Blohm Lab Wiki - User contributions [en-ca]

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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]].

Contact Konrad Kording if you need assistance.

'''[https://www.facebook.com/groups/626800380673076/ CoSMo 2013 Facebook group!!!]'''

== Introduction - overview of sensory-motor control ==
''Aug 5-6'' 
Lecturers: Gunnar Blohm, Niko Troje

[[Media:CoSMoTroje.pdf | Troje lecture]]: some introductory thoughts on modelling 
[[Media:SensoryMotorBlohm2013.pdf | Blohm sensory-motor lecture]]: a brief overview of the field 
[[Media:Howto_Model.pdf | Blohm how to model lecture]]: a practical guide

'''Afternoon tutorial 1''' 
Please first get the [[Media:MatlabIntro.pdf | Tutorial instructions]] 
Then download the [[Media:mdDisplay.m | Matlab code]] and [[Media:walker.mat | Data set]] for exercise 4.

'''Afternoon tutorial 2''' 
[[Media:DatasetReal.mat | Data set]] 
[[Media:tutorial_BayesianDecodingBlohm.pdf | 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 [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.

If you want "all" of DREAM (models, tools, and documentation), click here: [http://compneurosci.com/wiki/images/AllDream.zip 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 [[Media:LoadDreamPaths.m | 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).
*[[Media:Burns_2010.pdf | Burns]] -- reaching with head tilt and left/right visual perturbations 
*[[Media:Corbett_2013.pdf | Corbett]] -- reach trajectory predictions based on EMG and gaze movements 
*[[Media:Fernandes_2012_e1_published.pdf | Fernandes]] -- reaching with uncertain and rotated midpoint feedback 
*[[Media:Flint_2012.pdf | Flint]] -- decoding of reaching movements from local field potentials 
*[[Media:Kording_2004.pdf | Kording]] -- reaching with uncertain midpoint feedback 
*[[Media:Mattar_and_Ostry_2007.pdf | Mattar 07]] -- generalizing from one, two or multi targets to another direction 
*[[Media:Mattar_and_Ostry.pdf | Mattar 10]] -- reaching to a distance (short/long), generalizing to the other one (long/short) 
*[[Media:Somatosensory_Plasticity_and_Motor_Learning.pdf | Ostry]] -- move in force field, get an estimation of where the hand is 
*[[Media:Scott_2001.pdf | Scott]] -- monkey (no spike), center out: even and not evenly distributed targets, also a forward/back 
*[[Media:Stevenson2011.pdf | Stevenson]] -- center out, monkey with neural time stamps 
*[[Media:Thoroughman_2005.pdf | Thoroughman]] -- reach adaptation to perturbations with different complexity 
*[[Media:Vahdat_2011.pdf | Vahdat]] -- movement in force field with FMRI scans pre/post learning 
*[[Media:Wei_Relevance_Error_Motor_Adapt_2008.pdf | Wei 08]] -- visual perturbations, cursor shown only at target 
*[[Media:Wei_2010.pdf | Wei 10]] -- movement in differing force fields 
*[[Media:Young_2009.pdf | Young]] -- movement time stayed the same, but distance changed; fast, medium, slow reaches. 

== Limb motor control ==
''Aug 7-8'' 
Lecturers: Lena Ting, Stephen Scott

[[Media:ScottMotorSystemIntroCoSMo2013.pdf | Scott lecture]]: Introduction 
[[Media:Ting_Cosmo_2013_small.pdf | Ting lecture]]: Control through synergies 
[[Media:COSMO_Control_Theory_2013small.pdf | Scott lecture]]: biology of motor control 
[[Media:COSMO2013_OFC.pdf | Crevecoeur lecture]]: Mathematics of optimal feedback control

'''Afternoon tutorial 1''' 
[[Media:Ting_CoSMo_Lab.pdf | Instructions]] 
[[Media:Ting_Group_CoSMo_Code_Package.zip | Software package 1]] 
[[Media:wfANOVA.zip | Wavelet code]] 
Related papers: [[Media:Bingham_Choi_Ting_2011.pdf | Bingham (2011)]] and [[Media:Ting_and_Chvatal 2010.pdf | Ting (2010)]]

'''Afternoon tutorial 2''' 
[[Media:assignment_OFC.pdf | OFC tutorial]]

