Networks of coupled dynamical systems have been used to model biological oscillators, Josephson junction arrays, excitable media, neural networks, spatial games, genetic control networks and many other self-organizing systems. Ordinarily, the connection topology is assumed to be either completely regular or completely random. But many biological, technological and social networks lie somewhere between these two extremes. Here we explore simple models of networks that can be tuned through this middle ground: regular networks 'rewired' to introduce increasing amounts of disorder. We find that these systems can be highly clustered, like regular lattices, yet have small characteristic path lengths, like random graphs. We call them 'small-world' networks, by analogy with the small-world phenomenon (popularly known as six degrees of separation. The neural network of the worm Caenorhabditis elegans, the power grid of the western United States, and the collaboration graph of film actors are shown to be small-world networks. Models of dynamical systems with small-world coupling display enhanced signal-propagation speed, computational power, and synchronizability. In particular, infectious diseases spread more easily in small-world networks than in regular lattices.

/pdf/collective-dynamics-of-small-world-networks-205zhem3gm.pdf

Collective dynamics of small-world networks

There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

http://science.sciencemag.org/content/sci/291/5507/1304.full.pdf

The sequence of the human genome.

Probability Distributions.- Linear Models for Regression.- Linear Models for Classification.- Neural Networks.- Kernel Methods.- Sparse Kernel Machines.- Graphical Models.- Mixture Models and EM.- Approximate Inference.- Sampling Methods.- Continuous Latent Variables.- Sequential Data.- Combining Models.

Pattern Recognition and Machine Learning

Autonomous Maxwellian demons exploit structured environments as a resource to generate work: They randomize ordered inputs and leverage the increased Shannon entropy to transfer energy from a thermal reservoir to a work reservoir, respecting both Liouvillian state-space dynamics and the Second Law. To date, correctly determining such functional thermodynamic operating regimes was restricted to information engines for which correlations among information-bearing degrees of freedom can be calculated exactly via compact analytical forms---a highly restricted set of engines. Despite information-engine controllers being represented as finite hidden Markov chains and rate matrices, the restriction arose since the processes generated are notoriously complicated, defying closed-form analysis. Even when finite state (i) no finite expression for their Shannon entropy rate exists, (ii) the set of their predictive features is generically uncountably infinite, and (iii) their effective memory---the statistical complexity---diverges. When attempting to circumvent these challenges, previous analyses of thermodynamic function either heavily constrained controller structure, invoked approximations that misclassified thermodynamic functioning, or simply failed. Here, we adapt recent results from dynamical-system and ergodic theories that efficiently and accurately calculate the entropy rates and the rate of statistical complexity divergence of general hidden Markov processes. Applied to information ratchets, the results precisely determine the thermodynamic functionality for previously-studied Maxwellian Demons and open up analysis to a substantially broader class of information engines.

The Functional Thermodynamics of Finite-State Maxwellian Ratchets

Author(s): Loomis, SP; Crutchfield, JP | Abstract: Modularity dissipation identifies how locally implemented computation entails costs beyond those required by Landauer's bound on thermodynamic computing. We establish a general theorem for efficient local computation, giving the necessary and sufficient conditions for a local operation to have zero modularity cost. Applied to thermodynamically-generating stochastic processes it confirms a conjecture that classical generators are efficient if and only if they satisfy retrodiction, which places minimum-memory requirements on the generator. This extends immediately to quantum computation: Any quantum simulator that employs quantum memory compression cannot be thermodynamically efficient.

/pdf/thermodynamically-efficient-local-computation-and-the-ejgsi0yhdm.pdf

Thermodynamically-efficient local computation and the inefficiency of quantum memory compression

Author(s): Rupe, A; Crutchfield, JP; Kashinath, K; Prabhat | Abstract: Given that observational and numerical climate data are being produced at ever more prodigious rates, increasingly sophisticated and automated analysis techniques have become essential. Deep learning is quickly becoming a standard approach for such analyses and, while great progress is being made, major challenges remain. Unlike commercial applications in which deep learning has led to surprising successes, scientific data is highly complex and typically unlabeled. Moreover, interpretability and detecting new mechanisms are key to scientific discovery. To enhance discovery we present a complementary physics-based, data-driven approach that exploits the causal nature of spatiotemporal data sets generated by local dynamics (e.g. hydrodynamic flows). We illustrate how novel patterns and coherent structures can be discovered in cellular automata and outline the path from them to climate data.

/pdf/a-physics-based-approach-to-unsupervised-discovery-of-2lyvqdvj8h.pdf

A Physics-Based Approach to Unsupervised Discovery of Coherent Structures in Spatiotemporal Systems

Author(s): Ray, Kyle J; Wimsatt, Gregory W; Boyd, Alexander B; Crutchfield, James P | Abstract: All computation is physically embedded. Reflecting this, a growing body of results embraces rate equations as the underlying mechanics of thermodynamic computation and biological information processing. Strictly applying the implied continuous-time Markov chains, however, excludes a universe of natural computing. We show that expanding the toolset to continuous-time hidden Markov chains substantially removes the constraints. The general point is made concrete by our analyzing two eminently-useful computations that are impossible to describe with a set of rate equations over the memory states. We design and analyze a thermodynamically-costless bit flip, providing a first counterexample to rate-equation modeling. We generalize this to a costless Fredkin gate---a key operation in reversible computing that is computation universal. Going beyond rate-equation dynamics is not only possible, but necessary if stochastic thermodynamics is to become part of the paradigm for physical information processing.

/pdf/non-markovian-momentum-computing-universal-and-efficient-4uihb2t3ya.pdf

Non-Markovian Momentum Computing: Universal and Efficient

A general and basic model of primordial evolution--a soup of reacting finitary and discrete processes--is employed to identify and analyze fundamental mechanisms that generate and maintain complex structures in prebiotic systems. The processes--$\epsilon$-machines as defined in computational mechanics--and their interaction networks both provide well defined notions of structure. This enables us to quantitatively demonstrate hierarchical self-organization in the soup in terms of complexity. We found that replicating processes evolve the strategy of successively building higher levels of organization by autocatalysis. Moreover, this is facilitated by local components that have low structural complexity, but high generality. In effect, the finitary process soup spontaneously evolves a selection pressure that favors such components. In light of the finitary process soup's generality, these results suggest a fundamental law of hierarchical systems: global complexity requires local simplicity.

James P. Crutchfield

Papers

The Functional Thermodynamics of Finite-State Maxwellian Ratchets

Thermodynamically-efficient local computation and the inefficiency of quantum memory compression

A Physics-Based Approach to Unsupervised Discovery of Coherent Structures in Spatiotemporal Systems

Non-Markovian Momentum Computing: Universal and Efficient

Primordial Evolution in the Finitary Process Soup