Difference between revisions of "CoSMo 2013"
 
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This page contains course materials for the [http://www.compneurosci.com/CoSMo2013/program.html CoSMo 2013] summer school.   
 
This page contains course materials for the [http://www.compneurosci.com/CoSMo2013/program.html CoSMo 2013] summer school.   
 +
[[File:Cosmo 2013.jpg | thumb | CoSMo logo]]
  
 
To upload files, you must log in with an account that has upload access.  Here are some [[upload instructions]] or you can go straight to the [[Special:Upload | upload file page]].   
 
To upload files, you must log in with an account that has upload access.  Here are some [[upload instructions]] or you can go straight to the [[Special:Upload | upload file page]].   
  
−
Contact [[Konrad Kording]] if you need assistance.
+
Contact Konrad Kording if you need assistance.
 +
 
 +
 
 +
'''[https://www.facebook.com/groups/626800380673076/ CoSMo 2013 Facebook group!!!]'''
 +
 
 +
----
  
  
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Lecturers: Gunnar Blohm, Niko Troje
 
Lecturers: Gunnar Blohm, Niko Troje
  
−
Introduction on sensory processing (Troje) <br>
+
[[Media:CoSMoTroje.pdf | Troje lecture]]: some introductory thoughts on modelling <br>
−
'''Afternoon tutorials''' <br>
+
[[Media:SensoryMotorBlohm2013.pdf | Blohm sensory-motor lecture]]: a brief overview of the field <br>
−
files TBD
+
[[Media:Howto_Model.pdf | Blohm how to model lecture]]: a practical guide
 +
 
 +
 
 +
'''Afternoon tutorial 1''' <br>
 +
Please first get the [[Media:MatlabIntro.pdf | Tutorial instructions]] <br>
 +
Then download the [[Media:mdDisplay.m | Matlab code]] and [[Media:walker.mat | Data set]] for exercise 4.
 +
 
  
−
Introduction on sensory-motor control (Blohm) <br>
+
'''Afternoon tutorial 2''' <br>
−
How to model (Blohm) <br>
+
[[Media:DatasetReal.mat | Data set]] <br>
−
'''Afternoon tutorials''' <br>
+
[[Media:tutorial_BayesianDecodingBlohm.pdf | Instructions]]
−
files TBD
+
  
 +
----
  
 
== DREAM database - Introduction to the data and model sharing initiative==
 
== DREAM database - Introduction to the data and model sharing initiative==
Line 27: Line 39:
 
The DREAM project should be on the USB drives of a few different students.  If you haven't yet, find someone who has the data and get it from them.  DREAM can also be downloaded piece-wise (data sets, models, tools, and documentation) from CRCNS: http://crcns.org/data-sets/movements/dream/downloading-dream.  You will need to [https://crcns.org/join_form?came_from=http%3A//crcns.org/data-sets/movements/dream/downloading-dream create] an account on CRCNS to be able to download the project files.
 
The DREAM project should be on the USB drives of a few different students.  If you haven't yet, find someone who has the data and get it from them.  DREAM can also be downloaded piece-wise (data sets, models, tools, and documentation) from CRCNS: http://crcns.org/data-sets/movements/dream/downloading-dream.  You will need to [https://crcns.org/join_form?came_from=http%3A//crcns.org/data-sets/movements/dream/downloading-dream create] an account on CRCNS to be able to download the project files.
 
<!--[[File:AllDream.zip]]-->
 
<!--[[File:AllDream.zip]]-->
−
If you want "all" of DREAM (models, tools, and documentation), click here: [http://klab.smpp.northwestern.edu/wiki/images/d/d2/AllDream.zip AllDream.zip] <br>
+
If you want "all" of DREAM (models, tools, and documentation), click here: [http://compneurosci.com/wiki/images/AllDream.zip AllDream.zip] <br>
  
 
:If you're familiar with svn and would like info/credentials for code in the repository, contact [[Ben Walker]]
 
:If you're familiar with svn and would like info/credentials for code in the repository, contact [[Ben Walker]]
Line 35: Line 47:
  
