John C. Doyle 道耀
New Course Spring 2017 CDS 270-1 Complex networks, architecture, and evolution
Org meeting and first class: 2:30 Tu Apr 4 213 ANN
For more details: See Course details for more
Aims: Complex tech, bio, neuro, med, eco, and socio-econ networks have both strikingly universal shared architectural features and constraining "laws" but with extremely different domain specific details. This course will use familiar case studies to motivate a new mathematical framework for understanding these similarities and differences, emphasizing layering, dynamics, optimization, nonlinearity, learning, communications, and control, sparsity and structure, and tradeoffs between robustness, efficiency, and evolvability. The aim will be to establish a common core of concepts accessible to anyone at Caltech, with optional additional domain and math details more aimed at experts. Lectures will primarily be by video with class time devoted to discussions. Lots of live demos and games involving audience participation.
Grading: P/F only
Units: from 3 to 9 units by arrangement and in accordance with effort (e.g. from 3 units for videos and discussions to 9 units adding reading and project) Ideally, projects would involve teams of domain experts with CDS and CMS theorists. Projects can lead to papers or add to video materials.
Motivating case studies and projects will be drawn from a variety of areas. Students with domain expertise can help form teams to explore using new theory in these areas. There will be videos and reading on these topics, but students are urged to suggest others.
Neuroscience: sensorimotor control, spiking neurons, and limits to performance; planning and reflex; modularity, plasticity, learning, and evolution; vision and the vestibular ocular reflex (VOR); balance and bipedalism; automation and (un)conscious; fMRI and EEG analysis; throwing and hitting a 100 mph fastball;
Internet: Software defined networking (SDN), Internet of things (IOT), Application driven networking (ADN), content centric, operating systems, Network function virtualization (NFV), routing, congestion control, end-to-end and local, protocol stacks, aggregation
Microbial cell: metabolism; glycolytic oscillations; stress response; signal transduction; gene regulation; evolution, horizontal gene transfer; immune mechanisms; pathogenesis; microbiomes; phage physiology;
Power: Future smartgrid; optimization, control; cascading outages; challenge of renewables; role of storage and controllable loads
Ecosystems: wildfire ecology; Mediterranean climates; fire in the earth system
Medicine and physiology: cardiovascular physiology, heart rate variability, (an)aerobic metabolism, fatigue, training; sepsis and shock; electrocardiographic diagnosis of acute myocardial infarction; development, wound healing, and cancer
Physics: multiscale and complexity; high shear flows, turbulence, coherent structures, blunting, and drag; statistical mechanics, fluctuation-dissipation, back action and measurement, uncertainty principles, quantum measurement; phase transitions, criticality, optimization;
Social sciences: behavorial economics, casinos, the hot hand fallacy (fallacy), (non)stationary stochastic process, and evolutionary psychology; risk and uncertainty; chimps, bonobos, baboons, and gorillas; orcas and elephants; ants and bees; violence; patriarchy and matriarchy; fear, anger, hatred; empathy, compassion; language; bipedalism and weapons; agriculture and owners, soldiers, and slaves; Egypt, Sparta, Athens, Rome, China; Adam Smith; American Civil War ; technology, industrialization, and automation; World wars and depressions; wealth inequality; the 60s (1860s and 1960s) and "rights"; financialization; tech and social networks; current politics and media; Putin, Trump, and Brexit; Article on animal social justice
Transitions in evolution, architecture, and complexity: e.g. life, metabolism, ribosomes, oxygen, mitochondria, brains, flight, warm blood, maternal care, bipedalism, weapons, language, agriculture, states, money, industry, technology, IOT, ...
