Category: Complexity

🎧 Entanglement | Invisibilia (NPR)

Listened to Entanglement from Invisibilia | NPR.org
In Entanglement, you'll meet a woman with Mirror Touch Synesthesia who can physically feel what she sees others feeling. And an exploration of the ways in which all of us are connected — more literally than you might realize. The hour will start with physics and end with a conversation with comedian Maria Bamford and her mother. They discuss what it's like to be entangled through impersonation.
I can think of a few specific quirks I’ve got that touch tangentially on mirror synethesia. This story and some of the research behind it is truly fascinating. Particularly interesting are the ideas of the contagion of emotion. It would be interesting to take some complexity and network theory and add some mathematical models to see how this might look. In particular the recent political protests in the U.S. might make great models. This also makes me wonder where Donald Trump sits on this emotional empathy spectrum, if at all.

One of the more interesting take-aways: the thoughts and emotions of those around you can affect you far more than you imagine.

Four episodes in and this podcast is still impossibly awesome. I don’t know if I’ve had so many thought changing ideas since I read David Christian’s book Maps of Time: An Introduction to Big History. [1] The sad problem is that I’m listening to them at a far faster pace than they could ever continue to produce them.

References

[1]
D. Christian, Maps of Time: An Introduction to Big History. Univ of California Press, 2004.

🎧 How to Become Batman | Invisibilia (NPR)

Listened to How to Become Batman from Invisibilia | NPR.org
In "How to Become Batman," Alix and Lulu examine the surprising effect that our expectations can have on the people around us. You'll hear how people's expectations can influence how well a rat runs a maze. Plus, the story of a man who is blind and says expectations have helped him see. Yes. See. This journey is not without skeptics.
Expectations are much more important than we think.

Is it possible that this podcast is getting more interesting as it continues along?! In three episodes, I’ve gone from fan to fanboy.

NIMBioS Tutorial: Uncertainty Quantification for Biological Models

Bookmarked NIMBioS Tutorial: Uncertainty Quantification for Biological Models (nimbios.org)
NIMBioS will host an Tutorial on Uncertainty Quantification for Biological Models

Uncertainty Quantification for Biological Models

Meeting dates: June 26-28, 2017
Location: NIMBioS at the University of Tennessee, Knoxville

Organizers:
Marisa Eisenberg, School of Public Health, Univ. of Michigan
Ben Fitzpatrick, Mathematics, Loyola Marymount Univ.
James Hyman, Mathematics, Tulane Univ.
Ralph Smith, Mathematics, North Carolina State Univ.
Clayton Webster, Computational and Applied Mathematics (CAM), Oak Ridge National Laboratory; Mathematics, Univ. of Tennessee

Objectives:
Mathematical modeling and computer simulations are widely used to predict the behavior of complex biological phenomena. However, increased computational resources have allowed scientists to ask a deeper question, namely, “how do the uncertainties ubiquitous in all modeling efforts affect the output of such predictive simulations?” Examples include both epistemic (lack of knowledge) and aleatoric (intrinsic variability) uncertainties and encompass uncertainty coming from inaccurate physical measurements, bias in mathematical descriptions, as well as errors coming from numerical approximations of computational simulations. Because it is essential for dealing with realistic experimental data and assessing the reliability of predictions based on numerical simulations, research in uncertainty quantification (UQ) ultimately aims to address these challenges.

Uncertainty quantification (UQ) uses quantitative methods to characterize and reduce uncertainties in mathematical models, and techniques from sampling, numerical approximations, and sensitivity analysis can help to apportion the uncertainty from models to different variables. Critical to achieving validated predictive computations, both forward and inverse UQ analysis have become critical modeling components for a wide range of scientific applications. Techniques from these fields are rapidly evolving to keep pace with the increasing emphasis on models that require quantified uncertainties for large-scale applications. This tutorial will focus on the application of these methods and techniques to mathematical models in the life sciences and will provide researchers with the basic concepts, theory, and algorithms necessary to quantify input and response uncertainties and perform sensitivity analysis for simulation models. Concepts to be covered may include: probability and statistics, parameter selection techniques, frequentist and Bayesian model calibration, propagation of uncertainties, quantification of model discrepancy, adaptive surrogate model construction, high-dimensional approximation, random sampling and sparse grids, as well as local and global sensitivity analysis.

