Focuses on fundamental neural network architectures, circuits, and algorithms inspired by the primate brain. An emphasis will be placed on how humans learn as autonomous systems, while perceiving and interacting with their surroundings. Each week will address the modeling of different capabilities, such as sequence learning, motion perception, working memory, movement, self-motion and navigation, and boundary and surface perception. Students will implement and explore different neural systems through a progression of projects. The semester culminates with a presentation of a team project focused on simulation experiments of a neural system of the team’s choice.

Semester Spring 2020
Credits 4
Times & Locations

TR 11:00 - 12:15 pm, Davis 117

Instructor Oliver W. Layton
Office: Davis 115
Office hours:
M 11:00am - 12:00pm, 3:00pm - 5:00pm
R 2:00pm - 5:00pm
Course Goals
  1. Students understand, can implement, and appreciate the appropriate modeling context of different neural network architectures.
  2. Students understand how data collected from humans and primates inform us about human perception and fundamental mechanisms in vision and other systems of the brain.
  3. Students develop their systems model of motion processing and work in a team to design a model of another brain system or perceptual capability.
  4. Students present methods, algorithms, results, and designs in an organized and competently written manner.
  5. Students write, organize and manage a large software project.

There will be regular opportunities for you to practice what you have learned and to demonstrate your accomplishments.

The course grade will be determined as follows:

Projects 50% Hands-on opportunities to implement and explore concepts from lecture.
Assigned on average every 2 weeks, with weekly turn-in deadlines.
Students work in teams.
Quizzes 10% Short weekly in-class quizzes (given most Thursdays)
Classroom Participation 10% I expect you to be an active contributor in the classroom.
Team Participation 15% Peer assessment from group members on your collaboration and balanced contributions.
Final presentation 15% Thursday April 30 in Parker-Reid 12:30 - 2:00pm.
Group poster presentation at CLAS.

Students work in teams of 2.

Projects are assigned in class on Thursdays. There are two types of deadlines:

  • Draft submissions: Progress made on designated project tasks (ungraded).
    • Honest attempt is required to ultimately earn at least 26/30 on the final submission.
    • Absent draft submissions will result in a maximum score of 24/30.
  • Final submissions: Updated version of draft submission and remaining project tasks. Graded as follows:
    • 26/30: All tasks completed.
    • 27+: All tasks completed along with creative explorations beyond the scope of core tasks (extensions).
    • All the above scenarios assume honest attempt was made at the draft submission and the provided test code runs and returns the expected results.

Between draft and final submissions, code is turned in weekly.

The weekly deadline is Thursday at 11:59pm.

The draft and final submission schedule depends on the project length:

  • 1 week project: Graded submission only.
  • 2 week project: Draft submission due one week after project assigned, graded submission due the next week.
  • 3 week project: Draft submissions due weekly during the first two weeks, graded submission due on the third week.

Draft and final submissions should be placed in one of the team member's folder on Courses filer.

  • Place your draft submissions in User/Private/Project0X/DraftY, where X and Y are integers. Example: owlayton/Private/Project02/Draft1
  • Place your final submissions in Private/Project0X/Final.
Project Late Policy

Projects are an important part of the learning experience in this course. I do not want you to get behind with the project workload. To encourage this, projects later than 1 week past the due date will not be accepted.

Late projects will not be eligible for extension credit and will be capped at a maximum of 24/30.

Please contact me immediately in the event of illness and other unforeseen circumstances, we will work out accommodations.

Weekly quizzes

There will be a 10 minute quiz most Thursdays. The quizzes let you show me what you have learned. These should be quick and straightforward if you participate in lecture and review lecture notes.

I understand that everyone has a bad day; the quiz with the lowest grade will be dropped

Each quiz may be made up when a prior request is made or there is a documented health issue.

Please contact me immediately in the event of illness and other unforeseen circumstances, we will work out accommodations.

Class Participation You are expected to attend every class. If you must miss a class for any reason, I expect you to notify me in advance ASAP. For this course to be truly successful, your presence and participation is important. When you have a question, ask it. It is highly probable that one of your classmates has the same question.
Team Participation

Group work is an important component of the learning experience in this course. You and your team members should feel empowered to contribute with your maximum potential and creativity so that everyone can learn effectively. This requires open communication and respect for each other's contributions and time. To encourage everyone to reflect on this throughout the course, each team member will fill out a short form to evaluate the team experience when you submit each project. I understand that your workload outside of this course fluctuates during some weeks of the semester. The key is open communication and accountability with your team so that the workload can be distributed equitably and fairly. I expect you to reach out to your team members and me if this is not the case.