Universal laws and architectures: across all domains there are hard limits or "laws" on robustness vs efficiency, speed vs accuracy, with efficiency and robustness conservation laws that limit what is possible; universal architectures allow components to achieve what laws allow, and mix diverse components to create systems that achieve what no component can alone; universals including layering, hourglasses and bowties with thin waists and knots; planning and reflex layers; apps, OS, and hardware; horizontal swapping of apps, genes, memes; these are all largely unknown in science and poorly taught in engineering, with little or no theory, until recently; LEGOS as a model system; Darwin, Turing, Bode, Wiener, Shannon, Von Neumann, the death of cybernetics;
Infectious hijacking: layered architectures are vulnerable to infectious hijacking; mechanisms that swap apps, genes, and memes facilitate hijacking by viral, pathogenic versions; toxoplasmosis and zombie parasites; phage kill half the ocean's bacteria daily; network and automation technologies with increasingly dangerous, pervasive cybersecurity vulnerabilities; human's ultimate weakness may be strongly held beliefs (memes) that are contagious, false, dangerous, and unhealthy; parasites vs predators;
New “sciences”: complexity science; network science; edge of chaos; power laws; self-organized criticality; scale-free networks; small worlds; zombie science; hoaxiness; emergulence
Theory foundations: We will aim for a more integrated and accessible treatment of control theory, dynamical systems, optimization, probability and statistics, machine learning, communications theory, and computational complexity. Focus on "deep" fragilities. Previous familiarity or study is helpful but not essential as the questions arising in the case studies can be largely appreciated with minimal math, though the answers go through layers of increasing theory complexity. Students who do have backgrounds in these areas will be particularly useful in teams with domain experts.
For more details: See Course details for more
John Doyle is the Jean-Lou Chameau Professor of Control and Dynamical Systems, Electrical Engineer, and BioEngineering at Caltech, and received the BS&MS in EE, MIT (1977), and PhD in Math, UC Berkeley (1984)). He was a consultant at Honeywell Systems and Research Center from 1976 to 1990.
Research is on mathematical foundations for complex networks with applications in biology, technology, medicine, ecology, neuroscience, and multiscale physics that integrates theory from control, computation, communication, optimization, statistics (e.g. Machine Learning). An emphasis on universal laws and architectures, robustness/efficiency and speed/accuracy tradeoffs, adaptability, and evolvability and large scale systems with sparse, saturating, delayed, quantized, uncertain sensing, communications, computing, and actuation. Early work was on robustness of feedback control systems with applications to aerospace and process control. His students and research group developed software packages like the Matlab Robust Control Toolbox and the Systems Biology Markup Language (SBML).
Prizes, awards, records, championships include the 1990 IEEE Baker Prize (for all IEEE publications), also listed in the world top 10 “most important" papers in mathematics 1981-1993, IEEE Automatic Control Transactions Award (twice 1998, 1999), 1994 AACC American Control Conference Schuck Award, 2004 ACM Sigcomm Paper Prize and 2017 “test of time” award, and inclusion in Best Writing on Mathematics 2010. Individual awards include 1977 IEEE Power Hickernell, 1983 AACC Eckman, 1984 UC Berkeley Friedman, 1984 IEEE Centennial Outstanding Young Engineer (a one-time award for IEEE 100th anniversary), and 2004 IEEE Control Systems Field Award. Best known for fabulous friends, partner, colleagues, and students, with 16 of his advisees (mostly PhDs, some postdocs) now professors at “THE world top” universities (Berkeley(x3), MIT(x2), ETHZ (x2), Imperial (x2), Harvard, Stanford, Oxford, Cambridge, Hopkins, UCLA, Caltech). Has held world and national records and championships in various sports, but is otherwise quite fragile.