This tutorial is intended for graduate students, postdocs and researchers in mathematics, statistics, computer science and biology. A basic knowledge of probability, linear algebra, and differential equations is assumed.

Descriptive Flyer

Application deadline: March 1, 2017
To apply, you must complete an application on our online registration system:

  1. Click here to access the system
  2. Login or register
  3. Complete your user profile (if you haven’t already)
  4. Find this tutorial event under Current Events Open for Application and click on Apply

Participation in NIMBioS tutorials is by application only. Individuals with a strong interest in the topic are encouraged to apply, and successful applicants will be notified within two weeks after the application deadline. If needed, financial support for travel, meals, and lodging is available for tutorial attendees.

Summary Report. TBA

Live Stream. The Tutorial will be streamed live. Note that NIMBioS Tutorials involve open discussion and not necessarily a succession of talks. In addition, the schedule as posted may change during the Workshop. To view the live stream, visit http://www.nimbios.org/videos/livestream. A live chat of the event will take place via Twitter using the hashtag #uncertaintyTT. The Twitter feed will be displayed to the right of the live stream. We encourage you to post questions/comments and engage in discussion with respect to our Social Media Guidelines.

Source: NIMBioS Tutorial: Uncertainty Quantification for Biological Models

Mathematical Model Reveals the Patterns of How Innovations Arise | MIT Technology Review

Read Mathematicians have discovered how the universal patterns behind innovation arise (MIT Technology Review)
A mathematical model could lead to a new approach to the study of what is possible, and how it follows from what already exists.
Continue reading Mathematical Model Reveals the Patterns of How Innovations Arise | MIT Technology Review

🔖 Information theory, predictability, and the emergence of complex life

Bookmarked Information theory, predictability, and the emergence of complex life (arxiv.org)
Abstract: Despite the obvious advantage of simple life forms capable of fast replication, different levels of cognitive complexity have been achieved by living systems in terms of their potential to cope with environmental uncertainty. Against the inevitable cost associated to detecting environmental cues and responding to them in adaptive ways, we conjecture that the potential for predicting the environment can overcome the expenses associated to maintaining costly, complex structures. We present a minimal formal model grounded in information theory and selection, in which successive generations of agents are mapped into transmitters and receivers of a coded message. Our agents are guessing machines and their capacity to deal with environments of different complexity defines the conditions to sustain more complex agents.

Statistical Physics, Information Processing, and Biology Workshop at Santa Fe Institute

Bookmarked Information Processing and Biology by John Carlos Baez (Azimuth)
The Santa Fe Institute, in New Mexico, is a place for studying complex systems. I’ve never been there! Next week I’ll go there to give a colloquium on network theory, and also to participate in this workshop.
I just found out about this from John Carlos Baez and wish I could go! How have I not managed to have heard about it?

Stastical Physics, Information Processing, and Biology

Workshop

November 16, 2016 – November 18, 2016
9:00 AM
Noyce Conference Room

Abstract.
This workshop will address a fundamental question in theoretical biology: Does the relationship between statistical physics and the need of biological systems to process information underpin some of their deepest features? It recognizes that a core feature of biological systems is that they acquire, store and process information (i.e., perform computation). However to manipulate information in this way they require a steady flux of free energy from their environments. These two, inter-related attributes of biological systems are often taken for granted; they are not part of standard analyses of either the homeostasis or the evolution of biological systems. In this workshop we aim to fill in this major gap in our understanding of biological systems, by gaining deeper insight in the relation between the need for biological systems to process information and the free energy they need to pay for that processing.