  
−
Here is a [[Media:DataSetDescriptions.txt| description of data sets]] currently in Dream.  Dream is growing, but this list is accurate as of the time of the summer school.
+
Here is a description of data sets currently in Dream.  Dream is growing, but this list is accurate as of the time of the summer school (click on the link to access the related publication).
−
<!--*Burns -- reaching with head tilt and left/right visual perturbations
+
*[[Media:Burns_2010.pdf | Burns]] -- reaching with head tilt and left/right visual perturbations <br>
−
*Fernandes -- reaching with uncertain and rotated midpoint feedback  
+
*[[Media:Corbett_2013.pdf | Corbett]] -- reach trajectory predictions based on EMG and gaze movements <br>
−
*Kording -- reaching with uncertain midpoint feedback
+
*[[Media:Fernandes_2012_e1_published.pdf | Fernandes]] -- reaching with uncertain and rotated midpoint feedback <br>
−
*Mattar 07 -- generalizing from one, two or multi targets to another direction
+
*[[Media:Flint_2012.pdf | Flint]] -- decoding of reaching movements from local field potentials <br>
−
*Mattar 10 -- reaching to a distance (short/long), generalizing to the other one (long/short)
+
*[[Media:Kording_2004.pdf | Kording]] -- reaching with uncertain midpoint feedback <br>
−
*Ostry -- move in force field, get an estimation of where the hand is
+
*[[Media:Mattar_and_Ostry_2007.pdf | Mattar 07]] -- generalizing from one, two or multi targets to another direction <br>
−
*Scott -- monkey (no spike), center out: even and not evenly distributed targets, also a forward/back
+
*[[Media:Mattar_and_Ostry.pdf | Mattar 10]] -- reaching to a distance (short/long), generalizing to the other one (long/short) <br>
−
*Stevenson -- center out, monkey with neural time stamps
+
*[[Media:Somatosensory_Plasticity_and_Motor_Learning.pdf | Ostry]] -- move in force field, get an estimation of where the hand is <br>
−
*Vahdat -- movement in force field with FMRI scans pre/post learning
+
*[[Media:Scott_2001.pdf | Scott]] -- monkey (no spike), center out: even and not evenly distributed targets, also a forward/back <br>
−
*Wei 08 -- visual perturbations, cursor shown only at target
+
*[[Media:Stevenson2011.pdf | Stevenson]] -- center out, monkey with neural time stamps <br>
−
*Wei 10 -- movement in differing force fields
+
*[[Media:Thoroughman_2005.pdf | Thoroughman]] -- reach adaptation to perturbations with different complexity  <br>
−
*Young -- movement time stayed the same, but distance changed; fast, medium, slow reaches.
+
*[[Media:Vahdat_2011.pdf | Vahdat]] -- movement in force field with FMRI scans pre/post learning <br>
−
-->
+
*[[Media:Wei_Relevance_Error_Motor_Adapt_2008.pdf | Wei 08]] -- visual perturbations, cursor shown only at target <br>
 +
*[[Media:Wei_2010.pdf | Wei 10]] -- movement in differing force fields <br>
 +
*[[Media:Young_2009.pdf | Young]] -- movement time stayed the same, but distance changed; fast, medium, slow reaches. <br>
 +
 
 +
----
 +
 
  
 
== Limb motor control ==
 
== Limb motor control ==
Line 54: Line 71:
 
Lecturers: Lena Ting, Stephen Scott
 
Lecturers: Lena Ting, Stephen Scott
  
 +
[[Media:ScottMotorSystemIntroCoSMo2013.pdf | Scott lecture]]: Introduction <br>
 +
[[Media:Ting_Cosmo_2013_small.pdf | Ting lecture]]: Control through synergies<br>
 +
[[Media:COSMO_Control_Theory_2013small.pdf | Scott lecture]]: biology of motor control <br>
 +
[[Media:COSMO2013_OFC.pdf | Crevecoeur lecture]]: Mathematics of optimal feedback control
 +
 +
 +
'''Afternoon tutorial 1''' <br>
 +
[[Media:Ting_CoSMo_Lab.pdf | Instructions]] <br>
 +
[[Media:Ting_Group_CoSMo_Code_Package.zip | Software package 1]] <br>
 +
[[Media:wfANOVA.zip | Wavelet code]] <br>
 +
Related papers: [[Media:Bingham_Choi_Ting_2011.pdf | Bingham (2011)]] and [[Media:Ting_and_Chvatal 2010.pdf | Ting (2010)]]
 +
 +
 +
'''Afternoon tutorial 2''' <br>
 +
[[Media:assignment_OFC.pdf | OFC tutorial]]
 +
 +
----
  
