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Information and Entropy in Biological Systems

edited March 2015 in - Strategy

Here are the speakers at my workshop on Information and Entropy in Biological Systems, at the National Institute for Mathematical and Biological Synthesis, 8-10 April 2015:

  1. John Baez - overview
  2. Christina Cobbold - entropy-like measures of biodiversity
  3. Roderick Dewar - maximal entropy production in biology
  4. Matina Donaldson-Matasci - the fitness value of information
  5. Tobias Fritz - characterizations of Shannon and Renyi entropy
  6. John Harte - the maximum entropy method in population biology
  7. Marc Harper - information geometry in evolutionary game theory
  8. Chris Lee - information theory in experiment design
  9. Tom Leinster - entropy, biodiversity and related concepts of "magnitude"
  10. Annette Ostling - the neutral model and other theories of population biology: competitors to the principle of maximum entropy
  11. Susanne Still - the information bottleneck approach to predictive inference
  12. David Wolpert - the Landauer limit and bounds on entropy production by organisms

Most of these folks are described in the proposal. But there's one extra, David Wolpert. He's been working on an extension of Landauer's analysis of the heat cost of computation to quantify the heat cost of any Markov process.

Comments

  • 1.
    edited March 2015

    Here are the other invited participants:

    1. Romain Brasselet - postdoc in cognitive neuroscience knowledgeable about information-theoretic methods and methods of estimating entropy from samples of probability distributions.

    2. Katharina Brinck - grad student at Centre for Complexity Science at Imperial College; did masters at John Harte’s lab, where she extended his Maximum Entropy Theory of Ecology (METE) to trophic food webs, to study how entropy maximization on the macro scale together with MEP on the scale of individuals drive the structural development of model ecosystems.

    3. Troy Day - mathematical biologist, works with population dynamics, host-parasite dynamics, etc.; influential and could help move population dynamics to a more information-theoretic foundation.

    4. Charlotte de Vries - a biology master's student who studied particle physics to the master's level at Oxford and the Perimeter Institute. Interested in information theory.

    5. Andrew Eckford - ran conference on Bio-inspired Information Theory at Banff; he knows a lot about information theory in neurobiology but is eager to learn the applications to biodiversity and ecology.

    6. Chris Ellison - a postdoc who worked with James Crutchfield on "information-theoretic measures of structure and memory in stationary, stochastic systems - primarily, finite state hidden Markov models". He coauthored "Intersection Information based on Common Randomness", http://arxiv.org/abs/1310.1538. The idea: "The introduction of the partial information decomposition generated a flurry of proposals for defining an intersection information that quantifies how much of "the same information" two or more random variables specify about a target random variable. As of yet, none is wholly satisfactory." Works on in mutual information between organisms and environment (along with Donaldson-Matasci, invited), and also entropy rates.

    7. Cameron Freer - MIT postdoc in Brain and Cognitive Sciences working on maximum entropy production principles, algorithmic entropy etc.

    8. Dashiell Fryer - works with Marc Harper on information geometry and evolutionary game theory.

    9. Michael Gilchrist - an evolutionary biologist studying how errors and costs of protein translation affect the codon usage observed within a genome. Works at NIMBioS.

    10. Manoj Gopalkrishnan - an expert on chemical reaction networks who understands entropy-like Lyapunov functions for these systems.

    11. Ellen Hines - studies habitat modeling and mapping for marine endangered species and ecosystems, sea level change scenarios, documenting of human use and values. Her lab has used MaxEnt methods.

    12. Elizabeth Hobson - behavior ecology postdoc developing methods to quantify social complexity in animals. Works at NIMBioS.

    13. John Jungk - works on graph theory and biology.

    14. Maria Leites - works on dynamics, bifurcations and applications of coupled systems of non-linear ordinary differential equations with applications to ecology, epidemiology, and transcriptional regulatory networks. Interested in information theory.

    15. Timothy Lezon - a systems biologist in the Drug Discovery Institute at Pitt, who has used entropy to characterize phenotypic heterogeneity in populations of cultured cells.

    16. Yajun Mei - statistician who uses Kullback-Leibler divergence and how to efficiently compute entropy for the two-state hidden Markov models.

    17. David Murrugarra - works on discrete models in mathematical biology; interested in learning about information theory.

