Complex Systems Summer School 2013-Tutorials - Revision history

Seoane: /* Genetic Algorithms and Multi-Objective Optimization */

2013-06-12T16:40:54Z

Genetic Algorithms and Multi-Objective Optimization

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	We scheduled this tutorial for Tuesday at 3:00 pm, just before the time to work on projects. Hope that you find it interesting! -- [[Luís_Seoane \| Luíño]]		We scheduled this tutorial for Tuesday at 3:00 pm, just before the time to work on projects. Hope that you find it interesting! -- [[Luís_Seoane \| Luíño]]

			<strong>Material: </strong>

			Some material from the presentation:
			*Sildes, [[File:MOGA.pdf]]: These are from a larger, previously existing presentation; so you will find more stuff in there than I gave in the presentation. Feel free to come and ask about anything you want!
			*Websites:
			**The infamous [http://boxcar2d.com/ evolving car] that takes away attention from the speaker.
			**Website to [http://picbreeder.org/ evolve pictures] after successive selection.
			**[http://rogeralsing.com/2008/12/07/genetic-programming-evolution-of-mona-lisa/ This one] uses a genotype that encodes for polygons and evolve the Mona Lisa. You can find a gallery with other pictures evolved and an applet in [http://alteredqualia.com/visualization/evolve/ here]. By the way, I used this polygon genetic algorithm for my project on [http://briganraman.blogspot.com/2012/09/images-from-mind.html EEG-based image reconstruction], so you never now when something turns out useful in really distant parts of science.
			**You can find plenty of resources similar to these by just googling!
			*Some literature on the topic:
			**Nice, classic [http://www.astro.cornell.edu/~cordes/A6523/stephanie.forrest.pdf Science paper] on genetic algorithms by Stefanie Forrest (external SFI).
			**Does nature use MOO? Some answers [http://link.springer.com/article/10.1007%2Fs11284-009-0658-6#page-1 here] and [http://www.engr.colostate.edu/~krapf/biophysics/BPJC/FA2012/SauerScience2012.pdf here].
			*Code (in C++): I am not going to post it because I never made it thinking that someone but me could use... and my code is a relative mess. I will provide it to whoever requires it, specially if you are doing a CSSS project that would enjoy MOO. Just come talk to me! Most surely we would have to talk through some details about how it works, but I assure that it is very easy, it should be platform independent, and it should be trivial to make it work together with any arbitrary programming language that supports file I/O--i.e. any decent programming language... but please don't use [http://en.wikipedia.org/wiki/Whitespace_(programming_language) something like this].

	==Nix's Bag O' Mathematical Tools==		==Nix's Bag O' Mathematical Tools==

Seoane at 16:15, 12 June 2013

2013-06-12T16:15:31Z

← Older revision		Revision as of 16:15, 12 June 2013
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	~~'''~~Network Visualization Using [https://gephi.org/ Gephi]~~'''~~		==Network Visualization Using [https://gephi.org/ Gephi]==
	I will be showing people some basic features of using Gelphi to visualize networks this week. If there are other people who are also interested, we could turn it into a tutorial. -- [[Hua_Cai \| Hua]]		I will be showing people some basic features of using Gelphi to visualize networks this week. If there are other people who are also interested, we could turn it into a tutorial. -- [[Hua_Cai \| Hua]]

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	~~'''~~Bayesian Modeling~~'''~~		==Bayesian Modeling==
	I'd love to attend tutorials on Bayesian Modeling. I will be happy if someone can give a series of tutorials on this topic. [[Reniel_Cabral \| Ren]]		I'd love to attend tutorials on Bayesian Modeling. I will be happy if someone can give a series of tutorials on this topic. [[Reniel_Cabral \| Ren]]

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	~~'''~~Dynamics in Networks~~'''~~		==Dynamics in Networks==