  
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Lecturers: Angela Yu, Paul Schrater
 
Lecturers: Angela Yu, Paul Schrater
  
 +
[[Media:Cosmo2schrater.pdf | Schrater lecture]]: The Bayesian Brain <br>
 +
[[Media:YuKingston13.pdf | Yu lecture]]: Decisions, decisions, decisions
 +
 +
 +
'''Afternoon tutorial 1''' <br>
 +
[[Media:Cosmo2013Schrater.zip | Tutorial files]] <br>
 +
and relevant papers: [[Media:Kording_2004.pdf | Kording 2004]] and [[Media:haith-NIPS2008.pdf | Haith 2008]]
 +
 +
 +
'''Afternoon tutorial 2''' <br>
 +
[[Media:exercise_DM.pdf | Instructions]]
 +
 +
----
  
  
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Lecturer: Ken Rose
 
Lecturer: Ken Rose
  
 +
[[Media:RoseCoSMo2013grant_manship_101.pdf | Slides]]
 +
 +
----
  
  
Line 72: Line 122:
 
Lecturers: Kathy Cullen, Maurice Chacron
 
Lecturers: Kathy Cullen, Maurice Chacron
  
 +
[[Media:Chacron_lecture1.pptx | Chacron lecture 1]]: Linear Systems Theory <br>
 +
[[Media:CullenLinear_computational_lecture_2013.ppt | Cullen lecture 1]]: The VOR as a linear system <br>
 +
[[Media:CullenNon-linearComputationalLecture.pdf | Cullen lecture 2]]: Non-linear sensory-motor transformations <br>
 +
[[Media:Chacron_lecture2.pptx | Chacron lecture 2]]: Sensory-motor learning
 +
 +
 +
'''Afternoon tutorial 1''' <br>
 +
[[Media:KEC_CompNeuro OK.zip | Tutorial files]]
 +
 +
 +
'''Afternoon tutorial 2''' <br>
 +
[[Media:Exercise_day2.zip | Tutorial files]] <br>
 +
[[Media:Bol_2011_jneurosci.pdf | Related article]] <br>
 +
[[Media:dirac.m | Delta function]]
 +
 +
----
  
  
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Lecturer: Don Aldridge (IBM)
 
Lecturer: Don Aldridge (IBM)
  
 +
----
  
  
Line 84: Line 151:
 
Lecturers: Doug Tweed, Maurice Smith
 
Lecturers: Doug Tweed, Maurice Smith
  
 +
[[Media:Smithtalk_cosmo_2013a_final2.pdf | Smith slides]] <br>
 +
[[Media:TWEED_notes.pdf | Tweed notes]]
 +
 +
 +
'''Afternoon tutorial 1''' <br>
 +
[[Media:cosmo_exercises_smith.pdf | Instructions]]
 +
 +
 +
'''Afternoon tutorial 2''' <br>
 +
[[Media:TweedTutorial.zip | Tutorial files & instructions]]
 +
 +
----
  
  
 
==Computational neuroimaging & MVPA==
 
==Computational neuroimaging & MVPA==
 
''Aug 16-17'' <br>
 
''Aug 16-17'' <br>
−
Lecturers: Rhodri Cusack, Pat Stroman, Andy Connolly
+
Lecturers: Rhodri Cusack, Nick Oosterhof, Andy Connolly
 +
 
 +
[[Media:cusack_cosmo_2013_part1.pdf | Cusak lecture 1]] <br>
 +
[[Media:cusack_cosmo_2013_part2small.pdf | Cusak lecture 2]]
 +
 
