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Mapping Disciplinary StructuresUsing Network & Semantic Analysis           Greg Appelbaum                  &           Eli...
Cognitive neuroscientist…                             School books                            Tools of the trade
Cognitive Neuroscience Timeline                             “Cognitive Revolution”                       1950s - Broadbent...
Information Curve  Number of studies with fMRI of             Published entries by indexingfunctional MRI in their title/a...
Contemporary Meta-Analyses in Cognitive Neuroscience               http://neurosynth.org/Semantic Terminology             ...
Contemporary Meta-Analyses in Cognitive Neuroscience            http://www.cognitiveatlas.org/Semantic Terminology        ...
Scientometrics• The science of measuring and analyzing science.• Is a robust field, that incorporates numerous statistical...
Scientometrics                 2007 ”UCSD Map of Science”, Boyack and Klavans•   The largest maps of science to date (ISI ...
Content-Based Mapping•   As a result of the informatics revolution (particularly digital archiving) it is possible    to s...
Network Analysis• A network consists of nodes connected by links.• Formal network analysis was developed by sociologists, ...
Why Apply Network Analysis          to Cognitive Neuroscience• Cognitive neuroscience aims to understand relations between...
N e t w o r k Te x t A n a l y s i s                                 In a source   memory     study, we used two novel app...
The Corpus• Source:        • Nature Neuroscience, Neuron, Neuroimage, Journal of Neuroscience, Journal          of Cogniti...
Term Classification• Two semantic categories were defined for Anatomy and  Concept terms.   – Anatomy terms referred to on...
Text Preprocessing• Normalized for grammatical variants of terms• Because standard thesauri do not cover neuroanatomical  ...
T h e To p Te r m s                       Frequency                            Frequency1.    Vision             637      ...
Network Generation6 word sliding windowThese results supportthe hypothesis thatspecific subregions inthe MTL are associate...
3 NetworksConceptual Structure:    -- concept x conceptAnatomical Structure:     -- anatomy x anatomyFunctional Structure:...
Conceptual Structure     Weight > 51, Density 0.2801
Island Connectivity• Where is the waterline?• Are our inferences dependent on the choice of threshold?
Centrality Measures• DEGREE: The number of direct connections that a node has.   – Nodes with high degree are “connectors”...
Conceptual Structure                                                            Betweenness vs. Frequency                 ...
Anatomical Structure     Weight > 21, Density 0.1321
Anatomical Structure                                                                Betweenness vs. Frequency             ...
Anatomy x Anatomy     Drill Down on “Thalamus”
Functional Structure     Weight > 12, Density 0.0443
Structural Synonymity     Conceptual Network                       Anatomical Network• Second-level Positional Analyses   ...
Observations• Positive structure. Whereas concepts terms organize  around hubs for perception/attention, representation, a...
Limitations #1• A not B problem   – The co-occurrence of two terms in text could reflect a positive association, a negativ...
Limitations #2• Sensitivity of analytical parameters        Window size                         Proximity                 ...
Future Directions• Larger longitudinal corpus to  map relationships over time.• Extend these tool beyond  cognitive neuros...
Conclusions• Using this approach we are able to endogenously map the  knowledge space of cognitive neuroscience.• We are a...
CollaboratorsJordynn Jack                   Jim Moody               Scott Huettel
Thank You
An Integrated Approach to the Collection and Analysis of Network Data*Kathleen M. Carley, Jana Diesner, Jeffrey Reminga, M...
Cognitive Neuroscience:                      Journal Citation and Topic Maps• All articles from authors who contributed to...
Prospective Trace of a Sub-Discipline (Bruer, 2010)                                                               •    The...
Neuroeconomics          the neural basis of decision makingLevallois et al (under review) Translating Upwards: Linking the...
Betweenness/Frequency                                                    ?                        1995   2000   2005   201...
Scientometric Interpretations of           Network Structure                                           Future Directions① ...
Scientometrics                  2002 Map of Science: Boyack and KlavansBibliographic Coupling of SCI & SSCI to arrive at „...
ReferencesCarley, K. M. and Reminga, J. (2004) ORA: Organization Risk Analyzer. CASOS Technical     Report CMU-ISRI-04-106...