== The Bayesian Brain ==
''Aug 9-10'' 
Lecturers: Angela Yu, Paul Schrater

[[Media:Cosmo2schrater.pdf | Schrater lecture]]: The Bayesian Brain 
[[Media:YuKingston13.pdf | Yu lecture]]: Decisions, decisions, decisions

'''Afternoon tutorial 1''' 
[[Media:Cosmo2013Schrater.zip | Tutorial files]] 
and relevant papers: [[Media:Kording_2004.pdf | Kording 2004]] and [[Media:haith-NIPS2008.pdf | Haith 2008]]

'''Afternoon tutorial 2''' 
[[Media:exercise_DM.pdf | Instructions]]

==Grant writing 101 for Neuroscientists==
''Aug 9 (evening)'' 
Lecturer: Ken Rose

[[Media:RoseCoSMo2013grant_manship_101.pdf | Slides]]

== Sensory-motor transformations ==
''Aug 12-13'' 
Lecturers: Kathy Cullen, Maurice Chacron

[[Media:Chacron_lecture1.pptx | Chacron lecture 1]]: Linear Systems Theory 
[[Media:CullenLinear_computational_lecture_2013.ppt | Cullen lecture 1]]: The VOR as a linear system 
[[Media:CullenNon-linearComputationalLecture.pdf | Cullen lecture 2]]: Non-linear sensory-motor transformations 
[[Media:Chacron_lecture2.pptx | Chacron lecture 2]]: Sensory-motor learning

'''Afternoon tutorial 1''' 
[[Media:KEC_CompNeuro OK.zip | Tutorial files]]

'''Afternoon tutorial 2''' 
[[Media:Exercise_day2.zip | Tutorial files]] 
[[Media:Bol_2011_jneurosci.pdf | Related article]] 
[[Media:dirac.m | 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

[[Media:Smithtalk_cosmo_2013a_final2.pdf | Smith slides]] 
[[Media:TWEED_notes.pdf | Tweed notes]]

'''Afternoon tutorial 1''' 
[[Media:cosmo_exercises_smith.pdf | Instructions]]

'''Afternoon tutorial 2''' 
[[Media:TweedTutorial.zip | Tutorial files & instructions]]

==Computational neuroimaging & MVPA==
''Aug 16-17'' 
Lecturers: Rhodri Cusack, Nick Oosterhof, Andy Connolly

[[Media:cusack_cosmo_2013_part1.pdf | Cusak lecture 1]] 
[[Media:cusack_cosmo_2013_part2small.pdf | Cusak lecture 2]]

'''Afternoon tutorial 1''' 
[[Media:Tutorial.zip | Tutorial files and instructions]]

'''Workshop material day 2''' 
[http://discovery.dartmouth.edu/~aconnoll/cosmo_mvpa/index.html Workshop material] 
[http://www.nitrc.org/projects/mricron MRIcron visualization software package] 
Please download [http://discovery.dartmouth.edu/~aconnoll/cosmo_mvpa/_static/cosmo_mvpa_data.zip this file] (~170Mb!!!)

==Group projects==
''2-week duration'' 
The B.E.E.R (Behavioral Effects of Expected Reward) experimental competition results: [https://docs.google.com/spreadsheet/ccc?key=0ApTGNxJS3yoUdE1NdjhjREV5bzJ5ZmY0QXduNWZuNkE&usp=sharing 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 
[[Media:Different_Applications_of_TD-Learning_Using_an_Actor-Critic_Method.pdf | Slides]]

5:20pm - ''Using an OFC Model to Depict Motor Learning'' 
Team: Noor Al Dahhan, Edwin Cruz, Stephanie Durocher, Christophe Gerard, & Rajkumar Raveedndran 
[[Media:Raj_cosmo2013_Final.pdf | Slides]]

5:40pm - ''Motor Adaptation in a Model of Optimal Feedback Control'' 
Team: Kyle Blum, Andrew Kope, Kevin Trewartha, Julia Leonard 
[[Media:OFC_Learning_Cosmo2013GroupProj_final.pdf | Slides]]

''Dinner break''

7:00pm - ''Spatial and temporal re-analysis of fMRI data'' 
Team: Scott Macdonald, Conor Wild, Jason Gallivan, Nevena Savija 
[[Media:GallivanGroupPresentation_final.pdf | Slides]]