The goal of this workshop is to address these issues by focusing on a set three specific question:

  1. How has the fraction of free energy flux on earth that is used by biological computation changed with time?;
  2. What is the free energy cost of biological computation / function?;
  3. What is the free energy cost of the evolution of biological computation / function.

In all of these cases we are interested in the fundamental limits that the laws of physics impose on various aspects of living systems as expressed by these three questions.

Purpose: Research Collaboration
SFI Host: David Krakauer, Michael Lachmann, Manfred Laubichler, Peter Stadler, and David Wolpert

Hector Zenil

I’ve run across some of his work before, but I ran into some new material by Hector Zenil that will likely interest those following information theory, complexity, and computer science here. I hadn’t previously noticed that he refers to himself on his website as an “information theoretic biologist” — everyone should have that as a title, shouldn’t they? As a result, I’ve also added him to the growing list of ITBio Researchers.

If you’re not following him everywhere (?) yet, start with some of the sites below (or let me know if I’ve missed anything).

Hector Zenil:

His most recent paper on arXiv:
Low Algorithmic Complexity Entropy-deceiving Graphs | .pdf

A common practice in the estimation of the complexity of objects, in particular of graphs, is to rely on graph- and information-theoretic measures. Here, using integer sequences with properties such as Borel normality, we explain how these measures are not independent of the way in which a single object, such a graph, can be described. From descriptions that can reconstruct the same graph and are therefore essentially translations of the same description, we will see that not only is it necessary to pre-select a feature of interest where there is one when applying a computable measure such as Shannon Entropy, and to make an arbitrary selection where there is not, but that more general properties, such as the causal likeliness of a graph as a measure (opposed to randomness), can be largely misrepresented by computable measures such as Entropy and Entropy rate. We introduce recursive and non-recursive (uncomputable) graphs and graph constructions based on integer sequences, whose different lossless descriptions have disparate Entropy values, thereby enabling the study and exploration of a measure’s range of applications and demonstrating the weaknesses of computable measures of complexity.

Subjects: Information Theory (cs.IT); Computational Complexity (cs.CC); Combinatorics (math.CO)
Cite as: arXiv:1608.05972 [cs.IT] (or arXiv:1608.05972v4 [cs.IT]

YouTube

Yesterday he also posted two new introductory videos to his YouTube channel. There’s nothing overly technical here, but they’re nice short productions that introduce some of his work. (I wish more scientists did communication like this.) I’m hoping he’ll post them to his blog and write a bit more there in the future as well.

Universal Measures of Complexity

Relevant literature:

Reprogrammable World

Relevant literature:

Cross-boundary Behavioural Reprogrammability Reveals Evidence of Pervasive Turing Universality by Jürgen Riedel, Hector Zenil
Preprint available at http://arxiv.org/abs/1510.01671

Ed.: 9/7/16: Updated videos with links to relevant literature

Randomness And Complexity, from Leibniz To Chaitin | World Scientific Publishing

Bookmarked Randomness And Complexity, from Leibniz To Chaitin (amzn.to)
The book is a collection of papers written by a selection of eminent authors from around the world in honour of Gregory Chaitin s 60th birthday. This is a unique volume including technical contributions, philosophical papers and essays. Hardcover: 468 pages; Publisher: World Scientific Publishing Company (October 18, 2007); ISBN: 9789812770820

Network Science by Albert-László Barabási

Bookmarked Network Science by Albert-László BarabásiAlbert-László Barabási (Cambridge University Press)
I ran across a link to this textbook by way of a standing Google alert, and was excited to check it out. I was immediately disappointed to think that I would have to wait another month and change for the physical textbook to be released, but made my pre-order directly. Then with a bit of digging around, I realized that individual chapters are available immediately to quench my thirst until the physical text is printed next month.

The power of network science, the beauty of network visualization.

Network Science, a textbook for network science, is freely available under the Creative Commons licence. Follow its development on Facebook, Twitter or by signing up to our mailing list, so that we can notify you of new chapters and developments.