Illes, J. (2007) EMBO reports VOL 8
Appelbaum beam talk_library_digitalscholarship_final
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Presentation by Greg Appelbaum & Elizabeth Beam at Duke University Libraries' Text > Data digital scholarship series (2012 November 1)

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  • I show people stuff, record their brain activity, and try to figure out how the stuff in between works…The techniques measure changes in electrical voltage potentials or regional blood oxygenation when the brain is subjected to various stimuli
  • http://www.ica.luz.ve/~dfinol/NeuroCienciaCognitiva/What%20is%20Cognitive%20Neuroscience%20-%20an%20introduction%20by%20Jamie%20Ward.htm
  • And things have really taken off at this point for CNS… this plot just goes to 2007 but the growth is exponentialWhat is more, there is evidence that historically fMRI studies are cited ~3 times as often as other CNS methods (Fellows et al JOCN 2005)These information curves are reflective of the larger literature.. Need meta analysis tools
  • http://neurosynth.org/Activation coordinates are extracted from published neuroimaging articles using an automated parser. The full text of all articles is parsed, and each article is 'tagged' with a set of terms that occur at a high frequency in that article. A list of several thousand terms that occur at high frequency in 20 or more studies is generated. For each term of interest (e.g., 'emotion', 'language', etc.), the entire database of coordinates is divided into two sets: those that occur in articles containing the term, and those that don't. A giant meta-analysis is performed comparing the coordinates reported for studies with and without the term of interest. In addition to producing statistical inference maps (i.e., z and p value maps), we also compute posterior probability maps, which display the likelihood of a given term being used in a study if activation is observed at a particular voxel.Cognitiveatlas.orgThe Cognitive Atlas is a collaborative knowledge building project that aims to develop a knowledge base (or ontology) that characterizes the state of current thought in cognitive science. The project is led by Russell Poldrack, Professor of Psychology and Neurobiology at the University of Texas at Austin in collaboration with the UCLA Center for Computational Biology (A. Toga, PI) and UCLA Consortium for Neuropsychiatric Phenomics (R. Bilder, PI). It is supported by grant RO1MH082795 from the National Institute of Mental Health.
  • http://neurosynth.org/Activation coordinates are extracted from published neuroimaging articles using an automated parser. The full text of all articles is parsed, and each article is 'tagged' with a set of terms that occur at a high frequency in that article. A list of several thousand terms that occur at high frequency in 20 or more studies is generated. For each term of interest (e.g., 'emotion', 'language', etc.), the entire database of coordinates is divided into two sets: those that occur in articles containing the term, and those that don't. A giant meta-analysis is performed comparing the coordinates reported for studies with and without the term of interest. In addition to producing statistical inference maps (i.e., z and p value maps), we also compute posterior probability maps, which display the likelihood of a given term being used in a study if activation is observed at a particular voxel.Cognitiveatlas.orgThe Cognitive Atlas is a collaborative knowledge building project that aims to develop a knowledge base (or ontology) that characterizes the state of current thought in cognitive science. The project is led by Russell Poldrack, Professor of Psychology and Neurobiology at the University of Texas at Austin in collaboration with the UCLA Center for Computational Biology (A. Toga, PI) and UCLA Consortium for Neuropsychiatric Phenomics (R. Bilder, PI). It is supported by grant RO1MH082795 from the National Institute of Mental Health.
  • Meta data about institutions, countries of origin, patents, etc… can be included
  • Can be used to map institutional strategies… e.g. NSF and NIMHAre used to determine which fields are most closely connected, which produce the most patents, and which are the most intellectually vitalConnectedness coefficients between fields are calculated year-by-year to measure change. Authors found that connectivity is going up in ‘distant’ fields. This indicates that science is in a state of change.
  • A network consists of nodes connected by edges, in the mathematical lingo, or what we call “links.” When you’re clicking through pages on Facebook, you can imagine that you are a node linked to your friend John, another node, and that John is linked to a few of your friends in addition to people that you aren’t friends with. This sort of social network is a complex, hierarchical structure, in which you can be indirectly connected to millions of other people (750 million users) around the world through your few hundred friends. The idea of social networks is not new at all to sociologists, who in the 1930’s first used what they referred to as “sociograms” to describe interpersonal relations. More recently, social network analysis has been applied to study networks of terrorist cells and scientific journal co-authors. Sociologists have also developed mathematical tools to measure network properties, as well as computer programs to visualize large networks. The concept of networks is also important for neuroscientists. We all know that behaviors are not controlled by discrete brain areas working independently of each other, but rather by complex anatomical networks of a number of distally connected regions. In learning and memory research, a more sophisticated neural network model has been proposed for an associational organization of memories.
