Showing posts with label SNA. Show all posts
Showing posts with label SNA. Show all posts

Sunday, August 9, 2009

Links->Concepts Problem

George Siemens asked “what are the implications of people being connected in a certain way? (2009)”. That question is related to a corollary question: How do connections contribute to conceptual formation?

I am currently haunted by this question and I am writing here the leads that I found that may answer this profound problem.

My knowledge of how the brain works is quite superficial. I have always thought that the links are important as indexes for the brain, so that the entire semantic network need not be modeled in long term memory.

Indexing external semantic networks in memory


The indexes are either keywords, url, people you know, that will give you a semantic network. The semantic network's nodes may already exists in long term memory. It is the links that may be weak and even in danger of disappearing (forgetting). The equivalent or similar mental network in memory may be connected by weak links, so there is a need for a trigger to fire these links. That trigger is the indexes which may draw the semantic network structure in working memory and remind the brain of the path of the links to fire.

The question is whether the concepts in the semantic network of the external document is mapped in the declarative (semantic, episodic) or procedural memory in the cognitive architecture. Another is how many times do we need to keep drawing the external semantic network (e.g. asking a friend, rereading a blog) in order to strengthen the links and reduce the centrality or importance of the index.

Of course this is just my guess, I don't know whether this is true, I don't have any idea. But there may be a way to find out.

Simulating the CCK08 Moodle Forums

I am not a neuroscientist and the closest I can study a living brain is an artificial one. Fortunately cognitive scientists have developed cognitive architectures which are agents that tries to model the brain. One of these is Soar. I find Soar fascinating as it's underlying design of working memory is "organized as graph structures in states (Laird, 2008)". I was totally suprised to find nodes and links in their cognitive architecture. So I think it's not far fetched if someone has already found a way to relate this memory network to semantic networks and social networks. It's just a matter of time before I find those papers. Here is how I located the tools used in my on-going study of the CCK08 Moodle forums in Nigel Gilbert's diagram of the logic of simulation as a method (2005).


(based on Gilbert as cited in Gilbert & Troitzsch, 2005, p.17)

Ron Sun's Cascading Levels of Analysis

Although I have not fully read Ron Sun's "Cognition and multi-agent interaction (2006)" I found his idea of cascading levels of analysis providing some methodological meat to my skeleton of a general model of distance learning. I gather that he is advocating the integration of cognitive architectures and agent-based modeling in this book. He further states that "we may view different disciplines as different levels of abstraction in the process of exploring essentially the same broad set of questions (Sun, 2005)". His hierarchy of this different levels of abstractions are as follows:

Sun's Hierarchy of Four Levels

Level Object of Analysis Type of Analysis Model
1 inter-agent/collective processes social/cultural collections of agent models
2 agents psychological individual agent models
3 intra-agent processes componential modular construction of agent models
4 substrates physiological biological realization of models
(Source: Sun, 2006, p.7)

These levels looks similar to what I call modes in my skeletal model. And he further argue that we should engage in cross and mixed level analysis. I won't go any further on Sun's ideas since I still need to read the entire work, but I find it really exciting. His advocated approach may shed light on the problem of how linkages affect conceptual formation.

My skeletal model of distance learning


References

Laird, J.E. (2008, August 27). The Soar 9 tutorial. Part 1. Available in the software package here: http://sitemaker.umich.edu/soar/soar_software_downloads

Gilbert, N., & Troitzsch, K.G. (2005). Simulation for social scientist. (2nd ed.). England: Open University.

Siemens, G. (2009, July 30). Different Social Networks. Retrieved, August 9, 2009, from
http://www.elearnspace.org/blog/2009/07/30/different-social-networks/.

Sun, R. (2006). Cognition and multi-agent interaction. From cognitive modeling to social simulation. Cambridge: Cambridge University.

Monday, July 27, 2009

*ORA: Unifying Pajek net files has never been easier

Legal stuff of *ORA

*ORA is NOT free software, just like many of the network visualization tools out there.

According to it's "About *ORA" dialog box "Permission to use, copy and modify this version of the software or any parts of it and its documentation is hereby granted for RESEARCH ONLY purposes and provided that the above copyright notice and this permission notice appear intact in all copies of the software that, that you do not sell the software, nor include the software in a commercial package."

*ORA is a copyright (2001-2008 of the version I'm using) of Kathleen M. CArley, Center for Computational Analysis of Social and Organizational Systems (CASOS). Institute for Software Research International (ISRI), School of Computer Science (SCS), and Carnegie Mellon University(CMU).

The version I'm reviewing is 1.9.5.29 with a build date of July 2008 in Ubuntu. And version 1.9.5.4.3 in Vista with a build date of June 2009.

*ORA is available at http://www.casos.cs.cmu.edu/projects/ora/

I am not connected to the copyright holders.

Why is the union of networks in Pajek wrong?

When you hit Menu->Union of vertices in Pajek it doesn't seem to take into account labels. It will simply add all the vertices resulting in duplicate vertices with the same label.

What is *Ora?

According to its homepage at the Computational Analysis of Social and Organizational Systems (CASOS) "*ORA is a risk assessment tool for locating individuals or groups that are potential risks given social, knowledge and task network information." That description may mislead people to think that this tool is only a very specialized network visualization-analysis tool. I found that it is probably the most advance and user friendly, free network analysis tool out there that can be used for all kinds of networks. It is particularly powerful because of its application of metamatrices, and appear to be able to analyze semantic, social, organizational, communication, etc. networks at the same time.

