Controlling behavior in animals and robots
BIOENG-456
Media
Week6-Lecture-Navigation-Path-Integration
23.02.2023, 16:52
Week6-Lecture-Navigation-Path-Integration
23.02.2023, 16:52
Week6-Lecture-Navigation-Path-Integration
23.02.2023, 16:52
Week6-Lecture-Navigation-Path-Integration
23.02.2023, 16:52
Week6-Lecture-Navigation-Path-Integration
23.02.2023, 16:52
Week6-Lecture-Navigation-Path-Integration
23.02.2023, 16:52
This file is part of the content downloaded from Controlling behavior in animals and robots.
General Information
Controlling behavior in animals and robots
Teacher: Prof. Pavan Ramdya
https://www.epfl.ch/labs/ramdya-lab/pavan.ramdya@epfl.ch
Teaching assistants: Thomas Ka Chung Lam, Dominic Dall'Osto, Victor Alfred Stimpfling
When and Where
Tuesdays 13:15 - 18:00, in Room MED 2 2423
Students will acquire an integrative view on embodied behavioral control by focusing on the fruit fly, Drosophila melanogaster.
Students will synthesize and apply this knowledge through:
- (i) group Presentations and guided discussion of primary neuroscience literature
- (ii) guided computational simulation (Python) Exercises designed to test and consolidate knowledge
- (iii) a group Mini-Project intended to lead the students through the process of hands-on problem solving.
Course Format and Grading
Weekly computational modeling Exercises
will be performed independently.
Journal article Presentations and the Mini-Project will be carried out in small groups of 2-3 students.
A mid-term exam will be taken independently.
Exercises and the mini-project will require coding in Python on your own laptop. Some coding expertise is required.
Journal article Presentations and the Mini-Project will be carried out in small groups of 2-3 students.
A mid-term exam will be taken independently.
Exercises and the mini-project will require coding in Python on your own laptop. Some coding expertise is required.
Course grades are calculated from:
- Journal article Presentation (20%, group shares grade)
- Mid-term Exam (Week 7) on Week 1-6's Lectures, Required reading, and Exercises (40%, individual grade).
- Mini-project Report and Presentation (40%, group shares grade)
The Mini-project Report must be submitted by Friday, May 22, at 23h59.
The Mini-project Code must be submitted by Friday, May 22, at 23h59.
The Mini-project Code must be submitted by Friday, May 22, at 23h59.
The Mini-project Presentations will be presented on Tuesday, May 26, and slides should be submitted by 23h59 that night.
Organization and Timing
Each week for the first 6 weeks, you will have to:
Each week for the first 6 weeks, you will have to:
- Study introductory material (texts to read and videos to watch).
- (on Tuesday afternoons) Attend and participate in an interactive lecture, student group Journal Club presentations, and a computational modeling exercise session.
For weeks 8-14, you will work as a team to:
- (on Tuesday afternoons) The mini-project involves neuromechanical simulations of the fly (neuromechfly.org).
How to stay tuned
The 'Announcements Forum' is used by the teaching team to make announcements to the class. Only the teaching team will post in announcements.
The 'Announcements Forum' is used by the teaching team to make announcements to the class. Only the teaching team will post in announcements.
Contact and questions
Questions should be asked using the Moodle forums, the links are just below.
- Required: Programming experience (especially Python)
- Nice to have: Neuroscience II: cellular mechanisms of brain function (or the equivalent)
Week 1
Feb 17 - Introduction to the course
Course
Required reading (before class):
1. Insect-inspired AI for autonomous robots. [pdf]
2. The neuromechanics of animal locomotion: From biology to robotics and back [pdf]
="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">
="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">Note: Before the first class, please install Python and NeuroMechFly on your laptop using the following guide:="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr"> ="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">
https://github.com/NeLy-EPFL/cobar-exercises="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">Course
Required reading (before class):
1. Insect-inspired AI for autonomous robots. [pdf]
2. The neuromechanics of animal locomotion: From biology to robotics and back [pdf]
="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">
Exercise:
="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">
="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">
Learn FlyGym basics and explore kinematic replay (solutions)
="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">
- Week 1 slides (File)
- Paper presentation guidelines (File)
- How to read a paper (File)
- Paper presentation template (Keynote) (File)
- Paper presentation template (PowerPoint) (File)
Week 2
Feb 24 - Embodiment and motor control
="ltr">="ltr">
Course="ltr">="ltr">="ltr">="ltr">Required reading (before class):="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">
Exercise="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">:1. NeuroMechFly, a neuromechanical model of adult Drosophila melanogaster. [pdf]
2. NeuroMechFly v2: simulating embodied sensorimotor control in adult Drosophila. [pdf]
CPG controller for locomotion (solutions)
="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">
- Week 2 slides (File)
- Questions to consider - Week 2 (File)
- Questionnaire (Questionnaire)
- Student presentations (Folder)
Week 3
March 3 - Taxis toward an odor source
Course