    18. Ilya Nemenman - a coauthor with William Bialek and Naftali Tishby of "Predictability, complexity, and learning", and coauthor of "Information transduction capacity of noisy biochemical signaling networks".

    19. Maria Ortiz Mancera - statistician working at CONABIO, the National Commission for Knowledge and Use of Biodiversity, in Mexico.

    20. Connie Phong - grad student at Chicago's Institute of Genomics and System biology, working on how "certain biochemical network motifs are more attuned than others at maintaining strong input to output relationships under fluctuating conditions."

    21. Petr Plechak - works on information-theoretic tools for estimating and minimizing errors in coarse-graining stochastic systems. Wrote "Information-theoretic tools for parametrized coarse-graining of non-equilibrium extended systems", http://arxiv.org/abs/1304.7700.

    22. Blake Polllard - physics grad student working with John Baez on various generalizations of Shannon and Renyi entropy, and how these entropies change with time in Markov processes and open Markov processes.

    23. Timothee Poisot - works on species interaction networks; developed a "new suite of tools for probabilistic interaction networks".

    24. Richard Reeve - works on biodiversity studies and the spread of antibiotic resistance. Ran a program on entropy-based biodiversity measures at a mathematics institute in Barcelona.

    25. Matteo Smerlak - postdoc working on nonequilibrium thermodynamics and its applications to biology, especially population biology and cell replication.

    26. Alexander Wissner-Gross - Institute Fellow at the Harvard University Institute for Applied Computational Science and Research Affiliate at the MIT Media Laboratory, interested in lots of things.

    27. Matthew Zefferman - works on evolutionary game theory, institutional economics and models of gene-culture co-evolution. No work on information, but a postdoc at NIMBioS.

    Comment Source:Here are the other invited participants: 1. Romain Brasselet - postdoc in cognitive neuroscience knowledgeable about information-theoretic methods and methods of estimating entropy from samples of probability distributions. 2. Katharina Brinck - grad student at Centre for Complexity Science at Imperial College; did masters at John Harte’s lab, where she extended his Maximum Entropy Theory of Ecology (METE) to trophic food webs, to study how entropy maximization on the macro scale together with MEP on the scale of individuals drive the structural development of model ecosystems. 3. Troy Day - mathematical biologist, works with population dynamics, host-parasite dynamics, etc.; influential and could help move population dynamics to a more information-theoretic foundation. 4. Charlotte de Vries - a biology master's student who studied particle physics to the master's level at Oxford and the Perimeter Institute. Interested in information theory. 5. Andrew Eckford - ran conference on Bio-inspired Information Theory at Banff; he knows a lot about information theory in neurobiology but is eager to learn the applications to biodiversity and ecology. 6. Chris Ellison - a postdoc who worked with James Crutchfield on "information-theoretic measures of structure and memory in stationary, stochastic systems - primarily, finite state hidden Markov models". He coauthored "Intersection Information based on Common Randomness", http://arxiv.org/abs/1310.1538. The idea: "The introduction of the partial information decomposition generated a flurry of proposals for defining an intersection information that quantifies how much of "the same information" two or more random variables specify about a target random variable. As of yet, none is wholly satisfactory." Works on in mutual information between organisms and environment (along with Donaldson-Matasci, invited), and also entropy rates. 7. Cameron Freer - MIT postdoc in Brain and Cognitive Sciences working on maximum entropy production principles, algorithmic entropy etc. 8. Dashiell Fryer - works with Marc Harper on information geometry and evolutionary game theory. 9. Michael Gilchrist - an evolutionary biologist studying how errors and costs of protein translation affect the codon usage observed within a genome. Works at NIMBioS. 10. Manoj Gopalkrishnan - an expert on chemical reaction networks who understands entropy-like Lyapunov functions for these systems. 11. Ellen Hines - studies habitat modeling and mapping for marine endangered species and ecosystems, sea level change scenarios, documenting of human use and values. Her lab has used MaxEnt methods. 12. Elizabeth Hobson - behavior ecology postdoc developing methods to quantify social complexity in animals. Works at NIMBioS. 13. John Jungk - works on graph theory and biology. 14. Maria Leites - works on dynamics, bifurcations and applications of coupled systems of non-linear ordinary differential equations with applications to ecology, epidemiology, and transcriptional regulatory networks. Interested in information theory. 15. Timothy Lezon - a systems biologist in the Drug Discovery Institute at Pitt, who has used entropy to characterize phenotypic heterogeneity in populations of cultured cells. 17. Yajun Mei - statistician who uses Kullback-Leibler divergence and how to efficiently compute entropy for the two-state hidden Markov models. 18. David Murrugarra - works on discrete models in mathematical biology; interested in learning about information theory. 19. Ilya Nemenman - a coauthor with William Bialek and Naftali Tishby of "Predictability, complexity, and learning", and coauthor of "Information transduction capacity of noisy biochemical signaling networks". 20. Maria Ortiz Mancera - statistician working at CONABIO, the National Commission for Knowledge and Use of Biodiversity, in Mexico. 21. Connie Phong - grad student at Chicago's Institute of Genomics and System biology, working on how "certain biochemical network motifs are more attuned than others at maintaining strong input to output relationships under fluctuating conditions." 23. Petr Plechak - works on information-theoretic tools for estimating and minimizing errors in coarse-graining stochastic systems. Wrote "Information-theoretic tools for parametrized coarse-graining of non-equilibrium extended systems", http://arxiv.org/abs/1304.7700. 24. Blake Polllard - physics grad student working with John Baez on various generalizations of Shannon and Renyi entropy, and how these entropies change with time in Markov processes and open Markov processes. 25. Timothee Poisot - works on species interaction networks; developed a "new suite of tools for probabilistic interaction networks". 26. Richard Reeve - works on biodiversity studies and the spread of antibiotic resistance. Ran a program on entropy-based biodiversity measures at a mathematics institute in Barcelona. 27. Matteo Smerlak - postdoc working on nonequilibrium thermodynamics and its applications to biology, especially population biology and cell replication. 28. Alexander Wissner-Gross - Institute Fellow at the Harvard University Institute for Applied Computational Science and Research Affiliate at the MIT Media Laboratory, interested in lots of things. 29. Matthew Zefferman - works on evolutionary game theory, institutional economics and models of gene-culture co-evolution. No work on information, but a postdoc at NIMBioS.
  • 2.

