NetworkToolbox: Methods and Measures for Brain, Cognitive, and Psychometric Network Analysis in R

Christensen, Alexander P.

doi:10.31234/osf.io/6kmav

Cited by 18 publications

(14 citation statements)

References 34 publications

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“…This produced two 12 × 12 correlation matrices for each subject - one per task. We computed three measures to compare background connectivity between episodic encoding and retrieval within each subject: (1) Modularity, reflecting the degree to which our regions were operating as distinct networks, computed using the Louvain algorithm from R’s NetworkToolbox (Christensen, 2018). This method calculates a global modularity value (Q), reflecting the degree to which a set of ROIs are operating as a compartmentalized structure based on their covariation in activity.…”

Section: Methodsmentioning

confidence: 99%

Cortico-hippocampal network connections support the multidimensional quality of episodic memory

Cooper

Ritchey

2019

eLife

120

131

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Episodic memories reflect a bound representation of multimodal features that can be reinstated with varying precision. Yet little is known about how brain networks involved in memory, including the hippocampus and posterior-medial (PM) and anterior-temporal (AT) systems, interact to support the quality and content of recollection. Participants learned color, spatial, and emotion associations of objects, later reconstructing the visual features using a continuous color spectrum and 360-degree panorama scenes. Behaviorally, dependencies in memory were observed for the gist but not precision of event associations. Supporting this integration, hippocampus, AT, and PM regions showed increased connectivity and reduced modularity during retrieval compared to encoding. These inter-network connections tracked a multidimensional, objective measure of memory quality. Moreover, distinct patterns of connectivity tracked item color and spatial memory precision. These findings demonstrate how hippocampal-cortical connections reconfigure during episodic retrieval, and how such dynamic interactions might flexibly support the multidimensional quality of remembered events.

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Section: Methodsmentioning

confidence: 99%

Cortico-hippocampal network connections support the multidimensional quality of episodic memory

Cooper

Ritchey

2019

eLife

120

131

View full text Add to dashboard Cite

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“…In order to overcome the loss of information given by spurious associations, we used the Triangulated Maximally Filtered Graph ( TMFG—Massara et al 2016 ) method which, in the construction of a sub-network, is able to remove spurious connections and retain high correlations within the original graph ( see Kenett et al 2011 ). The TMFG filtering method was applied using the ‘NetworkToolbox’ package ( Christensen 2019 ; Kenett et al 2014 ) in R ( Rstudio Team 2020 ). Finally, we further binarized each group-similarity network in order to obtain in output an unweighted, undirected network.…”

Section: Methodsmentioning

confidence: 99%

“…The following network parameters were calculated for each network using the SemNeT ( Christensen and Kenett 2019 ) and NetworkToolbox ( Christensen 2019 ) packages in R: the clustering coefficient (CC) ( Watts and Strogatz 1998 ) the average shortest path length (ASPL), the modularity index (Q) ( Newman 2006 ), and the small-world-ness measure (S) ( Humphries and Gurney 2008 ). Based on previous studies ( Borodkin et al 2016 ; Christensen et al 2018 ; Kenett et al 2014 ), we empirically examined the validity of our findings by applying two reciprocal approaches.…”

Section: Methodsmentioning

confidence: 99%

Revealing the Role of Divergent Thinking and Fluid Intelligence in Children’s Semantic Memory Organization

2020

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The current theories suggest the fundamental role of semantic memory in creativity, mediating bottom-up (divergent thinking) and top-down (fluid intelligence) cognitive processes. However, the relationship between creativity, intelligence, and the organization of the semantic memory remains poorly-characterized in children. We investigated the ways in which individual differences in children’s semantic memory structures are influenced by their divergent thinking and fluid intelligence abilities. The participants (mean age 10) were grouped by their levels (high/low) of divergent thinking and fluid intelligence. We applied a recently-developed Network Science approach in order to examine group-based semantic memory graphs. Networks were constructed from a semantic fluency task. The results revealed that divergent thinking abilities are related to a more flexible structure of the semantic network, while fluid intelligence corresponds to a more structured semantic network, in line with the previous findings from the adult sample. Our findings confirm the crucial role of semantic memory organization in creative performance, and demonstrate that this phenomenon can be traced back to childhood. Finally, we also corroborate the network science methodology as a valid approach to the study of creative cognition in the developmental population.

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“…This produced two 12x12 correlation matrices for each subject one per task. We computed 3 measures to compare background connectivity between episodic encoding and retrieval within each subject: 1) Modularity, reflecting the degree to which our regions were operating as distinct networks, computed using the Louvain algorithm from R's NetworkToolbox (Christensen, 2018) . This method calculates a global modularity value (Q), reflecting the degree to which a set of ROIs are operating as a compartmentalized structure based on their covariation in activity.…”

Section: Task Background Connectivitymentioning

confidence: 99%

Cortico-hippocampal network connections support the multidimensional quality of episodic memory

Cooper

Ritchey

2019

Preprint

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Episodic memories reflect a bound representation of multimodal features that can be reinstated with varying levels of precision. Yet little is known about how brain networks involved in memory, including the hippocampus and posteriormedial (PM) and anteriortemporal (AT) cortical systems, functionally interact to support the quality and the content of recollection. Participants learned color, spatial, and emotion associations of objects, later reconstructing the visual features using a continuous color spectrum and 360degree panorama scenes. Behaviorally, dependencies in memory were observed for the gist but not precision of these event associations. Supporting this integration, hippocampus, AT, and PM regions showed increased internetwork connectivity and reduced modularity during retrieval compared to encoding. These network connections, particularly to hippocampus, tracked a multidimensional, continuous measure of objective memory quality. Moreover, distinct patterns of connectivity tracked item color precision and spatial memory precision. These findings demonstrate not only how hippocampalcortical connections reconfigure during episodic retrieval, but how such dynamic interactions might flexibly support the multidimensional quality of remembered events.

show abstract

NetworkToolbox: Methods and Measures for Brain, Cognitive, and Psychometric Network Analysis in R

Cited by 18 publications

References 34 publications

Cortico-hippocampal network connections support the multidimensional quality of episodic memory

Cortico-hippocampal network connections support the multidimensional quality of episodic memory

Revealing the Role of Divergent Thinking and Fluid Intelligence in Children’s Semantic Memory Organization

Cortico-hippocampal network connections support the multidimensional quality of episodic memory

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