Required reading (before class): ="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">
Required reading (before class): ="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">
Descending networks transform command signals into population motor control. [pdf]
2. Odour motion sensing enhances navigation of complex plumes. [pdf]="ltr">="ltr">="ltr">="ltr">
Exercise: Implement o="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">dor taxis with descending control of turning in NeuroMechFly.="ltr">="ltr">="ltr">="ltr">
2. Odour motion sensing enhances navigation of complex plumes. [pdf]="ltr">="ltr">="ltr">="ltr">
Exercise: Implement o="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">dor taxis with descending control of turning in NeuroMechFly.="ltr">="ltr">="ltr">="ltr">
- Turning controller (solutions)
- Odor-taxis (solutions)
Week 4
March 10 - Visual motion and tracking using neural networks
="ltr">
Course="ltr">="ltr">
Required reading (before class)="ltr">="ltr">
="ltr">="ltr">1. Connectome-constrained networks predict neural activity across the fly visual system [pdf]
2. Mapping model units to visual neurons reveals population code for social behaviour [pdf]
(2b. Optional News and Views of paper 2.: AI networks reveal how flies find a mate [pdf])
="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">
Exercise: Implement visual processing using artificial neural networks in NeuroMechFly.2. Mapping model units to visual neurons reveals population code for social behaviour [pdf]
(2b. Optional News and Views of paper 2.: AI networks reveal how flies find a mate [pdf])
="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">
- Vision basics (solutions)
- Neural network (solutions)
- Week 4 slides (File)
- Questions to consider - Week 4 (File)
- Quarter-semester Questionnaire (Questionnaire)
- Student presentations (Folder)
Week 5
Mating proximity blinds threat perceptionMarch 17 - Internal states and action selection
="ltr">
="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">
March 17 - Internal states and action selection
="ltr">
Course
Required reading (before class):
Required reading (before class):
1. Sexual arousal gates visual processing during Drosophila courtship [pdf]
2. Mating proximity blinds threat perception [pdf]
(2b. Optional News and Views articles about paper 2: [pdf1 , pdf2]
Head stabilization (solutions)
="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">
Week 6
March 24 - Path integration
Course
Required reading (before class):
1. Recorded lecture introduction to navigation and path integration
2. Seminar introducing Drosophila navigation circuits (from ~30 minutes - 50 minutes)
Required reading (before class):
1. Transforming representations of movement from body- to world-centric space. [pdf]
2. Transforming a head direction signal into a goal-oriented steering command. [pdf]
1. Recorded lecture introduction to navigation and path integration
2. Seminar introducing Drosophila navigation circuits (from ~30 minutes - 50 minutes)
Exercise: Implement path integration with feedback in NeuroMechFly.
="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">
1. Path integration (solution)="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">
- Week 6 slides (File)
- Questions to consider - Week 6 (File)
- Questionnaire: mini-project (Questionnaire)
- Course challenges questionnaire (Questionnaire)
- Student presentations (Folder)
Week 7
March 31 - Exam
13:15 - 17:00 - ="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">
Week 8
April 7 - Mini-project introduction
Short presentation of mini-project (Pr. and TAs)Discussion amongst group members to strategize approach
Miniproject repository: https://github.com/NeLy-EPFL/cobar-miniproject-2025/tree/main
Question spreadsheet: https://docs.google.com/spreadsheets/d/1wHoSIlYYBhN-fvrIGSlMGivsWuZLse4I7QxZd3NxRzo/edit?usp=sharing
Week 9
April 14 - Mini-project
13:15 - 18:00 - Open discussion for questions regarding the mini-projectWeek 10
April 28 - Mini-project
13:15 - 18:00 - Open discussion for questions regarding the mini-projectWeek 11
May 5 - Mini-project
13:15 - 18:00 - Open discussion for questions regarding the mini-projectWeek 12
May 12 - Mini-project - write report
="ltr">
13:15 - 18:00 - Open discussion for questions regarding mini-project data analysis & report writing
="ltr">
="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">
="ltr">
="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">
Week 13
May 19 - Mini-project - finalize report and prepare presentations
="ltr">
13:15 - 18:00 - Open discussion for questions regarding mini-project report and presentations
="ltr">
="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">="ltr">
Submit your mini-project report (*.pdf) and Github code link by 23:59 on Friday, May 22 (end of the week).
For the code submission:
- We prefer receiving the code through GitHub. If absolutely impossible please email all your code in a .zip file to the TAs and Pavan. If submitted through email please indicate: "Submitted through email" in the Moodle assignment.
- please title your code explicitly.
- We prefer receiving the code through GitHub. If absolutely impossible please email all your code in a .zip file to the TAs and Pavan. If submitted through email please indicate: "Submitted through email" in the Moodle assignment.
- please title your code explicitly.
Week 14
May 26 - Present mini-projects
="ltr">
13:15 - 18:00 - In-person mini-project presentations
="ltr">
="ltr">
="ltr">
Submit your mini-project presentation (*.pptx, *.key, or *.pdf) by 23:59 the day of class, May 26.
="ltr">="ltr">
="ltr">="ltr">
="ltr">
="ltr">