Month: June 2018

Complex Spreading Phenomena in Social Systems

This text is about spreading of information and influence in complex networks. Although previously considered similar and modeled in parallel approaches, there is now experimental evidence that epidemic and social spreading work in subtly different ways. While previously explored through modeling, there is currently an explosion of work on revealing the mechanisms underlying complex contagion based on big data and data-driven approaches.

This volume consists of four parts. Part 1 is an Introduction, providing an accessible summary of the state-of-the-art. Part 2 provides an overview of the central theoretical developments in the field. Part 3 describes the empirical work on observing spreading processes in real-world networks. Finally, Part 4 goes into detail with recent and exciting new developments: dedicated studies designed to measure specific aspects of the spreading processes, often using randomized control trials to isolate the network effect from confounders, such as homophily.

Each contribution is authored by leading experts in the field. This volume, though based on technical selections of the most important results on complex spreading, remains quite accessible to the newly interested. The main benefit to the reader is that the topics are carefully structured to take the novice to the level of expert on the topic of social spreading processes. This book will be of great importance to a wide field: from researchers in physics, computer science, and sociology to professionals in public policy and public health.

 

Complex Spreading Phenomena in Social Systems
Influence and Contagion in Real-World Social Networks
Editors: Sune Lehmann, Yong-Yeol Ahn

Source: link.springer.com

Semantic information, agency, and nonequilibrium statistical physics

Information theory provides various measures of correlations holding between the states of two systems, which are sometimes called measures of "syntactic information". At the same time, the concept of "semantic information" refers to information which is in some sense meaningful rather than merely correlational. Semantic information plays an important role in many fields — including biology, cognitive science, artificial intelligence — and there has been a long-standing interest in a quantitative theory of semantic information. In this work, we introduce such a theory, which defines semantic information as the syntactic information that a physical system has about its environment that is causally necessary for the system to maintain its own existence. We operationalize self-maintenance in terms of the ability of the system to maintain a low entropy state, which we use to make connections to results in nonequilibrium statistical physics. Our approach leads naturally to formal definitions of notions like "value of information", "semantic content", and "agency". Our approach is grounded purely in the intrinsic dynamics of a system coupled to some environment, and is applicable to any physical system.

Semantic information, agency, and nonequilibrium statistical physics
Artemy Kolchinsky, David H. Wolpert

Source: arxiv.org

The clock of chemical evolution

Chemical evolution is essential in understanding the origins of life. We present a theory for the evolution of molecule masses and show that small molecules grow by random diffusion and large molecules by a preferential attachment process leading eventually to life’s molecules. It reproduces correctly the distribution of molecules found via mass spectroscopy for the Murchison meteorite and estimates the start of chemical evolution back to 12.8 billion years following the birth of stars and supernovae. From the Frontier mass between the random and preferential attachment dynamics the birth time of molecule families can be estimated. Amino acids emerge about 165 million years after the start of evolution. Using the scaling of reaction rates with the distance of the molecules in space we recover correctly the few days emergence time of amino acids in the Miller-Urey experiment. The distribution of interstellar and extragalactic molecules are both consistent with the evolutionary mass distribution, and their age is estimated to 108 and 65 million years after the start of evolution. From the model, we can determine the number of different molecule compositions at the time of the creation of Earth to be 1.6 million and the number of molecule compositions in interstellar space to a mere 719.

The clock of chemical evolution
Stuart A. Kauffman, David P. Jelenfi, Gabor Vattay

Source: arxiv.org

Predicting perturbation patterns from the topology of biological networks

High-throughput technologies, offering unprecedented wealth of quantitative data underlying the makeup of living systems, are changing biology. Notably, the systematic mapping of the relationships between biochemical entities has fueled the rapid development of network biology, offering a suitable framework to describe disease phenotypes and predict potential drug targets. Yet, our ability to develop accurate dynamical models remains limited, due in part to the limited knowledge of the kinetic parameters underlying these interactions. Here, we explore the degree to which we can make reasonably accurate predictions in the absence of the kinetic parameters. We find that simple dynamically agnostic models are sufficient to recover the strength and sign of the biochemical perturbation patterns observed in 87 biological models for which the underlying kinetics is known. Surprisingly, a simple distance-based model achieves 65% accuracy. We show that this predictive power is robust to topological and kinetic parameters perturbations, and we identify key network properties that can increase up to 80% the recovery rate of the true perturbation patterns. We validate our approach using experimental data on the chemotactic pathway in bacteria, finding that a network model of perturbation spreading predicts with ~80% accuracy the directionality of gene expression and phenotype changes in knock-out and overproduction experiments. These findings show that the steady advances in mapping out the topology of biochemical interaction networks opens avenues for accurate perturbation spread modeling, with direct implications for medicine and drug development.

 

Predicting perturbation patterns from the topology of biological networks

Marc Santolini, Albert-Laszlo Barabasi
doi: https://doi.org/10.1101/349324

Source: www.biorxiv.org