|Slides - Readings - Links|
Graduate Seminar, Spring 2003
Tuesdays and Thursdays,
Web Page: http://www.cs.virginia.edu/bio
- Reading for Thursday, 3 April: Towards Differential Program Analysis, Workshop on Dynamic Analysis. 9 May 2003.
- Reading for Tuesday, 8 April: A Phylogenetic, Ontogenetic, and Epigenetic View of Bio-Inspired Hardware Systems, Moshe Sipper, Eduardo Sanchez, Daniel Mange, Marco Tomassini, Andres P4erez-Uribe and Andre Stauffer.
Extra reading: Toward Robust Integrated Circuits: The Embryonics Approach, Daniel Mange, Moshe Sipper, Andri Stauffer and Gianluca Tempesti.
- Tuesday will be on Chapter 5 from:
- 25 Mar: The paper for Thursday is:
- 18 Mar: The paper for Thursday is:
For Tuesday, Ting will present Chapter 1 and Chapter 4 from:
- Jacob Beal, An Algorithm for Bootstrapping Communications, International Conference on Complex Systems (ICCS), June 2002
- 4 Mar: Cells inspire spacecraft: NASA seeks inspiration from under microscope, Nature, 27 Feb 2003.
- 1 Mar: Inventors tiny robots earn big prize
- 13 Feb: Music of the Swarms, Discover, March 2003.
- 4 Feb: Project Description
- 30 Jan: Scientific American: Evolving Inventions, John Koza, Martin Keane and Matthew Streeter (summary only, need to buy it for the whole article)
- 23 Jan: Slides on Genetic Algorithms
- Please submit a Registration Survey
- Class time will be Tuesdays and Thursdays at 11am, as originally scheduled.
- 21 Jan: Introduction, Cell-Based Programming (Selvin George)
- 23 Jan: Genetic Algorithms (Jim Cohoon)
- 28 Jan: Wolfram, Ch 1-3
- 30 Jan: Wolfram, Chapter 3 (Matthew Ziegler)
- 4 Feb: Implications for Everyday Systems (Wolfram, Ch 8) (Selvin George)
- 6 Feb: Randomness in Cellular Automata (Wolfram, Ch 10) (Nate Paul)
- 11 Feb: Project Ideas Due
- 11 Feb: Two Dimensions and Beyond (Wolfram, Ch 5) (Hridesh Rajan)
- 13 Feb: Fundamental Physics (or Wolfram vs. Einstein, Podolsky, Rosen, Bell, Schrödinger, Bohr, Heisenberg, Planck, Born, Minkowski, Schwarzschild, Misner, Thorne, Wheeler, ... (Wolfram, Ch 9) (Ben Hocking)
- 18 Feb: Computational Equivalenct (Wolfram, Ch 12) (Ting Yan)
- 20 Feb: Swarm Intelligence: Ant Routing (Rajat Tikoo)
- 25 Feb: Swarm Intelligence: Self Organization (Qing Cao)
- 27 Feb: Project Proposals Due; Short Project Proposal Presentations
- 11 March: Swarm Intelligence: Humans — Actual, Imagined and Implied (Hridesh Rajan)
- 13 March: Swarm Intelligence: Implications and Speculations (Hongtao Zhang)
- 18 March: Swarm Intelligence: Implications and Speculations, cont. (Hongtao Zhang)
- 20 March: Amorphous Computing: Communications (Jun Wang)
- 25 March: Amorphous Computing: Paintable Computer (Ting Yan)
- 27 March: Biologically-Inspired Neural Nets (Ben Hocking)
- 1 April: Paintable Computer, Chapter 5 (Applications) (Rajat Tikoo)
- 3 April: Differential Program Analysis (Joel Winstead). Paper: Towards Differential Program Analysis, Workshop on Dynamic Analysis. 9 May 2003.
- 8 April: Embryonics (Matthew Ziegler). Paper: A Phylogenetic, Ontogenetic, and Epigenetic View of Bio-Inspired Hardware Systems, Moshe Sipper, Eduardo Sanchez, Daniel Mange, Marco Tomassini, Andres P4erez-Uribe and Andre Stauffer. Extra reading: Toward Robust Integrated Circuits: The Embryonics Approach, Daniel Mange, Moshe Sipper, Andri Stauffer and Gianluca Tempesti.
- 10 April: Organizing a Global Coordinate System from Local Information on an Ad Hoc Sensor Network (Radhika Nagpal, Howard Shrobe and Jonathan Bachrach) and A Scalable Location Service for Geographic Ad Hoc Routing (Jinyang Li, John Jannotti, Douglas S. J. De Couto, David R. Karger, Robert Morris) (Qing Cao)
- 15 April: Presentations; Slides
- 17 April: No Class
- 22 April: Project Presentations: Ben Hocking, Jun Wang, Nathanael Paul, Selvin George
- 24 April: Project Presentations: Matt Ziegler, Ting Yan, Rajat Tikoo
- 29 April: Project Presentations: Julian Dymacek, Hongtao Zhang, Qing Cao
Biology has developed effective solutions to tough engineering challenges through millions of years of evolution. Computer scientists can learn a great deal by observing nature and adopting biological approaches to problem solving. Biological systems tend to be decentralized, adaptive and environmentally aware, and as a result they have survivability, scalability and flexibility properties well beyond the best human-engineered systems. This seminar will survey work in computing that has drawn inspiration from biology, with a focus on security, survivability and optimization.
- Cellular Automata
- Neural Networks
- Genetic Algorithms
- Computer Immunology
- Amorphous Computing
- Biological Fault Tolerance
- Self-organization, self-reconfiguring robots
- Viruses, Agents
- Swarm intelligence, Stigmergic Systems
The first part of the course will involve reading and discussing selected chapters from Stephen Wolfram's A New Kind of Science. Later readings will be selected from books and research papers based on student interests.
All students are expected to contribute to the seminar regularly and to present one or two topics in depth.
In addition, students will work individually or in teams on an open-ended related research project relevant to the course. A project proposal will be due on February 27. The best projects should turn into conference papers.
No prior biology knowledge is expected, although students may find it helpful to read some introductory biology materials.
University of Virginia
Department of Computer Science
CS 851: Biologically-Inspired Computing