7:20pm - ''Diving into an ocean of biological motions: Clustering perceived attributes'' 
Team: Seamas Weech, Sophie Kenny, Sujaya Neupane, Benedict Chang 
[[Media:BioMotion_CoSMo2013.pdf | Slides]]

7:40pm - ''Image Reconstruction from Human Brain Activity'' 
Team: Mark Shaw, Christian Wolf, Gaurav Aggarwal 
[[Media:Mark_Image_Reconstruction.pptx | Slides]]

8:00pm - ''Modelling Reaching Behaviour'' 
Team: Vivian Paulun, Rubén Pinzón, Juan M. Galeazzi, Jolande Fooken 
[[Media:Galeazzi_PD3.pdf | Slides]]

8:20pm - ''What (some) models can and cannot do'' 
Team: Juan Chen, Paula Di Noto, Li-Ann Leow, Gabriella Levkov 
[[Media:CosMoJLPG.pdf | 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 
[[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!!!''' 
''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!!!''' 
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.

Blohm Lab Wiki:About

2018-01-31T00:16:28Z

Mike: Created blank page

2018-01-30T22:51:42Z

2018-01-30T22:33:24Z

Mike:

This page contains course materials for the [http://www.compneurosci.com/CoSMo/program.html CoSMo 2017] summer school.
[[File:CoSMoLogo2017.jpg | thumb | CoSMo logo]]

== Introduction ==
''Jul 31 - Aug 4'' 
Lecturers: Gunnar Blohm, Paul Schrater, Konrad Kording 

=== Day 1 - Overview of sensory-motor computations ===

[[Media:Organization_CoSMo2017.pdf | Organization slides]] 
[[Media:Philosophy_CoSMo2017.pdf | Philosophy of modelling slides]] 
[[Media:SensoryMotorBlohm2017.pdf | Sensorimotor overview slides]] 

'''Afternoon tutorial 1 - plotting neural data'''

Here is the file [[http://compneurosci.com/wiki/images/M1_Stevenson_Binned.mat Stevenson Data Set]]
As part of the tuning curve exercise we will understand it. 

Tutorial is available
[https://www.dropbox.com/sh/mqr7x1q8rk9129h/AAChwxoOwvQ3Y6U47cO8HRkVa?dl=0 here]

'''Afternoon tutorial 2: gain modulation for reference frame transformations'''

The goal of this tutorial is to understand how gain modulation can be used for reference frame transformations and how gain modulation can emerge from training a simple artificial neural network carrying out reference frame transformations. 
There are 2 different approaches to solving this:
* exact determination of read-out weights from eye-position gain-modulated neurons as in [[Media:Pouget_snyder_2000.pdf | this seminal paper]]. Here the solution can be found by computing the least-square optimal set of weights mapping the gain-modulated neurons (population code) to head-centered output neuron(s). For this to work, population code neurons need to be of the exponential function family.
* training a neural network to perform reference frame transformations using [[Media:Gain_fields_NNet_toolbox_CoSMo2016.m | this code]]. For this you can plot each individual neuron's receptive field for different eye positions and analyze how the receptive field changes with eye position in each network layer. 

=== Day 2 - Bayesian approaches ===

[https://drive.google.com/file/d/0B7BtxrHIZHgpUmUxXzl2WHVsUEk/view Bayesian perception - an introduction]: a tremendous book written by Wei Ji Ma, Konrad Kording, Daniel Goldreich 

'''AFTERNOON LECTURE TUTORIAL'''
[https://www.dropbox.com/sh/w1ajv6b1s1gc45u/AAAMIZR5FZUqNJn_8-yOgQ5ma?dl=0 Dropbox link to slides and tutorial]: Material for decision making lecture and tutorial 

=== Day 2 (evening) - How to model tutorial ===

Paul's Illusion exercise slides are in the afternoon tutorial dropbox. 

