<?xml version="1.0" encoding="UTF-8"?>
 <rdf:RDF xmlns="http://purl.org/rss/1.0/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:content="http://purl.org/rss/1.0/modules/content/" xmlns:taxo="http://purl.org/rss/1.0/modules/taxonomy/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:cc="http://web.resource.org/cc/" xmlns:syn="http://purl.org/rss/1.0/modules/syndication/" xmlns:admin="http://webns.net/mvcb/">
  <channel rdf:about="http://pinboard.in">
    <title>Pinboard (Vaguery)</title>
    <link>https://pinboard.in/u:Vaguery/public/</link>
    <description>recent bookmarks from Vaguery</description>
    <items>
      <rdf:Seq>	<rdf:li rdf:resource="https://arxiv.org/abs/1208.0482"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/2408.06691"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/2511.15533"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/2308.06277"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/2507.13253"/>
	<rdf:li rdf:resource="https://longnow.org/ideas/physics-life-complexity-assembly-theory/"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/2401.05375"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/2209.07505"/>
	<rdf:li rdf:resource="https://psyarxiv.com/27qba/"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1606.00101"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/2201.03582"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1805.02354"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1511.09203"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1907.13371"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1605.08070"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1711.02754"/>
	<rdf:li rdf:resource="https://occupymath.wordpress.com/2020/10/01/what-do-mathematicians-do-all-day-part-iv/"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1906.09465"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/2012.05437"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1606.00641"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1702.02764"/>
	<rdf:li rdf:resource="https://psyarxiv.com/2htkr/"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1012.0369"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1410.8001"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/cs/0008002"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1902.04174"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1907.10924"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1908.00971"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1808.06271"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1608.03145"/>
	<rdf:li rdf:resource="https://www.quantamagazine.org/with-food-webs-jennifer-dunne-puts-humans-back-into-ecology-20190321/"/>
	<rdf:li rdf:resource="http://advances.sciencemag.org/content/5/2/eaat1328"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1807.04437"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1811.11909"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1802.06668"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1808.05875"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1805.07360"/>
	<rdf:li rdf:resource="https://norabateson.wordpress.com/2015/11/03/symmathesy-a-word-in-progress/"/>
	<rdf:li rdf:resource="https://kappalanguage.org/"/>
	<rdf:li rdf:resource="https://www.complexityexplorer.org/courses"/>
	<rdf:li rdf:resource="http://www.complex-systems.com/index.html"/>
	<rdf:li rdf:resource="http://www.worldwidewanderings.net/science.html"/>
	<rdf:li rdf:resource="https://blogs.scientificamerican.com/sa-visual/in-silico-flurries/"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1709.08468"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1712.04499"/>
	<rdf:li rdf:resource="http://www.univie.ac.at/constructivism/journal/13/1/001.editorial"/>
	<rdf:li rdf:resource="http://www.joelsimon.net/ecosystem-modelling.html"/>
	<rdf:li rdf:resource="http://complex.upf.es/~ricard/INFONETS.pdf"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1702.01522"/>
	<rdf:li rdf:resource="https://mathenchant.wordpress.com/2017/07/17/swine-in-a-line/"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1611.01164"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1707.08905"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1709.02171"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/0801.3306"/>
	<rdf:li rdf:resource="http://smaldino.com/wp/wp-content/uploads/2017/01/Smaldino2017-ModelsAreStupid.pdf"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1705.00759"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1705.00692"/>
	<rdf:li rdf:resource="http://www.biorxiv.org/content/early/2017/05/25/142174?rss=1"/>
	<rdf:li rdf:resource="http://biorxiv.org/content/early/2016/08/25/071589?rss=1%2522"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1512.05259"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1306.0481"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/adap-org/9710002"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1012.1332"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1304.5109"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1703.04792"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1607.04474"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1109.4994"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1309.1837"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1406.2277"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1306.5533"/>
      </rdf:Seq>
    </items>
  </channel><item rdf:about="https://arxiv.org/abs/1208.0482">
    <title>[1208.0482] The concurrent evolution of cooperation and the population structures that support it</title>
    <dc:date>2026-05-24T12:27:54+00:00</dc:date>
    <link>https://arxiv.org/abs/1208.0482</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[The evolution of cooperation often depends upon population structure, yet nearly all models of cooperation implicitly assume that this structure remains static. This is a simplifying assumption, because most organisms possess genetic traits that affect their population structure to some degree. These traits, such as a group size preference, affect the relatedness of interacting individuals and hence the opportunity for kin or group selection. We argue that models that do not explicitly consider their evolution cannot provide a satisfactory account of the origin of cooperation, because they cannot explain how the prerequisite population structures arise. Here, we consider the concurrent evolution of genetic traits that affect population structure, with those that affect social behavior. We show that not only does population structure drive social evolution, as in previous models, but that the opportunity for cooperation can in turn drive the creation of population structures that support it. This occurs through the generation of linkage disequilibrium between socio-behavioral and population-structuring traits, such that direct kin selection on social behavior creates indirect selection pressure on population structure. We illustrate our argument with a model of the concurrent evolution of group size preference and social behavior.
]]></description>
<dc:subject>artificial-life machine-learning complexology rather-interesting hey-I-know-this-guy theoretical-biology to-simulate consider:performance-measures coevolution</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:b7f06f7b43d1/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:artificial-life"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:machine-learning"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:hey-I-know-this-guy"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:theoretical-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-simulate"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:performance-measures"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:coevolution"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/2408.06691">
    <title>[2408.06691] Complete ergodicity in one-dimensional reversible cellular automata</title>
    <dc:date>2026-05-24T10:53:42+00:00</dc:date>
    <link>https://arxiv.org/abs/2408.06691</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Exactly ergodicity in boundary-driven semi-infinite cellular automata (CA) are investigated. We establish all the ergodic rules in CA with 3, 4, and 5 states. We analytically prove the ergodicity for 12 rules in 3-state CA and 118320 rules in 5-state CA with any ergodic and periodic boundary condition, and numerically confirm all the other rules non-ergodic with some boundary condition. We classify ergodic rules into several patterns, which exhibit a variety of ergodic structure.
]]></description>
<dc:subject>nonlinear-dynamics cellular-automata ergodic-systems combinatorics complexology rather-interesting classification to-write-about to-simulate</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:163a69784c1b/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cellular-automata"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:ergodic-systems"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:combinatorics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:classification"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-simulate"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/2511.15533">
    <title>[2511.15533] Spatiotemporal Activity-Driven Networks</title>
    <dc:date>2026-01-18T20:44:41+00:00</dc:date>
    <link>https://arxiv.org/abs/2511.15533</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Temporal-network models have provided key insights into how time-varying connectivity shapes dynamical processes such as spreading. Among them, the activity-driven model is a widely used, analytically tractable benchmark. Yet many temporal networks, such as those of physical proximity, are also embedded in space, and spatial constraints are known to affect dynamics unfolding on the networks strongly. Despite this, there is a lack of similar simple and solvable models for spatiotemporal contact structures. Here, we introduce a spatial activity-driven model in which short-range contacts are more frequent. This model is analytically tractable and captures the joint effects of space and time. We show analytically and numerically that the model reproduces several characteristic features of social and contact networks, including strong and weak ties, clustering, and triangles having weights above the median. These traits can be attributed to space acting as a form of memory. Simulations of spreading dynamics on top of the model networks further illustrate the role of space, highlighting how localisation slows down spreading. Furthermore, the framework is well-suited for modelling social distancing in a principled way as an intervention measure aimed at reducing long-range links. We find that, unlike for non-spatial networks, even a small spatially targeted reduction in the total number of contacts can be very effective. More broadly, by offering a tractable framework, the model enables systematic exploration of dynamical processes on spatiotemporal networks.
]]></description>
<dc:subject>network-theory nonlinear-dynamics self-organization self-assembly rather-interesting complexology to-understand to-simulate consider:L1-geometry</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:d8d44de8f4c9/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:network-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-assembly"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-understand"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-simulate"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:L1-geometry"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/2308.06277">
    <title>[2308.06277] Descriptive complexity for neural networks via Boolean networks</title>
    <dc:date>2025-12-01T15:55:32+00:00</dc:date>
    <link>https://arxiv.org/abs/2308.06277</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We investigate the expressive power of neural networks from the point of view of descriptive complexity. We study neural networks that use floating-point numbers and piecewise polynomial activation functions from two perspectives: 1) the general scenario where neural networks run for an unlimited number of rounds and have unrestricted topologies, and 2) classical feedforward neural networks that have the topology of layered acyclic graphs and run for only a constant number of rounds. We characterize these neural networks via Boolean networks formalized via a recursive rule-based logic. In particular, we show that the sizes of the neural networks and the corresponding Boolean rule formulae are polynomially related. In fact, in the direction from Boolean rules to neural networks, the blow-up is only linear. Our translations result in a time delay, which is the number of rounds that it takes to simulate a single computation step. In the translation from neural networks to Boolean rules, the time delay of the resulting formula is polylogarithmic in the size of the neural network. In the converse translation, the time delay of the neural network is linear in the formula size. Ultimately, we obtain translations between neural networks, Boolean networks, the diamond-free fragment of modal substitution calculus, and a class of recursive Boolean circuits. Our translations offer a method, for almost any activation function F, of translating any neural network in our setting into an equivalent neural network that uses F at each node. This even includes linear activation functions, which is possible due to using floats rather than actual reals!
]]></description>
<dc:subject>boolean-networks neural-networks approximation rather-interesting nonlinear-dynamics complexology to-write-about to-simulate</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:d77e837ab688/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:boolean-networks"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:neural-networks"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:approximation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-simulate"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/2507.13253">
    <title>[2507.13253] Life Finds A Way: Emergence of Cooperative Structures in Adaptive Threshold Networks</title>
    <dc:date>2025-08-17T13:56:25+00:00</dc:date>
    <link>https://arxiv.org/abs/2507.13253</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[There has been a long debate on how new levels of organization have evolved. It might seem unlikely, as cooperation must prevail over competition. One well-studied example is the emergence of autocatalytic sets, which seem to be a prerequisite for the evolution of life. Using a simple model, we investigate how varying bias toward cooperation versus antagonism shapes network dynamics, revealing that higher-order organization emerges even amid pervasive antagonistic interactions. In general, we observe that a quantitative increase in the number of elements in a system leads to a qualitative transition.
We present a random threshold-directed network model that integrates node-specific traits with dynamic edge formation and node removal, simulating arbitrary levels of cooperation and competition. In our framework, intrinsic node values determine directed links through various threshold rules. Our model generates a multi-digraph with signed edges (reflecting support/antagonism, labeled ``help''/``harm''), which ultimately yields two parallel yet interdependent threshold graphs. Incorporating temporal growth and node turnover in our approach allows exploration of the evolution, adaptation, and potential collapse of communities and reveals phase transitions in both connectivity and resilience.
Our findings extend classical random threshold and Erdős-Rényi models, offering new insights into adaptive systems in biological and economic contexts, with emphasis on the application to Collective Affordance Sets. This framework should also be useful for making predictions that will be tested by ongoing experiments of microbial communities in soil.
]]></description>
<dc:subject>complexology Kauffmania simple-models-of-evolution agent-based to-write-about to-simulate consider:a-little-math-you-know-as-a-treat</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:6f2a7de90791/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:Kauffmania"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simple-models-of-evolution"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:agent-based"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-simulate"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:a-little-math-you-know-as-a-treat"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://longnow.org/ideas/physics-life-complexity-assembly-theory/">
    <title>Why the Physics Underlying Life is Fundamental and Computation is Not - Long Now</title>
    <dc:date>2025-04-13T19:30:13+00:00</dc:date>
    <link>https://longnow.org/ideas/physics-life-complexity-assembly-theory/</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Life is undeniably real. It defines the very boundary of our reality because it is what we are. Yet despite this fundamental presence, the nature of life has defied precise scientific explanation. While we recognize “life” colloquially and can characterize its more familiar biological forms, we struggle with frontier questions: how does life emerge from non-life? How can we engineer new forms of life? How might we recognize artificial or alien life? What are the sources of novelty and creativity that underlie biology and technology? 