Somewhat Recent Application Papers
For recent theory papers see Nikolai Matni
For fairly complete list of references see Google Scholar
Neuroscience and Machine Learning : Interpretation of the Precision Matrix and Its Application in Estimating Sparse Brain Connectivity during Sleep Spindles from Human Electrocorticography Recordings Das, Sampson, Lainscsek, Muller, Lin, Doyle, Cash, Halgren, Sejnowski, Neural Computation, 2017
Education and Neuroscience: Tutorial on education for Conference on Decision and Control, 2016
Medicine: Robust efficiency and actuator saturation explain healthy heart rate control and variability Li, Cruz, Chien, Sojoudi, Recht, Stone, Csete, Bahmiller, Doyle (2014), P Natl Acad Sci USA 111 (33)
Medicine: Sepsis: Something Old, Something New, and a Systems View J Crit Care. (2012)
Universal architectures: Architecture, constraints, and behavior, JC Doyle, MC Csete, P Natl Acad Sci USA, vol. 108, Sup 3 15624-15630
Biology: Gycolytic oscillations and limits on robust efficiency, FA Chandra, G Buzi, JC Doyle Science 333(6039):187-192, July 2011
Turbulence: Amplification and nonlinear mechanisms in plane Couette flow., D Gayme, B McKeon, B Bamieh, A Papachristodolou, and J Doyle. Physics of Fluids v23:6:065108 (2011)
Biology: Analysis of autocatalytic networks in biology, G Buzi, U Topcu, J Doyle, Automatica 47:1123-1130 (2011)
Earthquakes: The magnitude distribution of earthquakes near Southern California faults Page, Alderson, and Doyle JOURNAL OF GEOPHYSICAL RESEARCH, VOL. 116, (2011)
Physics: On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements, H Sandberg, JC Delvenne, JC Doyle, IEEE Trans Auto Control, v56:2, 293-308 (2011)
Wireless: Cross-layer design in multihop wireless networks, L Chen, SH Low, and JC Doyle, Computer Networks 55:480–496 (2011)
Circuits: Solving Large-Scale Hybrid Circuit-Antenna Problems Lavaei, Babakhani, Hajimiri and Doyle, IEEE Transactions on Circuits and Systems I, vol. 58, no. 2, pp. 374-387, Feb. 2011.
Complexity: Contrasting Views of Complexity and Their Implications For Network-Centric Infrastructures Alderson and Doyle, IEEE TRANSACTIONS ON SYSTEMS, MAN, AND CYBERNETICS—PART A: SYSTEMS AND HUMANS, VOL. 40, NO. 4, JULY 2010
Internet: Mathematics and the Internet: A Source of Enormous Confusion and Great Potential Willinger, Alderson, and Doyle, Notices of the AMS Volume 56, Number 5 (2009)
Fire: Fire in the Earth System, Science 324, 481 (2009)
Biology: Robustness of Cellular Functions, Stelling, Sauer, Szallasi, Doyle, and Doyle, Cell, 2004
Biology: Reverse Engineering of Biological Complexity, Csete and Doyle, Science, (2002)
Videos and slides
I have lots of slides and video material in this large dropbox folder.
The videos are in the subfolder called VideosSlidesPapers. I recommend downloading the videos since they may otherwise play in a truncated preview mode.
A good starting point is in 1.0.NewestIntroNeuroMed with more details in 2.0.OverviewWithNeuroEmphasis and 2.2 IntroLawsArchXtraDetails.
There are also 2 short intro videos in the top folder that give an overview of the rest, but then there are much more details in other subfolders, hopefully the names are suggestive...
There is also a whole subfolder on glycolytic oscillations and another on heart rate variability. These are our best and most accessible case studies in biology and medicine.
There are papers above with additional technical details.
- Dennice Gayme (Hopkins) named Carol Linde Croft Faculty Scholar.
- Na (Lina) Li (Harvard) gets NSF CAREER and AFOSR YI awards.
- Javad Lavaei (Berkeley) gets SIAM Control and Systems Theory Prize and AACC Eckman, and too many other awards to list.
- Old: Discover magazine "This man wants to control the internet" by Carl Zimmer, Discover magazine, 2008.
- Newer: Blog and new videos Follow link to dropbox folder with accessible introductory videos and case studies in neuroscience, cell biology, and medical physiology. Our you can go directly to the dropbox folder or see above video lists.
Please download the .mp4 files from the dropbox, otherwise they will run in preview mode, which limits the time.
Not very recent talk slides
U Wisc Madison CS Sept 2012 pdf
UCSB Sage lectures, May 2012. (These are pdf files. Ask me for the ppt if you want to steal anything. I would be very flattered.)
Old Teaching Material
- CDS 213, Robust Control (Spring 2012)
- CDS 212, Feedback Control Theory (Fall 2010)
- The Architecture of Robust, Evolvable Networks (Wi10)
E-mail: doyle AT caltech dot edu
Admin Assistant: Nikki Fountleroy