  • The sources of bias: (1) Across subfields, research on a given topic may be advanced to varying degrees. The boundaries between those subfields may be more or less permeable. (2) Imprecision in terminology leads to unnecessary distinctions and unwanted conflations. What one calls “working memory” may be referred to as “cognitive control” by another. (3) Once a brain function is linked to a function, knowledge of that link can shape the direction of future research. This may lead to reification of concepts as new researchers apply old labels to their findings.
  • We’ve applied the idea of a social network to study the semantic structure of cognitive neuroscience. Instead of people or neurons, our nodes are words from the abstracts of fMRI articles. The idea is that, typically speaking, authors use anatomy and concepts words together when they are describing a relationship between a brain area and a behavior or cognitive process. By searching for word co-associations, we extract this relational information. Then, we integrate these relationships across the literature into a network structure.
  • Functional MRI was selected largely because of its popularity: it was the most widely used human neuroimaging technique in the unfiltered pool. Additionally,by restricting our analysis to studies that employed a common neuroimaging method, we minimized differences in terminology and rhetoric. Because it was byfar the most common human neuroimaging method, fMRI was a good PROXY for the complete literature.The curation of the corpus involved parsing through those 7,675articles in the selected journals and time range to identify those that used fMRI to study human behavior or cognition. This meant excluding articles that referred to fMRI for atlas generation, in studies of fMRI methods or the hemodynamic response, etc.
  • Next, we generated alist of all words in the corpus of abstracts. This included over 15,000 unique words.The list sorted by frequency, and the 100 most frequent Anatomy and Concept terms were identified.
  • First, a bigram thesaurus was created to collapse word pairs to single words by replacing spaces with underscores. This involved generating a list of words that co-occurred together, and identifying those that fit one of our semantic categories. The process was then iterated for longer phrases: for example, “primary somatosensory cortex” was first converted to “primary_somatosensory.” A new co-occurrence list was generated, and we found that “primary somatosensory” appeared with “cortex.”Second, a generalization thesaurus was created to normalize for plurals, acronyms, and hyphenated compounds. To avoid manually searching the entire list, we only normalized for variants that were more common than the 100th most frequent words on the list. Finally, these terms were converted into presentable titles for the vsualization.
  • The terms used to generate the networks were the 100 most frequent word forms to appear in the text after preprocessing. The final judgment of term appropriateness for the two lists was made by two expert raters (authors LGA and SAH) who evaluated every candidate term.It is interesting to note that Ccncepts words are, on the whole, used more frequently. Though not shown, even the minimum frequencies for words to make the top-50 lists were higher for concepts than anatomy (50 vs. 15). This suggests that a larger portion of each abstract is devoted to discussing the behavioral components of the experiment, results, and implications. We’ll see that these frequency shifts bear implications for the networks, resulting in a higher network density for concepts vs. anatomy terms.
  • Automap software was used to generate a meta-network comprised of links within and between Anatomy and Concept node classes. A link was identified as the co-occurrence of two terms within a moving window of six adjacent words that appeared in the same sentence. Links were directed from the first to the second term, as read from left to right across the text within the window. Link weights were calculated from the sum of term co-occurrences throughout the corpus and were used to construct the three networks: Conceptual (Concepts to Concepts), Anatomical (Anatomy to Anatomy), and Functional (Anatomy to Concepts and Concepts to Anatomy).In order to create an interpretable visualization, we applied a filter to link weights so that only the top fifty nodes with the most highly weighted links are shown.
  • The Conceptual, Anatomical, and Functional networks are substructures within the larger meta-network.
  • Represents the “cognitive” or psychological underpinnings of the cognitive neuroscience field. Intuitive arrangement.... “Attention,” for example,” is connected to “control,” “top-down,” “selection,” “spatial,” and “vision.There appears to be a central hub of words including “control,” “attention,” “vision,” “object,” “representation,” and “motor” that relate to different domains in cognitive neuroscience. It is notable that “memory,” the second most frequent term, is disconnected from the central hub, appearing at the center of its own cluster off to the side.This is the densest network of the three. The minimum weight threshold is 51, which is the highest threshold of all the networks. Several disconnected islands -- e.g. neuroeconomics
  • Before going further, it is useful to considerthe connections within the island and between the mainland had we A) picked a lower threshold and B) picked a higher threshold.In either case the same set of nodes would have been largely isolated from the rest of the network.Bootstrapping empirical approaches will be useful in quantifying this further, but here is antidotal evidence
  • There are a few measures that can be used to quantify the relative position of a node in the network. Degree centrality is the raw number of a node’s connections, and this is highly correlated (r~.8) with frequency in our network. Note that we compute betweenness centrality that does incorporate link weight.