]]></description>
<dc:subject>assembly-theory self-organization complexology to-read overview philosophy-of-science representation</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:826b80edd2bf/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:assembly-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-read"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:overview"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:philosophy-of-science"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:representation"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/2401.05375">
    <title>[2401.05375] Classical Sorting Algorithms as a Model of Morphogenesis: self-sorting arrays reveal unexpected competencies in a minimal model of basal intelligence</title>
    <dc:date>2025-04-05T21:13:42+00:00</dc:date>
    <link>https://arxiv.org/abs/2401.05375</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[The emerging field of Diverse Intelligence seeks to identify, formalize, and understand commonalities in behavioral competencies across a wide range of implementations. Especially interesting are simple systems that provide unexpected examples of memory, decision-making, or problem-solving in substrates that at first glance do not appear to be complex enough to implement such capabilities. We seek to develop tools to help understand the minimal requirements for such capabilities, and to learn to recognize and predict basal forms of intelligence in unconventional substrates. Here, we apply novel analyses to the behavior of classical sorting algorithms, short pieces of code which have been studied for many decades. To study these sorting algorithms as a model of biological morphogenesis and its competencies, we break two formerly-ubiquitous assumptions: top-down control (instead, showing how each element within a array of numbers can exert minimal agency and implement sorting policies from the bottom up), and fully reliable hardware (instead, allowing some of the elements to be "damaged" and fail to execute the algorithm). We quantitatively characterize sorting activity as the traversal of a problem space, showing that arrays of autonomous elements sort themselves more reliably and robustly than traditional implementations in the presence of errors. Moreover, we find the ability to temporarily reduce progress in order to navigate around a defect, and unexpected clustering behavior among the elements in chimeric arrays whose elements follow one of two different algorithms. The discovery of emergent problem-solving capacities in simple, familiar algorithms contributes a new perspective to the field of Diverse Intelligence, showing how basal forms of intelligence can emerge in simple systems without being explicitly encoded in their underlying mechanics.
]]></description>
<dc:subject>artificial-life complexology rather-interesting problem-solving robustness to-write-about consider:evolved-solutions consider:local-and-global consider:performance-measures</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:181ddb4e6470/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:artificial-life"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:problem-solving"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:robustness"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:evolved-solutions"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:local-and-global"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:performance-measures"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/2209.07505">
    <title>[2209.07505] Temporal, structural, and functional heterogeneities extend criticality and antifragility in random Boolean networks</title>
    <dc:date>2023-10-10T10:08:10+00:00</dc:date>
    <link>https://arxiv.org/abs/2209.07505</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Most models of complex systems have been homogeneous, i.e., all elements have the same properties (spatial, temporal, structural, functional). However, most natural systems are heterogeneous: few elements are more relevant, larger, stronger, or faster than others. In homogeneous systems, criticality -- a balance between change and stability, order and chaos -- is usually found for a very narrow region in the parameter space, close to a phase transition. Using random Boolean networks -- a general model of discrete dynamical systems -- we show that heterogeneity -- in time, structure, and function -- can broaden additively the parameter region where criticality is found. Moreover, parameter regions where antifragility is found are also increased with heterogeneity. However, maximum antifragility is found for particular parameters in homogeneous networks. Our work suggests that the "optimal" balance between homogeneity and heterogeneity is non-trivial, context-dependent, and in some cases, dynamic.
]]></description>
<dc:subject>complexology Kauffmania boolean-networks nonlinear-dynamics automata to-write-about to-simulate define-your-terms</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:e4a365462d48/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:Kauffmania"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:boolean-networks"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:automata"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-simulate"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:define-your-terms"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://psyarxiv.com/27qba/">
    <title>PsyArXiv Preprints | Naturalising Agent Causation</title>
    <dc:date>2022-05-28T12:23:31+00:00</dc:date>
    <link>https://psyarxiv.com/27qba/</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[The idea of agent causation - that a system like a living organism can be a cause of things in the world - is often seen as mysterious and deemed to be at odds with the physicalist thesis that is now commonly embraced in science and philosophy. Instead, the causal power of organisms is attributed to mechanistic components within the system or derived from the causal activity at the lowest level of physical description. In either case, the ‘agent’ itself (i.e., the system as a whole) is left out of the picture entirely, and agent causation is explained away. We argue that this is not the right way to think about causation in biology, or in systems more generally. We present a framework of eight criteria that we argue, collectively, describe a system that overcomes the challenges concerning agent causality, in an entirely naturalistic and non-mysterious way. They are: 1) Thermodynamic Autonomy, 2) Persistence, 3) Endogenous Activity, 4) Holistic Integration, 5) Low-Level Indeterminacy, 6) Multiple Realisability, 7) Historicity, 8) Agent-Level Normativity. Each criterion is taken to be dimensional rather than categorical, and thus we conclude with a short discussion on how researchers working on quantifying agency may use this multi-dimensional framework to situate and guide their research.

]]></description>
<dc:subject>philosophy-of-science complexology agents representation individuation causality rather-interesting to-read to-understand consider:scale</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:e9a06e0f2215/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:philosophy-of-science"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:agents"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:representation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:individuation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:causality"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-read"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-understand"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:scale"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1606.00101">
    <title>[1606.00101] Exploratory Adaptation in Large Random Networks</title>
    <dc:date>2022-05-01T12:02:05+00:00</dc:date>
    <link>https://arxiv.org/abs/1606.00101</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[The capacity of cells and organisms to respond to challenging conditions in a repeatable manner is limited by a finite repertoire of pre-evolved adaptive responses. Beyond this capacity, cells can use exploratory dynamics to cope with a much broader array of conditions. However, the process of adaptation by exploratory dynamics within the lifetime of a cell is not well understood. Here we demonstrate the feasibility of exploratory adaptation in a high-dimensional network model of gene regulation. Exploration is initiated by failure to comply with a constraint and is implemented by random sampling of network configurations. It ceases if and when the network reaches a stable state satisfying the constraint. We find that successful convergence (adaptation) in high dimensions requires outgoing network hubs and is enhanced by their auto-regulation. The ability of these empirically-validated features of gene regulatory networks to support exploratory adaptation without fine-tuning, makes it plausible for biological implementation.
]]></description>
<dc:subject>reaction-networks complexology systems-biology nonlinear-dynamics rather-interesting looking-to-see to-write-about to-simulate consider:small-visual-examples</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:1a81afda7c08/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:reaction-networks"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:systems-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:looking-to-see"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-simulate"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:small-visual-examples"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/2201.03582">
    <title>[2201.03582] The Cultural Transmission of Tacit Knowledge</title>
    <dc:date>2022-04-02T12:13:08+00:00</dc:date>
    <link>https://arxiv.org/abs/2201.03582</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[A wide variety of cultural practices take the form of "tacit" knowledge, where the rules and principles are neither obvious to an observer nor known explicitly by the practitioners. This poses a problem for cultural evolution: if beginners cannot simply imitate experts, and experts cannot simply say or demonstrate what they are doing, how can tacit knowledge pass from generation to generation? We present a domain-general model of "tacit teaching", that shows how high-fidelity transmission of tacit knowledge is possible. It applies in cases where the underlying features of the practice are subject to interacting and competing constraints, as is expected both in embodied and in social practices. Our model makes predictions for key features of the teaching process. It predicts a tell-tale distribution of teaching outcomes: some students will be nearly perfect performers while others receiving the same instruction will be disastrously bad. This differs from most mainstream cultural evolution models centered on high-fidelity transmission with minimal copying errors, which lead to a much narrower distribution where students are mostly equally mediocre. The model also predicts generic features of the cultural evolution of tacit knowledge. The evolution of tacit knowledge is expected to be bursty, with long periods of stability interspersed with brief periods of dramatic change, and where tacit knowledge, once lost, becomes essentially impossible to recover.
]]></description>
<dc:subject>cultural-dynamics tacit-knowledge evolutionary-economics rather-interesting complexology agent-based to-write-about to-simulate</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:99bfaf6699a3/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cultural-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:tacit-knowledge"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:evolutionary-economics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:agent-based"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-simulate"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1805.02354">
    <title>[1805.02354] Transient phases in the Vicsek model of flocking</title>
    <dc:date>2022-03-19T12:11:35+00:00</dc:date>
    <link>https://arxiv.org/abs/1805.02354</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[The Vicsek model of flocking is studied by computer simulation. We confined our studies here to the morphologies and the lifetimes of transient phases. In our simulation, we have identified three distinct transient phases, namely, vortex phase, colliding phase and multi-domain phase. The mapping of Vicsek model to XY model in the v→0 limit prompted us to explore the possibility of finding any vortex kind of phases in the Vicsek model. We have obtained rotating vortex phase and measured the lifetime of this vortex phase. We have also measured the lifetimes of other two transient phases, i.e., colliding phase and multi-domain phase. We have measured the integrated lifetime (τt) of all these transient phases and studied this as function of density (ρ) and noise (η). In the low noise regime, we proposed here a scaling law τtN−a=F(ρN−b) where F(x) is a scaling function like F(x)∼x−s. By the method of data collapse, we have estimated the exponents as a=−0.110±0.010, b=0.950±0.010 and s=1.027±0.008. The integrated lifetime τ (defined in the text differently) was observed to decrease as the noise approaches the critical noise from below. This behaviour is quite unusual and contrary to the critical slowing down observed in the case of equilibrium phase transitions. We have provided a possible explanation from the time evolution of the distribution of the directions of velocities.
]]></description>
<dc:subject>flocking boids simulation complexology self-organization collective-behavior to-write-about to-visualize</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:c4d2ad67eead/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:flocking"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:boids"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:collective-behavior"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-visualize"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1511.09203">
    <title>[1511.09203] Statistical mechanics of complex economies</title>
    <dc:date>2022-03-15T15:55:57+00:00</dc:date>
    <link>https://arxiv.org/abs/1511.09203</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[In the pursuit of ever increasing efficiency and growth, our economies have evolved to remarkable degrees of complexity, with nested production processes feeding each other in order to create products of greater sophistication from less sophisticated ones, down to raw materials. The engine of such an expansion have been competitive markets that, according to General Equilibrium Theory (GET), achieve efficient allocations under specific conditions. We study large random economies within the GET framework, as templates of complex economies, and we find that a non-trivial phase transition occurs: the economy freezes in a state where all production processes collapse when either the number of primary goods or the number of available technologies fall below a critical threshold. As in other examples of phase transitions in large random systems, this is an unintended consequence of the growth in complexity. Our findings suggest that the Industrial Revolution can be regarded as a sharp transition between different phases, but also imply that well developed economies can collapse if too many intermediate goods are introduced.
]]></description>
<dc:subject>economics agent-based simulation looking-to-see complexology now-do-MMT to-write-about</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:8eb136b79800/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:economics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:agent-based"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:looking-to-see"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:now-do-MMT"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1907.13371">
    <title>[1907.13371] Proteins: the physics of amorphous evolving matter</title>
    <dc:date>2022-03-10T17:11:41+00:00</dc:date>
    <link>https://arxiv.org/abs/1907.13371</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Proteins are a matter of dual nature. As a physical object, a protein molecule is a folded chain of amino acids with multifarious biochemistry. But it is also an instantiation along an evolutionary trajectory determined by the function performed by the protein within a hierarchy of interwoven interaction networks of the cell, the organism and the population. A physical theory of proteins therefore needs to unify both aspects, the biophysical and the evolutionary. Specifically, it should provide a model of how the DNA gene is mapped into the functional phenotype of the protein. 
We review several physical approaches to the protein problem, focusing on a mechanical framework which treats proteins as evolvable condensed matter: Mutations introduce localized perturbations in the gene, which are translated to localized perturbations in the protein matter. A natural tool to examine how mutations shape the phenotype are Green's functions. They map the evolutionary linkage among mutations in the gene (termed epistasis) to cooperative physical interactions among the amino acids in the protein. We discuss how the mechanistic view can be applied to examine basic questions of protein evolution and design.
]]></description>
<dc:subject>structural-biology review everything-is-physics-again complexology oversimplifications-as-a-route-to-papers</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:df77874dd62d/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:structural-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:review"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:everything-is-physics-again"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:oversimplifications-as-a-route-to-papers"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1605.08070">
    <title>[1605.08070] Nonlinear Stochastic Dynamics of Complex Systems, I: A Chemical Reaction Kinetic Perspective with Mesoscopic Nonequilibrium Thermodynamics</title>
    <dc:date>2022-03-02T11:40:26+00:00</dc:date>
    <link>https://arxiv.org/abs/1605.08070</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We distinguish a mechanical representation of the world in terms of point masses with positions and momenta and the chemical representation of the world in terms of populations of different individuals, each with intrinsic stochasticity, but population wise with statistical rate laws in their syntheses, degradations, spatial diffusion, individual state transitions, and interactions. Such a formal kinetic system in a small volume V, like a single cell, can be rigorously treated in terms of a Markov process describing its nonlinear kinetics as well as nonequilibrium thermodynamics at a mesoscopic scale. We introduce notions such as open, driven chemical systems, entropy production, free energy dissipation, etc. Then in the macroscopic limit, we illustrate how two new "laws", in terms of a generalized free energy of the mesoscopic stochastic dynamics, emerge. Detailed balance and complex balance are two special classes of "simple" nonlinear kinetics. Phase transition is intrinsically related to multi-stability and saddle-node bifurcation phenomenon, in the limits of time t→∞ and system's size V→∞. Using this approach, we re-articulate the notion of inanimate equilibrium branch of a system and nonequilibrium state of a living matter, as originally proposed by Nicolis and Prigogine, and seek a logic consistency between this viewpoint and that of P. W. Anderson and J. J. Hopfield's in which macroscopic law emerges through symmetry breaking.
]]></description>
<dc:subject>statistical-mechanics nonlinear-dynamics emergence complexology rather-interesting to-understand</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:41b3b3b111c6/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:statistical-mechanics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:emergence"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-understand"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1711.02754">
    <title>[1711.02754] Hamming distance and mobility behavior in generalized rock-paper-scissors models</title>
    <dc:date>2022-02-17T11:30:43+00:00</dc:date>
    <link>https://arxiv.org/abs/1711.02754</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[This work reports on two related investigations of stochastic simulations which are widely used to study biodiversity and other related issues. We first deal with the behavior of the Hamming distance under the increase of the number of species and the size of the lattice, and then investigate how the mobility of the species contributes to jeopardize biodiversity. The investigations are based on the standard rules of reproduction, mobility and predation or competition, which are described by specific rules, guided by generalization of the rock-paper-scissors game, valid in the case of three species. The results on the Hamming distance indicate that it engenders universal behavior, independently of the number of species and the size of the square lattice. The results on the mobility confirm the prediction that it may destroy diversity, if it is increased to higher and higher values.
]]></description>
<dc:subject>complexology agent-based evolutionary-economics RPS theoretical-biology stress-testing rather-interesting to-write-about consider:other-distances consider:convolution</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:c86e755ee85d/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:agent-based"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:evolutionary-economics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:RPS"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:theoretical-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:stress-testing"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:other-distances"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:convolution"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://occupymath.wordpress.com/2020/10/01/what-do-mathematicians-do-all-day-part-iv/">
    <title>What do mathematicians do all day? Part IV – Occupy Math</title>
    <dc:date>2021-07-31T11:18:32+00:00</dc:date>
    <link>https://occupymath.wordpress.com/2020/10/01/what-do-mathematicians-do-all-day-part-iv/</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Occupy Math has been working on apoptotic cellular automata for eight years now. One thing that he has figured out is that there are billions and billions of rules that make pictures that die out at some point. This huge collection of pictures is a wonderful sandbox to test ideas about how to get evolution to do what is wanted, rather than some random thing. As an added bonus, even though it is a terrifically complex space with about 35 dimensions, the results of running evolution are pictures that are relatively easy to render and think about.