The book is the result of a collaboration between a number of individuals, shaping everything, from content (Albert-László Barabási), to visualizations and interactive tools (Gabriele Musella, Mauro Martino, Nicole Samay, Kim Albrecht), simulations and data analysis (Márton Pósfai). The printed version of the book will be published by Cambridge University Press in 2016. In the coming months the website will be expanded with an interactive version of the text, datasets, and slides to teach the material.

Book Contents

Personal Introduction
1. Introduction
2. Graph Theory
3. Random Networks
4. The Scale-Free Property
5. The Barabási-Albert Model
6. Evolving Networks
7. Degree Correlations
8. Network Robustness
9. Communities
10. Spreading Phenomena
Usage & Acknowledgements
About

Albert-László Barabási
on Network Science (book website)

Networks are everywhere, from the Internet, to social networks, and the genetic networks that determine our biological existence. Illustrated throughout in full colour, this pioneering textbook, spanning a wide range of topics from physics to computer science, engineering, economics and the social sciences, introduces network science to an interdisciplinary audience. From the origins of the six degrees of separation to explaining why networks are robust to random failures, the author explores how viruses like Ebola and H1N1 spread, and why it is that our friends have more friends than we do. Using numerous real-world examples, this innovatively designed text includes clear delineation between undergraduate and graduate level material. The mathematical formulas and derivations are included within Advanced Topics sections, enabling use at a range of levels. Extensive online resources, including films and software for network analysis, make this a multifaceted companion for anyone with an interest in network science.

Source: Cambridge University Press

The textbook is available for purchase in September 2016 from Cambridge University Press. Pre-order now on Amazon.com.

If you’re not already doing so, you should follow Barabási on Twitter.

Disconnected, Fragmented, or United? A Trans-disciplinary Review of Network Science

Bookmarked Disconnected, Fragmented, or United? A Trans-disciplinary Review of Network Science by César A. HidalgoCésar A. Hidalgo (Applied Network Science | SpringerLink)
Applied Network Science

Abstract

During decades the study of networks has been divided between the efforts of social scientists and natural scientists, two groups of scholars who often do not see eye to eye. In this review I present an effort to mutually translate the work conducted by scholars from both of these academic fronts hoping to continue to unify what has become a diverging body of literature. I argue that social and natural scientists fail to see eye to eye because they have diverging academic goals. Social scientists focus on explaining how context specific social and economic mechanisms drive the structure of networks and on how networks shape social and economic outcomes. By contrast, natural scientists focus primarily on modeling network characteristics that are independent of context, since their focus is to identify universal characteristics of systems instead of context specific mechanisms. In the following pages I discuss the differences between both of these literatures by summarizing the parallel theories advanced to explain link formation and the applications used by scholars in each field to justify their approach to network science. I conclude by providing an outlook on how these literatures can be further unified.

Design and Control of Self-organizing Systems

Bookmarked Design and Control of Self-organizing Systems by Carlos Gershenson (scifunam.fisica.unam.mx)
UNAM Mexico City has an available free download of Carlos Gershenson’s 2007 text.

Complex systems are usually difficult to design and control. There are several particular methods for coping with complexity, but there is no general approach to build complex systems. In this book I propose a methodology to aid engineers in the design and control of complex systems. This is based on the description of systems as self-organizing. Starting from the agent metaphor, the methodology proposes a conceptual framework and a series of steps to follow to find proper mechanisms that will promote elements to find solutions by actively interacting among themselves.

Design and Control of Self-organizing Systems by Carlos Gershenson (2007)
Design and Control of Self-organizing Systems by Carlos Gershenson (2007)

Introduction to Dynamical Systems and Chaos

Introduction to Dynamical Systems and Chaos (Summer, 2016)

About the Course:

In this course you’ll gain an introduction to the modern study of dynamical systems, the interdisciplinary field of applied mathematics that studies systems that change over time.

