Information Theory of the Heart Page - Revision history

Hashikaga: Replaced content with ''''Contact''': Hiroshi (hashika1@jhmi.edu)
Thank you for your interest in the project. Feel free to join us any time and share your thoughts!
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2014-07-03T06:30:51Z

Replaced content with ''''Contact''': Hiroshi (hashika1@jhmi.edu)<br> Thank you for your interest in the project. Feel free to join us any time and share your thoughts!<br>'

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Hashikaga at 06:11, 25 June 2014

2014-06-25T06:11:18Z

← Older revision		Revision as of 06:11, 25 June 2014
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	- Reproduce spiral waves, multiple wavelets and anatomical reentry in the CA model<br>		- Reproduce spiral waves, multiple wavelets and anatomical reentry in the CA model<br>
	- Extract time series data above from the CA model and convert them into sparse matrices<br>		- Extract time series data above from the CA model and convert them into sparse matrices<br>
			- Visualization of the final data<br>

	''Unanswered Questions:''<br>		''Unanswered Questions:''<br>

Hashikaga at 06:09, 25 June 2014

2014-06-25T06:09:16Z

← Older revision		Revision as of 06:09, 25 June 2014
Line 159:		Line 159:
	- Done - Code (Matlab/Java) to compute transfer entropy<br>		- Done - Code (Matlab/Java) to compute transfer entropy<br>
	- However, it turns out that local transfer entropy calculation of our model is computationally expensive...<br>		- However, it turns out that local transfer entropy calculation of our model is computationally expensive...<br>
			<br>
	'''06/24/2014(Tue) Progress'''<br>		'''06/24/2014(Tue) Progress'''<br>
	- Meeting with Simon to discuss the project - should focus on information transmission <br>		- Meeting with Simon to discuss the project - should focus on information transmission <br>
	- Done - Code (Matlab) to convert a dense matrix into a sparse matrix<br>		- Done - Code (Matlab) to convert a dense matrix into a sparse matrix<br>
	- Done - Code (Python) to compute mutual information for paired cells<br>		- Done - Code (Python) to compute mutual information for paired cells<br>
			- Done - Reproduce point stimulation in the CA model<br>
	[[File:photo01.jpg]]<br>		[[File:photo01.jpg]]<br>
			''To-Do List:''<br>
			- Reproduce spiral waves, multiple wavelets and anatomical reentry in the CA model<br>
			- Extract time series data above from the CA model and convert them into sparse matrices<br>

			''Unanswered Questions:''<br>
			- Mutual information in the diagnonal directions<br>
			- Adding noise (stochastic response) to the CA model to represent heterogeneous tissue<br>
			- Kullback–Leibler divergence computation - should be considered<br>
			- Measure of segmented regions vs. each cell<br>

	[[File:photo02.jpg]]<br>		[[File:photo02.jpg]]<br>

Hashikaga at 06:01, 25 June 2014

2014-06-25T06:01:42Z

← Older revision		Revision as of 06:01, 25 June 2014
Line 148:		Line 148:
	- Will follow up with Ryan as to refs<br>		- Will follow up with Ryan as to refs<br>
	- Will contact Dr. Lizier to get his insight as to the local information dynamics indices in 2-D CA model<br>		- Will contact Dr. Lizier to get his insight as to the local information dynamics indices in 2-D CA model<br>
			<br>
			'''06/21/2014(Sat) Unofficial Trip to Bandelier National Monument'''<br>
			<br>
			'''06/22/2014(Sun) Progress'''<br>
			- Done - Code (Matlab) to extract time series data from the CA model in the sparse representation format<br>
			- Done - Code (Matlab/Java) to compute transfer entropy<br>
			<br>
			'''06/23/2014(Mon) Progress'''<br>
			- Communicated with Dr. Joe Lizier regarding local information dynamics<br>
			- Done - Code (Matlab/Java) to compute transfer entropy<br>
			- However, it turns out that local transfer entropy calculation of our model is computationally expensive...<br>
			'''06/24/2014(Tue) Progress'''<br>
			- Meeting with Simon to discuss the project - should focus on information transmission <br>
			- Done - Code (Matlab) to convert a dense matrix into a sparse matrix<br>
			- Done - Code (Python) to compute mutual information for paired cells<br>
			[[File:photo01.jpg]]<br>
			[[File:photo02.jpg]]<br>