]]></description>
<dc:subject>cellular-automata evolutionary-algorithms complexology rather-interesting philosophy-of-science to-write-about to-visualize</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:d46eef9f1818/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cellular-automata"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:evolutionary-algorithms"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:philosophy-of-science"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-visualize"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1906.09465">
    <title>[1906.09465] Quantifying the Total Effect of Edge Interventions in Discrete Multistate Networks</title>
    <dc:date>2021-04-07T20:42:27+00:00</dc:date>
    <link>https://arxiv.org/abs/1906.09465</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Developing efficient computational methods to assess the impact of external interventions on the dynamics of a network model is an important problem in systems biology. This paper focuses on quantifying the global changes that result from the application of an intervention to produce a desired effect, which we define as the total effect of the intervention. The type of mathematical models that we will consider are discrete dynamical systems which include the widely used Boolean networks and their generalizations. The potential interventions can be represented by a set of nodes and edges that can be manipulated to produce a desired effect on the system. We use a class of regulatory rules called nested canalizing functions that frequently appear in published models and were inspired by the concept of canalization in evolutionary biology. In this paper, we provide a polynomial normal form based on the canalizing properties of regulatory functions. Using this polynomial normal form, we give a set of formulas for counting the maximum number of transitions that will change in the state space upon an edge deletion in the wiring diagram. These formulas rely on the canalizing structure of the target function since the number of changed transitions depends on the canalizing layer that includes the input to be deleted. We also present computations on random networks to compare the exact number of changes with the upper bounds provided by our formulas. Finally, we provide statistics on the sharpness of these upper bounds in random networks.
]]></description>
<dc:subject>boolean-networks rather-interesting theoretical-biology complexology Kauffmania to-write-about to-simulate consider:visualization consider:performance-measures</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:d8cc9f37d56e/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:boolean-networks"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:theoretical-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:Kauffmania"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-simulate"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:visualization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:performance-measures"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/2012.05437">
    <title>[2012.05437] Robustness and Stability of Spin Glass Ground States to Perturbed Interactions</title>
    <dc:date>2021-03-27T11:05:18+00:00</dc:date>
    <link>https://arxiv.org/abs/2012.05437</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Across many scientific and engineering disciplines, it is important to consider how much the output of a given system changes due to perturbations of the input. Here, we study the robustness of the ground states of ±J spin glasses on random graphs to flips of the interactions. For a sparse graph, a dense graph, and the fully connected Sherrington-Kirkpatrick model, we find relatively large sets of interactions that generate the same ground state. These sets can themselves be analyzed as sub-graphs of the interaction domain, and we compute many of their topological properties. In particular, we find that the robustness of these sub-graphs is much higher than one would expect from a random model. Most notably, it scales in the same logarithmic way with the size of the sub-graph as has been found in genotype-phenotype maps for RNA secondary structure folding, protein quaternary structure, gene regulatory networks, as well as for models for genetic programming. The similarity between these disparate systems suggests that this scaling may have a more universal origin.
]]></description>
<dc:subject>complexology fitness-landscapes spin-glasses scaling to-write-about to-simulate consider:nonrandom-graphs consider:feature-discovery</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:0c497321d865/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:fitness-landscapes"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:spin-glasses"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:scaling"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-simulate"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:nonrandom-graphs"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:feature-discovery"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1606.00641">
    <title>[1606.00641] The nonequilibrium glassy dynamics of self-propelled particles</title>
    <dc:date>2020-06-17T13:52:23+00:00</dc:date>
    <link>https://arxiv.org/abs/1606.00641</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We study the glassy dynamics taking place in dense assemblies of athermal active particles that are driven solely by a nonequilibrium self-propulsion mechanism. Active forces are modeled as an Ornstein-Uhlenbeck stochastic process, characterized by a persistence time and an effective temperature, and particles interact via a Lennard-Jones potential that yields well-studied glassy behavior in the Brownian limit, obtained as the persistence time vanishes. By increasing the persistence time, the system departs more strongly from thermal equilibrium and we provide a comprehensive numerical analysis of the structure and dynamics of the resulting active fluid. Finite persistence times profoundly affect the static structure of the fluid and give rise to nonequilibrium velocity correlations that are absent in thermal systems. Despite these nonequilibrium features, for any value of the persistence time we observe a nonequilibrium glass transition as the effective temperature is decreased. Surprisingly, increasing departure from thermal equilibrium is found to promote (rather than suppress) the glassy dynamics. Overall, our results suggest that with increasing persistence time, microscopic properties of the active fluid change quantitatively, but the broad features of the nonequilibrium glassy dynamics observed with decreasing the effective temperature remain qualitatively similar to those of thermal glass-formers.
]]></description>
<dc:subject>active-matter collective-behavior rather-interesting physics complexology to-write-about to-simulate consider:simplest-possible-vis</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:d7aa4aefa989/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:active-matter"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:collective-behavior"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:physics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-simulate"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:simplest-possible-vis"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1702.02764">
    <title>[1702.02764] A new method to reduce the number of time delays in a network</title>
    <dc:date>2020-05-07T12:30:09+00:00</dc:date>
    <link>https://arxiv.org/abs/1702.02764</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Time delays may cause dramatic changes to the dynamics of interacting oscillators. Coupled networks of interacting dynamical systems can behave unexpectedly when the signal between the vertices are time delayed. It has been shown for a very general class of systems that the time delays can be rearranged as long as the total time delay over the constitutive loops of the network is conserved. This fact allows to reduce the number of time delays of the problem without loss of information. There is a theoretical lower bound for this number, but in many cases we can find a numerical solution that beats this limit. Here we propose a formulation of the problem and a numerical method to even further reduce the number of time delays in a network.
]]></description>
<dc:subject>coupled-oscillators complexology inference rather-interesting dynamical-systems collective-behavior to-write-about to-simulate consider:looking-to-see consider:heuristics</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:28be316b5332/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:coupled-oscillators"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:inference"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:dynamical-systems"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:collective-behavior"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-simulate"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:looking-to-see"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:heuristics"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://psyarxiv.com/2htkr/">
    <title>PsyArXiv Preprints | Radical Embodied Computation: Reproduction of Similarity by Analogy as an Order Generating Mechanism in Complex Systems</title>
    <dc:date>2020-05-02T11:36:43+00:00</dc:date>
    <link>https://psyarxiv.com/2htkr/</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[About two decades ago, scholars from the scientific disciplines that study human behavior and cognition, suggested an era of post-cognitivism was imminent, in which the computer metaphor, computationalism and representationalism would be discarded as viable theoretical frameworks for explaining phenomena of the body and the mind. In the present paper I argue that explanations of complex adaptive behavior require a theory of meaning mechanics that explains how complex adaptive systems can use semantic information to coordinate their behavior. This calls for a unification of sorts between the insights obtained in ecological psychology and embodied embedded cognition with principles of natural computation (cf. Decastro, 2007) in the context of explaining the behavior and properties of complex adaptive systems and networks (see e.g., Freeman et al., 2001; Chialvo, 2010; Flack, 2017a; Scheffer et al., 2018). I will refer to this framework as Radical Embodied Computation (REC++) and discuss some of the philosophical and theoretical issues that have to be resolved. I conclude by suggesting a mechanism for the emergence of meaning that is based the conception of self-affine scaling as the reproduction of similarity by analogy.