Topics to be covered include: phase space, bifurcations, chaos, the butterfly effect, strange attractors, and pattern formation. The course will focus on some of the realizations from the study of dynamical systems that are of particular relevance to complex systems:

  1. Dynamical systems undergo bifurcations, where a small change in a system parameter such as the temperature or the harvest rate in a fishery leads to a large and qualitative change in the system’s
    behavior.
  2. Deterministic dynamical systems can behave randomly. This property, known as sensitive dependence or the butterfly effect, places strong limits on our ability to predict some phenomena.
  3. Disordered behavior can be stable. Non-periodic systems with the butterfly effect can have stable average properties. So the average or statistical properties of a system can be predictable, even if its details are not.
  4. Complex behavior can arise from simple rules. Simple dynamical systems do not necessarily lead to simple results. In particular, we will see that simple rules can produce patterns and structures of surprising complexity.

About the Instructor:

content_headshotDavid Feldman is Professor of Physics and Mathematics at College of the Atlantic. From 2004-2009 he was a faculty member in the Santa Fe Institute’s Complex Systems Summer School in Beijing, China. He served as the school’s co-director from 2006-2009. Dave is the author of Chaos and Fractals: An Elementary Introduction (Oxford University Press, 2012), a textbook on chaos and fractals for students with a background in high school algebra. Dave was a U.S. Fulbright Lecturer in Rwanda in 2011-12.

Course dates:

5 Jul 2016 9am PDT to
20 Sep 2016 3pm PDT

Prerequisites:

A familiarity with basic high school algebra. There will be optional lessons for those with stronger math backgrounds.

Syllabus

  • Introduction I: Iterated Functions
  • Introduction II: Differential Equations
  • Chaos and the Butterfly Effect
  • Bifurcations: Part I (Differential Equations)
  • Bifurcations: Part II (Logistic Map)
  • Universality
  • Phase Space
  • Strange Attractors
  • Pattern Formation
  • Summary and Conclusions

Source: Complexity Explorer

https://www.youtube.com/watch?v=li_YSEvdvvg&feature=youtu.be

Calculating the Middle Ages?

Bookmarked Calculating the Middle Ages? The Project "Complexities and Networks in the Medieval Mediterranean and Near East" (COMMED) [1606.03433] (arxiv.org)
The project "Complexities and networks in the Medieval Mediterranean and Near East" (COMMED) at the Division for Byzantine Research of the Institute for Medieval Research (IMAFO) of the Austrian Academy of Sciences focuses on the adaptation and development of concepts and tools of network theory and complexity sciences for the analysis of societies, polities and regions in the medieval world in a comparative perspective. Key elements of its methodological and technological toolkit are applied, for instance, in the new project "Mapping medieval conflicts: a digital approach towards political dynamics in the pre-modern period" (MEDCON), which analyses political networks and conflict among power elites across medieval Europe with five case studies from the 12th to 15th century. For one of these case studies on 14th century Byzantium, the explanatory value of this approach is presented in greater detail. The presented results are integrated in a wider comparison of five late medieval polities across Afro-Eurasia (Byzantium, China, England, Hungary and Mamluk Egypt) against the background of the {guillemotright}Late Medieval Crisis{guillemotleft} and its political and environmental turmoil. Finally, further perspectives of COMMED are outlined.

Network and Complexity Theory Applied to History

This interesting paper (summary below) appears to apply network and complexity science to history and is sure to be of interest to those working at the intersection of some of these types of interdisciplinary studies. In particular, I’d be curious to see more coming out of this type of area to support theses written by scholars like Francis Fukuyama in the development of societal structures. Those interested in the emerging area of Big History are sure to enjoy this type of treatment. I’m also curious how researchers in economics (like Cesar Hidalgo) might make use of available(?) historical data in such related analyses. I’m curious if Dave Harris might consider such an analysis in his ancient Near East work?

Those interested in a synopsis of the paper might find some benefit from an overview from MIT Technology Review: How the New Science of Computational History Is Changing the Study of the Past.

