scholarly journals Uncovering Dynamic Brain Reconfiguration in MEG Working Memory n-Back Task Using Topological Data Analysis

2019 ◽  
Vol 9 (6) ◽  
pp. 144 ◽  
Author(s):  
Ali Nabi Duman ◽  
Ahmet Emin Tatar ◽  
Harun Pirim
Keyword(s):  
Working Memory ◽  
Data Analysis ◽  
Response Time ◽  
Temporal Resolution ◽  
Generative Models ◽  
Topological Data Analysis ◽  
High Temporal Resolution ◽  
The Brain ◽  
Back Task ◽  
Topological Data

The increasing availability of high temporal resolution neuroimaging data has increased the efforts to understand the dynamics of neural functions. Until recently, there are few studies on generative models supporting classification and prediction of neural systems compared to the description of the architecture. However, the requirement of collapsing data spatially and temporally in the state-of-the art methods to analyze functional magnetic resonance imaging (fMRI), electroencephalogram (EEG) and magnetoencephalography (MEG) data cause loss of important information. In this study, we addressed this issue using a topological data analysis (TDA) method, called Mapper, which visualizes evolving patterns of brain activity as a mathematical graph. Accordingly, we analyzed preprocessed MEG data of 83 subjects from Human Connectome Project (HCP) collected during working memory n-back task. We examined variation in the dynamics of the brain states with the Mapper graphs, and to determine how this variation relates to measures such as response time and performance. The application of the Mapper method to MEG data detected a novel neuroimaging marker that explained the performance of the participants along with the ground truth of response time. In addition, TDA enabled us to distinguish two task-positive brain activations during 0-back and 2-back tasks, which is hard to detect with the other pipelines that require collapsing the data in the spatial and temporal domain. Further, the Mapper graphs of the individuals also revealed one large group in the middle of the stimulus detecting the high engagement in the brain with fine temporal resolution, which could contribute to increase spatiotemporal resolution by merging different imaging modalities. Hence, our work provides another evidence to the effectiveness of the TDA methods for extracting subtle dynamic properties of high temporal resolution MEG data without the temporal and spatial collapse.

scholarly journals Topological Data Analysis reveals robust alterations in the whole-brain and frontal lobe functional connectomes in Attention-Deficit/Hyperactivity Disorder

2019 ◽  
Author(s):  
Zeus Gracia-Tabuenca ◽  
Juan Carlos Díaz-Patiño ◽  
Isaac Arelio ◽  
Sarael Alcauter
Keyword(s):  
Attention Deficit Hyperactivity Disorder ◽  
Data Analysis ◽  
Frontal Lobe ◽  
Attention Deficit ◽  
Brain Network ◽  
Topological Data Analysis ◽  
Hyperactivity Disorder ◽  
The Brain ◽  
Connectivity Threshold ◽  
Topological Data

AbstractThe functional organization of the brain network (connectome) has been widely studied as a graph; however, methodological issues may affect the results, such as the brain parcellation scheme or the selection of a proper threshold value. Instead of exploring the brain in terms of a static connectivity threshold, this work explores its algebraic topology as a function of the filtration value (i.e., the connectivity threshold), a process termed the Rips filtration in Topological Data Analysis. Specifically, we characterized the transition from all nodes being isolated to being connected into a single component as a function of the filtration value, in a public dataset of children with attention-deficit/hyperactivity disorder (ADHD) and typically developing children. Results were highly congruent when using four different brain segmentations (atlases), and exhibited significant differences for the brain topology of children with ADHD, both at the whole brain network and at the functional sub-network levels, particularly involving the frontal lobe and the default mode network. Therefore, this approach may contribute to identify the neurophysio-pathology of ADHD, reducing the bias of connectomics-related methods.HighlightsTopological Data Analysis was implemented in functional connectomes.Betti curves were assessed based on the area under the curve, slope and kurtosis.The explored variables were robust along four different brain atlases.ADHD showed lower areas, suggesting decreased functional segregation.Frontal and default mode networks showed the greatest differences between groups.Graphical Abstract

scholarly journals Towards a new approach to reveal dynamical organization of the brain using topological data analysis

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Manish Saggar ◽  
Olaf Sporns ◽  
Javier Gonzalez-Castillo ◽  
Peter A. Bandettini ◽  
Gunnar Carlsson ◽  
...  
Keyword(s):  
Data Analysis ◽  
Topological Data Analysis ◽  
New Approach ◽  
The Brain ◽  
Topological Data

scholarly journals Development of the Functional Connectome Topology in Adolescence: evidence from Topological Data Analysis

