🔖 [1810.05095] The Statistical Physics of Real-World Networks | arXiv

Bookmarked [1810.05095] The Statistical Physics of Real-World Networks by Giulio Cimini, Tiziano Squartini, Fabio Saracco, Diego Garlaschelli, Andrea Gabrielli, Guido Caldarelli (arxiv.org)

Statistical physics is the natural framework to model complex networks. In the last twenty years, it has brought novel physical insights on a variety of emergent phenomena, such as self-organisation, scale invariance, mixed distributions and ensemble non-equivalence, which cannot be deduced from the behaviour of the individual constituents. At the same time, thanks to its deep connection with information theory, statistical physics and the principle of maximum entropy have led to the definition of null models reproducing some features of empirical networks, but otherwise as random as possible. We review here the statistical physics approach for complex networks and the null models for the various physical problems, focusing in particular on the analytic frameworks reproducing the local features of the network. We show how these models have been used to detect statistically significant and predictive structural patterns in real-world networks, as well as to reconstruct the network structure in case of incomplete information. We further survey the statistical physics frameworks that reproduce more complex, semi-local network features using Markov chain Monte Carlo sampling, and the models of generalised network structures such as multiplex networks, interacting networks and simplicial complexes.

Comments: To appear on Nature Reviews Physics. The revised accepted version will be posted 6 months after publication

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👓 Welcome to Voldemorting, the Ultimate SEO Dis | Wired

Read Welcome to Voldemorting, the Ultimate SEO Dis by Gretchen McCulloch (WIRED)
When writers swap Trump for Cheeto and 45, it's not just a put-down. Removing a keyword is the anti-SEO—transforming your subject into a slippery, ungraspable, swarm.

Surprised she didn’t mention the phenomena of subtweeting, snitch tagging, or dunking which are also closely related to voldemorting.

To my experience, the phrase “bird site” was generally used as a derogatory phrase on Mastodon (represented by a Mastodon character instead of a bird), by people who were fed up by Twitter and the interactions they found there. I recall instances of it as early as April 2017.

In addition to potential SEO implications, this phenomenon is also interesting for its information theoretic implications.

I particularly like the reference in the van der Nagle paper

[…] screenshotting, or making content visible without sending its website traffic – to demonstrate users’ understandings of the algorithms that seek to connect individuals to other people, platforms, content and advertisers, and their efforts to wrest back control.

This seems like an awesome way to skirt around algorithms in social sites as well as not rewarding negative sites with clicks.

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Reply to Andy Gonzalez about NIMBIOS Workshop

Replied to a tweet by Andy GonzalezAndy Gonzalez (Twitter)

Andrew Eckford et al. hosted a related conference a few months prior at BIRS which also has some great videos:

Biological and Bio-Inspired Information Theory(14w5170)

Perhaps it’s time for a follow up conference?

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👓 Tenured Faculty Position at Princeton University | IEEE Information Theory Society

Read Tenured Faculty Position at Princeton University (itsoc.org)
The Department of Electrical Engineering at Princeton University seeks outstanding applicants for a tenured appointment at the Associate or Full Professor level, effective as early as September 1, 2019. The search is open to candidates specializing in areas related to information sciences and systems, with strength in core fundamentals and an interest in applications areas such as networks, machine learning, energy systems, cyber-physical systems, robotics and control, wireless communications, biology, etc. The successful candidate should have a Ph.D. in Electrical Engineering or a related field, demonstrated excellence in academic research, and a proven track record of teaching and advising undergraduate and graduate students (if currently holding an academic appointment). We seek faculty members who will create a climate that embraces excellence and diversity, with a strong commitment to teaching and mentoring that will enhance the work of the department and attract and retain a diverse student body. Candidates must complete an online faculty application at: https://www.princeton.edu/acad-positions/position/4801; a detailed curriculum vitae, descriptions of teaching and research interests, reprints of selected publications, and the names and addresses of three references should be uploaded as .pdf documents via the on-line application. This position is subject to Princeton University's background check policy. To ensure full consideration, applications should be received by November 15, 2018, but the search will remain open until the position is filled.

