Author name cluster

Lloyd Elliott

Possible papers associated with this exact author name in Arrow. This page groups case-insensitive exact name matches and is not a full identity disambiguation profile.

5 papers

1 author row

YNIMG Journal 2023 Journal Article

Amplitudes of resting-state functional networks – investigation into their correlates and biophysical properties

Soojin Lee
Janine D. Bijsterbosch
Fidel Alfaro Almagro
Lloyd Elliott
Paul McCarthy
Bernd Taschler
Roser Sala-Llonch
Christian F. Beckmann

Resting-state fMRI studies have shown that multiple functional networks, which consist of distributed brain regions that share synchronised spontaneous activity, co-exist in the brain. As these resting-state networks (RSNs) have been thought to reflect the brain's intrinsic functional organization, intersubject variability in the networks' spontaneous fluctuations may be associated with individuals' clinical, physiological, cognitive, and genetic traits. Here, we investigated resting-state fMRI data along with extensive clinical, lifestyle, and genetic data collected from 37,842 UK Biobank participants, with the object of elucidating intersubject variability in the fluctuation amplitudes of RSNs. Functional properties of the RSN amplitudes were first examined by analyzing correlations with the well-established between-network functional connectivity. It was found that a network amplitude is highly correlated with the mean strength of the functional connectivity that the network has with the other networks. Intersubject clustering analysis showed the amplitudes are most strongly correlated with age, cardiovascular factors, body composition, blood cell counts, lung function, and sex, with some differences in the correlation strengths between sensory and cognitive RSNs. Genome-wide association studies (GWASs) of RSN amplitudes identified several significant genetic variants reported in previous GWASs for their implications in sleep duration. We provide insight into key factors determining RSN amplitudes and demonstrate that intersubject variability of the amplitudes primarily originates from differences in temporal synchrony between functionally linked brain regions, rather than differences in the magnitude of raw voxelwise BOLD signal changes. This finding additionally revealed intriguing differences between sensory and cognitive RSNs with respect to sex effects on temporal synchrony and provided evidence suggesting that synchronous coactivations of functionally linked brain regions, and magnitudes of BOLD signal changes, may be related to different genetic mechanisms. These results underscore that intersubject variability of the amplitudes in health and disease need to be interpreted largely as a measure of the sum of within-network temporal synchrony and amplitudes of BOLD signals, with a dominant contribution from the former.

Details DOI

NeurIPS Conference 2019 Conference Paper

Random Tessellation Forests

Shufei Ge
Shijia Wang
Yee Whye Teh
Liangliang Wang
Lloyd Elliott

Space partitioning methods such as random forests and the Mondrian process are powerful machine learning methods for multi-dimensional and relational data, and are based on recursively cutting a domain. The flexibility of these methods is often limited by the requirement that the cuts be axis aligned. The Ostomachion process and the self-consistent binary space partitioning-tree process were recently introduced as generalizations of the Mondrian process for space partitioning with non-axis aligned cuts in the plane. Motivated by the need for a multi-dimensional partitioning tree with non-axis aligned cuts, we propose the Random Tessellation Process, a framework that includes the Mondrian process as a special case. We derive a sequential Monte Carlo algorithm for inference, and provide random forest methods. Our methods are self-consistent and can relax axis-aligned constraints, allowing complex inter-dimensional dependence to be captured. We present a simulation study and analyze gene expression data of brain tissue, showing improved accuracies over other methods.

PDF Details

YNIMG Journal 2018 Journal Article

Directed functional connectivity using dynamic graphical models

Simon Schwab
Ruth Harbord
Valerio Zerbi
Lloyd Elliott
Soroosh Afyouni
Jim Q. Smith
Mark W. Woolrich
Stephen M. Smith

There are a growing number of neuroimaging methods that model spatio-temporal patterns of brain activity to allow more meaningful characterizations of brain networks. This paper proposes dynamic graphical models (DGMs) for dynamic, directed functional connectivity. DGMs are a multivariate graphical model with time-varying coefficients that describe instantaneous directed relationships between nodes. A further benefit of DGMs is that networks may contain loops and that large networks can be estimated. We use network simulations and human resting-state fMRI (N = 500) to investigate the validity and reliability of the estimated networks. We simulate systematic lags of the hemodynamic response at different brain regions to investigate how these lags potentially bias directionality estimates. In the presence of such lag confounds (0. 4–0. 8 s offset between connected nodes), our method has a sensitivity of 72%–77% to detect the true direction. Stronger lag confounds have reduced sensitivity, but do not increase false positives (i. e. , directionality estimates of the opposite direction). In human resting-state fMRI, the default mode network has consistent influence on the cerebellar, the limbic and the auditory/temporal networks. We also show a consistent reciprocal relationship between the visual medial and visual lateral network. Finally, we apply the method in a small mouse fMRI sample and discover a highly plausible relationship between areas in the hippocampus feeding into the cingulate cortex. We provide a computationally efficient implementation of DGM as a free software package for R.

Details DOI

NeurIPS Conference 2012 Conference Paper

Scalable imputation of genetic data with a discrete fragmentation-coagulation process

Lloyd Elliott
Yee Teh

We present a Bayesian nonparametric model for genetic sequence data in which a set of genetic sequences is modelled using a Markov model of partitions. The partitions at consecutive locations in the genome are related by their clusters first splitting and then merging. Our model can be thought of as a discrete time analogue of continuous time fragmentation-coagulation processes [Teh et al 2011], preserving the important properties of projectivity, exchangeability and reversibility, while being more scalable. We apply this model to the problem of genotype imputation, showing improved computational efficiency while maintaining the same accuracies as in [Teh et al 2011].

PDF Details

NeurIPS Conference 2011 Conference Paper

Modelling Genetic Variations using Fragmentation-Coagulation Processes

Yee Teh
Charles Blundell
Lloyd Elliott

We propose a novel class of Bayesian nonparametric models for sequential data called fragmentation-coagulation processes (FCPs). FCPs model a set of sequences using a partition-valued Markov process which evolves by splitting and merging clusters. An FCP is exchangeable, projective, stationary and reversible, and its equilibrium distributions are given by the Chinese restaurant process. As opposed to hidden Markov models, FCPs allow for flexible modelling of the number of clusters, and they avoid label switching non-identifiability problems. We develop an efficient Gibbs sampler for FCPs which uses uniformization and the forward-backward algorithm. Our development of FCPs is motivated by applications in population genetics, and we demonstrate the utility of FCPs on problems of genotype imputation with phased and unphased SNP data.

PDF Details