2021 ◽  
Author(s):  
Zeus Gracia-Tabuenca ◽  
Juan Carlos Díaz-Patiño ◽  
Isaac Arelio ◽  
Sarael Alcauter
Keyword(s):  
Data Analysis ◽  
Functional Organization ◽  
Developmental Trajectories ◽  
Local Level ◽  
Topological Data Analysis ◽  
Typically Developing ◽  
Fixed Set ◽  
The Individual ◽  
The Brain ◽  
Topological Data

Adolescence is a crucial developmental period in terms of behavior and mental health. Therefore, understanding how the brain develops during this stage is a fundamental challenge for neuroscience. Recent studies have modelled the brain as a network or connectome, mainly applying measures from graph theory, showing a change in its functional organization such as an increase in its segregation and integration. Topological Data Analysis (TDA) complements such modelling by extracting high-dimensional features across the whole range of connectivity values, instead of exploring a fixed set of connections. This study enquiries into the developmental trajectories of such properties using a longitudinal sample of typically developing participants (N = 98; 53/45 F/M; 6.7-18.1 years), applying TDA into their functional connectomes. In addition, we explore the effect of puberty on the individual developmental trajectories. Results showed that compared to random networks, the adolescent brain is more segregated at the global level, but more densely connected at the local level. Furthermore, developmental effects showed nonlinear trajectories for the integration of the whole brain and fronto-parietal networks, with an inflection point and increasing trajectories after puberty onset. These results add to the insights in the development of the functional organization of the adolescent.

scholarly journals Topological Data Analysis Approaches to Uncovering the Timing of Ring Structure Onset in Filamentous Networks

2021 ◽  
Vol 83 (3) ◽  
Author(s):  
Maria-Veronica Ciocanel ◽  
Riley Juenemann ◽  
Adriana T. Dawes ◽  
Scott A. McKinley
Keyword(s):  
Time Series ◽  
Data Analysis ◽  
Actin Filaments ◽  
Time Series Data ◽  
Polymer Networks ◽  
Topological Data Analysis ◽  
Series Data ◽  
Topological Features ◽  
Topological Data

AbstractIn developmental biology as well as in other biological systems, emerging structure and organization can be captured using time-series data of protein locations. In analyzing this time-dependent data, it is a common challenge not only to determine whether topological features emerge, but also to identify the timing of their formation. For instance, in most cells, actin filaments interact with myosin motor proteins and organize into polymer networks and higher-order structures. Ring channels are examples of such structures that maintain constant diameters over time and play key roles in processes such as cell division, development, and wound healing. Given the limitations in studying interactions of actin with myosin in vivo, we generate time-series data of protein polymer interactions in cells using complex agent-based models. Since the data has a filamentous structure, we propose sampling along the actin filaments and analyzing the topological structure of the resulting point cloud at each time. Building on existing tools from persistent homology, we develop a topological data analysis (TDA) method that assesses effective ring generation in this dynamic data. This method connects topological features through time in a path that corresponds to emergence of organization in the data. In this work, we also propose methods for assessing whether the topological features of interest are significant and thus whether they contribute to the formation of an emerging hole (ring channel) in the simulated protein interactions. In particular, we use the MEDYAN simulation platform to show that this technique can distinguish between the actin cytoskeleton organization resulting from distinct motor protein binding parameters.

scholarly journals Classification of apatite structures via topological data analysis: a framework for a ‘Materials Barcode’ representation of structure maps

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Scott Broderick ◽  
Ruhil Dongol ◽  
Tianmu Zhang ◽  
Krishna Rajan
Keyword(s):  
Machine Learning ◽  
Data Analysis ◽  
Crystal Chemistry ◽  
Persistent Homology ◽  
Hierarchical Classification ◽  
Topological Data Analysis ◽  
Learning Tool ◽  
Coordination Polyhedra ◽  
Machine Learning Tool ◽  
Topological Data

AbstractThis paper introduces the use of topological data analysis (TDA) as an unsupervised machine learning tool to uncover classification criteria in complex inorganic crystal chemistries. Using the apatite chemistry as a template, we track through the use of persistent homology the topological connectivity of input crystal chemistry descriptors on defining similarity between different stoichiometries of apatites. It is shown that TDA automatically identifies a hierarchical classification scheme within apatites based on the commonality of the number of discrete coordination polyhedra that constitute the structural building units common among the compounds. This information is presented in the form of a visualization scheme of a barcode of homology classifications, where the persistence of similarity between compounds is tracked. Unlike traditional perspectives of structure maps, this new “Materials Barcode” schema serves as an automated exploratory machine learning tool that can uncover structural associations from crystal chemistry databases, as well as to achieve a more nuanced insight into what defines similarity among homologous compounds.

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