A New Thermodynamics Theory of the Origin of Life | Quanta Magazine

Bookmarked A New Physics Theory of Life by Natalie Wolchover (quantamagazine.org)
Jeremy England, a 31-year-old physicist at MIT, thinks he has found the underlying physics driving the origin and evolution of life.
References:

Hypothesis annotations

[ hypothesis user = 'chrisaldrich' tags = 'EnglandQM']

Introduction to Information Theory | SFI’s Complexity Explorer

Many readers often ask me for resources for delving into the basics of information theory. I hadn’t posted it before, but the Santa Fe Institute recently had an online course Introduction to Information Theory through their Complexity Explorer, which has some other excellent offerings. It included videos, fora, and other resources and was taught by the esteemed physicist and professor Seth Lloyd. There are a number of currently active students still learning and posting there.

Introduction to Information Theory

About the Tutorial:

This tutorial introduces fundamental concepts in information theory. Information theory has made considerable impact in complex systems, and has in part co-evolved with complexity science. Research areas ranging from ecology and biology to aerospace and information technology have all seen benefits from the growth of information theory.

In this tutorial, students will follow the development of information theory from bits to modern application in computing and communication. Along the way Seth Lloyd introduces valuable topics in information theory such as mutual information, boolean logic, channel capacity, and the natural relationship between information and entropy.

Lloyd coherently covers a substantial amount of material while limiting discussion of the mathematics involved. When formulas or derivations are considered, Lloyd describes the mathematics such that less advanced math students will find the tutorial accessible. Prerequisites for this tutorial are an understanding of logarithms, and at least a year of high-school algebra.

About the Instructor(s):

Professor Seth Lloyd is a principal investigator in the Research Laboratory of Electronics (RLE) at the Massachusetts Institute of Technology (MIT). He received his A.B. from Harvard College in 1982, the Certificate of Advanced Study in Mathematics (Part III) and an M. Phil. in Philosophy of Science from Cambridge University in 1983 and 1984 under a Marshall Fellowship, and a Ph.D. in Physics in 1988 from Rockefeller University under the supervision of Professor Heinz Pagels.

From 1988 to 1991, Professor Lloyd was a postdoctoral fellow in the High Energy Physics Department at the California Institute of Technology, where he worked with Professor Murray Gell-Mann on applications of information to quantum-mechanical systems. From 1991 to 1994, he was a postdoctoral fellow at Los Alamos National Laboratory, where he worked at the Center for Nonlinear Systems on quantum computation. In 1994, he joined the faculty of the Department of Mechanical Engineering at MIT. Since 1988, Professor Lloyd has also been an adjunct faculty member at the Sante Fe Institute.

Professor Lloyd has performed seminal work in the fields of quantum computation and quantum communications, including proposing the first technologically feasible design for a quantum computer, demonstrating the viability of quantum analog computation, proving quantum analogs of Shannon’s noisy channel theorem, and designing novel methods for quantum error correction and noise reduction.

Professor Lloyd is a member of the American Physical Society and the Amercian Society of Mechanical Engineers.

Tutorial Team:

Yoav Kallus is an Omidyar Fellow at the Santa Fe Institute. His research at the boundary of statistical physics and geometry looks at how and when simple interactions lead to the formation of complex order in materials and when preferred local order leads to system-wide disorder. Yoav holds a B.Sc. in physics from Rice University and a Ph.D. in physics from Cornell University. Before joining the Santa Fe Institute, Yoav was a postdoctoral fellow at the Princeton Center for Theoretical Science in Princeton University.

How to use Complexity Explorer: How to use Complexity Explore
Prerequisites: At least one year of high-school algebra
Like this tutorial? 

Syllabus

  1. Introduction
  2. Forms of Information
  3. Information and Probability
  4. Fundamental Formula of Information
  5. Computation and Logic: Information Processing
  6. Mutual Information
  7. Communication Capacity
  8. Shannon’s Coding Theorem
  9. The Manifold Things Information Measures
  10. Homework