Spiking Networks on the Cusp of Chaos - Revision history

Watson: /* Participants */

2009-06-29T04:23:31Z

Participants

← Older revision		Revision as of 04:23, 29 June 2009
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	* [[watson]]		* [[watson]]
	* [[Corinne Teeter]]
	* [[Rosemary Braun]]		* [[Rosemary Braun]]
	* [[Massimo Mastrangeli]]		* [[Massimo Mastrangeli]]
	* [[Andrew Berdahl]]		* [[Andrew Berdahl]]
	* [[Angela Onslow]]		* [[Angela Onslow]]

Watson: /* 6/25 Dinner Meeting: 6PM */

2009-06-26T03:59:04Z

6/25 Dinner Meeting: 6PM

← Older revision		Revision as of 03:59, 26 June 2009
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	Let's meet to discuss some specific experiments we want to run. And exactly how we want to run them. These should be informed by desired/possible outcomes. I can lead this discussion. I should be able to show you the code in action with a GUI and everything as well. We can chat about the spectral analysis stuff that Greg and I were discussing too. Corinne and others: maybe you have some insight into this method now? [[watson]]		Let's meet to discuss some specific experiments we want to run. And exactly how we want to run them. These should be informed by desired/possible outcomes. I can lead this discussion. I should be able to show you the code in action with a GUI and everything as well. We can chat about the spectral analysis stuff that Greg and I were discussing too. Corinne and others: maybe you have some insight into this method now? [[watson]]

			====Notes from [[watson]]====

			Demoed the software to the group and went over some of the code with Rosemary. Generated some ideas but we need another meeting to decide on specific experiments and tools etc.

			===6/26 Lunch Meeting: 12:45 in Dining Hall===

			Agenda: decide on some experiments we're interested in running, figure out the tools/machinery/configurations we need for that and set a work time (probably later in the day) where we can all be in the same place and when I will be available to you for questions about my code, the model and python generally. [[watson]]

	==Participants==		==Participants==

Watson: /* 6/25 Dinner Meeting */

2009-06-25T06:50:45Z

6/25 Dinner Meeting

← Older revision		Revision as of 06:50, 25 June 2009
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	Today I also had a really good chat with Greg L. on how to think about characterizing/clustering the structure of networks. For example if we determine that 16 particular networks have very similar behavioral properties then how do we check to see if they also have structural properties in common? One way is to do some eigenanalysis on the adjacency matrix and pay attention to the first couple of eigenvectors (since the networks are so small). Plotting the first couple of eigenvectors of each network adjacency matrix in phase space, do those 16 cluster together? There are still many questions in my mind about the specific method and how to best utilize it (e.g. would we still run a Laplacian? Do we run a separate analysis on each individual network or somehow on all of them?), but this is an inspiring start to understanding ways to characterize the structural nature of the networks and compare across several networks of the same size. (or of different sizes? Greg also pointed out that eigenanalysis methods can scale up to larger matricies pretty naturally)		Today I also had a really good chat with Greg L. on how to think about characterizing/clustering the structure of networks. For example if we determine that 16 particular networks have very similar behavioral properties then how do we check to see if they also have structural properties in common? One way is to do some eigenanalysis on the adjacency matrix and pay attention to the first couple of eigenvectors (since the networks are so small). Plotting the first couple of eigenvectors of each network adjacency matrix in phase space, do those 16 cluster together? There are still many questions in my mind about the specific method and how to best utilize it (e.g. would we still run a Laplacian? Do we run a separate analysis on each individual network or somehow on all of them?), but this is an inspiring start to understanding ways to characterize the structural nature of the networks and compare across several networks of the same size. (or of different sizes? Greg also pointed out that eigenanalysis methods can scale up to larger matricies pretty naturally)

	===6/25 Dinner Meeting===		===6/25 Dinner Meeting: 6PM===

	Let's meet to discuss some specific experiments we want to run. And exactly how we want to run them. These should be informed by desired/possible outcomes. I can lead this discussion. [[watson]]		Let's meet to discuss some specific experiments we want to run. And exactly how we want to run them. These should be informed by desired/possible outcomes. I can lead this discussion. I should be able to show you the code in action with a GUI and everything as well. We can chat about the spectral analysis stuff that Greg and I were discussing too. Corinne and others: maybe you have some insight into this method now? [[watson]]

	==Participants==		==Participants==

Watson: /* 6/25 Dinner Meeting */

2009-06-25T06:44:52Z

6/25 Dinner Meeting

← Older revision		Revision as of 06:44, 25 June 2009
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	===6/25 Dinner Meeting===		===6/25 Dinner Meeting===

	Let's meet to discuss some specific experiments we want to run. And exactly how we want to run them. These should be informed by desired/possible outcomes. I ~~will~~ lead this discussion. [[watson]]		Let's meet to discuss some specific experiments we want to run. And exactly how we want to run them. These should be informed by desired/possible outcomes. I can lead this discussion. [[watson]]

