arXiv subjects

Peter J. Hellyer

Publications and source records attributed to Peter J. Hellyer.

4 recordsLinked to original sources

arXiv2019

Analysis of an Automated Machine Learning Approach in Brain Predictive Modelling: A data-driven approach to Predict Brain Age from Cortical Anatomical Measures

The use of machine learning (ML) algorithms has significantly increased in neuroscience. However, from the vast extent of possible ML algorithms, which one is the optimal model to predict the target variable? What are the hyperparameters for such a model? Given the plethora of possible answers to these questions, in the last years, automated machine learning (autoML) has been gaining attention. Here, we apply an autoML library called TPOT which uses a tree-based representation of machine learning pipelines and conducts a genetic-programming based approach to find the model and its hyperparameters that more closely predicts the subject's true age. To explore autoML and evaluate its efficacy within neuroimaging datasets, we chose a problem that has been the focus of previous extensive study: brain age prediction. Without any prior knowledge, TPOT was able to scan through the model space and create pipelines that outperformed the state-of-the-art accuracy for Freesurfer-based models using only thickness and volume information for anatomical structure. In particular, we compared the performance of TPOT (mean accuracy error (MAE): $4.612 \pm .124$ years) and a Relevance Vector Regression (MAE $5.474 \pm .140$ years). TPOT also suggested interesting combinations of models that do not match the current most used models for brain prediction but generalise well to unseen data. AutoML showed promising results as a data-driven approach to find optimal models for neuroimaging applications.

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arXiv2016

Balanced activation in a simple embodied neural simulation

In recent years, there have been many computational simulations of spontaneous neural dynamics. Here, we explore a model of spontaneous neural dynamics and allow it to control a virtual agent moving in a simple environment. This setup generates interesting brain-environment feedback interactions that rapidly destabilize neural and behavioral dynamics and suggest the need for homeostatic mechanisms. We investigate roles for both local homeostatic plasticity (local inhibition adjusting over time to balance excitatory input) as well as macroscopic task negative activity (that compensates for task positive, sensory input) in regulating both neural activity and resulting behavior (trajectories through the environment). Our results suggest complementary functional roles for both local homeostatic plasticity and balanced activity across brain regions in maintaining neural and behavioral dynamics. These findings suggest important functional roles for homeostatic systems in maintaining neural and behavioral dynamics and suggest a novel functional role for frequently reported macroscopic task-negative patterns of activity (e.g., the default mode network).

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arXiv2015

Local inhibitory plasticity tunes global brain dynamics and allows the emergence of functional brain networks

Rich, spontaneous brain activity has been observed across a range of different temporal and spatial scales. These dynamics are thought to be important t for efficient neural functioning. Experimental evidence suggests that these neural dynamics are maintained across a variety of different cognitive states, in response to alterations of the environment and to changes in brain configuration (e.g., across individuals, development and in many neurological disorders). This suggests that the brain has evolved mechanisms to stabilize dynamics and maintain them across a range of situations. Here, we employ a local homeostatic inhibitory plasticity mechanism, balancing inhibitory and excitatory activity in a model of macroscopic brain activity based on white-matter structural connectivity. We demonstrate that the addition of homeostatic plasticity regulates network activity and allows for the emergence of rich, spontaneous dynamics across a range of brain configurations. Furthermore, the presence of homeostatic plasticity maximises the overlap between empirical and simulated patterns of functional connectivity. Therefore, this work presents a simple, local, biologically plausible inhibitory mechanism that allows stable dynamics to emerge in the brain and which facilitates the formation of functional connectivity networks.

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arXiv2014

Exploring spatiotemporal network transitions in task functional MRI

A critical question for cognitive neuroscience regards how transitions between cognitive states emerge from the dynamic activity of functional brain networks. However, current methodologies cannot easily evaluate both the spatial and temporal changes in brain networks with cognitive state. Here we combine a simple data reorganization with spatial ICA, enabling a spatiotemporal ICA (stICA) which captures the consistent evolution of networks during onset and offset of a task. The technique was applied to FMRI datasets involving alternating between rest and task and to simple synthetic data. Starting and finishing time-points of periods of interest (anchors) were defined at task block onsets and offsets. For each subject, the ten volumes following each anchor were extracted and concatenated spatially, producing a single 3D sample. Samples for all anchors and subjects were concatenated along the fourth dimension. This 4D dataset was decomposed using ICA into spatiotemporal components. One component exhibited the transition with task onset from a default mode network (DMN) becoming less active to a fronto-parietal control network (FPCN) becoming more active. We observed other changes with relevance to understanding network dynamics, e.g., the DMN showed a changing spatial distribution, shifting to an anterior/superior pattern of deactivation during task from a posterior/inferior pattern during rest. By anchoring analyses to periods associated with the onsets and offsets of task, our approach reveals novel aspects of the dynamics of network activity accompanying these transitions. Importantly, these findings were observed without specifying a priori either the spatial networks or the task time courses.

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