Although I haven't explored it's full potential yet, one particular application is the union of pajek networks. I can't seem to import netdraw files yet, or include the vector files associated with the pajek networks. But perhaps there is a way I haven't found yet.



How to make a union of networks in *ORA



1. In *ORA click menu->File->Data import wizard... or Ctrl-O 2. A dialogue box will appear, select "Create a meta-network from separate network files" and click "Next"
3. In the next dialogue box, I just left the default value of "Create a new meta-network with ID: Meta Network" then I hit Next.


4. A dialogue box for choosing the networks to load in *ORA will appear. Just Browse for your file and hit OK.

I you have more than one network file just click the plus (+) button and another browsing textbox will appear.

I've experienced *ORA complained about the filename of networks like forum1.net, forum2.net. It interpreted it as being the same network. So what I did was to import one network at a time. I don't know if it would be different had I changed the names of the second network.

You can select the type of metamatrix from the drop-down boxes. Since mine is composed of actors, I selected "Agent" as Source type and Target type. I also set "Source node labels: Yes".

Click Finish.


5. A small dialogue box will appear asking "Would you like to anonymize the data?" I hit "No" because I need the labels for the union network. You can always anonymize the data later with menu->Data Management->Meta-Network Anonymize...

6.All your loaded network will appear in the left panel. This should be familiar to people using the Network Workbench Tool.

7. To make a union of the two network (in my example one is size 83 and the other is size 61) click menu->Data Management->Meta-Network Union...

A dialogue box will appear. I kept the default "Currently loaded in ORA" and set "Select how to combine link weights" to Sum.

Then hit Compute.


8. It will create a new Network in the left panel with the name Union. Mine produced a network with 108 vertices from size 83 and 61 networks. Whereas Pajek will create a 144 size network.

9. To Anonymize the network select the Union network in the panel click menu->Data Management->Meta-Network Anonymize... or simply right click the Union network in the panel and select Anonymize...


It will show a dialogue box wherein I checked "Anonymize node titles". You can even create decoder files. Then hit the Anonymize button.

To examine your labels, just select Agent in the panel like in the figure. YOu can see the Node Titles are A-1, A-2 etc.

10. You can examine your Union network with menu->Visualization->Network visualizer->View Entire Meta-Network. It's visualizer is still sluggish and not as impressive as Pajek, but it could be because I'm using the wrong OS platform. See below. It seems it's using JUNG (http://jung.sourceforge.net) library for visualization.

Then click ORA Network Visualizer->menu->Save Image To File...


You can save the graph in PNG, JPG, SVG, and PDF formats.

And here's the output.

11. Converting from *ORA's DynetML to NetDraw's VNA

*ORA'S Network Format Converter will convert from DyNetML, ASSAMML, UCINET, CSV, and DL to DyNetML, UCINET, DL, CSV, and VNA.


Click on File->Network Format Converter and a dialogue box will appear. In the Load tab, select Format DYNETML and Load your Union file that was saved as .xml.


Then go to the Save tab, and select VNA and save.

Here's a graph render of the VNA output in NetDraw.




Problems encountered

I installed the Windows version in a Vista machine. But I coudld not import any network files. It resulted in Java errors.

I was able to import graphs in the Ubuntu Linux Jaunty installation. But *ORA seems 32 bit and I had 64 bit installed. It had a lot of GTK related errors, particularly with the canberra-gtk-module. So it was a bit buggy and I couldn't use the Network Format Converter because it would not open.

I had to shift to the Windows version with the saved DyNetML xml file, and convert it there. I don't think it converts back to Pajek net file though.

Perhaps if I can resolve the 32 bit GTK problem in my installation or install a 32 bit Ubuntu things will be better. But I managed to make a proper union of the networks without resorting to cumbersome spreadsheet techniques.

Unfortunately, I haven't been able to unify the vectors yet.

Aside from that, I don't know how *ORA will handle very large networks.

I think, if the developers continue to improve *ORA, particularly its visualizer it will become even better than Pajek in the future.

But remember that *ORA is NOT free software and is available only for research. Pajek too is proprietary and according to its "About Pajek" dialogue box is free (as in free beer) for noncommercial use only. I personally haven't found a free (beer) tool that equals Pajek in speed, visualization, and analysis.

The Network Workbench Tool (version 12.0.0 beta), a copyright of Indiana University is licensed under Apache License Version 2.0. Gephi version 0.5 Beta is GPL 3.0 (gephi.org) but it is only a graph editor. Perhaps Gephi can be partnered with the sna 2.0 R package (http://erzuli.ss.uci.edu/R.stuff) from Carter Butts which is GPL 2.0 and later.

References

Kathleen M. CArley, Center for Computational Analysis of Social and Organizational Systems (CASOS), Institute for Software Research International (ISRI), School of Computer Science (SCS), and Carnegie Mellon University(CMU). *ORA [Software]. Available at http://www.casos.cs.cmu.edu/projects/ora/

Butts, C.T. The SNA Package, v2.0 [Software]. Available at http://erzuli.ss.uci.edu/R.stuff

Indiana University. The Network Workbench Tool [Software]. Available at http://nwb.slis.indiana.edu/download.html.

R Development Core Team (2009). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org.


V. Batagelj, A. Mrvar: Pajek – Program for Large Network Analysis. Home page: http://vlado.fmf.uni-lj.si/pub/networks/pajek/
 
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