 +
 
 +
'''Afternoon tutorial 1''' <br>
 +
[[Media:Tutorial.zip | Tutorial files and instructions]]
 +
 
 +
 
 +
'''Workshop material day 2''' <br>
 +
[http://www.cosmomvpa.org Workshop material] <br>
 +
[http://www.nitrc.org/projects/mricron MRIcron visualization software package] <br>
 +
Please download [http://github.com/CoSMoMVPA/CoSMoMVPA this file] (~170Mb!!!)
 +
 
 +
----
 +
 
 +
==Group projects==
 +
''2-week duration'' <br>
 +
The B.E.E.R (Behavioral Effects of Expected Reward) experimental competition results: [https://docs.google.com/spreadsheet/ccc?key=0ApTGNxJS3yoUdE1NdjhjREV5bzJ5ZmY0QXduNWZuNkE&usp=sharing Scores] <br>
 +
First prize (best group): 2 pitchers of beer (or equivalent) at the Grad Club <br>
 +
Second prize: 1 pitcher of beer for the team
 +
 
 +
 
 +
'''Presentation schedule: Fri, Aug 16''' <br>
 +
5:00pm - ''Different Applications of TD-Learning Using an Actor-Critic Method'' <br>
 +
Team: Susanna Summa, Camilla Pierella, Chiara Baston, Ashley Parr <br>
 +
[[Media:Different_Applications_of_TD-Learning_Using_an_Actor-Critic_Method.pdf | Slides]]
 +
 
 +
 
 +
5:20pm - ''Using an OFC Model to Depict Motor Learning'' <br>
 +
Team: Noor Al Dahhan, Edwin Cruz, Stephanie Durocher, Christophe Gerard, & Rajkumar Raveedndran <br>
 +
[[Media:Raj_cosmo2013_Final.pdf | Slides]]
 +
 
 +
 
 +
5:40pm - ''Motor Adaptation in a Model of Optimal Feedback Control'' <br>
 +
Team: Kyle Blum, Andrew Kope, Kevin Trewartha, Julia Leonard <br>
 +
[[Media:OFC_Learning_Cosmo2013GroupProj_final.pdf | Slides]]
 +
 
 +
 
 +
''Dinner break''
 +
 
 +
 
 +
7:00pm - ''Spatial and temporal re-analysis of fMRI data'' <br>
 +
Team: Scott Macdonald, Conor Wild, Jason Gallivan, Nevena Savija <br>
 +
[[Media:GallivanGroupPresentation_final.pdf | Slides]]
 +
 
 +
 
 +
7:20pm - ''Diving into an ocean of biological motions: Clustering perceived attributes'' <br>
 +
Team: Seamas Weech, Sophie Kenny, Sujaya Neupane, Benedict Chang <br>
 +
[[Media:BioMotion_CoSMo2013.pdf | Slides]]
 +
 
 +
 
 +
7:40pm - ''Image Reconstruction from Human Brain Activity'' <br>
 +
Team: Mark Shaw, Christian Wolf, Gaurav Aggarwal <br>
 +
[[Media:Mark_Image_Reconstruction.pptx | Slides]]
 +
 
 +
 
 +
8:00pm - ''Modelling Reaching Behaviour'' <br>
 +
Team: Vivian Paulun, Rubén Pinzón, Juan M. Galeazzi, Jolande Fooken <br>
 +
[[Media:Galeazzi_PD3.pdf | Slides]]
 +
 
 +
 
 +
8:20pm - ''What (some) models can and cannot do'' <br>
 +
Team: Juan Chen, Paula Di Noto, Li-Ann Leow, Gabriella Levkov <br>
 +
[[Media:CosMoJLPG.pdf | Slides]]
 +
 
 +
 
 +
8:40pm - ''The B.E.E.R (Behavioral Effects of Expected Reward) experimental competition''  '''WINNER'''<br>
 +
''Optimality under fire: Dissociating learning from Bayesian integration'' <br>
 +
Team: Luigi Acerbi, Feryal Behbahani, Megan Peters, Marius 't Hart <br>
 +
[[Media:OptimalityUnderFire_Acerbi_tHart_Behbahani_Peters.pdf | Slides]]
 +
 
