaluation on various benchmark KGs supports the validity of this approach, which we term Trace KGE. Trace KGE, in particular, contributes to increased interpretability and understanding of the perplexing KGE model's behavior

    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

    ScribFormer: Transformer Makes CNN Work Better for Scribble-based Medical Image Segmentation

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    Most recent scribble-supervised segmentation methods commonly adopt a CNN framework with an encoder-decoder architecture. Despite its multiple benefits, this framework generally can only capture small-range feature dependency for the convolutional layer with the local receptive field, which makes it difficult to learn global shape information from the limited information provided by scribble annotations. To address this issue, this paper proposes a new CNN-Transformer hybrid solution for scribble-supervised medical image segmentation called ScribFormer. The proposed ScribFormer model has a triple-branch structure, i.e., the hybrid of a CNN branch, a Transformer branch, and an attention-guided class activation map (ACAM) branch. Specifically, the CNN branch collaborates with the Transformer branch to fuse the local features learned from CNN with the global representations obtained from Transformer, which can effectively overcome limitations of existing scribble-supervised segmentation methods. Furthermore, the ACAM branch assists in unifying the shallow convolution features and the deep convolution features to improve model’s performance further. Extensive experiments on two public datasets and one private dataset show that our ScribFormer has superior performance over the state-of-the-art scribble-supervised segmentation methods, and achieves even better results than the fully-supervised segmentation methods. The code is released at https://github.com/HUANGLIZI/ScribFormer