Final Presentation

Your team will give a poster presentation at CLAS. There are a few options for the topic:

  1. Develop one of your projects further.
  2. Run additional simulation experiments with one of the systems that you implement in the projects.
  3. Develop and/or implement a system related to or inspired by one of the systems in the projects.

A crucial component of presentation grade will be on developing your poster, explaining your neural system, and communicating the significance/motivation of your project to non-expects in a clear, cogent manner. Your friends who have not taken CS343/CS443 (or are not CS majors) should be able to understand the general arc of your project.


It should go without saying that you should back up any files related to this course. If the code you submit to us is somehow lost (through your fault or our fault), I must be able to get another copy from you. I suggest you use at least the college's personal server ( and one other cloud-based storage service (e.g. Google Drive) to store your work in this class.

Team Collaboration

Here are the expectations for collaboration in a team-based environment:

  • You are free to share, exchange, and jointly write code, solve problems, and answer project questions within your team.
  • You may discuss problems and solutions with other teams, but you must NOT see, share, or exchange code or responses to written project questions.
Academic Honesty

Computer science, both academically and professionally, is a collaborative discipline. In any collaboration, however, all parties are expected to make their own contributions and to generously credit the contributions of others. In our class, therefore, collaboration on assignments is encouraged, but you as an individual are responsible for understanding all the material in the assignment and doing your own work. Always strive to do your best, give generous credit to others, start early, and seek help early from both your professors and classmates.

The following rules are intended to help you get the most out of your education and to clarify the line between honest and dishonest work. We reserve the right to ask you to verbally explain the reasoning behind any answer or code that you turn in and to modify your project grade based on your answers. It is vitally important that you turn in work that is your own. We do use automated plagiarism detection software, so please be sure to abide by these, rather minimal, rules. Reports of academic dishonesty are handled by an academic review board and a finding of academic dishonesty may result in significant sanctions. For more details on Colby's Academic Integrity policies and procedures, see

  • If you have had a substantive discussion of any homework or programming solution with a classmate, then be sure to cite them in your write-up. If you are unsure of what constitutes "substantive", then ask me or err on the side of caution. As one rule of thumb, you may discuss your approach to solving a problem, but you must not share or look at another classmate's code or written answers to project questions.
  • You must not copy answers or code from another student either by hand or electronically. Another way to think about it is that you should communicate with one another in natural human sentences, not in lines of code from a programming language.
The Colby Affirmation

Colby College is a community dedicated to learning and committed to the growth and well-being of all its members.

As a community devoted to intellectual growth, we value academic integrity. We agree to take ownership of our academic work, to submit only work that is our own, to fully acknowledge the research and ideas of others in our work, and to abide by the instructions and regulations governing academic work established by the faculty.

As a community built on respect for ourselves, each other, and our physical environment, we recognize the diversity of people who have gathered here and that genuine inclusivity requires active, honest, and compassionate engagement with one another. We agree to respect each other, to honor community expectations, and to comply with College policies.

As a member of this community, I pledge to hold myself and others accountable to these values. More ...

Academic Accommodations

I am available to discuss academic accommodations that any student with a documented disability may require. Please note that you’ll need to provide a letter from the Dean of Studies Office documenting your approved accommodations. Please meet with me to make a request for accommodations at the beginning of the semester--and at a minimum two weeks before any key due dates--so that we can work together with the College to make the appropriate arrangements for you.

Title IX Statement

Colby College prohibits and will not tolerate sexual misconduct or gender-based discrimination of any kind. Colby is legally obligated to investigate sexual misconduct (including, but not limited to, sexual assault and sexual harassment) and other specific forms of behavior that violate federal and state laws (Title IX and Title VII, and the Maine Human Rights Act). Such behavior also requires the College to fulfill certain obligations under two other federal laws, the Violence Against Women Act (VAWA) and the Jeanne Clery Disclosure of Campus Security Policy and Campus Statistics Act (Clery Act).

To learn more about what constitutes sexual misconduct or to report an incident, see:

If you wish to speak confidentially about an incident of sexual misconduct, you may contact:

  • Counseling Center: 207-859-4490
  • Gender and Sexual Diversity Program: Director Emily Schusterbauer ( 207-859-4093)
  • Office of Religious & Spiritual Life: 207-859-4272
    • Dean of Religious & Spiritual Life, Kurt Nelson (
    • Jewish Chaplain, Erica Asch (
    • Catholic Campus Minister, Charles Demm (

Students should be aware that faculty members are considered "responsible employees"; as such, if you disclose an incident of sexual misconduct to a faculty member, they have an obligation to report it to Colby's Title IX Coordinator. "Disclosure" may include communication in-person, via email/phone/text, or through class assignments.

© 2019 Oliver Layton