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General Information | Resources | Reading List | Weekly Schedule | Lecture Notes | Course Material |
I. General Information |
Dr. Yoonsuck Choe
Email: choe(a)tamu.edu
Office: HRBB 322B
Phone: 845-5466
Office hours: M 10:30am-11:30am, WF 4-5pm
CPSC 420, 625, 636, or 633 (or equivalent) and graduate classification; or consent of instructor.
MWF 3-3:50pm, HRBB 126
From the course catalog: The architecture of the mammalian cerebral cortex; its modular organization and its network for distributed and parallel processing; cortical networks in perception and memory; neuronal microstructure and dynamical simulation of cortical networks; the cortical network as a proven paradigm for the design of cognitive machines.About this semester: This course will provide necessary background for modeling the structure (anatomy), function (physiology), and growth (development) of neurons, neuronal circuits, and neuronal networks. Various computational concepts, techniques, and tools necessary for modeling neural systems will be introduced. A selected set of latest papers in the field of computational neuroscience and neuroinformatics will be surveyed.
See the Weekly Schedule section for more details.
Grading will be on the absolute scale. The cutoff for an `A' will be at most 90% of total score, 80% for a `B', 70% for a `C', and 60% for a `D'. However, these cutoffs might be lowered at the end of the semester to accomodate the actual distribution of grades.
AGGIE HONOR CODE: An Aggie does not lie, cheat, or steal or tolerate those who do.Upon accepting admission to Texas A&M University, a student immediately assumes a commitment to uphold the Honor Code, to accept responsibility for learning, and to follow the philosophy and rules of the Honor System. Students will be required to state their commitment on examinations, research papers, and other academic work. Ignorance of the rules does not exclude any member of the TAMU community from the requirements or the processes of the Honor System.
For additional information please visit: http://www.tamu.edu/aggiehonor/
Local Course Policy:
- Collaboration is allowed, but final submitted material should be in your own words.
The Americans with Disabilities Act (ADA) is a federal anti-discrimination statute that provides comprehensive civil rights protection for persons with disabilities. Among other things, this legislation requires that all students with disabilities be guaranteed a learning environment that provides for reasonable accommodation of their disabilities. If you believe you have a disability requiring an accommodation, please contact the Department of Student Life, Services for Students with Disabilities, in Cain Hall or call 845-1637.
III. Weekly Schedule and Class Notes |
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1 | 8/27 | Introduction | Course overview | slide01
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1 | 8/29 | Introduction | Essential terminology and neuroanatomy | slide02
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1 | 8/31 | Neuron: Physiology | Shepherd: Chapter 2 | slide03
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2 | 9/3 | Neuron: Computational models | Dayan and Abbott: Chapter 5, Appendix A.4 | slide04
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2 | 9/5 | Neuron: Computational models | Dayan and Abbott: Chapter 5, Appendix A.4 | slide05
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2 | 9/7 | Neuron: Computational models | Dayan and Abbott: Chapter 5, Appendix A.4 | slide05
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3 | 9/10 | Thalamus | Shepherd: Chapter 8 | slide06 slide07 |
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3 | 9/12 | Thalamus Model | Choe (2004) [PDF] | slide08
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3 | 9/14 | Thalamus Model | Choe (2004) [PDF] | slide08
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4 | 9/17 | Neuron: Plasticity | Dayan and Abbott: Chapter 8 | slide09
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4 | 9/19 | Neuron: Plasticity | Dayan and Abbott: Chapter 8 | slide09
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4 | 9/21 | No class | View this TED talk Sebastian Seung, on Connectomics | |||
5 | 9/24 | Neural Encoding | Dayan and Abbott: Chapter 1 | slide10
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5 | 9/26 | Visual System: Computation | Miikkulainen et al. [eBook]: Chapter 1,2,3 | slide11
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5 | 9/28 | Visual System: Development | Miikkulainen et al.: Chapters 4 and 5 | slide11
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6 | 10/1 | Visual System: Development | Miikkulainen et al.: Chapters 4 and 5 | slide11
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6 | 10/3 | Visual cortical response power law and perceptual salience | Choe and Sarma (2006) [PDF] | slide12
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6 | 10/5 | Neocortex | Shepherd: Chapter 12; Douglas and Martin (2004) [PDF] | slide13
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7 | 10/8 | Basal Ganglia | Shepherd: Chapter 9 | Homework 1 due 11:59pm | slide14
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7 | 10/10 | Motor System: Decoding Internal State | Choe and Smith (2006) [PDF], Choe (2011) | slide15
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7 | 10/12 | Motor System: Decoding Internal State | Choe and Smith (2006) [PDF], Choe et al. (2008), Choe (2011) | slide15
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8 | 10/15 | Online guest lectures | See this TED Talk Daniel Wolpert: The real reason for brains, and this one VS Ramachandran: 3 clues to understanding your brain | |||
8 | 10/17 | Online guest lecture | See this TED Talk Jeff Hawkins: How brain science will change computing | |||
8 | 10/19 | Texture: Tactile or visual ? | Bai et al. (2008), Park et al. (2009) | slide16
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9 | 10/22 | Texture: Tactile or visual ? | Bai et al. (2008), Park et al. (2009) | slide16
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9 | 10/24 | Emergence of memory | Chung and Choe (2011) | slide17
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9 | 10/26 | Predictive dynamics | Kwon and Choe (2008) | slide17
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10 | 10/29 | Computational Tools Showcase | Topographica, xppaut, octave, SIDA, neuroevolution | slide16-suppl
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10 | 10/31 | Delay Compensation | Lim and Choe (2006) [PDF] | slide18
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10 | 11/2 | Natural Images: Statistical Structure | Xiuwen Liu and DeLiang Wang (2002) [PDF] | slide19
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11 | 11/5 | Neuron Morphology | De Schutter: Chapter 6 and 7 | slide20
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11 | 11/7 | Neuron Morphology | De Schutter: Chapter 6 and 7 | slide20
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11 | 11/9 | Neuron Morphology: Statistical Description; Neuroinformatics | Ascoli et al. (2001) [PDF]; Chung et al. (2011) | slide21 slide22 |
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12 | 11/12 | Network Analysis: Complexity | Sporns and Tononi (2002) [PDF]; Sporns et al. (2004) [PDF] | slide23
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12 | 11/14 | Network Analysis: Shortest Path | Kaiser and Hilgetag (2006) [PDF] | slide24
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12 | 11/16 | Network Analysis: Dynamics | Thiel et al. (2003) [PDF] | slide25
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13 | 11/19 | Behavioral constraints affecting sensory representations | Salinas (2006) | slide26
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13 | 11/21 | Systems Neuroscience | Van Hemmen and Sejnowski: Chapters 1, 13, and 19 | slide27
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13 | 11/23 | No Class (Thanksgiving) | ||||
14 | 11/26 | Neuroevolution for computational neuroscience | Stanley and Miikkulainen (2002); Ruppin (2002); Floreano et al. (2005) | slide28
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14 | 11/28 | Neuroevolution for computational neuroscience, Course wrap-up | Stanley and Miikkulainen (2002); Ruppin (2002); Floreano et al. (2005) | slide28 slide29 |
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14 | 11/30 | Project Presentation | ||||
15 | 12/3 | Project Presentation |