	==Participants==		==Participants==

Watson: /* Meetings */

2009-06-25T06:43:39Z

Meetings

← Older revision		Revision as of 06:43, 25 June 2009
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	Today I also had a really good chat with Greg L. on how to think about characterizing/clustering the structure of networks. For example if we determine that 16 particular networks have very similar behavioral properties then how do we check to see if they also have structural properties in common? One way is to do some eigenanalysis on the adjacency matrix and pay attention to the first couple of eigenvectors (since the networks are so small). Plotting the first couple of eigenvectors of each network adjacency matrix in phase space, do those 16 cluster together? There are still many questions in my mind about the specific method and how to best utilize it (e.g. would we still run a Laplacian? Do we run a separate analysis on each individual network or somehow on all of them?), but this is an inspiring start to understanding ways to characterize the structural nature of the networks and compare across several networks of the same size. (or of different sizes? Greg also pointed out that eigenanalysis methods can scale up to larger matricies pretty naturally)		Today I also had a really good chat with Greg L. on how to think about characterizing/clustering the structure of networks. For example if we determine that 16 particular networks have very similar behavioral properties then how do we check to see if they also have structural properties in common? One way is to do some eigenanalysis on the adjacency matrix and pay attention to the first couple of eigenvectors (since the networks are so small). Plotting the first couple of eigenvectors of each network adjacency matrix in phase space, do those 16 cluster together? There are still many questions in my mind about the specific method and how to best utilize it (e.g. would we still run a Laplacian? Do we run a separate analysis on each individual network or somehow on all of them?), but this is an inspiring start to understanding ways to characterize the structural nature of the networks and compare across several networks of the same size. (or of different sizes? Greg also pointed out that eigenanalysis methods can scale up to larger matricies pretty naturally)

			===6/25 Dinner Meeting===

			Let's meet to discuss some specific experiments we want to run. And exactly how we want to run them. These should be informed by desired/possible outcomes. I will lead this discussion. [[watson]]

	==Participants==		==Participants==

Watson: /* 6/24 Morning Meeting @ SFI */

2009-06-25T06:23:50Z

6/24 Morning Meeting @ SFI

← Older revision		Revision as of 06:23, 25 June 2009
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	Meet at SFI at 10:45 to go over code and hash out some ideas for experiments and conceptualize desired/possible outcomes.		Meet at SFI at 10:45 to go over code and hash out some ideas for experiments and conceptualize desired/possible outcomes.

			====Notes from [[watson]]====

			Angela, Max, Andrew and myself met to go over the current code. I didn't have it up and running on my new laptop but do now. See new notes on installing on OSX linked from [[#Code]] section above.

			Today I also had a really good chat with Greg L. on how to think about characterizing/clustering the structure of networks. For example if we determine that 16 particular networks have very similar behavioral properties then how do we check to see if they also have structural properties in common? One way is to do some eigenanalysis on the adjacency matrix and pay attention to the first couple of eigenvectors (since the networks are so small). Plotting the first couple of eigenvectors of each network adjacency matrix in phase space, do those 16 cluster together? There are still many questions in my mind about the specific method and how to best utilize it (e.g. would we still run a Laplacian? Do we run a separate analysis on each individual network or somehow on all of them?), but this is an inspiring start to understanding ways to characterize the structural nature of the networks and compare across several networks of the same size. (or of different sizes? Greg also pointed out that eigenanalysis methods can scale up to larger matricies pretty naturally)

	==Participants==		==Participants==

Watson: /* Participants */

2009-06-25T06:04:54Z

Participants

← Older revision		Revision as of 06:04, 25 June 2009
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	* [[Massimo Mastrangeli]]		* [[Massimo Mastrangeli]]
	* [[Andrew Berdahl]]		* [[Andrew Berdahl]]
			* [[Angela Onslow]]

Watson: /* Meetings */

2009-06-24T04:28:40Z

Meetings

← Older revision		Revision as of 04:28, 24 June 2009
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	Good meeting today. Glad to see some interest. Plans to meet tomorrow morning to go over code.		Good meeting today. Glad to see some interest. Plans to meet tomorrow morning to go over code.

	To get the code yourself, head up to the [[#Code\|code]] section above. My code is of course a miniscule download. Downloading python is more involved and the two packages you'll need in addition are ~13 MB total.		To get the code yourself, head up to the [[#Code\|code]] section above. My code is of course a miniscule download. The most important (and smallest!) bit of code to understand is the SpikingNetwork.py file. MATLAB users: see the SpikeInformation.py file for a link to some documentation online that helps understand the equivalent ways of doing most things in both languages.

			Downloading python is more involved and the two packages you'll need in addition to the base install (which you already have if you have OSX) are ~13 MB total.

			===6/24 Morning Meeting @ SFI===

			Meet at SFI at 10:45 to go over code and hash out some ideas for experiments and conceptualize desired/possible outcomes.

	==Participants==		==Participants==

Watson: /* Notes */

2009-06-24T03:58:36Z

Notes

← Older revision		Revision as of 03:58, 24 June 2009
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	Good meeting today. Glad to see some interest. Plans to meet tomorrow morning to go over code.		Good meeting today. Glad to see some interest. Plans to meet tomorrow morning to go over code.

	To get the code yourself, head up to the [[#Code\|code]] section above.		To get the code yourself, head up to the [[#Code\|code]] section above. My code is of course a miniscule download. Downloading python is more involved and the two packages you'll need in addition are ~13 MB total.

	==Participants==		==Participants==

Watson: /* Code */

2009-06-24T03:41:56Z

Code

← Older revision		Revision as of 03:41, 24 June 2009
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	* [http://www.math.ucdavis.edu/~watson/spiking/#download Directions] on downloading Python and two other necessary packages.		* [http://www.math.ucdavis.edu/~watson/spiking/#download Directions] on downloading Python and two other necessary packages.
	* [http://www.math.ucdavis.edu/~watson/spiking/info/#~~download~~ My code] for the Spiking Network software we're starting with.		* [http://www.math.ucdavis.edu/~watson/spiking/info/#code My code] for the Spiking Network software we're starting with.
	* [http://networkx.lanl.gov/ NetworkX], which we'll eventually use.		* [http://networkx.lanl.gov/ NetworkX], which we'll eventually use.


	==Polyrhythmic Music==		==Polyrhythmic Music==