 +
 
 +
'''Survey: please click [http://www.surveymonkey.com/s/VYM7LM8 here] to evaluate projects'''
 +
 
 +
 
 +
'''Winner of the 2-week project competition: B.E.E.R team!!!''' <br>
 +
''Prize'': A poster presentation at the [http://www.seas.harvard.edu/motorlab/acmc/openconf.php TCMC] satellite meeting to the [http://www.sfn.org/annual-meeting/neuroscience-2013 SfN] annual meeting in San Diego.
 +
 
 +
----
 +
 
 +
 
 +
==Sunset dinner cruise==
 +
For everyone having signed up: please meet at 6pm AT THE LATEST @ 1 Brock Street (East end of Confederation Park, just by city hall). '''Please be on time!!!''' <br>
 +
We will board the "Island Queen" all together at 6pm. This is a CoSMo-sponsored event. Food is included and there will be a cash bar.

Latest revision as of 14:43, 6 February 2018

This page contains course materials for the CoSMo 2013 summer school.

CoSMo logo

To upload files, you must log in with an account that has upload access. Here are some upload instructions or you can go straight to the upload file page.

Contact Konrad Kording if you need assistance.


CoSMo 2013 Facebook group!!!


Introduction - overview of sensory-motor control

Aug 5-6
Lecturers: Gunnar Blohm, Niko Troje

Troje lecture: some introductory thoughts on modelling
Blohm sensory-motor lecture: a brief overview of the field
Blohm how to model lecture: a practical guide


Afternoon tutorial 1
Please first get the Tutorial instructions
Then download the Matlab code and Data set for exercise 4.


Afternoon tutorial 2
Data set
Instructions

DREAM database - Introduction to the data and model sharing initiative

Aug 5 (evening)

Lecturer: Gunnar Blohm

The DREAM project should be on the USB drives of a few different students. If you haven't yet, find someone who has the data and get it from them. DREAM can also be downloaded piece-wise (data sets, models, tools, and documentation) from CRCNS: http://crcns.org/data-sets/movements/dream/downloading-dream. You will need to create an account on CRCNS to be able to download the project files. If you want "all" of DREAM (models, tools, and documentation), click here: AllDream.zip

If you're familiar with svn and would like info/credentials for code in the repository, contact Ben Walker


Update: Here's the fixed version of LoadDreamPaths.m. (The originally distributed version had Windows directory formatting using '/' and would not work for *nix. This script should work for all OSes.)


Here is a description of data sets currently in Dream. Dream is growing, but this list is accurate as of the time of the summer school (click on the link to access the related publication).

  • Burns -- reaching with head tilt and left/right visual perturbations
  • Corbett -- reach trajectory predictions based on EMG and gaze movements
  • Fernandes -- reaching with uncertain and rotated midpoint feedback
  • Flint -- decoding of reaching movements from local field potentials
  • Kording -- reaching with uncertain midpoint feedback
  • Mattar 07 -- generalizing from one, two or multi targets to another direction
  • Mattar 10 -- reaching to a distance (short/long), generalizing to the other one (long/short)
  • Ostry -- move in force field, get an estimation of where the hand is
  • Scott -- monkey (no spike), center out: even and not evenly distributed targets, also a forward/back
  • Stevenson -- center out, monkey with neural time stamps
  • Thoroughman -- reach adaptation to perturbations with different complexity
  • Vahdat -- movement in force field with FMRI scans pre/post learning
  • Wei 08 -- visual perturbations, cursor shown only at target
  • Wei 10 -- movement in differing force fields
  • Young -- movement time stayed the same, but distance changed; fast, medium, slow reaches.


