Decoding Task-Based fMRI Data Using Graph Neural Networks, Considering Individual Differences

Functional magnetic resonance imaging (fMRI) is a non-invasive technology that provides high spatial resolution in determining the human brain\u27s responses and measures regional brain activity through metabolic changes in blood oxygen consumption associated with neural activity. Task fMRI provides an opportunity to analyze the working mechanisms of the human brain during specific task performance. Over the past several years, a variety of computational methods have been proposed to decode task fMRI data that can identify brain regions associated with different task stimulations. Despite the advances made by these methods, several limitations exist due to graph representations and graph embeddings transferred from task fMRI signals. In the present study, we proposed an end-to-end graph convolutional network by combining the convolutional neural network with graph representation, with three convolutional layers to classify task fMRI data from the Human Connectome Project (302 participants, 22–35 years of age). One goal of this dissertation was to improve classification performance. We applied four of the most widely used node embedding algorithms—NetMF, RandNE, Node2Vec, and Walklets—to automatically extract the structural properties of the nodes in the brain functional graph, then evaluated the performance of the classification model. The empirical results indicated that the proposed GCN framework accurately identified the brain\u27s state in task fMRI data and achieved comparable macro F1 scores of 0.978 and 0.976 with the NetMF and RandNE embedding methods, respectively. Another goal of the dissertation was to assess the effects of individual differences (i.e., gender and fluid intelligence) on classification performance. We tested the proposed GCN framework on sub-datasets divided according to gender and fluid intelligence. Experimental results indicated significant differences in the classification predictions of gender, but not high/low fluid intelligence fMRI data. Our experiments yielded promising results and demonstrated the superior ability of our GCN in modeling task fMRI data

Modelos matemáticos para lesões em redes neurais com padrões complexos de conectividade

Orientador: Prof. Dr. Ricardo Luiz VianaTese (Doutorado) - Universidade Federal do Paraná, Setor de Ciências Exatas, Programa de Pós-Graduação em Física. Defesa: Curitiba, 18/09/2015Inclui referências : f. 139-146Resumo: O cérebro contem cerca de cem bilhões de neurônios que se conectam através de um padrão complexo de conectividade, que opera no sentido de otimizar o processo de transmissão de informação. Os neurônios, ao estabelecerem uma conexão entre si podem muitas vezes exibir sincronização. A presença de traumas e doenças degenerativas em regiões específicas do cérebro podem, através de efeitos locais, danificar o funcionamento cerebral como um todo. O propósito deste trabalho é tentar responder a questões do tipo: em uma rede neural, quais são as formas de lesões que causam maior impacto na dinâmica da rede? É possível identificar um tipo de lesão a partir do seu efeito? Existem topologias de rede que são mais robustas à lesões? Neste sentido, analisamos a sincronização de fase para uma rede de neurônios com diferentes topologias de rede, comparamos os resultados com um modelo de osciladores e analisamos diferentes tipos de lesões. Nossos resultados apontam que para o estudo de sincronização de fase, os neurônios podem ser considerados como osciladores, porém, o comportamento das frequências no estado sincronizado em redes neurais, em geral, não é similar ao comportamento de osciladores. No estudo das lesões, do ponto de vista dinâmico, para cada tipo de rede existe um comportamento distinto aos diferentes tipos de lesões. Entre neurônios globalmente acoplados, é possível distinguir a partir da dinâmica global se a lesão destrói apenas as conexões ou destrói os neurônios. Em redes complexas, o efeito das lesões é maior quando a lesão afeta os neurônios mais conectados ou com maior centralidade de intermediação. Em redes de pequeno mundo, a diferença entre os tipos de lesão é perceptível, porém, mais sutil do que para redes aleatórias e sem escala.Abstract: The brain is composed of around one hundread billion of neurons connected through synapses forming a complex pattern of connectivity. This complex connectivity is responsible to optimize the information process. When neurons are connected among themselves they can exhibit synchronization. The presence of traumas and neurodegenerative diseases in some brain areas causes not only local effects, but in the whole brain. The purpose of this work is to answer questions like: which are the type of lesions with bigger dynamical effects in the neural network? Is it possible to identify a type of lesion just looking at its dynamical effects in the network? Are there topologies against lesions which are more robust than others? In this sense, we analyse phase synchronization in a neural network with different network topologies. We compare the obtained results with a model of phase oscillators and we analysed different types of lesions. Our results show that neuronal phase synchronization is similar to phase synchronization in oscillators, however, frequency synchronization usually is different in both models. Related to lesions, from the dynamical point of view, for each type of network there is a distinct behavior for each type of lesion. Among globally coupled neurons, it is possible to dynamically distinguish when the lesion either disrupt or destroy the neurons. For complex networks, the most effective lesions are those that affects the most connected neurons or those with the largest betweenness. For small-world networks, the difference among types of lesions are distinguishable, though, they are subtle in comparison with random and scale-free networks

Computing Interpretable Representations of Cell Morphodynamics

Shape changes (morphodynamics) are one of the principal ways cells interact with their environments and perform key intrinsic behaviours like division. These dynamics arise from a myriad of complex signalling pathways that often organise with emergent simplicity to carry out critical functions including predation, collaboration and migration. A powerful method for analysis can therefore be to quantify this emergent structure, bypassing the low-level complexity. Enormous image datasets are now available to mine. However, it can be difficult to uncover interpretable representations of the global organisation of these heterogeneous dynamic processes. Here, such representations were developed for interpreting morphodynamics in two key areas: mode of action (MoA) comparison for drug discovery (developed using the economically devastating Asian soybean rust crop pathogen) and 3D migration of immune system T cells through extracellular matrices (ECMs). For MoA comparison, population development over a 2D space of shapes (morphospace) was described using two models with condition-dependent parameters: a top-down model of diffusive development over Waddington-type landscapes, and a bottom-up model of tip growth. A variety of landscapes were discovered, describing phenotype transitions during growth, and possible perturbations in the tip growth machinery that cause this variation were identified. For interpreting T cell migration, a new 3D shape descriptor that incorporates key polarisation information was developed, revealing low-dimensionality of shape, and the distinct morphodynamics of run-and-stop modes that emerge at minute timescales were mapped. Periodically oscillating morphodynamics that include retrograde deformation flows were found to underlie active translocation (run mode). Overall, it was found that highly interpretable representations could be uncovered while still leveraging the enormous discovery power of deep learning algorithms. The results show that whole-cell morphodynamics can be a convenient and powerful place to search for structure, with potentially life-saving applications in medicine and biocide discovery as well as immunotherapeutics.Open Acces