Hashikaga at 08:16, 21 June 2014

2014-06-21T08:16:25Z

← Older revision		Revision as of 08:16, 21 June 2014
Line 138:		Line 138:
	2) Time series likely too short - Should compute entropy, mutual information using a longer time series (>10 heart beats) to dilute aperiodic effects<br>		2) Time series likely too short - Should compute entropy, mutual information using a longer time series (>10 heart beats) to dilute aperiodic effects<br>
	3) Transfer entropy - neutral. Need to see the data to get a better feel.<br>		3) Transfer entropy - neutral. Need to see the data to get a better feel.<br>
	4) Multivariate mutual information among neighboring cells - ~~perhaps premature at this point; get more~~ data first<br>		4) Multivariate mutual information among neighboring cells - Get other data first<br>
	5) Local Information Dynamics (Dr. Lizier) - Very promising<br>		5) Local Information Dynamics (Dr. Lizier) - Very promising<br>
	6) Local causal structure using cellular automata - Ryan will send us refs<br>		6) Local causal structure using cellular automata - Ryan will send us refs<br>

Hashikaga at 08:15, 21 June 2014

2014-06-21T08:15:50Z

← Older revision		Revision as of 08:15, 21 June 2014
Line 138:		Line 138:
	2) Time series likely too short - Should compute entropy, mutual information using a longer time series (>10 heart beats) to dilute aperiodic effects<br>		2) Time series likely too short - Should compute entropy, mutual information using a longer time series (>10 heart beats) to dilute aperiodic effects<br>
	3) Transfer entropy - neutral. Need to see the data to get a better feel.<br>		3) Transfer entropy - neutral. Need to see the data to get a better feel.<br>
	4) Multivariate mutual information - perhaps premature at this point; get more data first<br>		4) Multivariate mutual information among neighboring cells - perhaps premature at this point; get more data first<br>
	5) Local Information Dynamics (Dr. Lizier) - Very promising<br>		5) Local Information Dynamics (Dr. Lizier) - Very promising<br>
	6) Local causal structure using cellular automata - Ryan will send us refs<br>		6) Local causal structure using cellular automata - Ryan will send us refs<br>

Hashikaga at 08:15, 21 June 2014

2014-06-21T08:15:16Z

← Older revision		Revision as of 08:15, 21 June 2014
Line 138:		Line 138:
	2) Time series likely too short - Should compute entropy, mutual information using a longer time series (>10 heart beats) to dilute aperiodic effects<br>		2) Time series likely too short - Should compute entropy, mutual information using a longer time series (>10 heart beats) to dilute aperiodic effects<br>
	3) Transfer entropy - neutral. Need to see the data to get a better feel.<br>		3) Transfer entropy - neutral. Need to see the data to get a better feel.<br>
	4) Local Information Dynamics (Dr. Lizier) - Very promising<br>		4) Multivariate mutual information - perhaps premature at this point; get more data first<br>
	5) Local causal structure using cellular automata - Ryan will send us refs<br>		5) Local Information Dynamics (Dr. Lizier) - Very promising<br>
	6) Licor reconstruction - Ryan will send us refs<br>		6) Local causal structure using cellular automata - Ryan will send us refs<br>
			7) Licor reconstruction - Ryan will send us refs<br>
	[[File:photo1.JPG]]<br>		[[File:photo1.JPG]]<br>
	''To-Do List:''<br>		''To-Do List:''<br>

