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Please bring a laptop to every class session. If this is a problem, talk to Prof. Nelson.

Week 1: introduction; evolution of intelligence

Tue, Jan 17

Topics: intro to the course; emergence of life; evolution of intelligence; intro to p5js/Processing.
Readings: Hawking S (1994) Life in the Universe
Timeline of evolutionary history of life (focus on Hadeon and Archean Eons for this week)
Slides: PowerPoint 1
Videos: Hello p5js (~5 minutes)
Dan Shiffman, Intro I.0 The Nature of Code (23:46)
Dan Shiffman, p5.js - 1.0 Intro: What is it? (12:05)
Dan Shiffman, p5.js - 1.1 Basics of Drawing (15:11)
Dan Shiffman, p5.js - 1.2 Color (15:18)

Thu, Jan 19

Topics: hands-on p5js/Processing tutorial; random numbers, random walks, random noise.
Readings: Shiffman D (2012) Introduction, The Nature of Code, Sections I.1-I.5
Videos: Shiffman, Intro I.1 Random Walker (9:26)
Dan Shiffman, p5.js - 2.3 Javascript Objects (9:23)
Dan Shiffman, p5.js - 6.1 What is an array? (13:49)
Dan Shiffman, p5.js - 6.2 Arrays and loops (8:09)
Dan Shiffman, p5.js - 6.3 Arrays of objects (12:41)
Dan Shiffman, p5.js - 6.4 The Constructor function (12:39)
Code: Nature of Code, Introduction
Week 2: Modeling organisms as physical objects; object-oriented programming

Tue, Jan 24

Topics: p5js tutorial, objects, arrays
Readings: Shiffman D (2012) Introduction, Sections I.6-I.7
Shiffman D (2012) Chapter 1. Vectors, Sections 1.1-1.6
Videos: Shiffman, Intro I.5 Perlin Noise (13:43)
FYI: TED talk: Martin Hanczyc, The line between life and not-life
NEWS: No signs of alien life? Maybe they're all extinct.
Chopra and Lineweaver (2016) The Case for a Gaian Bottleneck: The Biology of Habitability.

Thu, Jan 26

Topics: week03 homework assignment, simple foraging example
Readings: none
Videos: none
Homework: week03_hw_template (foraging efficiency vs. noise)
(due Tu Jan 31, 9:00 PM)
Week 3: behavior without a nervous system, bacterial chemotaxis

Tue, Jan 31

Topics: Topics: single-cell intelligence; kinesis and taxis
Slides: PowerPoint 3
Readings: Dusenbery DB (1996) Life at Small Scale. Scientific American Library. Chapter 1, Invisible Organisms, pp 2-17 (16 pp). microbes, food chains, hunting vs farming
Zupanc GKH (2004) Behavioral Neurobiology: An Integrative Approach. Oxford Press. 80-88 (9 pp) classification of orienting movements; orienting behavior without a nervous system
Videos: none
Homework: Week 03 homework due by 9:00 PM (foraging efficiency)

Thu, Feb 2

Topics: Topics: bacterial chemotaxis; run-tumble behavior
Slides: PowerPoint 4
Readings: Jurica MS, Stoddard BL (1998) Mind your Bs and Rs: Bacterial Chemotaxis, signal transduction, and protein recognition" Structure 6:809-813 (5 pp) bacterial chemotaxis, coupling sensors to effectors
Videos: Biochemical signalling network in bacterial chemotaxis
Sample code: estimating pi
Homework: week04_hw_template (kinesis strategies)
(due Tu Feb 7, 9:00 PM)
Week 4: sensory information processing

Tue, Feb 7

Topics: obstacle avoidance in paramecia; electrical signaling; emergence of multicellular organisms; Braitenberg vehicles;
Slides: PowerPoint 5
Readings: Braitenberg V (1984) Vehicles: Experiments in Synthetic Psychology. MIT Press. pp. 1-14 (14 pp) Braitenberg Vehicles
Videos: Paramecium caudatum
Homework: Week 04 homework due today by 9:00 PM (kinesis strategies)

