33 research outputs found
Modeling Dynamic Functional Connectivity with Latent Factor Gaussian Processes
Dynamic functional connectivity, as measured by the time-varying covariance
of neurological signals, is believed to play an important role in many aspects
of cognition. While many methods have been proposed, reliably establishing the
presence and characteristics of brain connectivity is challenging due to the
high dimensionality and noisiness of neuroimaging data. We present a latent
factor Gaussian process model which addresses these challenges by learning a
parsimonious representation of connectivity dynamics. The proposed model
naturally allows for inference and visualization of time-varying connectivity.
As an illustration of the scientific utility of the model, application to a
data set of rat local field potential activity recorded during a complex
non-spatial memory task provides evidence of stimuli differentiation
Whole MILC: generalizing learned dynamics across tasks, datasets, and populations
Behavioral changes are the earliest signs of a mental disorder, but arguably,
the dynamics of brain function gets affected even earlier. Subsequently,
spatio-temporal structure of disorder-specific dynamics is crucial for early
diagnosis and understanding the disorder mechanism. A common way of learning
discriminatory features relies on training a classifier and evaluating feature
importance. Classical classifiers, based on handcrafted features are quite
powerful, but suffer the curse of dimensionality when applied to large input
dimensions of spatio-temporal data. Deep learning algorithms could handle the
problem and a model introspection could highlight discriminatory
spatio-temporal regions but need way more samples to train. In this paper we
present a novel self supervised training schema which reinforces whole sequence
mutual information local to context (whole MILC). We pre-train the whole MILC
model on unlabeled and unrelated healthy control data. We test our model on
three different disorders (i) Schizophrenia (ii) Autism and (iii) Alzheimers
and four different studies. Our algorithm outperforms existing self-supervised
pre-training methods and provides competitive classification results to
classical machine learning algorithms. Importantly, whole MILC enables
attribution of subject diagnosis to specific spatio-temporal regions in the
fMRI signal.Comment: Accepted at MICCAI 2020. arXiv admin note: substantial text overlap
with arXiv:1912.0313
Construction of embedded fMRI resting state functional connectivity networks using manifold learning
We construct embedded functional connectivity networks (FCN) from benchmark
resting-state functional magnetic resonance imaging (rsfMRI) data acquired from
patients with schizophrenia and healthy controls based on linear and nonlinear
manifold learning algorithms, namely, Multidimensional Scaling (MDS), Isometric
Feature Mapping (ISOMAP) and Diffusion Maps. Furthermore, based on key global
graph-theoretical properties of the embedded FCN, we compare their
classification potential using machine learning techniques. We also assess the
performance of two metrics that are widely used for the construction of FCN
from fMRI, namely the Euclidean distance and the lagged cross-correlation
metric. We show that the FCN constructed with Diffusion Maps and the lagged
cross-correlation metric outperform the other combinations
mSPD-NN: A Geometrically Aware Neural Framework for Biomarker Discovery from Functional Connectomics Manifolds
Connectomics has emerged as a powerful tool in neuroimaging and has spurred
recent advancements in statistical and machine learning methods for
connectivity data. Despite connectomes inhabiting a matrix manifold, most
analytical frameworks ignore the underlying data geometry. This is largely
because simple operations, such as mean estimation, do not have easily
computable closed-form solutions. We propose a geometrically aware neural
framework for connectomes, i.e., the mSPD-NN, designed to estimate the geodesic
mean of a collections of symmetric positive definite (SPD) matrices. The
mSPD-NN is comprised of bilinear fully connected layers with tied weights and
utilizes a novel loss function to optimize the matrix-normal equation arising
from Fr\'echet mean estimation. Via experiments on synthetic data, we
demonstrate the efficacy of our mSPD-NN against common alternatives for SPD
mean estimation, providing competitive performance in terms of scalability and
robustness to noise. We illustrate the real-world flexibility of the mSPD-NN in
multiple experiments on rs-fMRI data and demonstrate that it uncovers stable
biomarkers associated with subtle network differences among patients with
ADHD-ASD comorbidities and healthy controls.Comment: Accepted into IPMI 202