scholarly journals Deep Neural Networks Carve the Brain at its Joints

2020 ◽  
Author(s):  
Maxwell A. Bertolero ◽  
Danielle S. Bassett
Keyword(s):  
Neural Networks ◽  
Deep Neural Networks ◽  
Linear Models ◽  
Brain Connectivity ◽  
Network Models ◽  
Brain Regions ◽  
Linear Functions ◽  
Complex Relationships ◽  
And Behavior ◽  
The Brain

AbstractHow an individual’s unique brain connectivity determines that individual’s cognition, behavior, and risk for pathology is a fundamental question in basic and clinical neuroscience. In seeking answers, many have turned to machine learning, with some noting the particular promise of deep neural networks in modelling complex non-linear functions. However, it is not clear that complex functions actually exist between brain connectivity and behavior, and thus if deep neural networks necessarily outperform simpler linear models, or if their results would be interpretable. Here we show that, across 52 subject measures of cognition and behavior, deep neural networks fit to each brain region’s connectivity outperform linear regression, particularly for the brain’s connector hubs—regions with diverse brain connectivity—whereas the two approaches perform similarly when fit to brain systems. Critically, averaging deep neural network predictions across brain regions results in the most accurate predictions, demonstrating the ability of deep neural networks to easily model the various functions that exists between regional brain connectivity and behavior, carving the brain at its joints. Finally, we shine light into the black box of deep neural networks using multislice network models. We determined that the relationship between connector hubs and behavior is best captured by modular deep neural networks. Our results demonstrate that both simple and complex relationships exist between brain connectivity and behavior, and that deep neural networks can fit both. Moreover, deep neural networks are particularly powerful when they are first fit to the various functions of a system independently and then combined. Finally, deep neural networks are interpretable when their architectures are structurally characterized using multislice network models.

scholarly journals Unified AI framework to uncover deep interrelationships between gene expression and Alzheimer’s disease neuropathologies

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nicasia Beebe-Wang ◽  
Safiye Celik ◽  
Ethan Weinberger ◽  
Pascal Sturmfels ◽  
Philip L. De Jager ◽  
...  
Keyword(s):  
Gene Expression ◽  
Alzheimer’S Disease ◽  
Neural Networks ◽  
Alzheimer's Disease ◽  
Immune Response ◽  
Deep Neural Networks ◽  
Linear Models ◽  
Joint Analysis ◽  
Analysis Framework ◽  
Complex Relationships

AbstractDeep neural networks (DNNs) capture complex relationships among variables, however, because they require copious samples, their potential has yet to be fully tapped for understanding relationships between gene expression and human phenotypes. Here we introduce an analysis framework, namely MD-AD (Multi-task Deep learning for Alzheimer’s Disease neuropathology), which leverages an unexpected synergy between DNNs and multi-cohort settings. In these settings, true joint analysis can be stymied using conventional statistical methods, which require “harmonized” phenotypes and tend to capture cohort-level variations, obscuring subtler true disease signals. Instead, MD-AD incorporates related phenotypes sparsely measured across cohorts, and learns interactions between genes and phenotypes not discovered using linear models, identifying subtler signals than cohort-level variations which can be uniquely recapitulated in animal models and across tissues. We show that MD-AD exploits sex-specific relationships between microglial immune response and neuropathology, providing a nuanced context for the association between inflammatory genes and Alzheimer’s Disease.

scholarly journals Multilayer Network Approach in EEG Motor Imagery with an Adaptive Threshold

Sensors ◽  
2021 ◽  
Vol 21 (24) ◽  
pp. 8305
Author(s):  
César Covantes-Osuna ◽  
Jhonatan B. López ◽  
Omar Paredes ◽  
Hugo Vélez-Pérez ◽  
Rebeca Romo-Vázquez
Keyword(s):  
Motor Imagery ◽  
Brain Connectivity ◽  
Single Layer ◽  
Network Models ◽  
Brain Regions ◽  
Adaptive Threshold ◽  
Brain Network ◽  
Multilayer Network ◽  
Brain Models ◽  
The Brain