    Serverless Strategies and Tools in the Cloud Computing Continuum

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    Tesis por compendio[ES] En los últimos años, la popularidad de la computación en nube ha permitido a los usuarios acceder a recursos de cómputo, red y almacenamiento sin precedentes bajo un modelo de pago por uso. Esta popularidad ha propiciado la aparición de nuevos servicios para resolver determinados problemas informáticos a gran escala y simplificar el desarrollo y el despliegue de aplicaciones. Entre los servicios más destacados en los últimos años se encuentran las plataformas FaaS (Función como Servicio), cuyo principal atractivo es la facilidad de despliegue de pequeños fragmentos de código en determinados lenguajes de programación para realizar tareas específicas en respuesta a eventos. Estas funciones son ejecutadas en los servidores del proveedor Cloud sin que los usuarios se preocupen de su mantenimiento ni de la gestión de su elasticidad, manteniendo siempre un modelo de pago por uso de grano fino. Las plataformas FaaS pertenecen al paradigma informático conocido como Serverless, cuyo propósito es abstraer la gestión de servidores por parte de los usuarios, permitiéndoles centrar sus esfuerzos únicamente en el desarrollo de aplicaciones. El problema del modelo FaaS es que está enfocado principalmente en microservicios y tiende a tener limitaciones en el tiempo de ejecución y en las capacidades de computación (por ejemplo, carece de soporte para hardware de aceleración como GPUs). Sin embargo, se ha demostrado que la capacidad de autoaprovisionamiento y el alto grado de paralelismo de estos servicios pueden ser muy adecuados para una mayor variedad de aplicaciones. Además, su inherente ejecución dirigida por eventos hace que las funciones sean perfectamente adecuadas para ser definidas como pasos en flujos de trabajo de procesamiento de archivos (por ejemplo, flujos de trabajo de computación científica). Por otra parte, el auge de los dispositivos inteligentes e integrados (IoT), las innovaciones en las redes de comunicación y la necesidad de reducir la latencia en casos de uso complejos han dado lugar al concepto de Edge computing, o computación en el borde. El Edge computing consiste en el procesamiento en dispositivos cercanos a las fuentes de datos para mejorar los tiempos de respuesta. La combinación de este paradigma con la computación en nube, formando arquitecturas con dispositivos a distintos niveles en función de su proximidad a la fuente y su capacidad de cómputo, se ha acuñado como continuo de la computación en la nube (o continuo computacional). Esta tesis doctoral pretende, por lo tanto, aplicar diferentes estrategias Serverless para permitir el despliegue de aplicaciones generalistas, empaquetadas en contenedores de software, a través de los diferentes niveles del continuo computacional. Para ello, se han desarrollado múltiples herramientas con el fin de: i) adaptar servicios FaaS de proveedores Cloud públicos; ii) integrar diferentes componentes software para definir una plataforma Serverless en infraestructuras privadas y en el borde; iii) aprovechar dispositivos de aceleración en plataformas Serverless; y iv) facilitar el despliegue de aplicaciones y flujos de trabajo a través de interfaces de usuario. Además, se han creado y adaptado varios casos de uso para evaluar los desarrollos conseguidos.[CA] En els últims anys, la popularitat de la computació al núvol ha permès als usuaris accedir a recursos de còmput, xarxa i emmagatzematge sense precedents sota un model de pagament per ús. Aquesta popularitat ha propiciat l'aparició de nous serveis per resoldre determinats problemes informàtics a gran escala i simplificar el desenvolupament i desplegament d'aplicacions. Entre els serveis més destacats en els darrers anys hi ha les plataformes FaaS (Funcions com a Servei), el principal atractiu de les quals és la facilitat de desplegament de petits fragments de codi en determinats llenguatges de programació per realitzar tasques específiques en resposta a esdeveniments. Aquestes funcions són executades als servidors del proveïdor Cloud sense que els usuaris es preocupen del seu manteniment ni de la gestió de la seva elasticitat, mantenint sempre un model de pagament per ús de gra fi. Les plataformes FaaS pertanyen al paradigma informàtic conegut com a Serverless, el propòsit del qual és abstraure la gestió de servidors per part dels usuaris, permetent centrar els seus esforços únicament en el desenvolupament d'aplicacions. El problema del model FaaS és que està enfocat principalment a microserveis i tendeix a tenir limitacions en el temps d'execució i en les capacitats de computació (per exemple, no té suport per a maquinari d'acceleració com GPU). Tot i això, s'ha demostrat que la capacitat d'autoaprovisionament i l'alt grau de paral·lelisme d'aquests serveis poden ser molt adequats per a més aplicacions. A més, la seva inherent execució dirigida per esdeveniments fa que les funcions siguen perfectament adequades per ser definides com a passos en fluxos de treball de processament d'arxius (per exemple, fluxos de treball de computació científica). D'altra banda, l'auge dels dispositius intel·ligents i integrats (IoT), les innovacions a les xarxes de comunicació i la necessitat de reduir la latència en casos d'ús complexos han donat lloc al concepte d'Edge computing, o computació a la vora. L'Edge computing consisteix en el processament en dispositius propers a les fonts de dades per millorar els temps de resposta. La combinació d'aquest paradigma amb la computació en núvol, formant arquitectures amb dispositius a diferents nivells en funció de la proximitat a la font i la capacitat de còmput, s'ha encunyat com a continu de la computació al núvol (o continu computacional). Aquesta tesi doctoral pretén, doncs, aplicar diferents estratègies Serverless per permetre el desplegament d'aplicacions generalistes, empaquetades en contenidors de programari, a través dels diferents nivells del continu computacional. Per això, s'han desenvolupat múltiples eines per tal de: i) adaptar serveis FaaS de proveïdors Cloud públics; ii) integrar diferents components de programari per definir una plataforma Serverless en infraestructures privades i a la vora; iii) aprofitar dispositius d'acceleració a plataformes Serverless; i iv) facilitar el desplegament d'aplicacions i fluxos de treball mitjançant interfícies d'usuari. A més, s'han creat i s'han adaptat diversos casos d'ús per avaluar els desenvolupaments aconseguits.[EN] In recent years, the popularity of Cloud computing has allowed users to access unprecedented compute, network, and storage resources under a pay-per-use model. This popularity led to new services to solve specific large-scale computing challenges and simplify the development and deployment of applications. Among the most prominent services in recent years are FaaS (Function as a Service) platforms, whose primary appeal is the ease of deploying small pieces of code in certain programming languages to perform specific tasks on an event-driven basis. These functions are executed on the Cloud provider's servers without users worrying about their maintenance or elasticity management, always keeping a fine-grained pay-per-use model. FaaS platforms belong to the computing paradigm known as Serverless, which aims to abstract the management of servers from the users, allowing them to focus their efforts solely on the development of applications. The problem with FaaS is that it focuses on microservices and tends to have limitations regarding the execution time and the computing capabilities (e.g. lack of support for acceleration hardware such as GPUs). However, it has been demonstrated that the self-provisioning capability and high degree of parallelism of these services can be well suited to broader applications. In addition, their inherent event-driven triggering makes functions perfectly suitable to be defined as steps in file processing workflows (e.g. scientific computing workflows). Furthermore, the rise of smart and embedded devices (IoT), innovations in communication networks and the need to reduce latency in challenging use cases have led to the concept of Edge computing. Edge computing consists of conducting the processing on devices close to the data sources to improve response times. The coupling of this paradigm together with Cloud computing, involving architectures with devices at different levels depending on their proximity to the source and their compute capability, has been coined as Cloud Computing Continuum (or Computing Continuum). Therefore, this PhD thesis aims to apply different Serverless strategies to enable the deployment of generalist applications, packaged in software containers, across the different tiers of the Cloud Computing Continuum. To this end, multiple tools have been developed in order to: i) adapt FaaS services from public Cloud providers; ii) integrate different software components to define a Serverless platform on on-premises and Edge infrastructures; iii) leverage acceleration devices on Serverless platforms; and iv) facilitate the deployment of applications and workflows through user interfaces. Additionally, several use cases have been created and adapted to assess the developments achieved.Risco Gallardo, S. (2023). Serverless Strategies and Tools in the Cloud Computing Continuum [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/202013Compendi