]]></description>
<dc:subject>cognition philosophy-of-mind complexology rather-interesting to-write-about pragmatism psychology</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:7a3cd854134f/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cognition"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:philosophy-of-mind"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pragmatism"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:psychology"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1012.0369">
    <title>[1012.0369] Jammed particulate systems are inherently nonharmonic</title>
    <dc:date>2020-01-23T02:10:12+00:00</dc:date>
    <link>https://arxiv.org/abs/1012.0369</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Jammed particulate systems, such as granular media, colloids, and foams, interact via one-sided forces that are nonzero only when particles overlap. We find that systems with one-sided repulsive interactions possess no linear response regime in the large system limit (N→∞) for all pressures p (or compressions Δϕ), and for all N near jamming onset p→0. We perform simulations on 2D frictionless bidisperse mechanically stable disk packings over a range of packing fractions Δϕ=ϕ−ϕJ above jamming onset ϕJ. We apply perturbations with amplitude δ to the packings along each eigen-direction from the dynamical matrix and determine whether the response of the system evolving at constant energy remains in the original eigenmode of the perturbation. For δ>δc, which we calculate analytically, a single contact breaks and fluctuations abruptly spread to all harmonic modes. As δ increases further all discrete harmonic modes disappear into a continuous frequency band. We find that <δc>∼Δϕ/Nλ, where 1>λ>0.5, and thus jammed particulate systems are inherently nonharmonic with no linear vibrational response regime as N→∞ over the full range of Δϕ, and as Δϕ→0 at any N.
]]></description>
<dc:subject>granular-materials physics! nonlinear-dynamics complexology rather-interesting simulation looking-to-see have-you-tried-thwacking-it? ah-yes-I-see-you-did</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:ad58ef1f419b/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:granular-materials"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:physics!"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:looking-to-see"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:have-you-tried-thwacking-it?"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:ah-yes-I-see-you-did"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1410.8001">
    <title>[1410.8001] The hipster effect: When anticonformists all look the same</title>
    <dc:date>2020-01-10T20:55:37+00:00</dc:date>
    <link>https://arxiv.org/abs/1410.8001</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[In such different domains as neurosciences, spin glasses, social science, economics and finance, large ensemble of interacting individuals following (mainstream) or opposing (hipsters) to the majority are ubiquitous. In these systems, interactions generally occur after specific delays associated to transport, transmission or integration of information. We investigate here the impact of anti-conformism combined to delays in the emergent dynamics of large populations of mainstreams and hipsters. To this purpose, we introduce a class of simple statistical systems of interacting agents composed of (i) mainstreams and anti-conformists in the presence of (ii) delays, possibly heterogeneous, in the transmission of information. In this simple model, each agent can be in one of two states, and can change state in continuous time with a rate depending on the state of others in the past. We express the thermodynamic limit of these systems as the number of agents diverge, and investigate the solutions of the limit equation, with a particular focus on synchronized oscillations induced by delayed interactions. We show that when hipsters are too slow in detecting the trends, they will consistently make the same choice, and realizing this too late, they will switch, all together to another state where they remain alike. Similar synchronizations arise when the impact of mainstreams on hipsters choices (and reciprocally) dominate the impact of other hipsters choices, and we show that these may emerge only when the randomness in the hipsters decisions is sufficiently large. Beyond the choice of the best suit to wear this winter, this study may have important implications in understanding synchronization of nerve cells, investment strategies in finance, or emergent dynamics in social science, domains in which delays of communication and the geometry of information accessibility are prominent.
]]></description>
<dc:subject>complexology agent-based collective-behavior evolutionary-economics simulation to-write-about to-simulate coupled-oscillators</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:83f6fd17d7a3/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:agent-based"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:collective-behavior"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:evolutionary-economics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-simulate"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:coupled-oscillators"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/cs/0008002">
    <title>[cs/0008002] Structure of some sand pile model</title>
    <dc:date>2019-12-26T13:15:43+00:00</dc:date>
    <link>https://arxiv.org/abs/cs/0008002</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[SPM (Sand Pile Model) is a simple discrete dynamical system used in physics to represent granular objects. It is deeply related to integer partitions, and many other combinatorics problems, such as tilings or rewriting systems. The evolution of the system started with n stacked grains generates a lattice, denoted by SPM(n). We study here the structure of this lattice. We first explain how it can be constructed, by showing its strong self-similarity property. Then, we define SPM(infini), a natural extension of SPM when one starts with an infinite number of grains. Again, we give an efficient construction algorithm and a coding of this lattice using a self-similar tree. The two approaches give different recursive formulae for the cardinal of SPM(n), where no closed formula have ever been found.
]]></description>
<dc:subject>sandpiles complexology combinatorics rather-interesting nonlinear-dynamics to-simulate to-write-about</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:e239f6bbcbf7/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:sandpiles"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:combinatorics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-simulate"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1902.04174">
    <title>[1902.04174] Cut-off for sandpiles on tiling graphs</title>
    <dc:date>2019-11-25T17:40:16+00:00</dc:date>
    <link>https://arxiv.org/abs/1902.04174</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Sandpile dynamics are considered on graphs constructed from periodic plane and space tilings by assigning a growing piece of the tiling either torus or open boundary conditions. A general method of obtaining the Green's function of the tiling is given, and a total variation cut-off phenomenon is demonstrated under general conditions. It is shown that the boundary condition does not affect the mixing time for planar tilings, nor does it change the asymptotic mixing time for the cubic lattice $\zed^d$ for all sufficiently large d. In a companion paper, computational methods are used to demonstrate that the mixing time is altered for the $\Dfour$ lattice in dimension 4.
]]></description>
<dc:subject>sandpiles boundary-conditions complexology rather-interesting to-simulate to-write-about consider:arbitrary-graphs</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:a0c17be6329b/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:sandpiles"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:boundary-conditions"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-simulate"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:arbitrary-graphs"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1907.10924">
    <title>[1907.10924] Influence of the size of the intruder on the reorganization of a 2D granular medium</title>
    <dc:date>2019-09-08T14:38:35+00:00</dc:date>
    <link>https://arxiv.org/abs/1907.10924</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We consider the rearrangements of a vertical twodimensional granular packing induced by the withdrawal of an intruder. Here, we focus on the influence of the size of the intruder on the reorganization process. The long term evolution of the granular packing is investigated as well as the avalanche dynamics that characterize the short term rearrangements around the intruder. For small enough intruder, we observe the formation of arches that periodically destabilize and influence the reorganization dynamics of the two-dimensional packing through larger rearrangement events.
]]></description>
<dc:subject>granular-materials nonlinear-dynamics complexology rather-interesting experiment looking-to-see robustness self-organization mesoscale-structure-formation to-simulate consider:dominoes</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:7fbc72d6344c/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:granular-materials"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:experiment"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:looking-to-see"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:robustness"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:mesoscale-structure-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-simulate"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:dominoes"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1908.00971">
    <title>[1908.00971] Physical machine learning outperforms &quot;human learning&quot; in Quantum Chemistry</title>
    <dc:date>2019-08-07T11:21:25+00:00</dc:date>
    <link>https://arxiv.org/abs/1908.00971</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Two types of approaches to modeling molecular systems have demonstrated high practical efficiency. Density functional theory (DFT), the most widely used quantum chemical method, is a physical approach predicting energies and electron densities of molecules. Recently, numerous papers on machine learning (ML) of molecular properties have also been published. ML models greatly outperform DFT in terms of computational costs, and may even reach comparable accuracy, but they are missing physicality - a direct link to Quantum Physics - which limits their applicability. Here, we propose an approach that combines the strong sides of DFT and ML, namely, physicality and low computational cost. We derive general equations for exact electron densities and energies that can naturally guide applications of ML in Quantum Chemistry. Based on these equations, we build a deep neural network that can compute electron densities and energies of a wide range of organic molecules not only much faster, but also closer to exact physical values than current versions of DFT. In particular, we reached a mean absolute error in energies of molecules with up to eight non-hydrogen atoms as low as 0.9 kcal/mol relative to CCSD(T) values, noticeably lower than those of DFT (approaching ~2 kcal/mol) and ML (~1.5 kcal/mol) methods. A simultaneous improvement in the accuracy of predictions of electron densities and energies suggests that the proposed approach describes the physics of molecules better than DFT functionals developed by "human learning" earlier. Thus, physics-based ML offers exciting opportunities for modeling, with high-theory-level quantum chemical accuracy, of much larger molecular systems than currently possible.
]]></description>
<dc:subject>emergent-design machine-learning neural-networks quantums molecular-design complexology to-write-about</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:6d7b4ecfd102/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:emergent-design"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:machine-learning"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:neural-networks"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:quantums"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:molecular-design"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1808.06271">
    <title>[1808.06271] Transforming mesoscale granular plasticity through particle shape</title>
    <dc:date>2019-05-02T08:55:06+00:00</dc:date>
    <link>https://arxiv.org/abs/1808.06271</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[When an amorphous material is strained beyond the point of yielding it enters a state of continual reconfiguration via dissipative, avalanche-like slip events that relieve built-up local stress. However, how the statistics of such events depend on local interactions among the constituent units remains debated. To address this we perform experiments on granular material in which we use particle shape to vary the interactions systematically. Granular material, confined under constant pressure boundary conditions, is uniaxially compressed while stress is measured and internal rearrangements are imaged with x-rays. We introduce volatility, a quantity from economic theory, as a powerful new tool to quantify the magnitude of stress fluctuations, finding systematic, shape-dependent trends. For all 22 investigated shapes the magnitude s of relaxation events is well-fit by a truncated power law distribution P(s)∼s−τexp(−s/s∗), as has been proposed within the context of plasticity models. The power law exponent τ for all shapes tested clusters around τ= 1.5, within experimental uncertainty covering the range 1.3 - 1.7. The shape independence of τ and its compatibility with mean field models indicate that the granularity of the system, but not particle shape, modifies the stress redistribution after a slip event away from that of continuum elasticity. Meanwhile, the characteristic maximum event size s∗ changes by two orders of magnitude and tracks the shape dependence of volatility. Particle shape in granular materials is therefore a powerful new factor influencing the distance at which an amorphous system operates from scale-free criticality. These experimental results are not captured by current models and suggest a need to reexamine the mechanisms driving mesoscale plastic deformation in amorphous systems.
]]></description>
<dc:subject>granular-materials condensed-matter rather-interesting looking-to-see experiment engineering-design consider:simulation consider:performance-measures complexology</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:ae5ff6a5ef63/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:granular-materials"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:condensed-matter"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:looking-to-see"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:experiment"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:engineering-design"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:performance-measures"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1608.03145">
    <title>[1608.03145] Physical model of the genotype-to-phenotype map of proteins</title>
    <dc:date>2019-04-24T15:24:51+00:00</dc:date>
    <link>https://arxiv.org/abs/1608.03145</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[How DNA is mapped to functional proteins is a basic question of living matter. We introduce and study a physical model of protein evolution which suggests a mechanical basis for this map. Many proteins rely on large-scale motion to function. We therefore treat protein as learning amorphous matter that evolves towards such a mechanical function: Genes are binary sequences that encode the connectivity of the amino acid network that makes a protein. The gene is evolved until the network forms a shear band across the protein, which allows for long-range, soft modes required for protein function. The evolution reduces the high-dimensional sequence space to a low-dimensional space of mechanical modes, in accord with the observed dimensional reduction between genotype and phenotype of proteins. Spectral analysis of the space of 106 solutions shows a strong correspondence between localization around the shear band of both mechanical modes and the sequence structure. Specifically, our model shows how mutations of the gene and their correlations occur at amino acids whose interactions determine the functional mode.
]]></description>
<dc:subject>complexology rather-interesting theoretical-biology abstract-models combinatorics bioinformatics structural-biology structure-function-cartoons to-write-about to-simulate lattice-polymers</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:63c4d1b88c21/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:theoretical-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:abstract-models"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:combinatorics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:bioinformatics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:structural-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:structure-function-cartoons"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-simulate"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:lattice-polymers"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://www.quantamagazine.org/with-food-webs-jennifer-dunne-puts-humans-back-into-ecology-20190321/">
    <title>With Food Webs, Jennifer Dunne Puts Humans Back Into Ecology | Quanta Magazine</title>
    <dc:date>2019-03-29T13:01:07+00:00</dc:date>
    <link>https://www.quantamagazine.org/with-food-webs-jennifer-dunne-puts-humans-back-into-ecology-20190321/</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[In 2016 Dunne co-authored the first comprehensive, detailed food web that explicitly included humans. That paper looked at the Aleut people who inhabited Alaska’s Sanak Archipelago for thousands of years. Since then, she and other researchers have described food webs that include humans from other ecosystems, both past and present-day. While they built these food webs, Dunne and some of her ecologist and archaeologist colleagues also started brainstorming about other ways to explore how humans have interacted with ecosystems throughout history.