The brain has been understood as an interconnected neural network generally modeled as a graph to outline the functional topology and dynamics of brain processes. Classic graph modeling is based on single-layer models that constrain the traits conveyed to trace brain topologies. Multilayer modeling, in contrast, makes it possible to build whole-brain models by integrating features of various kinds. The aim of this work was to analyze EEG dynamics studies while gathering motor imagery data through single-layer and multilayer network modeling. The motor imagery database used consists of 18 EEG recordings of four motor imagery tasks: left hand, right hand, feet, and tongue. Brain connectivity was estimated by calculating the coherence adjacency matrices from each electrophysiological band (δ, θ, α and β) from brain areas and then embedding them by considering each band as a single-layer graph and a layer of the multilayer brain models. Constructing a reliable multilayer network topology requires a threshold that distinguishes effective connections from spurious ones. For this reason, two thresholds were implemented, the classic fixed (average) one and Otsu’s version. The latter is a new proposal for an adaptive threshold that offers reliable insight into brain topology and dynamics. Findings from the brain network models suggest that frontal and parietal brain regions are involved in motor imagery tasks.

scholarly journals Category representations in the brain are both discretely localized and widely distributed

2018 ◽  
Vol 119 (6) ◽  
pp. 2256-2264 ◽  
Author(s):  
Zarrar Shehzad ◽  
Gregory McCarthy
Keyword(s):  
Functional Mri ◽  
Brain Connectivity ◽  
Strong Support ◽  
Brain Regions ◽  
Distributed Representations ◽  
Domain Specific ◽  
Category Information ◽  
Shared Information ◽  
Unique Domain ◽  
The Brain

Whether category information is discretely localized or represented widely in the brain remains a contentious issue. Initial functional MRI studies supported the localizationist perspective that category information is represented in discrete brain regions. More recent fMRI studies using machine learning pattern classification techniques provide evidence for widespread distributed representations. However, these latter studies have not typically accounted for shared information. Here, we find strong support for distributed representations when brain regions are considered separately. However, localized representations are revealed by using analytical methods that separate unique from shared information among brain regions. The distributed nature of shared information and the localized nature of unique information suggest that brain connectivity may encourage spreading of information but category-specific computations are carried out in distinct domain-specific regions. NEW & NOTEWORTHY Whether visual category information is localized in unique domain-specific brain regions or distributed in many domain-general brain regions is hotly contested. We resolve this debate by using multivariate analyses to parse functional MRI signals from different brain regions into unique and shared variance. Our findings support elements of both models and show information is initially localized and then shared among other regions leading to distributed representations being observed.

scholarly journals Brain hierarchy score: Which deep neural networks are hierarchically brain-like?

2020 ◽  
Author(s):  
Soma Nonaka ◽  
Kei Majima ◽  
Shuntaro C. Aoki ◽  
Yukiyasu Kamitani
Keyword(s):  
Neural Networks ◽  
Image Recognition ◽  
High Performance ◽  
Deep Neural Networks ◽  
Recognition Performance ◽  
Brain Activity ◽  
Spatial Integration ◽  
Hierarchical Processing ◽  
Visual Areas ◽  
The Brain

SummaryAchievement of human-level image recognition by deep neural networks (DNNs) has spurred interest in whether and how DNNs are brain-like. Both DNNs and the visual cortex perform hierarchical processing, and correspondence has been shown between hierarchical visual areas and DNN layers in representing visual features. Here, we propose the brain hierarchy (BH) score as a metric to quantify the degree of hierarchical correspondence based on the decoding of individual DNN unit activations from human brain activity. We find that BH scores for 29 pretrained DNNs with varying architectures are negatively correlated with image recognition performance, indicating that recently developed high-performance DNNs are not necessarily brain-like. Experimental manipulations of DNN models suggest that relatively simple feedforward architecture with broad spatial integration is critical to brain-like hierarchy. Our method provides new ways for designing DNNs and understanding the brain in consideration of their representational homology.

scholarly journals Resting-state brain activity can predict target-independent aptitude in fMRI-neurofeedback training

2021 ◽  
Author(s):  
Takashi Nakano ◽  
Masahiro Takamura ◽  
Haruki Nishimura ◽  
Maro Machizawa ◽  
Naho Ichikawa ◽  
...  
Keyword(s):  
Resting State ◽  
Brain Connectivity ◽  
Brain Activity ◽  
Resting State Fmri ◽  
Brain Regions ◽  
Posterior Cingulate Cortex ◽  
Fmri Data ◽  
Independent Test ◽  
The Individual ◽  
The Brain