	I am very interested in learning about network dynamics. Anyone else interested in having a tutorial on that? [[Regina_Martinez \| Regina]]		I am very interested in learning about network dynamics. Anyone else interested in having a tutorial on that? [[Regina_Martinez \| Regina]]
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	~~'''~~Cross impact balances and Markov chains~~'''~~		==Cross impact balances and Markov chains==

	For anyone who could not make the tutorial, [https://docs.google.com/file/d/0B_w3ogGtuejzVG1Ma2tKenN2QjQ/edit?usp=sharing here is a copy of the slides], which provide another way of interpreting [http://www.cross-impact.de/english/CIB_e_Alg.htm web pages explaining the CIB algorithm]. Note that from the cross-impact balance analysis web site, you can download the free software to play with CIB analysis yourself. I am also happy to talk more one-on-one if needed! --[[User:Vanessas\|Vanessas]] 02:24, 6 June 2013 (UTC)		For anyone who could not make the tutorial, [https://docs.google.com/file/d/0B_w3ogGtuejzVG1Ma2tKenN2QjQ/edit?usp=sharing here is a copy of the slides], which provide another way of interpreting [http://www.cross-impact.de/english/CIB_e_Alg.htm web pages explaining the CIB algorithm]. Note that from the cross-impact balance analysis web site, you can download the free software to play with CIB analysis yourself. I am also happy to talk more one-on-one if needed! --[[User:Vanessas\|Vanessas]] 02:24, 6 June 2013 (UTC)
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	~~'''~~Genetic Algorithms and Multi-Objective Optimization~~'''~~		==Genetic Algorithms and Multi-Objective Optimization==

	I have seen many people interested in implementing GAs to evolve networks, which is something I have done for some of my research. I also worked with Multi-Objective Optimization (MOO), which is perfectly possible with GAs and has been around for a while; but it has not become so mainstream. I propose to make a brief tutorial of <i>classic</i> Genetic Algorithm vs. Multi-Objective Genetic Algorithm. Enough people interested? If we are a few of us, we could just meet up and I'll tell you the basics! -- [[Luís_Seoane \| Luíño]]		I have seen many people interested in implementing GAs to evolve networks, which is something I have done for some of my research. I also worked with Multi-Objective Optimization (MOO), which is perfectly possible with GAs and has been around for a while; but it has not become so mainstream. I propose to make a brief tutorial of <i>classic</i> Genetic Algorithm vs. Multi-Objective Genetic Algorithm. Enough people interested? If we are a few of us, we could just meet up and I'll tell you the basics! -- [[Luís_Seoane \| Luíño]]
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	~~'''~~Nix's Bag O' Mathematical Tools~~'''~~
			==Nix's Bag O' Mathematical Tools==

	I'm planning on giving a number of tutorials to supplement Jim Crutchfield and I's lectures. The purpose of these should be to help you with your projects ( and encourage usage of our methods ;) ). I think it'd be cool for people to use this area to suggest topics to focus on. I started an empty bulleted list below. This will become more clear after we've given our lectures, but feel free to throw ideas out there when they come up. General topics might be: Information theory, time series analysis/modeling/prediction, symbolic dynamics (coarse-graining dynamical systems, i.e. what Liz Bradley discussed briefly), hidden Markov models, signal processing, bayesian inference, complexity measures, etc. [[Nix_Barnett \| Nix]]		I'm planning on giving a number of tutorials to supplement Jim Crutchfield and I's lectures. The purpose of these should be to help you with your projects ( and encourage usage of our methods ;) ). I think it'd be cool for people to use this area to suggest topics to focus on. I started an empty bulleted list below. This will become more clear after we've given our lectures, but feel free to throw ideas out there when they come up. General topics might be: Information theory, time series analysis/modeling/prediction, symbolic dynamics (coarse-graining dynamical systems, i.e. what Liz Bradley discussed briefly), hidden Markov models, signal processing, bayesian inference, complexity measures, etc. [[Nix_Barnett \| Nix]]
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	== ~~'''~~Python~~'''~~ ==		==Python==

	Downloads:		Downloads:

Caih at 02:39, 12 June 2013

2013-06-12T02:39:39Z

← Older revision		Revision as of 02:39, 12 June 2013
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	I will be showing people some basic features of using Gelphi to visualize networks this week. If there are other people who are also interested, we could turn it into a tutorial. -- [[Hua_Cai \| Hua]]		I will be showing people some basic features of using Gelphi to visualize networks this week. If there are other people who are also interested, we could turn it into a tutorial. -- [[Hua_Cai \| Hua]]

	This tutorial will be held on Wednesday (June 12th) at 1:30 (after lunch) at the main lecture hall. Stephan and I will show step by step network visualization and analysis in the tutorial. If you want to play with Gephi hands on during the tutorial, please download and install Gephi ahead of time. Link to Download [https://gephi.org/ Gephi]. The example we will use can be downloaded from [http://gephi.org/datasets/airlines.gexf.zip/ here].		This tutorial will be held on Wednesday (June 12th) at 1:30 (after lunch) at the main lecture hall. Stephan and I will show step by step network visualization and analysis in the tutorial. If you want to play with Gephi hands on during the tutorial, please download and install Gephi ahead of time. Link to Download [https://gephi.org/ Gephi]. The example we will use can be downloaded from [http://gephi.org/datasets/airlines.gexf.zip here].

	* I'm in -- Mauricio		* I'm in -- Mauricio

Caih at 02:38, 12 June 2013

2013-06-12T02:38:36Z

← Older revision		Revision as of 02:38, 12 June 2013
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	I will be showing people some basic features of using Gelphi to visualize networks this week. If there are other people who are also interested, we could turn it into a tutorial. -- [[Hua_Cai \| Hua]]		I will be showing people some basic features of using Gelphi to visualize networks this week. If there are other people who are also interested, we could turn it into a tutorial. -- [[Hua_Cai \| Hua]]

	This tutorial will be held on Wednesday (June 12th) at 1:30 (after lunch) at the main lecture hall. Stephan and I will show step by step network visualization and analysis in the tutorial. If you want to play with Gephi hands on during the tutorial, please download and install Gephi ahead of time. Link to Download [https://gephi.org/ Gephi]. ~~Data~~ we will use ~~in the tutorials are~~ [~~File~~:~~airlines_Nodes~~.~~csv]] and [[File:airlines_Edges~~.~~csv]~~].		This tutorial will be held on Wednesday (June 12th) at 1:30 (after lunch) at the main lecture hall. Stephan and I will show step by step network visualization and analysis in the tutorial. If you want to play with Gephi hands on during the tutorial, please download and install Gephi ahead of time. Link to Download [https://gephi.org/ Gephi]. The example we will use can be downloaded from [http://gephi.org/datasets/airlines.gexf.zip/ here].

	* I'm in -- Mauricio		* I'm in -- Mauricio

Caih at 02:35, 12 June 2013

2013-06-12T02:35:19Z

← Older revision		Revision as of 02:35, 12 June 2013
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	'''Network Visualization Using [https://gephi.org/ Gephi]'''		'''Network Visualization Using [https://gephi.org/ Gephi]'''
	I will be showing people some basic features of using Gelphi to visualize networks this week. If there are other people who are also interested, we could turn it into a tutorial. -- [[Hua_Cai \| Hua]]		I will be showing people some basic features of using Gelphi to visualize networks this week. If there are other people who are also interested, we could turn it into a tutorial. -- [[Hua_Cai \| Hua]]
	~~I'm in -- Mauricio~~

			This tutorial will be held on Wednesday (June 12th) at 1:30 (after lunch) at the main lecture hall. Stephan and I will show step by step network visualization and analysis in the tutorial. If you want to play with Gephi hands on during the tutorial, please download and install Gephi ahead of time. Link to Download [https://gephi.org/ Gephi]. Data we will use in the tutorials are [File:airlines_Nodes.csv]] and [[File:airlines_Edges.csv]].