Wow! Verdu hasn’t even started experiencing entropy yet…

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👓 U. confirms Verdu’s dismissal following misconduct investigation | The Princetonian

Read U. confirms Verdu's dismissal following misconduct investigation (The Princetonian)
On Friday night, Assistant Vice President for Communications Dan Day confirmed that professor Sergio Verdú was dismissed from the faculty as of Sept. 24 following a University investigation into his conduct in relation to University policies that prohibit consensual relations with students and require honesty and cooperation in University matters.
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🔖 Categorical informatics

Bookmarked Categorical informatics by David Spivak (math.mit.edu)

"Category theory is a universal modeling language."

Background.

Success is founded on information. A tight connection between success (in anything) and information. It follows that we should (if we want to be more successful) study what information is.

Grant proposals. These are several grant proposals, some funded, some in the pipeline, others not funded, that explain various facets of my research project.

Introductory talk (video, slides).

Blog post, on John Baez's blog Azimuth, about my motivations for studying this subject. (Here's a .pdf version.)

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🔖 Theory Of Self Reproducing Automata by John Von Neumann, Arthur W. Burks (Editor) | 9780252727337

Bookmarked Theory Of Self Reproducing Automata by John von Neumann (University of Illinois Press)

Waiting for the price of some of these to drop.

Digital copy available on Archive.org.

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👓 Disconnected, fragmented, or united? a trans-disciplinary review of network science | Applied Network Science | César A. Hidalgo

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

Highlights, Quotes, Annotations, & Marginalia

Social scientists focus on explaining how context specific social and economic mechanisms drive the structure of networks and on how networks shape social and economic outcomes. By contrast, natural scientists focus primarily on modeling network characteristics that are independent of context, since their focus is to identify universal characteristics of systems instead of context specific mechanisms.  

August 25, 2018 at 10:18PM

Science and Complexity (Weaver 1948); explained the three eras that according to him defined the history of science. These were the era of simplicity, disorganized complexity, and organized complexity. In the eyes of Weaver what separated these three eras was the development of mathematical tools allowing scholars to describe systems of increasing complexity.  

August 25, 2018 at 10:19PM

Problems of disorganized complexity are problems that can be described using averages and distributions, and that do not depend on the identity of the elements involved in a system, or their precise patterns of interactions. A classic example of a problem of disorganized complexity is the statistical mechanics of Ludwig Boltzmann, James-Clerk Maxwell, and Willard Gibbs, which focuses on the properties of gases.  

August 25, 2018 at 10:20PM

Soon after Weaver’s paper, biologists like Francois Jacob (Jacob and Monod 1961), (Jacob et al. 1963) and Stuart Kaufmann (Kauffman 1969), developed the idea of regulatory networks. Mathematicians like Paul Erdos and Alfred Renyi, advanced graph theory (Erdős and Rényi 1960) while Benoit Mandelbrot worked on Fractals (Mandelbrot and Van Ness 1968), (Mandelbrot 1982). Economists like Thomas Schelling (Schelling 1960) and Wasily Leontief (Leontief 1936), (Leontief 1936), respectively explored self-organization and input-output networks. Sociologists, like Harrison White (Lorrain and White 1971) and Mark Granovetter (Granovetter 1985), explored social networks, while psychologists like Stanley Milgram (Travers and Milgram 1969) explored the now famous small world problem.   

Some excellent references
August 25, 2018 at 10:24PM

First, I will focus in these larger groups because reviews that transcend the boundary between the social and natural sciences are rare, but I believe them to be valuable. One such review is Borgatti et al. (2009), which compares the network science of natural and social sciences arriving at a similar conclusion to the one I arrived.  

August 25, 2018 at 10:27PM

Links are the essence of networks. So I will start this review by comparing the mechanisms used by natural and social scientists to explain link formation.  

August 25, 2018 at 10:32PM

When connecting the people that acted in the same movie, natural scientists do not differentiate between people in leading or supporting roles.  

But they should because it’s not often the case that these are relevant unless they are represented by the same agent or agency.
August 25, 2018 at 10:51PM

For instance, in the study of mobile phone networks, the frequency and length of interactions has often been used as measures of link weight (Onnela et al. 2007), (Hidalgo and Rodriguez-Sickert 1008), (Miritello et al. 2011).  

And they probably shouldn’t because typically different levels of people are making these decisions. Studio brass and producers typically have more to say about the lead roles and don’t care as much about the smaller ones which are overseen by casting directors or sometimes the producers. The only person who has oversight of all of them is the director, and even then they may quit caring at some point.
August 25, 2018 at 10:52PM

Social scientists explain link formation through two families of mechanisms; one that finds it roots in sociology and the other one in economics. The sociological approach assumes that link formation is connected to the characteristics of individuals and their context. Chief examples of the sociological approach include what I will call the big three sociological link-formation hypotheses. These are: shared social foci, triadic closure, and homophily.  