  • The plot of frequency shows thatbetweenness and frequency are loosely correlated, as the more frequent terms tend to serve linking roles in the network. Nonetheless there are a number of interesting nodes which are more or less between than predicted by frequency. There is a cluster of highly frequent terms in the bottom right corner below the regression line, indicating that they have lower betweenness than expected by their frequency. This suggests that words like “vision,” “memory,” and “reward,” which refer to distinct domains, tend to be used in the context of only their own domains.At the top of the plot, words like “selection,” “emotion,” and “control” refer to processes that span those domains. While not as frequent, these terms create bridges throughout the network.
  • The network of anatomy terms is considerably less dense than the concepts network, and it lacks a central hub or self-organized clusters. Instead, it appears to be dominated by three terms: “PFC,” “amygdala,” and “ACC.” From these and other common terms, branches emerge relating to processing pathways. For example, “insula” gives rise to a sensorimotor pathway linking cortical and subcortical regions.Finally, there are several groups of terms that are entirely disconnected from the network. These correspond to visual regions and prefrontal regions.
  • The plot of betweennes vs. frequency shows a cluster of terms in the top left which are considerably more between than expected by frequency. Insula, for example, has the second highest betweenness despite coming in only 9th on the frequency list. This is likely due to its important role in connecting the somatosensory branch to the main network.The most notable outlier is “thalamus,” which is the most highly between term despite its relatively low position at 15th on the frequency list. Its high betweenness is likely due to its direct connections to both “amygdala” and “ACC,” two of the most frequent and central nodes in the network. .
  • Drilling down on “thalamus” shows that it is connected to a great many more nodes than shown on the thresholded network. Its low-level connections to “hippocampus,” “mPFC,” and “parietal cortex” likely contribute to its high betweenness. This is an important reminder that although the network visualization only displays nodes with the strongest connections, the measures are based on the connectivity of the entire network.
  • The most direct representation of cognitive neuroscience. The network structure appears to be driven by anatomy terms which have a higher relative betweenness centralityConversely, high-frequency concepts terms show up on the margins of the network. Several are pendants with only one other connection, such as “emotion” and “observation.” There are also quite a few dyads and triads of words disconnected from the network and with only one or two above-threshold connections. The disconnectedness and low density of this network suggest that there is room to strengthen the links between anatomy and function in the field of cognitive neuroscience.
  • Clearly, the anatomy and concepts terms fall along different regression lines. The anatomy terms have higher betweenness, reflecting their central positions on the network. Because the anatomical terms are less frequent, the network structure depends on how concepts are arranged around the anatomical terms.
  • Second-order projection networks were computed by correlating across each row in the adjancy matrix of link weights. They show links between terms that occupy similar positions in the network, and we thus call them “semantic synonyms.”Have similar meaning (e.g. Anticipation and Future) Come from the same circumscribed area of the literature (risk and reward)Suggest aspects of the literature that deserve further refinement
  • Retrodictive forecasting
  • Produces an unbiased synthesis Our approach characterizes how cognitive neuroscience presents itself to the larger scientific community, through the summaries of individual articles within their titles and abstracts.Additionalstudies of their function would have the greatest effects on the overall character of the network, so we identify them as particularly important targets for future research
  • Bruer Himself characterizes these as “toy maps” that may not be representative of the whole discipline.1988 and 2007 journal citation map. Asymmetric between journal co-citation (not author-wise or directional) Hub‐authority journals are black nodes, authority journals dark grey nodes, hub journals light grey nodes. Nodes are proportional to hub scores, authority scores, and hub + authority score for the black nodes.1988 & 2007 cognitive neuroscience topic map. Topic maps are generated from “stop-listed title words” of all the articles in the citation maps. Co-occurrence matrices are computed for words that occur at least 11 times in the article titles-that year and the spatial arrangement is ‘spring loaded using the Kamada-Kawai algorithm. Node size proportional to log of word occurrences.