[[Media:HowtoMode_CoSMo2017.pdf | How to model tutorial slides]] 

=== Day 3 - Linear systems ===

'''Morning lectures and tutorials (Theory and saccades)''' 
[[Media:SystemsTheory_CoSMo2017.pdf | Linear systems theory slides]] 
[[Media:SystemsEyeMovements_CoSMo2017.pdf | Modelling saccades slides]] 

[[Media:CoSMo2015-vOpstal.pdf | van Opstal syllabus - linear systems theory]]: a great syllabus developed by John van Opstal for CoSMo on using linear systems to model gaze control with theory, exercises and answers to exercises 

'''Afternoon lectures and tutorials (Kalman filter)''' 

[https://drive.google.com/open?id=0B8bK-gM8hHDpRlBiRTRRZlZsT3c Face attractiveness and decision tutorials, and lecture slides] 

[https://docs.google.com/document/d/1a5uEJepjmRpdzr0d26feRgQfVKVMzOvuGX83NAGhEow/edit?usp=sharing Here] are modeling tutorial instructions. Please also read the papers by [[Media:Lappe,_Bremmer,_&_van_der_Berg_1999.pdf | Lappe]] and [[Media:Seno_&_Fukuda_2012.pdf | Seno]]. 

=== Day 3 (evening) - paper writing 101 ===

Konrad talked about [http://klab.smpp.northwestern.edu/wiki/index.php5/Paper_Writing_101 paper writing 101]. This is also formalized in the [http://www.biorxiv.org/content/early/2016/12/17/088278 Ten simple rules for structuring papers] article. 

=== Day 4 - Optimal Feedback Control ===

[[Media:OFC_CoSMo2017.pdf | OFC slides]] 

[[Media:inverted_pendulum_LQGproblem.m | Inverted pendulum problem]] 
[[Media:kalman_lqg.m | LQG code]] 

=== Day 5 - optimality and model fitting ===

Konrad discussed if we can understand a micro-processor. This is published [http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005268 here]

''' BADS model fitting (afternoon) ''' 

[[Media:Acerbi-CoSMo2017.pdf | Luigi Acerbi's slides]] 
[https://github.com/lacerbi/cosmo-2017-tutorial Tutorial files]

''' Model evaluation discussion ''' 

[[Media:Model_evaluation_CoSMo2017.pdf | Model evaluation slides]] also containing the brainstorming outcome

== The Bayesian Brain ==
''Aug 5'' 
Lecturer: Jan Drugowitsch

[[Media:Drugowitsch_cosmo2017-perceptual_decisions.pdf | Jan's slides]] 
[https://github.com/DrugowitschLab/CoSMo2017 Jan's tutorial material] 

== Motor control & learning ==
''Aug 7-8'' 
Lecturers: Alaa Ahmed and Reza Shadmehr 

''' Morning Lectures '''

''' Afternoon Problems and Lecture slides '''

[https://www.dropbox.com/sh/uhe0bbgkyohlhx5/AABO9rIeIXlt-Q8JjpM4OwuUa?dl=0 SLIDES AND PROBLEMS] 

== From basic insights to clinical applications ==
"Aug 9-10" 
Lecturer: Dagmar Sternad 

[https://drive.google.com/a/husky.neu.edu/file/d/0B8XrhP_fMLgETmloWW50NWRxZzA/view?usp=drive_web DAY 1 MATERIALS] 
[https://drive.google.com/drive/folders/0B8XrhP_fMLgEY2xUaDdDQWl6clE DAY 2 MATERIALS] 

== DREAM database - Shared data and models for CoSMo projects ==
''Jul 31 - Aug 13'' 
Curtesy: Konrad Kording 

You can get the DREAM project from Gunnar on a USB drive. 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.

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] 

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

Here's the latest version of [[Media:LoadDreamPaths.m | LoadDreamPaths.m]]. (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).
*[[Media:Burns_2010.pdf | Burns]] -- reaching with head tilt and left/right visual perturbations 
*[[Media:Corbett_2013.pdf | Corbett]] -- reach trajectory predictions based on EMG and gaze movements 
*[[Media:Fernandes_2012_e1_published.pdf | Fernandes]] -- reaching with uncertain and rotated midpoint feedback 
*[[Media:Flint_2012.pdf | Flint]] -- decoding of reaching movements from local field potentials 
*[[Media:Kording_2004.pdf | Kording]] -- reaching with uncertain midpoint feedback 
*[[Media:Mattar_and_Ostry_2007.pdf | Mattar 07]] -- generalizing from one, two or multi targets to another direction 
*[[Media:Mattar_and_Ostry.pdf | Mattar 10]] -- reaching to a distance (short/long), generalizing to the other one (long/short) 
*[[Media:Somatosensory_Plasticity_and_Motor_Learning.pdf | Ostry]] -- move in force field, get an estimation of where the hand is 
*[[Media:Scott_2001.pdf | Scott]] -- monkey (no spike), center out: even and not evenly distributed targets, also a forward/back 
*[[Media:Stevenson2011.pdf | Stevenson]] -- center out, monkey with neural time stamps 
*[[Media:Thoroughman_2005.pdf | Thoroughman]] -- reach adaptation to perturbations with different complexity 
*[[Media:Vahdat_2011.pdf | Vahdat]] -- movement in force field with FMRI scans pre/post learning 
*[[Media:Wei_Relevance_Error_Motor_Adapt_2008.pdf | Wei 08]] -- visual perturbations, cursor shown only at target 
*[[Media:Wei_2010.pdf | Wei 10]] -- movement in differing force fields 
*[[Media:Young_2009.pdf | Young]] -- movement time stayed the same, but distance changed; fast, medium, slow reaches. 