Thu, Feb 9

Topics: Dusenbery: What is information?;
Cariani: Information relationships (syntactic, semantic, pragmatic)
Slides: PowerPoint 6
Readings: Dusenbery DB (1996) Information is where you find it. Biol. Bull. 191:124-128 (5 pp) Information from a biological perspective; genome (evolutionary times), memory (lifetime), sensory (current state).
Cariani P. (1991) Some epistemological implications of devices which construct their own sensors and effectors. In: Varela F, Bourgine P eds. Towards a practice of autonomous systems. Cambridge, MA: MIT Press, 484-493 (10 pp) Information relationships (syntactic, semantic, pragmatic)
Videos: Braitenberg Vehicles
Quiz: Paper-based quiz (multiple-choice, true-false, short-answer) over movement strategies: kinesis, taxis, Braitenberg vehicles.
Homework: week05_hw_template (Braitenberg vehicles)
(due Tu Feb 14, 9:00 PM)
Week 5: natural selection, genetic algorithms

Tue, Feb 14

Topics: evolutionary computation, genetic algorithms
Readings: Shiffman, Chapter 9 - Evolution of Code, Sections 9.1-9.8
Videos: Shiffman, 9.1 Evolutionary Computing(20:00) (Watch FIRST 20 minutes)
Sample code: Nature of Code, GA Examples
GA_text demo
Homework: Week 05 homework due today by 9:00 PM (Braitenberg vehicles)

Thu, Feb 16

Topics: evolutionary computation, genetic algorithms
Readings: Shiffman, Chapter 9 - Evolution of Code, Sections 9.9-9.13
Videos: Shiffman, 9.1 Evolutionary Computing(20:00) (Watch LAST 20 minutes)
Homework: Week 06: GAs / evolving Braitenberg controllers (due Tu Feb 21, 9:00 PM)
Brait TESTING environment (you will report results, but not modify this code)
Brait EVOLVE environment (you will need to clone and modify this code)

Week 6: emergence of animals and nervous systems

Tue, Feb 21

Topics: emergence of animals and nervous systems, intro to C. elegans
Readings: Ferree TC, Lockery SR (1999) Computational rules for chemotaxis in the nematode C. elegans. J Comput Neurosci 6:263-277 (15 pp)
Videos: A brief introduction to C. elegans (2:11)
Slides: PowerPoint 7
Homework: Week 06 homework due by 9:00 PM (GAs / evolving Brait controllers)

Thu, Feb 23

Topics: area-restricted search in C. elegans, neuromodulation
Readings: Hills T, Brockie PJ, Maricq AV (2004) Dopamine and glutamate control area-restricted search behavior in Caenorhabditis elegans. J Neurosci 24:1217-1225 (9 pp)
Code: RC filters
Slides: PowerPoint 8
Homework: Week 07: Evolving worm chemotaxis controllers (due Tu Feb 28, 9:00 PM)
C. elegans TESTING environment
C. elegans EVOLVE environment
Week 7: Cambrian explosion, insect brains, vertebrate brains

Tue, Feb 28

Topics: Cambrian explosion, insect brains
Readings: Beer R, Chiel J, Sterling L (1991) An artificial insect. American Scientist, 79:444-452 (9 pp)
Videos: none
Slides: PowerPoint 09
Homework: Week 07 homework due by 9:00 PM (evolving worm controllers)

Thu, Mar 2

Topics: vertebrate brains, toad visuomotor behaviors, prey capture
Readings: Carew TJ (2000) Behavioral Neurobiology, Chapter 4, Feature Analysis in Toads. 95-119 (25 pp)
Videos: Neuroethology of Toads (Part 1: Behavior)
Neuroethology of Toads (Part 2: Neural Basis)
Slides: PowerPoint 10
Homework: week08_hw_template (action selection / FSM / ARS)
(due Tu Mar 7, 9:00 PM)
Week 8: spike-based models, vertebrate visuomotor circuits

Tue, Mar 7

Topics: threshold logic, integrate-and-fire models, lamprey model I
Readings: Braitenberg V (1984) Vehicles: Experiments in Synthetic Psychology. pp. 15-25 (11 pp)
Videos: Visually Guided Locomotion in Lamprey
Slides: PowerPoint 11
Demo: Demo: Braitenberg spiking model
Exercise: Threshold Logic_template (threshold-logic programming)
Homework: Week 08 homework due by 9:00 PM (action selection / FSM / ARS)