August 25, 2018 at 10:55PM

The social foci hypothesis predicts that links are more likely to form among individuals who, for example, are classmates, co-workers, or go to the same gym (they share a social foci). The triadic closure hypothesis predicts that links are more likely to form among individuals that share “friends” or acquaintances. Finally, the homophily hypothesis predicts that links are more likely to form among individuals who share social characteristics, such as tastes, cultural background, or physical appearance (Lazarsfeld and Merton 1954), (McPherson et al. 2001).  

definitions of social foci, triadic closure, and homophily within network science.
August 26, 2018 at 11:39AM

Yet, strategic games look for equilibrium in the formation and dissolution of ties in the context of the game theory advanced first by (Von Neumann et al. 2007), and later by (Nash 1950).  

August 25, 2018 at 10:58PM

Preferential attachment is the idea that connectivity begets connectivity.  

August 25, 2018 at 10:59PM

Preferential attachment is an idea advanced originally by the statisticians John Willis and Udny Yule in (Willis and Yule 1922), but has been rediscovered numerous times during the twentieth century.  

August 25, 2018 at 11:00PM

Rediscoveries of this idea in the twentieth century include the work of (Simon 1955) (who did cite Yule), (Merton 1968), (Price 1976) (who studied citation networks), and (Barabási and Albert 1999), who published the modern reference for this model, which is now widely known as the Barabasi-Albert model.  

August 25, 2018 at 11:01PM

preferential attachment. In the eyes of the social sciences, however, understanding which of all of these hypotheses drives the formation of the network is what one needs to explore.  

For example what drives attachment of political candidates?
August 26, 2018 at 08:15AM

Finally it is worth noting that trust, through the theory of social capital, has been connected with long-term economic growth—even though these results are based on regressions using extremely sparse datasets.  

And this is an example of how Trump is hurting the economy.
August 26, 2018 at 08:33AM

Nevertheless, the evidence suggests that social capital and social institutions are significant predictors of economic growth, after controlling for the effects of human capital and initial levels of income (Knack and Keefer 1997), (Knack 2002).4 So trust is a relevant dimension of social interactions that has been connected to individual dyads, network formation, labor markets, and even economic growth.  

August 26, 2018 at 08:35AM

Social scientist, on the other hand, have focused on what ties are more likely to bring in new information, which are primarily weak ties (Granovetter 1973), and on why weak ties bring new information (because they bridge structural holes (Burt 2001), (Burt 2005)).  

August 26, 2018 at 09:45AM

heterogeneous networks have been found to be effective promoters of the evolution of cooperation, since there are advantages to being a cooperator when you are a hub, and hubs tend to stabilize networks in equilibriums where levels of cooperation are high (Ohtsuki et al. 2006), (Pacheco et al. 2006), (Lieberman et al. 2005), (Santos and Pacheco 2005).  

August 26, 2018 at 09:49AM

These results, however, have also been challenged by human experiments finding no such effect (Gracia-Lázaro et al. 2012). The study of cooperation in networks has also been performed in dynamic settings, where individuals are allowed to cut ties (Wang et al. 2012), promoting cooperation, and are faced with different levels of knowledge about the reputation of peers in their network (Gallo and Yan 2015). Moreover, cooperating behavior has seen to spread when people change the networks where they participate in (Fowler and Christakis 2010).  

Open questions
August 26, 2018 at 09:50AM

References

1.
Hidalgo CA. Disconnected, fragmented, or united? a trans-disciplinary review of network science. ANS. 2016;1(1). doi:10.1007/s41109-016-0010-3
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👓 The harm of harmless jokes | lu popolvuh – Medium

Read The harm of harmless jokes by lu popolvuh (lu popolvuh – Medium)
A #MeTooSTEM story about requesting a change in tradition

I’ve followed bits of this story for a while since it touches on an area I follow, but I had no idea the harassment was so terrible. The Romeo and Juliette business is just deplorable.