			* I'm in -- Mauricio
	* Hua, thanks!. I'm in! [[Regina_Martinez \| Regina]]		* Hua, thanks!. I'm in! [[Regina_Martinez \| Regina]]
	* I will attend- Susanne		* I will attend- Susanne

Caih at 22:53, 11 June 2013

2013-06-11T22:53:18Z

← Older revision		Revision as of 22:53, 11 June 2013
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	'''Network Visualization Using [https://gephi.org/ \| Gephi]'''		'''Network Visualization Using [https://gephi.org/ Gephi]'''
	I will be showing people some basic features of using Gelphi to visualize networks this week. If there are other people who are also interested, we could turn it into a tutorial. -- [[Hua_Cai \| Hua]]		I will be showing people some basic features of using Gelphi to visualize networks this week. If there are other people who are also interested, we could turn it into a tutorial. -- [[Hua_Cai \| Hua]]
	I'm in -- Mauricio		I'm in -- Mauricio

Caih at 22:53, 11 June 2013

2013-06-11T22:53:01Z

← Older revision		Revision as of 22:53, 11 June 2013
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	'''Network Visualization Using Gephi'''		'''Network Visualization Using [https://gephi.org/ \| Gephi]'''
	I will be showing people some basic features of using Gelphi to visualize networks this week. If there are other people who are also interested, we could turn it into a tutorial. -- [[Hua_Cai \| Hua]]		I will be showing people some basic features of using Gelphi to visualize networks this week. If there are other people who are also interested, we could turn it into a tutorial. -- [[Hua_Cai \| Hua]]
	I'm in -- Mauricio		I'm in -- Mauricio

Caih at 22:45, 11 June 2013

2013-06-11T22:45:56Z

← Older revision		Revision as of 22:45, 11 June 2013
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	'''Network Visualization Using ~~Gelphi~~'''		'''Network Visualization Using Gephi'''
	I will be showing people some basic features of using Gelphi to visualize networks this week. If there are other people who are also interested, we could turn it into a tutorial. -- [[Hua_Cai \| Hua]]		I will be showing people some basic features of using Gelphi to visualize networks this week. If there are other people who are also interested, we could turn it into a tutorial. -- [[Hua_Cai \| Hua]]
	I'm in -- Mauricio		I'm in -- Mauricio

Nix at 15:21, 11 June 2013

2013-06-11T15:21:12Z

← Older revision		Revision as of 15:21, 11 June 2013
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	* I'm in! Thanks. [[Regina_Martinez \| Regina]]		* I'm in! Thanks. [[Regina_Martinez \| Regina]]

			* Max and I will probably schedule this tutorial for next week (after my lecture). [[Nix_Barnett \| Nix]]


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	* i'm in also! [[Ivana_Stankov \| Ivana]]		* i'm in also! [[Ivana_Stankov \| Ivana]]
	* I'm in -- Mauricio		* I'm in -- Mauricio
			Okay, I'll try to cover info theory, hidden markof model inference, and bayesian inference next week. Some of this will be covered this week in Jim's lectures and my labs. [[Nix_Barnett \| Nix]]

SKortsch at 03:15, 11 June 2013

2013-06-11T03:15:15Z

← Older revision		Revision as of 03:15, 11 June 2013
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	* I'm in! Thanks. [[Regina_Martinez \| Regina]]		* I'm in! Thanks. [[Regina_Martinez \| Regina]]

	* I will come, Susanne

	'''Dynamics in Networks'''		'''Dynamics in Networks'''
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	Yes! [[James_Magdanz \| Jim]]		Yes! [[James_Magdanz \| Jim]]

			* I will come, Susanne

	We scheduled this tutorial for Tuesday at 3:00 pm, just before the time to work on projects. Hope that you find it interesting! -- [[Luís_Seoane \| Luíño]]		We scheduled this tutorial for Tuesday at 3:00 pm, just before the time to work on projects. Hope that you find it interesting! -- [[Luís_Seoane \| Luíño]]