Thu, Mar 9

Topics: lamprey model continued, place-code to rate-code conversion
Readings: Kamali Sarvestani I, Kozlov A, Harischandra N, Grillner S, Ekeberg O (2012) A computational model of visually guided locomotion in lamprey. Biol. Cybern Nov 2012 (16 pp)
Videos: none
Slides: none
HW: week09_hw_template (lamprey place-code to rate-code conversion)
(due Tu Mar 14, 9:00 PM)
Week 9: Midterm Exam

Tue, Mar 14

Topics: Review session for midterm exam
Slides: Midterm Review
Homework: Week 09 homework due by 9:00 PM (lamprey place- to rate-code)

Thu, Mar 16

Midterm Exam

Enjoy your SPRING BREAK!
Week 10: Associative learning

Tue, Mar 28

Topics: learning and memory, honeybee foraging, proboscis extension reflex (PER)
Slides: PowerPoint 15
Readings: Carew TJ (2000) Behavioral Neurobiology, Chapter 9, Associative Learning in Honeybees. 271-300 (30 pp)

Thu, Mar 30

Topics: neural basis of PER, associative learning models, delta rule
Slides: PowerPoint 16
Readings: Montague PR, Dayan P, Person C, Sejnowski TJ (1995) Bee foraging in uncertain environments using predictive Hebbian learning. Nature 377:725-728 (4 pp)
Demo: Bee two-choice demo
HW: week11_hw_template (bee-inspired foraging)
(due Tu Apr 4, 9:00 PM)
Week 11: Spatial navigation, memory systems, reinforcement learning

Tue, Apr 4

Topics: spatial navigation, desert ants; intro to reinforcement learning
Slides: PowerPoint 17
Readings: Wehner R (2003) Desert ant navigation: how miniature brains solve complex tasks. J. Comp. Physiol. A 189: 579-588 (10 pp).

Thu, Apr 6

Topics: Memory systems; Reinforcement learning; SARSA algorithm
Slides: PowerPoint 19
Readings: (1) Squire LR (2004) Memory systems of the brain: A brief history and current perspective. Neurobiol Learn Mem 82:171-177 (7 pp.)
(2) Clayton NS, Bussey TJ, Dickinson A (2003) Can animals recall the past and plan for the future? Nat Rev Neurosci 4:685-691 (7 pp.)
Homework: week12_hw_template (Q-learning, grid world)
(due Tu Apr 11, 9:00 PM)
Week 12: Neural Networks, Q-learning with neural nets

Tue, Apr 11

Topics: Neural networks, supervised learning, classification, regression
Readings: Hacker's guide to Neural Networks
Slides: PowerPoint 20
Demos: ConvNetJS

Thu, Apr 13

Topics: Q-learning with neural nets
Readings: Mnih V, et al. (2015) Human Level Control Through Deep Reinforcement Learning. Nature 518, 539-533.
Video: Inside DeepMind
Demos: ConvNetJS: Deep Q Learning Demo
Homework: week13_hw_template (Q-learning with neural nets)
(due Tu Apr 18, 9:00 PM)

Week 13: Communication between agents, Final project overview

Tue, Apr 18

Topics: Agent communication, ant pheromone trails, discussion of final projects
Slides: PowerPoint 21

Thu, Apr 20

Topics: Discussion and sign-off on project ideas.
Homework: project_proposal_template
(due Tu Apr 26, 9:00 PM)
Week 14: Final project work week

Tue, Apr 25

Office hours consulting for final project.
Click here to schedule

Project proposals due by 9:00 PM
(submit zip file to

Thu, Apr 27

Office hours consulting for final project.
Click here to schedule

Week 15: Final project presentations

Tue, May 02

Final project presentations and peer review.
Final project submission due by 9:00 PM
(submit zip file to

Thu, May 04

Reading Day - NO CLASS

Mark E. Nelson, University of Illinois at Urbana-Champaign, 2005-2016.