  • From Bruer 2004) “On the small scale employed in this study, one might hope to see how cognitiveneuroscience emerged from its progenitor disciplines (systems neuroscience, cognitivepsychology, neuropsychology) by noting changes in co‐citation patterns among theprogenitor discipline journals and possibly through the appearance of new cognitiveneuroscience journals. These maps also allow us to visualize the citation flow amongjournals and to assess how results and ideas flowed among them. For aninterdisciplinary field emerging from a multi‐disciplinary foundation, like cognitiveneuroscience, one might be able to see how, for example, ideas and results fromneuroscience fed into psychology, from psychology into neuroscience, or both.”
  • The global structure includes all of the nodes within the defined boundaries of the network. It can be described by density, or the degree of interconnectedness of the nodes. It can also be described by topology, defined as “the shape, or form, of a network,” i.e., which nodes are connected to which other nodes (Moody). The global structure can be expected to change in datasets collected from different time periods. The intrinsic structure of a network arises from the position, connectivity, and centrality of individual nodes. Connectivity refers to the direct relations a node has to other nodes. Its position within the network is dependent on the connectivity of all nodes, and its centrality is the degree to which the node is located at an important position within the network.
  • Uses Bibliographic Coupling of SCI & SSCI to arrive at ‘Neighborhoods’ and ‘Disciplines’.Cog Neuro Lives out hereWill contact Klavas about “science Locating it”
  • Transcript of "Appelbaum beam talk_library_digitalscholarship_final"

    1. 1. Mapping Disciplinary StructuresUsing Network & Semantic Analysis Greg Appelbaum & Elizabeth Beam Duke University Library Digital Scholarship Series November 1, 2012
    2. 2. Cognitive neuroscientist… School books Tools of the trade
    3. 3. Cognitive Neuroscience Timeline “Cognitive Revolution” 1950s - Broadbent, Chomsky, Miller… PET TMS EEG is developed Reivich (1979) Barker et al (1985) (Berger 1929)1925 1950 1975 2000Action potentials discovered MRI developed Hodgkin & Huxley (1938) Lauterbur (1973) fMRI BOLD response first measured Ogawa et al (1990) Gazzaniga and Miller coined the name “cognitive neuroscience” over martinis at the Rockefeller Faculty Club (1976) Adapted from: The Students Guide to Cognitive Neuroscience by Jamie Ward, 2006
    4. 4. Information Curve Number of studies with fMRI of Published entries by indexingfunctional MRI in their title/abstract service per year Blowup shows new influx of sources (Wikipedia) Literature review is now somewhat of an intractable problem… There is a profound need for tools that can synthesize.
    5. 5. Contemporary Meta-Analyses in Cognitive Neuroscience http://neurosynth.org/Semantic Terminology Brain Locations
    6. 6. Contemporary Meta-Analyses in Cognitive Neuroscience http://www.cognitiveatlas.org/Semantic Terminology Ontology
    7. 7. Scientometrics• The science of measuring and analyzing science.• Is a robust field, that incorporates numerous statistical and mathematical methods to reveal quantitative features of science.• The lion’s share of these involve citation-based methods and clustering algorithms to arrive at ‘knowledge-bearing units’
    8. 8. Scientometrics 2007 ”UCSD Map of Science”, Boyack and Klavans• The largest maps of science to date (ISI and Scopus databases).• 7.2 million papers published in more than 16,000 journals between 2001-2005.
    9. 9. Content-Based Mapping• As a result of the informatics revolution (particularly digital archiving) it is possible to scrutinize the content of science on large scales with relative ease.• In turn new meta-analytic techniques can provide powerful tools for the critical scrutiny of what is known…. Metaknowledge! Evans and Foster (2011) Metaknowledge, Science.
    10. 10. Network Analysis• A network consists of nodes connected by links.• Formal network analysis was developed by sociologists, who have studied links between friends, terrorist cells, and disease carriers.• You may be familiar with other popular applications of network concepts.
    11. 11. Why Apply Network Analysis to Cognitive Neuroscience• Cognitive neuroscience aims to understand relations between brain anatomy and behavioral function.• These relations are linked through experimental findings to create a network consisting of the core empirical support of the discipline.• The rhetoric used to express these relations should be a suitable target for meta-analysis.