Hashikaga at 07:11, 21 June 2014

2014-06-21T07:11:29Z

← Older revision		Revision as of 07:11, 21 June 2014
Line 134:		Line 134:
	- Done - Code (Matlab) to visualize entropy and mutual information in 3-D<br>		- Done - Code (Matlab) to visualize entropy and mutual information in 3-D<br>
	- Permission obtained to use CA model (2005 Atienza, Matlab). Thank you!<br>		- Permission obtained to use CA model (2005 Atienza, Matlab). Thank you!<br>
	- Meeting with ~~Dr.~~ Ryan ~~James~~ to review the preliminary data: <br>		- Meeting with Ryan to review the preliminary data: <br>
	1) Action potential duration (APD) likely overestimated with threshold at 0.01 -> change to 0.1 with reasonable estimate<br>		1) Action potential duration (APD) likely overestimated with threshold at 0.01 -> change to 0.1 with reasonable estimate<br>
	2) Time series likely too short - Should compute entropy, mutual information using a longer time series (>10 heart beats) to dilute aperiodic effects<br>		2) Time series likely too short - Should compute entropy, mutual information using a longer time series (>10 heart beats) to dilute aperiodic effects<br>
	3) Transfer entropy - neutral. Need to see the data to get a better feel.<br>		3) Transfer entropy - neutral. Need to see the data to get a better feel.<br>
	4) Local Information Dynamics (Dr. Lizier) - Very promising<br>		4) Local Information Dynamics (Dr. Lizier) - Very promising<br>
			5) Local causal structure using cellular automata - Ryan will send us refs<br>
			6) Licor reconstruction - Ryan will send us refs<br>
	[[File:photo1.JPG]]<br>		[[File:photo1.JPG]]<br>
	''To-Do List:''<br>		''To-Do List:''<br>
	- Code to extract time series data from the CA model in the sparse representation format<br>		- Code to extract time series data from the CA model in the sparse representation format<br>
	- Code to compute transfer entropy and local information dynamics (minor modifications of existing codes)<br>		- Code to compute transfer entropy and local information dynamics (minor modifications of existing codes)<br>
			- Will follow up with Ryan as to refs<br>
	- Will contact Dr. Lizier to get his insight as to the local information dynamics indices in 2-D CA model<br>		- Will contact Dr. Lizier to get his insight as to the local information dynamics indices in 2-D CA model<br>

Hashikaga at 07:02, 21 June 2014

2014-06-21T07:02:42Z

← Older revision		Revision as of 07:02, 21 June 2014
Line 139:		Line 139:
	3) Transfer entropy - neutral. Need to see the data to get a better feel.<br>		3) Transfer entropy - neutral. Need to see the data to get a better feel.<br>
	4) Local Information Dynamics (Dr. Lizier) - Very promising<br>		4) Local Information Dynamics (Dr. Lizier) - Very promising<br>
	[[File:~~photo[1]~~.JPG]]<br>		[[File:photo1.JPG]]<br>
	''To-Do List:''<br>		''To-Do List:''<br>
	- Code to extract time series data from the CA model in the sparse representation format<br>		- Code to extract time series data from the CA model in the sparse representation format<br>
	- Code to compute transfer entropy and local information dynamics (minor modifications of existing codes)<br>		- Code to compute transfer entropy and local information dynamics (minor modifications of existing codes)<br>
	- Will contact Dr. Lizier to get his insight.<br>		- Will contact Dr. Lizier to get his insight as to the local information dynamics indices in 2-D CA model<br>

Hashikaga at 07:02, 21 June 2014

2014-06-21T07:02:05Z

← Older revision		Revision as of 07:02, 21 June 2014
Line 139:		Line 139:
	3) Transfer entropy - neutral. Need to see the data to get a better feel.<br>		3) Transfer entropy - neutral. Need to see the data to get a better feel.<br>
	4) Local Information Dynamics (Dr. Lizier) - Very promising<br>		4) Local Information Dynamics (Dr. Lizier) - Very promising<br>
	[[File:photo[1].JPG]]		[[File:photo[1].JPG]]<br>
	''To-Do List:''<br>		''To-Do List:''<br>
	- Code to extract time series data from the CA model in the sparse representation format<br>		- Code to extract time series data from the CA model in the sparse representation format<br>
	- Code to compute transfer entropy and local information dynamics (minor modifications of existing codes)<br>		- Code to compute transfer entropy and local information dynamics (minor modifications of existing codes)<br>
	- Will contact Dr. Lizier to get his insight.<br>		- Will contact Dr. Lizier to get his insight.<br>

Information Theory of the Heart Page - Revision history

Hashikaga: Replaced content with ''''Contact''': Hiroshi (hashika1@jhmi.edu) Thank you for your interest in the project. Feel free to join us any time and share your thoughts!'

Hashikaga at 06:11, 25 June 2014

Hashikaga at 06:09, 25 June 2014

Hashikaga at 06:01, 25 June 2014

Hashikaga at 08:16, 21 June 2014

Hashikaga at 08:15, 21 June 2014

Hashikaga at 08:15, 21 June 2014

Hashikaga at 07:11, 21 June 2014

Hashikaga at 07:02, 21 June 2014

Hashikaga at 07:02, 21 June 2014

Hashikaga: Replaced content with ''''Contact''': Hiroshi (hashika1@jhmi.edu)
Thank you for your interest in the project. Feel free to join us any time and share your thoughts!
'