AbstractNeurofeedback (NF) aptitude, which refers to an individual’s ability to change its brain activity through NF training, has been reported to vary significantly from person to person. The prediction of individual NF aptitudes is critical in clinical NF applications. In the present study, we extracted the resting-state functional brain connectivity (FC) markers of NF aptitude independent of NF-targeting brain regions. We combined the data in fMRI-NF studies targeting four different brain regions at two independent sites (obtained from 59 healthy adults and six patients with major depressive disorder) to collect the resting-state fMRI data associated with aptitude scores in subsequent fMRI-NF training. We then trained the regression models to predict the individual NF aptitude scores from the resting-state fMRI data using a discovery dataset from one site and identified six resting-state FCs that predicted NF aptitude. Next we validated the prediction model using independent test data from another site. The result showed that the posterior cingulate cortex was the functional hub among the brain regions and formed predictive resting-state FCs, suggesting NF aptitude may be involved in the attentional mode-orientation modulation system’s characteristics in task-free resting-state brain activity.

scholarly journals Strategic Cognitive Sequencing: A Computational Cognitive Neuroscience Approach

2013 ◽  
Vol 2013 ◽  
pp. 1-18 ◽  
Author(s):  
Seth A. Herd ◽  
Kai A. Krueger ◽  
Trenton E. Kriete ◽  
Tsung-Ren Huang ◽  
Thomas E. Hazy ◽  
...  
Keyword(s):  
Cognitive Process ◽  
Network Models ◽  
Brain Regions ◽  
Human Cognition ◽  
Neural Network Models ◽  
Future Directions ◽  
Error Learning ◽  
Cognitive Actions ◽  
Self Instruction ◽  
The Brain

We address strategic cognitive sequencing, the “outer loop” of human cognition: how the brain decides what cognitive process to apply at a given moment to solve complex, multistep cognitive tasks. We argue that this topic has been neglected relative to its importance for systematic reasons but that recent work on how individual brain systems accomplish their computations has set the stage for productively addressing how brain regions coordinate over time to accomplish our most impressive thinking. We present four preliminary neural network models. The first addresses how the prefrontal cortex (PFC) and basal ganglia (BG) cooperate to perform trial-and-error learning of short sequences; the next, how several areas of PFC learn to make predictions of likely reward, and how this contributes to the BG making decisions at the level of strategies. The third models address how PFC, BG, parietal cortex, and hippocampus can work together to memorize sequences of cognitive actions from instruction (or “self-instruction”). The last shows how a constraint satisfaction process can find useful plans. The PFC maintains current and goal states and associates from both of these to find a “bridging” state, an abstract plan. We discuss how these processes could work together to produce strategic cognitive sequencing and discuss future directions in this area.

scholarly journals Frequency-based brain networks: From a multiplex framework to a full multilayer description

2018 ◽  
Vol 2 (4) ◽  
pp. 418-441 ◽  
Author(s):  
Javier M. Buldú ◽  
Mason A. Porter
Keyword(s):  
Brain Networks ◽  
Network Models ◽  
Real Data ◽  
Laplacian Matrix ◽  
Brain Regions ◽  
Brain Diseases ◽  
Multilayer Networks ◽  
Frequency Bands ◽  
Multiplex Network ◽  
The Brain

We explore how to study dynamical interactions between brain regions by using functional multilayer networks whose layers represent different frequency bands at which a brain operates. Specifically, we investigate the consequences of considering the brain as (i) a multilayer network, in which all brain regions can interact with each other at different frequency bands; and as (ii) a multiplex network, in which interactions between different frequency bands are allowed only within each brain region and not between them. We study the second-smallest eigenvalue λ2 of the combinatorial supra-Laplacian matrix of both the multiplex and multilayer networks, as λ2 has been used previously as an indicator of network synchronizability and as a biomarker for several brain diseases. We show that the heterogeneity of interlayer edge weights and, especially, the fraction of missing edges crucially modify the value of λ2, and we illustrate our results with both synthetic network models and real data obtained from resting-state magnetoencephalography. Our work highlights the differences between using a multiplex approach and a full multilayer approach when studying frequency-based multilayer brain networks.