    12. 12. N e t w o r k Te x t A n a l y s i s In a source memory study, we used two novel approaches to data analysis that allowed item memory strength and source memory strength to be assessed independently. First, we identified regions in both hippocampus and perirhinal_cortex in which activity varied as a function of subsequent item memory strength while source memory strength was held constant at chance levels. Second, we identified regions in prefrontal_cortex in which activity varied as a function of subsequent source memory strength while item memory strength was held constant. These findings suggest that activity in the medial_temporal_lobe is predictive of subsequent memory strength, whereas activity in prefrontal_cortex is predictive of subsequent recollection.• Network text analysis takes words as nodes.• Two nodes are linked if they co-occur in the same window of adjacent words in the text.• To represent the field of cognitive neuroscience, we visualized links between anatomy and concepts terms.
    13. 13. The Corpus• Source: • Nature Neuroscience, Neuron, Neuroimage, Journal of Neuroscience, Journal of Cognitive Neuroscience • January 1, 2008 through June 30, 2010 • 7,675 articles• Criteria for inclusion: • Use of functional magnetic resonance imaging (fMRI) for primary data collection. • Stated goals of understanding links between the human brain and some function. • A report of empirical data collected for the current article.• Final Corpus: Abstracts and Titles from 1,127 fMRI studies • Versus: EEG (346), PET (120), and TMS (109)
    14. 14. Term Classification• Two semantic categories were defined for Anatomy and Concept terms. – Anatomy terms referred to one of the following: 1. A brain structure (e.g., “hippocampus”) 2. A functionally defined region (e.g., “fusiform face area”) – Concept terms belonged to one of the following categories: 1. A domain of cognitive neuroscience (e.g., “memory”) 2. A process within a domain (e.g., “working memory”) 3. A stimulus property (e.g., “face” or “risk”)
    15. 15. Text Preprocessing• Normalized for grammatical variants of terms• Because standard thesauri do not cover neuroanatomical terms, nor the jargon of cognitive neuroscience, we authored custom thesauri. – BIGRAM THESAURUS: • prefrontal cortex  prefrontal_cortex – GENERALIZATION THESAURUS: • pfc, prefrontal, prefrontal cortices  prefrontal_cortex
    16. 16. T h e To p Te r m s Frequency Frequency1. Vision 637 1. PFC 3562. Memory 556 2. Amygdala 3293. Behavior 497 3. ACC 2724. Information 490 4. Hippocampus 2695. Attention 488 5. Parietal Cortex 2276. Representation 450 6. Visual Cortex 1777. Control 449 7. Intraparietal Sulcus 1528. Object 442 8. mPFC 1389. Perception 439 9. Insula 13110. Cognition 434 10. Cerebellum 129
    17. 17. Network Generation6 word sliding windowThese results supportthe hypothesis thatspecific subregions inthe MTL are associatedwith item memory andmemory for context. ~50 highest weighted links
    18. 18. 3 NetworksConceptual Structure: -- concept x conceptAnatomical Structure: -- anatomy x anatomyFunctional Structure: -- (anatomy x concept + concept x anatomy)
    19. 19. Conceptual Structure Weight > 51, Density 0.2801
    20. 20. Island Connectivity• Where is the waterline?• Are our inferences dependent on the choice of threshold?
    21. 21. Centrality Measures• DEGREE: The number of direct connections that a node has. – Nodes with high degree are “connectors” or “hubs.” – is highly correlated (r~.8) with frequency• BETWEENNESS: It is equal to the number of shortest paths from all vertices to all other paths that pass through that node. – Nodes with high betweenness are “brokers.”
    22. 22. Conceptual Structure Betweenness vs. Frequency 0.06 Emotion Cognition Selection Learning 0.05 ControlBetweenness Centrality Recognition Spatial 0.04 Word Movement 0.03 Inhibition Representation Priming Encoding Prediction Sensory Action Auditory Face Observation Vision 0.02 Error Memory Suppression Perception Working Memory Reward Verbal Category Speech Attention 0.01 Semantic Load Motion Retrieval Motor Object Social Executive Future Risk 0 0 100 200 300 400 500 600 Frequency
    23. 23. Anatomical Structure Weight > 21, Density 0.1321
    24. 24. Anatomical Structure Betweenness vs. Frequency 0.12 Thalamus 0.1Betweenness Centrality dlPFC Insula 0.08 Premotor Cortex Frontal Pre-SMA Precuneus 0.06 Cerebellum PFC SMA Putamen Amygdala 0.04 Hippocampus Caudate Parietal Cortex IPL IFG Anterior Insula Intraparietal Sulcus 0.02 Fusiform OFC mPFC Parahippocampus MTL V1 S1 Cingulate Visual Cortex Basal Ganglia 0 0 50 100 150 200 250 300 350 400 Frequency
    25. 25. Anatomy x Anatomy Drill Down on “Thalamus”
    26. 26. Functional Structure Weight > 12, Density 0.0443
    27. 27. Structural Synonymity Conceptual Network Anatomical Network• Second-level Positional Analyses – Second-order projections link terms that occupy similar positions in the network and therefore represent semantic synonyms. – Computed as the correlation coefficient between each row in the adjacency matrix of link weights
    28. 28. Observations• Positive structure. Whereas concepts terms organize around hubs for perception/attention, representation, and control, a few highly central anatomy terms lead into branches representing processing streams.• Negative structure. Islands appear as collections of isolated terms on the networks, while gaps are revealed by network measures as terms with high betweenness centrality relative to frequency.