They arrived at the idea of a new kind of network: not a food web, but a web of use. Their working group, which first came together in early 2017, looks at six populations of preindustrial or nonindustrial humans, cataloging every way that people interacted with the species around them: pelts for clothing, wood for shelter, leaves for medicine and so on. To visualize the results, the researchers map a culture’s five or six most-used species onto a circular plot, along with a “taxonomy of uses.” The result resembles a thickly woven dreamcatcher.

]]></description>
<dc:subject>ecology complexology define-your-terms rather-interesting ontology seeing-the-data to-write-about the-mangle-in-practice the-docile-body-of-the-scientist seeing-as-a-feature nature-and-man-sittin-in-a-tree</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:c69e22eb600c/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:ecology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:define-your-terms"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:ontology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:seeing-the-data"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:the-mangle-in-practice"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:the-docile-body-of-the-scientist"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:seeing-as-a-feature"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nature-and-man-sittin-in-a-tree"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://advances.sciencemag.org/content/5/2/eaat1328">
    <title>Best reply structure and equilibrium convergence in generic games | Science Advances</title>
    <dc:date>2019-02-23T13:31:36+00:00</dc:date>
    <link>http://advances.sciencemag.org/content/5/2/eaat1328</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Game theory is widely used to model interacting biological and social systems. In some situations, players may converge to an equilibrium, e.g., a Nash equilibrium, but in other situations their strategic dynamics oscillate endogenously. If the system is not designed to encourage convergence, which of these two behaviors can we expect a priori? To address this question, we follow an approach that is popular in theoretical ecology to study the stability of ecosystems: We generate payoff matrices at random, subject to constraints that may represent properties of real-world games. We show that best reply cycles, basic topological structures in games, predict nonconvergence of six well-known learning algorithms that are used in biology or have support from experiments with human players. Best reply cycles are dominant in complicated and competitive games, indicating that in this case equilibrium is typically an unrealistic assumption, and one must explicitly model the dynamics of learning.
]]></description>
<dc:subject>game-theory dynamical-systems complexology it's-more-complicated-than-you-think simulation to-write-about rather-interesting nudge-targets collective-behavior</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:4297fe75f59b/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:game-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:dynamical-systems"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:collective-behavior"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1807.04437">
    <title>[1807.04437] Finite-State Classical Mechanics</title>
    <dc:date>2019-02-07T11:01:26+00:00</dc:date>
    <link>https://arxiv.org/abs/1807.04437</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Reversible lattice dynamics embody basic features of physics that govern the time evolution of classical information. They have finite resolution in space and time, don't allow information to be erased, and easily accommodate other structural properties of microscopic physics, such as finite distinct state and locality of interaction. In an ideal quantum realization of a reversible lattice dynamics, finite classical rates of state-change at lattice sites determine average energies and momenta. This is very different than traditional continuous models of classical dynamics, where the number of distinct states is infinite, the rate of change between distinct states is infinite, and energies and momenta are not tied to rates of distinct state change. Here we discuss a family of classical mechanical models that have the informational and energetic realism of reversible lattice dynamics, while retaining the continuity and mathematical framework of classical mechanics. These models may help to clarify the informational foundations of mechanics.
]]></description>
<dc:subject>nonlinear-dynamics cellular-automata lattice-gases complexology representation review</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:dd62d76a1230/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cellular-automata"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:lattice-gases"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:representation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:review"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1811.11909">
    <title>[1811.11909] Synchronization of chaotic systems: A microscopic description</title>
    <dc:date>2019-02-07T10:56:30+00:00</dc:date>
    <link>https://arxiv.org/abs/1811.11909</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[The synchronization of coupled chaotic systems represents a fundamental example of self organization and collective behavior. This well-studied phenomenon is classically characterized in terms of macroscopic parameters, such as Lyapunov exponents, that help predict the systems transitions into globally organized states. However, the local, microscopic, description of this emergent process continues to elude us. Here we show that at the microscopic level, synchronization is captured through a gradual process of topological adjustment in phase space, in which the strange attractors of the two coupled systems continuously converge, taking similar form, until complete topological synchronization ensues. We observe the local nucleation of topological synchronization in specific regions of the systems attractor, providing early signals of synchrony, that appear significantly before the onset of complete synchronization. This local synchronization initiates at the regions of the attractor characterized by lower expansion rates, in which the chaotic trajectories are least sensitive to slight changes in initial conditions. Our findings offer an alternative description of synchronization in chaotic systems, exposing its local embryonic stages that are overlooked by the currently established global analysis. Such local topological synchronization enables the identification of configurations where prediction of the state of one system is possible from measurements on that of the other, even in the absence of global synchronization.
]]></description>
<dc:subject>nonlinear-dynamics coupled-oscillators rather-interesting synchronization to-read complexology physics! dynamical-systems</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:cff7a91c3c14/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:coupled-oscillators"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:synchronization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-read"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:physics!"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:dynamical-systems"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1802.06668">
    <title>[1802.06668] Sequentializing cellular automata</title>
    <dc:date>2018-11-01T09:57:44+00:00</dc:date>
    <link>https://arxiv.org/abs/1802.06668</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We study the problem of sequentializing a cellular automaton without introducing any intermediate states, and only performing reversible permutations on the tape. We give a decidable characterization of cellular automata which can be written as a single left-to-right sweep of a bijective rule from left to right over an infinite tape.
]]></description>
<dc:subject>cellular-automata representation rather-interesting a-bit-backwards-though complexology computational-complexity to-write-about consider:looking-to-see</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:a8a677a0bfe9/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cellular-automata"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:representation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:a-bit-backwards-though"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:computational-complexity"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:looking-to-see"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1808.05875">
    <title>[1808.05875] Co-evolution of nodes and links: diversity driven coexistence in cyclic competition of three species</title>
    <dc:date>2018-08-20T11:35:14+00:00</dc:date>
    <link>https://arxiv.org/abs/1808.05875</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[When three species compete cyclically in a well-mixed, stochastic system of N individuals, extinction is known to typically occur at times scaling as the system size N. This happens, for example, in rock-paper-scissors games or conserved Lotka-Volterra models in which every pair of individuals can interact on a complete graph. Here we show that if the competing individuals also have a "social temperament" to be either introverted or extroverted, leading them to cut or add links respectively, then long-living state in which all species coexist can occur when both introverts and extroverts are present. These states are non-equilibrium quasi-steady states, maintained by a subtle balance between species competition and network dynamcis. Remarkably, much of the phenomena is embodied in a mean-field description. However, an intuitive understanding of why diversity stabilizes the co-evolving node and link dynamics remains an open issue.]]></description>
<dc:subject>coevolution theoretical-biology rather-interesting population-biology social-norms to-write-about to-simulate artificial-life it's-more-complicated-than-you-think complexology agent-based</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:f60dbf50ce32/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:coevolution"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:theoretical-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:population-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:social-norms"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-simulate"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:artificial-life"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:agent-based"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1805.07360">
    <title>[1805.07360] Prediction in Projection: A new paradigm in delay-coordinate reconstruction</title>
    <dc:date>2018-06-21T10:59:23+00:00</dc:date>
    <link>https://arxiv.org/abs/1805.07360</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Delay-coordinate embedding is a powerful, time-tested mathematical framework for reconstructing the dynamics of a system from a series of scalar observations. Most of the associated theory and heuristics are overly stringent for real-world data, however, and real-time use is out of the question due to the expert human intuition needed to use these heuristics correctly. The approach outlined in this thesis represents a paradigm shift away from that traditional approach. I argue that perfect reconstructions are not only unnecessary for the purposes of delay-coordinate based forecasting, but that they can often be less effective than reduced-order versions of those same models. I demonstrate this using a range of low- and high-dimensional dynamical systems, showing that forecast models that employ imperfect reconstructions of the dynamics---i.e., models that are not necessarily true embeddings---can produce surprisingly accurate predictions of the future state of these systems. I develop a theoretical framework for understanding why this is so. This framework, which combines information theory and computational topology, also allows one to quantify the amount of predictive structure in a given time series, and even to choose which forecast method will be the most effective for those data.
]]></description>
<dc:subject>nonlinear-dynamics representation complexology rather-interesting to-write-about to-understand</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:f3cfac4b0635/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:representation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-understand"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://norabateson.wordpress.com/2015/11/03/symmathesy-a-word-in-progress/">
    <title>Symmathesy: A Word in Progress | norabateson</title>
    <dc:date>2018-06-21T10:56:32+00:00</dc:date>
    <link>https://norabateson.wordpress.com/2015/11/03/symmathesy-a-word-in-progress/</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[I would like to propose a new word for “System” that refers specifically to living systems – that is, to systems which emerge from the communications and interactions of living vitae (another new term, one which will be defined later). The new word, and concept, for “system” that I propose is one which highlights the expression and communication of interdependency and, particularly, mutual learning. The existing word, “system”, while useful for discussion of many kinds of systems, does not communicate contextual fields of simultaneous learning as is necessary for life. The inclusion of mutual learning in the terminology is specifically meant to preclude the models of engineering and mechanism that are implicit in much systems theorizing today.   We have learned that when dealing with living systems, the many variables of developing interaction become untenable to consider in such mechanistic parameters. This change in concept should spark a significant shift in our work, in the sciences, applied professions, communication, arts, that addresses or depends upon our understanding of life and evolution. The discourse with which we discuss and study the living world should be representative of the living world, and should cautiously avoid connotations that imply or are derived from engineering.

The notion of systems as being an arrangement of parts and wholes has become a distraction from the new systemic vision, which we are trying to encourage, that sees life as relational mutual learning contexts. As studies ranging from cognitive science to epigenetics, social science, ecology and evolutionary theory, are increasingly showing, evolution emerges in interrelationality, not in arrangement. Therefore the need is acute to create a differentiation between living systems and other systems.

]]></description>
<dc:subject>complexology representation define-your-terms rather-interesting to-write-about philosophy-of-science</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:9e46d74fc25a/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:representation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:define-your-terms"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:philosophy-of-science"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://kappalanguage.org/">
    <title>Home | Kappa Language</title>
    <dc:date>2018-05-28T12:03:17+00:00</dc:date>
    <link>https://kappalanguage.org/</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[By separating a rule from a patch on which it acts we gain a much clearer approach to mechanistic causality. If causal analysis were to proceed at the level of patches, it would obfuscate the causal structure of a system by dragging along context irrelevant to an event. In addition to simulation and static analysis, the Kappa platform also extracts the causal structure of a rule system from its simulation traces.

]]></description>
<dc:subject>bioinformatics representation hey-I-know-this-guy complexology pattern-discovery rather-interesting to-write-about</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:2f4be5227079/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:bioinformatics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:representation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:hey-I-know-this-guy"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-discovery"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://www.complexityexplorer.org/courses">
    <title>Complexity Explorer</title>
    <dc:date>2018-04-27T00:29:39+00:00</dc:date>
    <link>https://www.complexityexplorer.org/courses</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[New for 2018, our flagship course, Introduction to Complexity, will be open year round. All units will be available at all times, so you can learn the fundamentals of Complex Systems Science at your own pace, and earn your certificate at any time. 

All other courses are designed to be similar to a semester-long course, offering the chance to delve into a subject deeply. Courses are available in two ways: as a course session, or an archived course.  Each course is usually offered in one session per calendar year.

Tutorials are short, self-paced “mini-courses” designed to introduce students to important techniques and to provide illustrations of their application in complex systems.

Complexity Explorer's courses and tutorials are supported by user donations and contributions from the Santa Fe Institute.  Please consider donating to support further course and tutorial development.