Limb motor control

Aug 7-8
Lecturers: Lena Ting, Stephen Scott

Scott lecture: Introduction
Ting lecture: Control through synergies
Scott lecture: biology of motor control
Crevecoeur lecture: Mathematics of optimal feedback control


Afternoon tutorial 1
Instructions
Software package 1
Wavelet code
Related papers: Bingham (2011) and Ting (2010)


Afternoon tutorial 2
OFC tutorial


The Bayesian Brain

Aug 9-10
Lecturers: Angela Yu, Paul Schrater

Schrater lecture: The Bayesian Brain
Yu lecture: Decisions, decisions, decisions


Afternoon tutorial 1
Tutorial files
and relevant papers: Kording 2004 and Haith 2008


Afternoon tutorial 2
Instructions


Grant writing 101 for Neuroscientists

Aug 9 (evening)
Lecturer: Ken Rose

Slides


Sensory-motor transformations

Aug 12-13
Lecturers: Kathy Cullen, Maurice Chacron

Chacron lecture 1: Linear Systems Theory
Cullen lecture 1: The VOR as a linear system
Cullen lecture 2: Non-linear sensory-motor transformations
Chacron lecture 2: Sensory-motor learning


Afternoon tutorial 1
Tutorial files


Afternoon tutorial 2
Tutorial files
Related article
Delta function


From academia to industry - a practical guide

Aug 12 (evening)
Lecturer: Don Aldridge (IBM)


Adaptation & learning

Aug 14-15
Lecturers: Doug Tweed, Maurice Smith

Smith slides
Tweed notes


Afternoon tutorial 1
Instructions


Afternoon tutorial 2
Tutorial files & instructions


Computational neuroimaging & MVPA

Aug 16-17
Lecturers: Rhodri Cusack, Nick Oosterhof, Andy Connolly

Cusak lecture 1
Cusak lecture 2


Afternoon tutorial 1
Tutorial files and instructions


Workshop material day 2
Workshop material
MRIcron visualization software package
Please download this file (~170Mb!!!)

Group projects

2-week duration
The B.E.E.R (Behavioral Effects of Expected Reward) experimental competition results: Scores
First prize (best group): 2 pitchers of beer (or equivalent) at the Grad Club
Second prize: 1 pitcher of beer for the team


Presentation schedule: Fri, Aug 16
5:00pm - Different Applications of TD-Learning Using an Actor-Critic Method
Team: Susanna Summa, Camilla Pierella, Chiara Baston, Ashley Parr
Slides


5:20pm - Using an OFC Model to Depict Motor Learning
Team: Noor Al Dahhan, Edwin Cruz, Stephanie Durocher, Christophe Gerard, & Rajkumar Raveedndran
Slides


5:40pm - Motor Adaptation in a Model of Optimal Feedback Control
Team: Kyle Blum, Andrew Kope, Kevin Trewartha, Julia Leonard
Slides


Dinner break


7:00pm - Spatial and temporal re-analysis of fMRI data
Team: Scott Macdonald, Conor Wild, Jason Gallivan, Nevena Savija
Slides


7:20pm - Diving into an ocean of biological motions: Clustering perceived attributes
Team: Seamas Weech, Sophie Kenny, Sujaya Neupane, Benedict Chang
Slides


7:40pm - Image Reconstruction from Human Brain Activity
Team: Mark Shaw, Christian Wolf, Gaurav Aggarwal
Slides


8:00pm - Modelling Reaching Behaviour
Team: Vivian Paulun, Rubén Pinzón, Juan M. Galeazzi, Jolande Fooken
Slides


8:20pm - What (some) models can and cannot do
Team: Juan Chen, Paula Di Noto, Li-Ann Leow, Gabriella Levkov
Slides


8:40pm - The B.E.E.R (Behavioral Effects of Expected Reward) experimental competition WINNER
Optimality under fire: Dissociating learning from Bayesian integration
Team: Luigi Acerbi, Feryal Behbahani, Megan Peters, Marius 't Hart
Slides


Survey: please click here to evaluate projects


Winner of the 2-week project competition: B.E.E.R team!!!
Prize: A poster presentation at the TCMC satellite meeting to the SfN annual meeting in San Diego.


Sunset dinner cruise

For everyone having signed up: please meet at 6pm AT THE LATEST @ 1 Brock Street (East end of Confederation Park, just by city hall). Please be on time!!!
We will board the "Island Queen" all together at 6pm. This is a CoSMo-sponsored event. Food is included and there will be a cash bar.

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