== Group projects ==
''Jul 31 - Aug 12'' 

[https://docs.google.com/document/d/1uSXjGmlbal8-Y3qmbntZYRA9in3Re2bCTWcA19c00yI/edit?usp=sharing Here] are some ideas for 2-week project topics. 

[[Media:HowtoMode_CoSMo2017.pdf | How to model tutorial slides]] 

[[Media:GroupProjectPresentationTemplate2017.pptx | Group project presentation template]] 

'''Instructions:''' Every group will have a 30min slot (20min presentation, 10min questions). The research question, hypotheses and rationale for the choice of the approach should be clearly presented. Models, simulations, results, discussion etc should be detailed enough for everyone to follow. 

'''Best group gets a free short talk at Advances in Motor Control and Motor Learning 2017 (SfN satellite workshop)!!!''' (confirmed by John Krakauer) 
Here is a link to the SfN [https://www.sfn.org/annual-meeting/neuroscience-2017/sessions-and-events/satellite-events satellite events] - submission deadline Sept 15 !!! The winner has to apply too and specify you are CoSMo 2017 project winner... 

'''PROJECT PRESENTATIONS (Sat, Aug 12)''' 

''12:30-1pm - Kalman Kong and four Monkeys'' 
"Does uncertainty in visual and proprioceptive hand estimates determine the degree of sensory recalibration?" 
Group: Eugene Poh, Gaiqing Kong, Jianfei Guo, Pierre Petitet, Zhaoran Zhang 

''1-1:30pm - Buzzfeed LAMAS'' 
"You won't BELIEVE how S1 spiking activity encodes sensory feedback for goal directed movements in a grasping task!" 
Group: Liza Okorokova, Alex Kaiser, Monica Liu, Spencer Arbuckle, Angelica Herrera

''1:30-2pm - The Acronym'' 
"Influence of task difficulty history on the adaptation rate in a motion prediction task" 
Group: Chloe, Moji, Ben, Jonny and Corson 

''2-2:30pm - Too Bayesic'' 
"Copy-mechanism explains transfer in visual perceptual learning" 
Group: Suraj Chakravarthi Raja, Pedro Cisneros-Velarde, Wanying Jiang, Katrin Sutter 

''2:30-3pm - Cucumber Nation'' 
"Modelling savings using a probabilistic estimate of the environment" 
Group: Kevin Day, Hyosub Kim, Rory Flemming, Agustin Solano, Jing Huang

''3-3:30pm - The encoders'' 
"Bayesian Decision Making in Biological Motion" 
Group: Anakani Chattoraj, Deepak Gopinath, Khashayar Misaghian, Albert Buchard, Santiago Alonso-Diaz 

''3:30-4pm - Where-The-Fovea? (WTF)'' 
"Do natural scenes influence the development of the preferred retinal location with foveal scotoma?" 
Group: Yangzi, Rakesh, Ali, Charlotte, & Immo 

''4-4:30pm - Eurovision'' 
"Can people make optimal decisions when both visual evidence and reward vary over time?" 
Group: Ioanna Polyzou, Baptiste Caziot, Jozsef Arató, David Aguilar-Lleyda 

''4:30-5pm - Team Locomotion'' 
"Predicting optimal gaze direction as a function of running speed when running on targets" 
Group: Nidhi Seethapathi, Tzu-Hsiang Lin, Yashar Aucie