]]></description>
<dc:subject>MOOC complexology hey-I-know-this-guy to-watch to-write-about</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:a2bfca577661/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:MOOC"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:hey-I-know-this-guy"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-watch"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://www.complex-systems.com/index.html">
    <title>Complex Systems</title>
    <dc:date>2018-03-11T10:30:55+00:00</dc:date>
    <link>http://www.complex-systems.com/index.html</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Founded by Stephen Wolfram in 1987 »
The original journal devoted to the science, mathematics and engineering of systems with simple components but complex overall behavior.

Hundreds of published papers, encompassing three decades of leading-edge complex systems research, are available for free and immediate download.]]></description>
<dc:subject>journal complexology nudge-targets open-access</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:8ebdb78c97c3/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:journal"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:open-access"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://www.worldwidewanderings.net/science.html">
    <title>World Wide Wanderings</title>
    <dc:date>2018-02-03T23:02:31+00:00</dc:date>
    <link>http://www.worldwidewanderings.net/science.html</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Over the years I have worked on many different research and computing projects, all over the world. Most of my scientific work is related to the origin of life, evolution, and complex systems & emergence. Below is a brief overview of the main projects that I am currently working on. Preprints of my publications on this work are available for download (see the list of publications).
]]></description>
<dc:subject>hey-I-know-this-guy science complexology to-write-about</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:27b3cf1036cf/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:hey-I-know-this-guy"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:science"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://blogs.scientificamerican.com/sa-visual/in-silico-flurries/">
    <title>In Silico Flurries - Scientific American Blog Network</title>
    <dc:date>2018-01-27T23:30:44+00:00</dc:date>
    <link>https://blogs.scientificamerican.com/sa-visual/in-silico-flurries/</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[The complexity and detail in the patterns from such reaction-diffusion systems can be truly surprising—a relatively simple process and small number of parameters can yield an endless variety of familiar patterns and shapes. One season-appropriate example of this is snowflakes, known for their variety and complexity. 
]]></description>
<dc:subject>simulation self-organization self-assembly complexology rather-interesting to-write-about Purdy-pitchers</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:def6c3aa39d1/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-assembly"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:Purdy-pitchers"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1709.08468">
    <title>[1709.08468] Local equilibrium in the Bak-Sneppen model</title>
    <dc:date>2018-01-26T00:02:34+00:00</dc:date>
    <link>https://arxiv.org/abs/1709.08468</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[The Bak Sneppen (BS) model is a very simple model that exhibits all the richness of self-organized criticality theory. At the thermodynamic limit, the BS model converges to a situation where all particles have a fitness that is uniformly distributed between a critical value pc and 1. The pc value is unknown, as are the variables that influence and determine this value. Here, we study the Bak Sneppen model in the case in which the lowest fitness particle interacts with an arbitrary even number of m nearest neighbors. We show that pc,m verifies a simple local equilibrium relationship. Based on this relationship, we can determine bounds for pc,m.]]></description>
<dc:subject>self-organization SOC complexology to-write-about consider:animations</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:8216ce198c8d/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:SOC"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:animations"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1712.04499">
    <title>[1712.04499] Colloquium: Criticality and dynamical scaling in living systems</title>
    <dc:date>2018-01-20T13:15:20+00:00</dc:date>
    <link>https://arxiv.org/abs/1712.04499</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[A celebrated and controversial hypothesis conjectures that some biological systems --parts, aspects, or groups of them-- may extract important functional benefits from operating at the edge of instability, halfway between order and disorder, i.e. in the vicinity of the critical point of a phase transition. Criticality has been argued to provide biological systems with an optimal balance between robustness against perturbations and flexibility to adapt to changing conditions, as well as to confer on them optimal computational capabilities, huge dynamical repertoires, unparalleled sensitivity to stimuli, etc. Criticality, with its concomitant scale invariance, can be conjectured to emerge in living systems as the result of adaptive and evolutionary processes that, for reasons to be fully elucidated, select for it as a template upon which higher layers of complexity can rest. This hypothesis is very suggestive as it proposes that criticality could constitute a general and common organizing strategy in biology stemming from the physics of phase transitions. However, despite its thrilling implications, this is still in its embryonic state as a well-founded theory and, as such, it has elicited some healthy skepticism. From the experimental side, the advent of high-throughput technologies has created new prospects in the exploration of biological systems, and empirical evidence in favor of criticality has proliferated, with examples ranging from endogenous brain activity and gene-expression patterns, to flocks of birds and insect-colony foraging, to name but a few...
]]></description>
<dc:subject>self-organization SOC power-laws complexology to-write-about</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:00a768f4a0ef/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:SOC"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:power-laws"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://www.univie.ac.at/constructivism/journal/13/1/001.editorial">
    <title>Vörös S. &amp; Riegler A. (2017) A Plea for not Watering Down the Unseemly: Reconsidering Francisco Varela’s Contribution to Science. Constructivist Foundations 13(1): 1–10</title>
    <dc:date>2017-12-26T12:44:45+00:00</dc:date>
    <link>http://www.univie.ac.at/constructivism/journal/13/1/001.editorial</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Context: In the past three decades, the work of Varela has had an enormous impact on current developments in contemporary science. Problem: Varela’s thought was extremely complex and multifaceted, and while some aspects - notably his contributions to the autopoietic theory of living and enactivist approach to cognition - have gained widespread acclaim, others have been ignored or watered down. Method: We identify three dimensions of Varela’s thought: (i) anti-realism of the “middle way”; (ii) anti-foundationalism of the circular/recursive onto-epistemology; and (iii) ethical/social implications of the circularity/recursivity. The discussion of these dimensions is followed by a concise overview of the individual target articles in this issue and the topics they cover. Finally, we discuss in what ways the articles extend and relate to Varela’s work. We do this by means of a concrete example: the relation between “enaction” and “enactivism. Results: We show that the ignoring-cum-watering-down process of Varela’s contributions to science is at least partly linked to the three dimensions of Varela’s thought. Based on our examination we also find that the more narrow research topics are always interrelated with broader philosophical reflection. Researching into ignored and watered-down aspects of Varela’s work enables us to not only gain fresh insights into Varela’s overall philosophy and rekindle interest in the topics and themes that have been brushed aside, but also cast a fresh light on those that are currently in full bloom. Implications: Reviving interest in Varela’s work in toto could lead to fruitful research and discussion in numerous scientific fields. To illustrate this idea, we delineate, tentatively, three domains - theoretical, empirical, and existential - where Varela’s contribution to philosophy and science could instigate prolific exchange of views. Constructivist content: All three dimensions of Varela’s philosophy have strong affinities with radical constructivist critique of realism and some of its epistemological and ethical implications.

]]></description>
<dc:subject>complexology philosophy-of-science philosophy rather-interesting cannot-read</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:39ce445e6939/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:philosophy-of-science"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:philosophy"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cannot-read"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://www.joelsimon.net/ecosystem-modelling.html">
    <title>Joel Simon</title>
    <dc:date>2017-12-23T10:14:53+00:00</dc:date>
    <link>http://www.joelsimon.net/ecosystem-modelling.html</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[An abstract plant multi-agent ecosystem simulation for artistic and research purposes. Individuals are simple circles that grow, collect resources, spread seeds and compete with others each timestep. Models are used in ecology by using the output, and its discrepancy from observation, to generate new hypotheses about ecological mechanics. I was inspired to do this project while working on an upcoming project modeling coral growth. I don't have a background in ecosystem modeling but the ideas came from conversations with a PhD student who does. I did an interview on my design and research interest in this project and its relationship to my virtual coral project. The code is available on Github.

]]></description>
<dc:subject>generative-art computational-art complexology agent-based</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:bec9654b4931/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:generative-art"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:computational-art"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:agent-based"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://complex.upf.es/~ricard/INFONETS.pdf">
    <title>Information Theory of Complex Networks</title>
    <dc:date>2017-12-03T13:39:12+00:00</dc:date>
    <link>http://complex.upf.es/~ricard/INFONETS.pdf</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Complex networks are characterized by highly heterogeneous distributions of links, often pervading the presence of key properties such as robustness under node removal. Several correlation measures have been defined in order to characterize the structure of these nets. Here we show that mutual information, noise and joint entropies can be properly defined on a static graph. These measures are computed for a number of real networks and analytically estimated for some simple standard models. It is shown that real networks are clustered in a well-defined domain of the entropy- noise space. By using simulated annealing optimization, it is shown that optimally heterogeneous nets actually cluster around the same narrow domain, suggesting that strong constraints actually operate on the possible universe of complex networks. The evolutionary implications are discussed]]></description>
<dc:subject>via:twitter complexology network-theory information-theory to-read hey-I-know-this-guy</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:77e4ed6b4aeb/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:via:twitter"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:network-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:information-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-read"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:hey-I-know-this-guy"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1702.01522">
    <title>[1702.01522] Inverse statistical problems: from the inverse Ising problem to data science</title>
    <dc:date>2017-11-17T13:25:26+00:00</dc:date>
    <link>https://arxiv.org/abs/1702.01522</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Inverse problems in statistical physics are motivated by the challenges of `big data' in different fields, in particular high-throughput experiments in biology. In inverse problems, the usual procedure of statistical physics needs to be reversed: Instead of calculating observables on the basis of model parameters, we seek to infer parameters of a model based on observations. In this review, we focus on the inverse Ising problem and closely related problems, namely how to infer the coupling strengths between spins given observed spin correlations, magnetisations, or other data. We review applications of the inverse Ising problem, including the reconstruction of neural connections, protein structure determination, and the inference of gene regulatory networks. For the inverse Ising problem in equilibrium, a number of controlled and uncontrolled approximate solutions have been developed in the statistical mechanics community. A particularly strong method, pseudolikelihood, stems from statistics. We also review the inverse Ising problem in the non-equilibrium case, where the model parameters must be reconstructed based on non-equilibrium statistics.]]></description>
<dc:subject>data-science statistics inverse-problems complexology rather-interesting inference to-write-about review to-simulate philosophy-of-science</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:18875f985d44/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:data-science"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:statistics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:inverse-problems"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:inference"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:review"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-simulate"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:philosophy-of-science"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://mathenchant.wordpress.com/2017/07/17/swine-in-a-line/">
    <title>Swine in a Line |</title>
    <dc:date>2017-11-09T16:49:20+00:00</dc:date>
    <link>https://mathenchant.wordpress.com/2017/07/17/swine-in-a-line/</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[What I hope you take away from this essay is a sense that there’s an interestingly tangled relationship between games, numbers, and the devices we use for representing and manipulating numbers. The abacus was introduced as a way to represent and manipulate numbers for purposes of counting. On the other hand, we can play games with an abacus (the Swine in a Line games) that don’t immediately seem to be about numbers at all, but if we play with those games for long enough, we come to see that underlying the chaos of one configuration giving rise to another, and then another, there is a pattern, and this pattern is most naturally expressed in the language of number.