    ClusterFix: A Cluster-Based Debiasing Approach without Protected-Group Supervision

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    The failures of Deep Networks can sometimes be ascribed to biases in the data or algorithmic choices. Existing debiasing approaches exploit prior knowledge to avoid unintended solutions; we acknowledge that, in real-world settings, it could be unfeasible to gather enough prior information to characterize the bias, or it could even raise ethical considerations. We hence propose a novel debiasing approach, termed ClusterFix, which does not require any external hint about the nature of biases. Such an approach alters the standard empirical risk minimization and introduces a per-example weight, encoding how critical and far from the majority an example is. Notably, the weights consider how difficult it is for the model to infer the correct pseudo-label, which is obtained in a self-supervised manner by dividing examples into multiple clusters. Extensive experiments show that the misclassification error incurred in identifying the correct cluster allows for identifying examples prone to bias-related issues. As a result, our approach outperforms existing methods on standard benchmarks for bias removal and fairness

    Dconformer: A denoising convolutional transformer with joint learning strategy for intelligent diagnosis of bearing faults

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    Rolling bearings are the core components of rotating machinery, and their normal operation is crucial to entire industrial applications. Most existing condition monitoring methods have been devoted to extracting discriminative features from vibration signals that reflect bearing health status. However, the complex working conditions of rolling bearings often make the fault-related information easily buried in noise and other interference. Therefore, it is challenging for existing approaches to extract sufficient critical features in these scenarios. To address this issue, this paper proposes a novel CNN-Transformer network, referred to as Dconformer, capable of extracting both local and global discriminative features from noisy vibration signals. The main contributions of this research include: (1) Developing a novel joint-learning strategy that simultaneously enhances the performance of signal denoising and fault diagnosis, leading to robust and accurate diagnostic results; (2) Constructing a novel CNN-transformer network with a multi-branch cross-cascaded architecture, which inherits the strengths of CNNs and transformers and demonstrates superior anti-interference capability. Extensive experimental results reveal that the proposed Dconformer outperforms five state-of-the-art approaches, particularly in strong noisy scenarios
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