Computational Methods in Interdisciplinary Science
Welcome & Introduction
Kia ora koutou!
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Senior Lecturer
School of Computer Science
Room 303.491
email: phone: 09 923 7027
internal extension: 87027
website: www.matthewegbert.com
Open office hours, but better to email first.
My professional trajectory
Undergraduate in Computer Science at the University of St Andrews.
Software Engineer
Web Developer
Desire to return to academia to re-train
Remembered Karl Sims’ Evolved Virtual Creatures
KarlSims:EvolvedVirtualCreatures (1994) https://www.youtube.com/watch?v=JBgG_VSP7f8&feature=youtu.be
My research…
Evolutionary Robotics
Evolutionary Robotics
Evolving controllers for robots to understand biology.
What kinds of systems does evolution make?
How are they different from the systems that human engineers create?
sensory input
sensor input
motor output
motor output
lagged recurrent connection
Unconventional Computing
Transforming chemistry into computational machinery
Biologically inspired AI
AI research has been hugely successful at producing more and more impressive problem solving devices.
Nevertheless, AI remains very different from natural (i.e. biological) forms of intelligence.
– intrinsic goals (as opposed to goals given by a designer)
– experience (consciousness)
– meaning and value
How can we bridge that gap?
Artificial Life
Simulating life-like systems to explore life “as it could be” so as to understand life as it really is.
Interdisciplinary
– computer models
– philosophy
(what is life? what are minds?)
– chemistry
– mathematics
Course Structure
David Overview of Computational Biology Dynamical Systems Modelling
String-matching algorithms in genome analysis and assembly; Stochastic Processes; Hidden Markov Models; Bayesian Phylogenetics
If you have questions about material taught by me, ask me! Other questions (course structure, etc.) should go to David as he is the course coordinator.
All the information you need is on canvas. Look there for the latest and most accurate information.
Note the links at the top of the home page.
Each week…
We will meet three times per week for face-to-face learning sessions (lectures). In addition you will have one lab each week.
No lab in Week 1. Instead you are to read…
Reading Assignment: Read Part I “Preliminaries” of Introduction to the Modeling and Analysis of Complex Systems by H. Sayama (pps. 1–26)
On the ‘modules’ page, I have added a link to this free text book, which we use in my portion of the paper.
Wednesday 9-10 Thursdays 9-10 Fridays 10-11
Thursdays 2-3 Fridays 2-3
Assessment
Breakdown:
– assignments 30% (4 assignments @ 7.5% each)
– written midterm test 10%
– written final examination 60%
This course has separate theory and practical pass requirement, i.e., you will need to pass both the theory (test+exam) and the practical (assignments) individually.
We use the standard university grade boundaries. >89.5 for A+, then 5 mark increments down to >49.5 for C-.
Assignments
These are essentially exercises to give you a chance to practice what you have learned.
The first will involve building a basic simulation of ecological homeostasis (how populations of living systems can stabilize their environment) and investigating its dynamics.
This is a simplification of a model that is being used in current scientific debate concerning ways that ecological systems might regulate themselves.
FYI: Some of the assignments and labs will use jupyter notebooks.
https://jupyter.org/
This will take place online on Wed, 13 Apr 2022 (Week 7)
Material covered on the test may also be on the exam, but it will be less heavily emphasized there
A mixture of all content from the course, with later materials emphasized a bit more.
Mostly short-answer questions.
Academic Integrity
The University of Auckland will not tolerate cheating or the assisting others to cheat, and views cheating in coursework as a serious academic offence. The work that a student submits for grading must be the student’s own work, reflecting his or her learning. Where work from other sources is used, it must be properly acknowledged and referenced. This requirement also applies to sources on the world-wide web. A student’s assessed work may be reviewed against electronic source material using computerised detection mechanisms. Upon reasonable request, students may be required to provide an electronic version of their work for computerised review.
Please refer to
http://www.auckland.ac.nz/uoa/home/about/teaching-learning/honesty
Also this document outlines the School of Computer Science’s philosophy of learning and teaching and our expectations for student engagement https://docs.google.com/document/d/1vT5_czzIj4jZ96Uds7Ytq1yAav0zS83VP z2fSYLU7Sc/edit?usp=sharing
(links are in the Modules section of canvas)
What does it mean to be a class rep?
VIDEO: http://www.ausa.org.nz/wp-content/uploads/2019/07/AUSA-CLASS-REPS-AD.mp4
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