]]></description>
<dc:subject>number-theory mathematical-recreations math pedagogy ludics to-write-about sandpiles complexology</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:7ed7761a7e7c/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:number-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:mathematical-recreations"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:math"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pedagogy"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:ludics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:sandpiles"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1611.01164">
    <title>[1611.01164] Sensitive Dependence of Optimal Network Dynamics on Network Structure</title>
    <dc:date>2017-10-15T12:29:36+00:00</dc:date>
    <link>https://arxiv.org/abs/1611.01164</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[The relation between network structure and dynamics is determinant for the behavior of complex systems in numerous domains. An important longstanding problem concerns the properties of the networks that optimize the dynamics with respect to a given performance measure. Here we show that such optimization can lead to sensitive dependence of the dynamics on the structure of the network. Specifically, using diffusively coupled systems as examples, we demonstrate that the stability of a dynamical state can exhibit sensitivity to unweighted structural perturbations (i.e., link removals and node additions) for undirected optimal networks and to weighted perturbations (i.e., small changes in link weights) for directed optimal networks. As mechanisms underlying this sensitivity, we identify discontinuous transitions occurring in the complement of undirected optimal networks and the prevalence of eigenvector degeneracy in directed optimal networks. These findings establish a unified characterization of networks optimized for dynamical stability, which we illustrate using Turing instability in activator-inhibitor systems, synchronization in power-grid networks, network diffusion, and several other network processes. Our results suggest that the network structure of a complex system operating near an optimum can potentially be fine-tuned for a significantly enhanced stability compared to what one might expect from simple extrapolation. On the other hand, they also suggest constraints on how close to the optimum the system can be in practice. Finally, the results have potential implications for biophysical networks, which have evolved under the competing pressures of optimizing fitness while remaining robust against perturbations.
]]></description>
<dc:subject>network-theory nonlinear-dynamics emergent-design complexology rather-interesting to-write-about to-simulate nudge-targets consider:looking-to-see</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:11ff4ab2caf6/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:network-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:emergent-design"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-simulate"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:looking-to-see"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1707.08905">
    <title>[1707.08905] Delegated Causality of Complex Systems</title>
    <dc:date>2017-10-03T11:11:21+00:00</dc:date>
    <link>https://arxiv.org/abs/1707.08905</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We introduce a simple but subtle, overlooked kind of causality provoked by critical dynamical systems with rich behavior and moderate sensitivity to the environment. By taking clues from Godel's incompleteness theorem, evolutionary biology, Eastern philosophy, we argue that conspicuously complex natural systems build up on interactions of this provoked, delegated causality.
]]></description>
<dc:subject>complexology cause-and-effect philosophy-of-science to-understand emergence</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:bc00778edbd5/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cause-and-effect"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:philosophy-of-science"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-understand"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:emergence"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1709.02171">
    <title>[1709.02171] On the stability and instability of finite dynamical systems with prescribed interaction graphs</title>
    <dc:date>2017-09-26T15:00:25+00:00</dc:date>
    <link>https://arxiv.org/abs/1709.02171</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[The dynamical properties of finite dynamical systems (FDSs) have been investigated in the context of coding theoretic problems, such as network coding, and in the context of hat games, such as the guessing game and Winkler's hat game. The instability of an FDS is the minimum Hamming distance between a state and its image under the FDS, while the stability is the minimum of the reciprocal of the Hamming distance; they are both directly related to Winkler's hat game. In this paper, we study the value of the (in)stability of FDSs with prescribed interaction graphs. The first main contribution of this paper is the study of the maximum stability for interaction graphs with a loop on each vertex. We determine the maximum (in)stability for large enough alphabets and also prove some lower bounds for the Boolean alphabet. We also compare the maximum stability for arbitrary functions compared to monotone functions only. The second main contribution of the paper is the study of the average (in)stability of FDSs with a given interaction graph. We show that the average stability tends to zero with high alphabets, and we then investigate the average instability. In that study, we give bounds on the number of FDSs with positive instability (i.e fixed point free functions). We then conjecture that all non-acyclic graphs will have an average instability which does not tend to zero when the alphabet is large. We prove this conjecture for some classes of graphs, including cycles.
]]></description>
<dc:subject>boolean-networks cellular-automata automata combinatorics graph-theory representation complexology dynamical-systems to-write to-cartoon-about</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:1978edb008fa/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:boolean-networks"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cellular-automata"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:automata"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:combinatorics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:graph-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:representation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:dynamical-systems"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-cartoon-about"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/0801.3306">
    <title>[0801.3306] Chip-Firing and Rotor-Routing on Directed Graphs</title>
    <dc:date>2017-09-26T14:30:23+00:00</dc:date>
    <link>https://arxiv.org/abs/0801.3306</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We give a rigorous and self-contained survey of the abelian sandpile model and rotor-router model on finite directed graphs, highlighting the connections between them. We present several intriguing open problems.
]]></description>
<dc:subject>sandpiles complexology graph-theory dynamical-systems feature-construction to-write-about nudge-targets consider:classification consider:feature-discovery</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:5de54da81778/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:sandpiles"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:graph-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:dynamical-systems"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:feature-construction"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:classification"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:feature-discovery"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://smaldino.com/wp/wp-content/uploads/2017/01/Smaldino2017-ModelsAreStupid.pdf">
    <title>Models Are Stupid, and We Need More of Them [PDF]</title>
    <dc:date>2017-09-23T14:06:56+00:00</dc:date>
    <link>http://smaldino.com/wp/wp-content/uploads/2017/01/Smaldino2017-ModelsAreStupid.pdf</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[It is my belief that the widespread inability to grasp the solution to the Monty Hall problem stems from a failure to properly model the scenario. You should switch doors because regardless of which door you picked initially, the host can always show you one with a goat. Being shown a goat therefore has no bearing on the probability that your initial choice was correct. Since that probability is 1/3, there is a 2/3 chance that you were wrong and the cash is behind the remaining door. Thus, two out of three times, switching is the right move. The common intuition that the choice is instead a 50-50 split between two options is erroneous.
Readers of this chapter are likely to be interested in social behaviors and their underlying psychological mechanisms. These systems tend to be quite a bit more complicated than a simple game show problem. This should concern us. Being an expert does not inoculate us from the failure of our limited imaginations, which evolved to solve problems quite different from those of interest to behavioral scientists. We could use some help.]]></description>
<dc:subject>models philosophy-of-science psychology complex-systems define-your-terms via:? complexology visualization learning-by-watching</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:8759d7cd82c0/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:models"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:philosophy-of-science"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:psychology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complex-systems"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:define-your-terms"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:via:?"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:visualization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:learning-by-watching"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1705.00759">
    <title>[1705.00759] Controllability of Conjunctive Boolean Networks with Application to Gene Regulation</title>
    <dc:date>2017-08-14T13:10:42+00:00</dc:date>
    <link>https://arxiv.org/abs/1705.00759</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[A Boolean network is a finite state discrete time dynamical system. At each step, each variable takes a value from a binary set. The value update rule for each variable is a local function which depends only on a selected subset of variables. Boolean networks have been used in modeling gene regulatory networks. We focus in this paper on a special class of Boolean networks, namely the conjunctive Boolean networks (CBNs), whose value update rule is comprised of only logic AND operations. It is known that any trajectory of a Boolean network will enter a periodic orbit. Periodic orbits of a CBN have been completely understood. In this paper, we investigate the orbit-controllability and state-controllability of a CBN: We ask the question of how one can steer a CBN to enter any periodic orbit or to reach any final state, from any initial state. We establish necessary and sufficient conditions for a CBN to be orbit-controllable and state-controllable. Furthermore, explicit control laws are presented along the analysis.
]]></description>
<dc:subject>boolean-networks Kauffmania engineering-design emergent-design rather-interesting to-write-about nudge-targets consider:feature-discovery dynamical-systems complexology</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:0d55044fd5ad/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:boolean-networks"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:Kauffmania"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:engineering-design"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:emergent-design"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:feature-discovery"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:dynamical-systems"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1705.00692">
    <title>[1705.00692] Diffusion limited aggregation in the Boolean lattice</title>
    <dc:date>2017-08-13T13:56:47+00:00</dc:date>
    <link>https://arxiv.org/abs/1705.00692</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[In the Diffusion Limited Aggregation (DLA) process on on ℤ2, or more generally ℤd, particles aggregate to an initially occupied origin by arrivals on a random walk. The scaling limit of the result, empirically, is a fractal with dimension strictly less than d. Very little has been shown rigorously about the process, however. 
We study an analogous process on the Boolean lattice {0,1}n, in which particles take random decreasing walks from (1,…,1), and stick at the last vertex before they encounter an occupied site for the first time; the vertex (0,…,0) is initially occupied. In this model, we can rigorously prove that lower levels of the lattice become full, and that the process ends by producing an isolated path of unbounded length reaching (1,…,1).]]></description>
<dc:subject>to-simulate to-write-about consider:slight-relaxations probability-theory complexology</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:065ecaed062a/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-simulate"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:slight-relaxations"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:probability-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://www.biorxiv.org/content/early/2017/05/25/142174?rss=1">
    <title>Breakdown Of Modularity In Complex Networks | bioRxiv</title>
    <dc:date>2017-08-06T12:13:04+00:00</dc:date>
    <link>http://www.biorxiv.org/content/early/2017/05/25/142174?rss=1</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[The presence of modular organisation is a common property of a wide range of complex systems, from cellular or brain networks to technological graphs. Modularity allows some degree of segregation between different parts of the network and has been suggested to be a prerequisite for the evolvability of biological systems. In technology, modularity defines a clear division of tasks and it is an explicit design target. However, many natural and artificial systems experience a breakdown in their modular pattern of connections, which has been associated to failures in hub nodes or the activation of global stress responses. In spite of its importance, no general theory of the breakdown of modularity and its implications has been advanced yet. Here we propose a new, simple model of network landscape where it is possible to exhaustively characterise the breakdown of modularity in a well-defined way. We found that evolution cannot reach maximally modular networks under the presence of functional and cost constraints, implying the breakdown of modularity is an adaptive feature.

]]></description>
<dc:subject>fitness-landscapes network-theory modularity rather-interesting boolean-networks to-write-about complexology simple-models nudge-targets evolvability</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:91c41af58b59/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:fitness-landscapes"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:network-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:modularity"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:boolean-networks"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simple-models"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:evolvability"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://biorxiv.org/content/early/2016/08/25/071589?rss=1%2522">
    <title>Dynamics Robustness of Cascading Systems | bioRxiv</title>
    <dc:date>2017-06-11T11:52:04+00:00</dc:date>
    <link>http://biorxiv.org/content/early/2016/08/25/071589?rss=1%2522</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[A most important property of biochemical systems is robustness. Static robustness, e.g., homeostasis, is the insensitivity of a state against perturbations, whereas dynamics robustness, e.g., homeorhesis, is the insensitivity of a dynamic process. In contrast to the extensively studied static robustness, dynamics robustness, i.e., how a system creates an invariant temporal profile against perturbations, is little explored despite transient dynamics being crucial for cellular fates and are reported to be robust experimentally. For example, the duration of a stimulus elicits different phenotypic responses, and signaling networks process and encode temporal information. Hence, robustness in time courses will be necessary for functional biochemical networks. Based on dynamical systems theory, we uncovered a general mechanism to achieve dynamics robustness. Using a three-stage linear signaling cascade as an example, we found that the temporal profiles and response duration post-stimulus is robust to perturbations against certain parameters. Then analyzing the linearized model, we elucidated the criteria of how such dynamics robustness emerges in signaling networks. We found that changes in the upstream modules are masked in the cascade, and that the response duration is mainly controlled by the rate-limiting module and organization of the cascade's kinetics. Specifically, we found two necessary conditions for dynamics robustness in signaling cascades: 1) Constraint on the rate-limiting process: The phosphatase activity in the perturbed module is not the slowest. 2) Constraints on the initial conditions: The kinase activity needs to be fast enough such that each module is saturated even with fast phosphatase activity and upstream information is attenuated. We discussed the relevance of such robustness to several biological examples and the validity of the above conditions therein. Given the applicability of dynamics robustness to a variety of systems, it will provide a general basis for how biological systems function dynamically.