    Hi John, Will this workshop be videotaped?

    Comment Source:Hi John, Will this workshop be videotaped?
  • 3.

    Good question! They write:

    NIMBioS offers free live streaming of many NIMBioS events. See box below for live stream events and link to log in. After you log in by entering your name, organization, and email address, you will be taken to the live stream, which will be active only during the event.

    The live stream will not be archived, but individual talks will be videotaped and available soon on the NIMBioS YouTube channel.

    There are already some videos there. I'll try to persuade them to video as many talks as possible! Thanks!

    Comment Source:Good question! [They write](http://www.nimbios.org/videos/livestream): > NIMBioS offers free live streaming of many NIMBioS events. See box below for live stream events and link to log in. After you log in by entering your name, organization, and email address, you will be taken to the live stream, **which will be active only during the event**. > The live stream will **not** be archived, but individual talks will be videotaped and available soon on the [NIMBioS YouTube channel](https://www.youtube.com/user/NIMBioS). There are already some videos there. I'll try to persuade them to video as many talks as possible! Thanks!
  • 4.

    Great, Thanks John.

    Comment Source:Great, Thanks John.
  • 5.

    At the urging of the NIMBioS staff, I started a blog for my workshop:

    I doubt it will see much action, but it allows participants to post their talks, links to papers, etc. Right now the welcome post just says the rough program of the workshop, who the participants are, etc.

    Comment Source:At the urging of the NIMBioS staff, I started a blog for my workshop: * [NIMBioS investigative workshops: information and entropy in biological systems: welcome!](http://www.nimbios.org/wordpress-training/entropy/2015/03/05/welcome/) I doubt it will see much action, but it allows participants to post their talks, links to papers, etc. Right now the welcome post just says the rough program of the workshop, who the participants are, etc.
  • 6.
    edited June 2015

    You can see videos of 7 of the 12 talks at our workshop here, along with talk slides, abstracts, and links to papers:

    I'm also putting up blog articles about the talks. I'm too busy to write nice explanations of stuff, so they're mostly just full of links.

    Comment Source:You can see videos of 7 of the 12 talks at our workshop here, along with talk slides, abstracts, and links to papers: * [Information and entropy in biological systems](http://math.ucr.edu/home/baez/nimbios/). I'm also putting up blog articles about the talks. I'm too busy to write nice explanations of stuff, so they're mostly just full of links.
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