Normalization Principles in Computational Neuroscience

2019 ◽  
Author(s):  
Kenway Louie ◽  
Paul W. Glimcher
Keyword(s):  
Information Processing ◽  
Computational Neuroscience ◽  
Linear Models ◽  
Brain Regions ◽  
Information Coding ◽  
Brain Organization ◽  
Contextual Modulation ◽  
Early Visual Cortex ◽  
And Function ◽  
And Behavior

A core question in systems and computational neuroscience is how the brain represents information. Identifying principles of information coding in neural circuits is critical to understanding brain organization and function in sensory, motor, and cognitive neuroscience. This provides a conceptual bridge between the underlying biophysical mechanisms and the ultimate behavioral goals of the organism. Central to this framework is the question of computation: what are the relevant representations of input and output, and what algorithms govern the input-output transformation? Remarkably, evidence suggests that certain canonical computations exist across different circuits, brain regions, and species. Such computations are implemented by different biophysical and network mechanisms, indicating that the unifying target of conservation is the algorithmic form of information processing rather than the specific biological implementation. A prime candidate to serve as a canonical computation is divisive normalization, which scales the activity of a given neuron by the activity of a larger neuronal pool. This nonlinear transformation introduces an intrinsic contextual modulation into information coding, such that the selective response of a neuron to features of the input is scaled by other input characteristics. This contextual modulation allows the normalization model to capture a wide array of neural and behavioral phenomena not captured by simpler linear models of information processing. The generality and flexibility of the normalization model arises from the normalization pool, which allows different inputs to directly drive and suppress a given neuron, effectively separating information that drives excitation and contextual modulation. Originally proposed to describe responses in early visual cortex, normalization has been widely documented in different brain regions, hierarchical levels, and modalities of sensory processing; furthermore, recent work shows that the normalization extends to cognitive processes such as attention, multisensory integration, and decision making. This ubiquity reinforces the canonical nature of the normalization computation and highlights the importance of an algorithmic framework in linking biological mechanism and behavior.

Effective brain connectivity estimation between active brain regions in autism using the dual Kalman-based method

2020 ◽  
Vol 65 (1) ◽  
pp. 23-32
Author(s):  
Mehdi Rajabioun ◽  
Ali Motie Nasrabadi ◽  
Mohammad Bagher Shamsollahi ◽  
Robert Coben
Keyword(s):  
Resting State ◽  
Brain Connectivity ◽  
Effective Connectivity ◽  
Estimation Error ◽  
Brain Regions ◽  
Estimation Methods ◽  
Estimation Errors ◽  
Normal Children ◽  
Brain Functions ◽  
The Brain

AbstractBrain connectivity estimation is a useful method to study brain functions and diagnose neuroscience disorders. Effective connectivity is a subdivision of brain connectivity which discusses the causal relationship between different parts of the brain. In this study, a dual Kalman-based method is used for effective connectivity estimation. Because of connectivity changes in autism, the method is applied to autistic signals for effective connectivity estimation. For method validation, the dual Kalman based method is compared with other connectivity estimation methods by estimation error and the dual Kalman-based method gives acceptable results with less estimation errors. Then, connectivities between active brain regions of autistic and normal children in the resting state are estimated and compared. In this simulation, the brain is divided into eight regions and the connectivity between regions and within them is calculated. It can be concluded from the results that in the resting state condition the effective connectivity of active regions is decreased between regions and is increased within each region in autistic children. In another result, by averaging the connectivity between the extracted active sources of each region, the connectivity between the left and right of the central part is more than that in other regions and the connectivity in the occipital part is less than that in others.

scholarly journals Lessons From Deep Neural Networks for Studying the Coding Principles of Biological Neural Networks

2021 ◽  
Vol 14 ◽  
Author(s):  
Hyojin Bae ◽  
Sang Jeong Kim ◽  
Chang-Eop Kim
Keyword(s):  
Neural Networks ◽  
Neural Coding ◽  
Deep Neural Networks ◽  
Neural Response ◽  
Feature Representation ◽  
Network Feature ◽  
Biological Neural Networks ◽  
Stimulus Features ◽  
The Comparative Study ◽  
The Brain

One of the central goals in systems neuroscience is to understand how information is encoded in the brain, and the standard approach is to identify the relation between a stimulus and a neural response. However, the feature of a stimulus is typically defined by the researcher's hypothesis, which may cause biases in the research conclusion. To demonstrate potential biases, we simulate four likely scenarios using deep neural networks trained on the image classification dataset CIFAR-10 and demonstrate the possibility of selecting suboptimal/irrelevant features or overestimating the network feature representation/noise correlation. Additionally, we present studies investigating neural coding principles in biological neural networks to which our points can be applied. This study aims to not only highlight the importance of careful assumptions and interpretations regarding the neural response to stimulus features but also suggest that the comparative study between deep and biological neural networks from the perspective of machine learning can be an effective strategy for understanding the coding principles of the brain.

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