]]></description>
<dc:subject>systems-biology self-organization complexology nonlinear-dynamics emergent-design to-write-about nudge-targets consider:feature-discovery robustness</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:c12a55e66e64/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:systems-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:emergent-design"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:feature-discovery"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:robustness"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1512.05259">
    <title>[1512.05259] Dynamical criticality: overview and open questions</title>
    <dc:date>2017-06-11T11:50:00+00:00</dc:date>
    <link>https://arxiv.org/abs/1512.05259</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Systems that exhibit complex behaviours are often found in a particular dynamical condition, poised between order and disorder. This observation is at the core of the so-called criticality hypothesis, which states that systems in a dynamical regime between order and disorder attain the highest level of computational capabilities and achieve an optimal trade-off between robustness and flexibility. Recent results in cellular and evolutionary biology, neuroscience and computer science have revitalised the interest in the criticality hypothesis, emphasising its role as a viable candidate general law in adaptive complex systems. In this paper we provide an overview of the works on dynamical criticality that are -to the best of our knowledge- particularly relevant for the criticality hypothesis. We review the main contributions concerning dynamics and information processing at the edge of chaos, and we illustrate the main achievements in the study of critical dynamics in biological systems. Finally, we discuss open questions and propose an agenda for future work.
]]></description>
<dc:subject>edge-of-chaos complexology boolean-networks Kauffmania self-organization to-write-about to-do</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:1da88e50d623/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:edge-of-chaos"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:boolean-networks"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:Kauffmania"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-do"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1306.0481">
    <title>[1306.0481] Run-and-tumble in a crowded environment: persistent exclusion process for swimmers</title>
    <dc:date>2017-05-05T11:02:49+00:00</dc:date>
    <link>https://arxiv.org/abs/1306.0481</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[The effect of crowding on the run-and-tumble dynamics of swimmers such as bacteria is studied using a discrete lattice model of mutually excluding particles that move with constant velocity along a direction that is randomized at a rate α. In stationary state, the system is found to break into dense clusters in which particles are trapped or stopped from moving. The characteristic size of these clusters predominantly scales as α−0.5 both in 1D and 2D. For a range of densities, due to cooperative effects, the stopping time scales as 0.851d and as 0.82d, where d is the diffusive time associated with the motion of cluster boundaries. Our findings might be helpful in understanding the early stages of biofilm formation.
]]></description>
<dc:subject>active-matter self-organization dynamical-systems complexology simulation rather-interesting to-write-about consider:looking-to-see</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:2e3db554efe4/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:active-matter"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:dynamical-systems"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:looking-to-see"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/adap-org/9710002">
    <title>[adap-org/9710002] Self-Organized Criticality with Complex Scaling Exponents in the Train Model</title>
    <dc:date>2017-04-29T13:29:39+00:00</dc:date>
    <link>https://arxiv.org/abs/adap-org/9710002</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[The train model which is a variant of the Burridge-Knopoff earthquake model is investigated for a velocity-strengthening friction law. It shows self-organized criticality with complex scaling exponents. That is, the probability density function of the avalanche strength is a power law times a log-periodic function. Exact results (scaling exponent: 3/2+2πi/ln4) are found for a nonlocal cellular automaton which approximates the overdamped train model. Further the influence of random static friction is discussed.]]></description>
<dc:subject>dynamical-systems complexology agent-based nudge-targets consider:looking-to-see to-write-about</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:7f401dd88b03/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:dynamical-systems"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:agent-based"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:looking-to-see"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1012.1332">
    <title>[1012.1332] Time-Symmetric Cellular Automata</title>
    <dc:date>2017-04-22T12:19:05+00:00</dc:date>
    <link>https://arxiv.org/abs/1012.1332</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Together with the concept of reversibility, another relevant physical notion is time-symmetry, which expresses that there is no way of distinguishing between backward and forward time directions. This notion, found in physical theories, has been neglected in the area of discrete dynamical systems. Here we formalize it in the context of cellular automata and establish some basic facts and relations. We also state some open problems that may encourage further research on the topic.]]></description>
<dc:subject>cellular-automata artificial-life complexology computational-complexity information-theory representation</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:a47488701a5f/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cellular-automata"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:artificial-life"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:computational-complexity"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:information-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:representation"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1304.5109">
    <title>[1304.5109] Kadanoff Sand Pile Model. Avalanche Structure and Wave Shape</title>
    <dc:date>2017-04-19T23:57:55+00:00</dc:date>
    <link>https://arxiv.org/abs/1304.5109</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Sand pile models are dynamical systems describing the evolution from N stacked grains to a stable configuration. It uses local rules to depict grain moves and iterate it until reaching a fixed configuration from which no rule can be applied. Physicists L. Kadanoff {\em et al} inspire KSPM, extending the well known {\em Sand Pile Model} (SPM). In KSPM(D), we start from a pile of N stacked grains and apply the rule: D−1 grains can fall from column i onto columns i+1,i+2,…,i+D−1 if the difference of height between columns i and i+1 is greater or equal to D. Toward the study of fixed points (stable configurations on which no grain can move) obtained from N stacked grains, we propose an iterative study of KSPM evolution consisting in the repeated addition of one grain on a heap of sand, triggering an avalanche at each iteration. We develop a formal background for the study of avalanches, resumed in a finite state word transducer, and explain how this transducer may be used to predict the form of fixed points. Further precise developments provide a plain formula for fixed points of KSPM(3), showing the emergence of a wavy shape.]]></description>
<dc:subject>sandpile self-organization complexology dynamical-systems to-write-about consider:simulation nudge-targets consider:extensive-properties</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:c7c0eca53467/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:sandpile"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:dynamical-systems"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:extensive-properties"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1703.04792">
    <title>[1703.04792] Frustration and thermalisation in an artificial magnetic quasicrystal</title>
    <dc:date>2017-04-17T12:04:12+00:00</dc:date>
    <link>https://arxiv.org/abs/1703.04792</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We have created and studied artificial magnetic quasicrystals based on Penrose tiling patterns of interacting nanomagnets that lack the translational symmetry of spatially periodic artificial spin ices. Vertex-level degeneracy and frustration induced by the network topology of the Penrose pattern leads to a low energy configuration that we propose as a ground state. It has two parts, a quasi-one-dimensional rigid "skeleton" that spans the entire pattern and is capable of long-range order, and clusters of macrospins within it that are degenerate in a nearest neighbour model, and so are "flippable". These lead to macroscopic degeneracy for the array as a whole. Magnetic force microscopy imaging of Penrose tiling arrays revealed superdomains that are larger for more strongly coupled arrays. The superdomain size is larger after AC-demagnetisation and especially after annealing the array above its blocking temperature.
]]></description>
<dc:subject>experiment frustrated-networks complexology quasicrystals looking-to-see rather-interesting</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:871598a61766/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:experiment"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:frustrated-networks"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:quasicrystals"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:looking-to-see"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1607.04474">
    <title>[1607.04474] The Influence of Canalization on the Robustness of Boolean Networks</title>
    <dc:date>2017-04-17T10:41:53+00:00</dc:date>
    <link>https://arxiv.org/abs/1607.04474</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Time- and state-discrete dynamical systems are frequently used to model molecular networks. This paper provides a collection of mathematical and computational tools for the study of robustness in Boolean network models. The focus is on networks governed by k-canalizing functions, a recently introduced class of Boolean functions that contains the well-studied class of nested canalizing functions. The activities and sensitivity of a function quantify the impact of input changes on the function output. This paper generalizes the latter concept to c-sensitivity and provides formulas for the activities and c-sensitivity of general k-canalizing functions as well as canalizing functions with more precisely defined structure. A popular measure for the robustness of a network, the Derrida value, can be expressed as a weighted sum of the c-sensitivities of the governing canalizing functions, and can also be calculated for a stochastic extension of Boolean networks. These findings provide a computationally efficient way to obtain Derrida values of Boolean networks, deterministic or stochastic, that does not involve simulation.
]]></description>
<dc:subject>boolean-networks Kauffmania nonlinear-dynamics complexology systems-biology rather-interesting to-write-about nudge-targets consider:looking-to-see consider:feature-discovery open-questions</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:83974cf96eb5/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:boolean-networks"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:Kauffmania"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:systems-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:looking-to-see"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:feature-discovery"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:open-questions"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1109.4994">
    <title>[1109.4994] The finite-state character of physical dynamics</title>
    <dc:date>2017-03-24T23:32:00+00:00</dc:date>
    <link>https://arxiv.org/abs/1109.4994</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Finite physical systems have only a finite amount of distinct state. This finiteness is fundamental in statistical mechanics, where the maximum number of distinct states compatible with macroscopic constraints defines entropy. Here we show that finiteness of distinct state is similarly fundamental in ordinary mechanics: energy and momentum are defined by the maximum number of distinct states possible in a given time or distance. More generally, any moment of energy or momentum bounds distinct states in time or space. These results generalise both the Nyquist bandwidth-bound on distinct values in classical signals, and quantum uncertainty bounds. The new certainty bounds are achieved by finite-bandwidth evolutions in which time and space are effectively discrete, including quantum evolutions that are effectively classical. Since energy and momentum count distinct states, they are defined in classical finite-state dynamics, and they relate classical relativity to finite-state evolution.
]]></description>
<dc:subject>hey-I-know-this-guy physics automata theoretical-physics complexology quantum discrete-mathematics philosophy-of-science representation</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:ea2f914506cd/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:hey-I-know-this-guy"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:physics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:automata"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:theoretical-physics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:quantum"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:discrete-mathematics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:philosophy-of-science"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:representation"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1309.1837">
    <title>[1309.1837] Evolution and non-equilibrium physics. A study of the Tangled Nature Model</title>
    <dc:date>2017-03-24T12:45:27+00:00</dc:date>
    <link>https://arxiv.org/abs/1309.1837</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We argue that the stochastic dynamics of interacting agents which replicate, mutate and die constitutes a non-equilibrium physical process akin to aging in complex materials. Specifically, our study uses extensive computer simulations of the Tangled Nature Model (TNM) of biological evolution to show that punctuated equilibria successively generated by the model's dynamics have increasing entropy and are separated by increasing entropic barriers. We further show that these states are organized in a hierarchy and that limiting the values of possible interactions to a finite interval leads to stationary fluctuations within a component of the latter. A coarse-grained description based on the temporal statistics of quakes, the events leading from one component of the hierarchy to the next, accounts for the logarithmic growth of the population and the decaying rate of change of macroscopic variables. Finally, we question the role of fitness in large scale evolution models and speculate on the possible evolutionary role of rejuvenation and memory effects.
]]></description>
<dc:subject>theoretical-biology artificial-life complexology ecology Bak-Sneppen-stuff fitness-landscapes Oh Physics!</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:f5e82efaeef8/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:theoretical-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:artificial-life"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:ecology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:Bak-Sneppen-stuff"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:fitness-landscapes"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:Oh"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:Physics!"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1406.2277">
    <title>[1406.2277] Designing Complex Dynamics in Cellular Automata with Memory</title>
    <dc:date>2017-03-24T00:13:14+00:00</dc:date>
    <link>https://arxiv.org/abs/1406.2277</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Since their inception at {\it Macy conferences} in later 1940s complex systems remain the most controversial topic of inter-disciplinary sciences. The term `complex system' is the most vague and liberally used scientific term. Using elementary cellular automata (ECA), and exploiting the CA classification, we demonstrate elusiveness of `complexity' by shifting space-time dynamics of the automata from simple to complex by enriching cells with {\it memory}. This way, we can transform any ECA class to another ECA class --- without changing skeleton of cell-state transition function --- and vice versa by just selecting a right kind of memory. A systematic analysis display that memory helps `discover' hidden information and behaviour on trivial --- uniform, periodic, and non-trivial --- chaotic, complex --- dynamical systems.
]]></description>
<dc:subject>emergent-design cellular-automata to-write-about feature-construction complexology</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:89056cd81e93/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:emergent-design"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cellular-automata"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:feature-construction"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1306.5533">
    <title>[1306.5533] Evolving Gene Regulatory Networks with Mobile DNA Mechanisms</title>
    <dc:date>2017-03-24T00:09:00+00:00</dc:date>
    <link>https://arxiv.org/abs/1306.5533</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[This paper uses a recently presented abstract, tuneable Boolean regulatory network model extended to consider aspects of mobile DNA, such as transposons. The significant role of mobile DNA in the evolution of natural systems is becoming increasingly clear. This paper shows how dynamically controlling network node connectivity and function via transposon-inspired mechanisms can be selected for in computational intelligence tasks to give improved performance. The designs of dynamical networks intended for implementation within the slime mould Physarum polycephalum and for the distributed control of a smart surface are considered.
]]></description>
<dc:subject>gene-regulatory-networks Kauffmania engineering-design emergent-design complexology rather-interesting nudge-targets consider:looking-to-see</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:b820ef636191/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:gene-regulatory-networks"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:Kauffmania"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:engineering-design"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:emergent-design"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:looking-to-see"/>
</rdf:Bag></taxo:topics>
</item>
</rdf:RDF>