    29. 29. Limitations #1• A not B problem – The co-occurrence of two terms in text could reflect a positive association, a negative association, or even the speculation about an unknown association. – Without further (difficult) coding, we cannot resolve this problem. – See however, typical Google search queries…• Curration – How to move this to an autonomous process?
    30. 30. Limitations #2• Sensitivity of analytical parameters Window size Proximity Scrambled network
    31. 31. Future Directions• Larger longitudinal corpus to map relationships over time.• Extend these tool beyond cognitive neuroscience.• Develop web-based tools …that interface with other existing meta-analysis tools. Contour density maps show a birds eye view of the landscape.
    32. 32. Conclusions• Using this approach we are able to endogenously map the knowledge space of cognitive neuroscience.• We are able to identify terms that are understudied compared to their importance.• These results can provide prescriptive recommendations for topics whose further study will most efficiently build new links between structure and function.
    33. 33. CollaboratorsJordynn Jack Jim Moody Scott Huettel
    34. 34. Thank You
    35. 35. An Integrated Approach to the Collection and Analysis of Network Data*Kathleen M. Carley, Jana Diesner, Jeffrey Reminga, Maksim Tsvetovat
    36. 36. Cognitive Neuroscience: Journal Citation and Topic Maps• All articles from authors who contributed to the Summer Institute Cognitive Neuroscience. (5 year intervals) Journal Citation Map 1988 2007CNS Topic MapsBruer (2004) Mapping Cognitive Neuroscience: Two‐dimensional perspectives on twenty years of cognitive neuroscience research
    37. 37. Prospective Trace of a Sub-Discipline (Bruer, 2010) • The author set consists of 28 authors highly active in attentional research in the mid-1980s. • “By 1990 a distinct cognitive neuroscience specialty cluster emerges, dominated by authors engaged in brain imaging research” Bruer, J.T. (2010) Can we talk? How the cognitive neuroscience of attention emerged from neurobiology and psychology, 1980–2005. Scientometrics.
    38. 38. Neuroeconomics the neural basis of decision makingLevallois et al (under review) Translating Upwards: Linking the Neural and SocialSciences via Neuroeconomics,
    39. 39. Betweenness/Frequency ? 1995 2000 2005 2010 2015
    40. 40. Scientometric Interpretations of Network Structure Future Directions① Intrinsic structure – Connectivity and position of nodes – Clusters within the network② Global structure – Network density and topology – Changes in networks over time The local neighborhood of our 5 Contour density maps show a birds eye journals (around here) view of the landscape.
    41. 41. Scientometrics 2002 Map of Science: Boyack and KlavansBibliographic Coupling of SCI & SSCI to arrive at „Neighborhoods‟ and „Disciplines‟. – 730,000 papers, 7,300 journals, 671 “disciplines”
    42. 42. ReferencesCarley, K. M. and Reminga, J. (2004) ORA: Organization Risk Analyzer. CASOS Technical Report CMU-ISRI-04-106, 1-45.Carley, K. M. (2006) A dynamic network approach to the assessment of terrorist groups and the impact of alternative courses of action. Visualizing Network Information KN1, 1-10.Moody, J. and Light, R. (2006) A view from above: the evolving sociological landscape. The American Sociologist 37.2, 67-86.Moody, J. (2011) Introduction to Social Network Analysis. Social Science Research Institute Workshop.Moreno, J. L. (1953) Who shall survive? New York: Beacon House.Newman, M. E. J. (2004) Co-authorship networks and patterns of collaboration. Proceedings of the National Academy of Sciences 101.s1, 5200-5205.
    43. 43. Illes, J. (2007) EMBO reports VOL 8

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