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👓 A Songwriting Mystery Solved: Math Proves John Lennon Wrote ‘In My Life’ | NPR

Read A Songwriting Mystery Solved: Math Proves John Lennon Wrote 'In My Life' (NPR | Weekend Edition Saturday)

Over the years, Lennon and McCartney have revealed who really wrote what, but some songs are still up for debate. The two even debate between themselves — their memories seem to differ when it comes to who wrote the music for 1965's "In My Life."

Mathematics professor Jason Brown spent 10 years working with statistics to solve the magical mystery. Brown's the findings were presented on Aug. 1 at the Joint Statistical Meeting in a presentation called "Assessing Authorship of Beatles Songs from Musical Content: Bayesian Classification Modeling from Bags-Of-Words Representations."

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🔖 Proceedings for ALIFE 2018: The 2018 Conference on Artificial Life

Bookmarked Proceedings ALIFE 2018: The 2018 Conference on Artificial Life by Takashi Ikegami, Nathaniel Virgo, Olaf Witkowski, Mizuki Oka, Reiji Suzuki, Hiroyuki Iizuka (eds.) (MIT Press Journals)
This volume presents the proceedings of ALIFE 2018, the 2018 Conference on Artificial Life, held July 23rd-27th. It took place in Tokyo, Japan (http://2018.alife.org). The ALIFE and ECAL conferences have been the major meeting of the artificial life (ALife) research community since 1987 and 1991, respectively. As a Hybrid of the European Conference on Artificial Life (ECAL) and the International Conference on the Synthesis and Simulation of Living Systems (ALIFE), the 2018 Conference on Artificial Life (ALIFE 2018) will take place outside both Europe and the US, in Tokyo, Japan.
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🔖 CNS*2018 Workshop on Methods of Information Theory in Computational Neuroscience

Read Information Theory in Computational Neuroscience Workshop (CNS*2018) by Joseph Lizier (lizier.me)
Methods originally developed in Information Theory have found wide applicability in computational neuroscience. Beyond these original methods there is a need to develop novel tools and approaches that are driven by problems arising in neuroscience. A number of researchers in computational/systems neuroscience and in information/communication theory are investigating problems of information representation and processing. While the goals are often the same, these researchers bring different perspectives and points of view to a common set of neuroscience problems. Often they participate in different fora and their interaction is limited. The goal of the workshop is to bring some of these researchers together to discuss challenges posed by neuroscience and to exchange ideas and present their latest work. The workshop is targeted towards computational and systems neuroscientists with interest in methods of information theory as well as information/communication theorists with interest in neuroscience.
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Following Mark Stanley Everitt

Followed Mark Stanley Everitt (Qubyte Codes)

Mark Stanley Everitt headshot Welcome to qubyte.codes! The personal site of Mark Stanley Everitt.

I'm a programmer specialising in JavaScript, living and working in Brighton, UK. This blog is a place for me to write about stuff I find interesting or useful. Probably JavaScript for the most part, but certainly not limited to it. By day I spend most of my programming time writing Node.js applications, with a little browser stuff when I can.

I'm also interested in the social side and ethics of software development. I'm a regular mentor at Codebar in Brighton.

I lived and worked in Tokyo for a number of years, initially as an academic (I hold a PhD in quantum optics and quantum information), and later as a programmer. I speak a little Japanese.

If you have and questions of comments, tweet to me @qubyte or toot to me at @qubyte@mastodon.social .

If you're interested in code I've published, I'm qubyte on GitHub.

A blogger/coder who was into quantum mechanics, information theory, supports webmentions, and speaks some Japanese? How could I not follow?!

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👓 The role of information theory in chemistry | Chemistry World

Read The role of information theory in chemistry by Philip Ball (Chemistry World)
Is chemistry an information science after all?

Discussion of some potential interesting directions for application of information theory to chemistry (and biology).

In the 1990s, Nobel laureate Jean-Marie Lehn argued that the principles of spontaneous self-assembly and self-organisation, which he had helped to elucidate in supramolecular chemistry, could give rise to a science of ‘informed matter’ beyond the molecule.

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👓 Andrew Jordan reviews Peter Woit’s Quantum Theory, Groups and Representations and finds much to admire. | Inference

Read Woit’s Way by Andrew Jordan (Inference: International Review of Science)
Andrew Jordan reviews Peter Woit's Quantum Theory, Groups and Representations and finds much to admire.

For the tourists, I’ve noted before that Peter maintains a free copy of his new textbook on his website.

I also don’t think I’ve ever come across the journal Inference before, but it looks quite nice in terms of content and editorial.

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