Fibration symmetries uncover the building blocks of biological networks

A major ambition of systems science is to uncover the building blocks of any biological network to decipher how cellular function emerges from their interactions. Here, we introduce a graph representation of the information flow in these networks as a set of input trees, one for each node, which contains all pathways along which information can be transmitted in the network. In this representation, we find remarkable symmetries in the input trees that deconstruct the network into functional building blocks called fibers. Nodes in a fiber have isomorphic input trees and thus process equivalent dynamics and synchronize their activity. Each fiber can then be collapsed into a single representative base node through an information-preserving transformation called 'symmetry fibration', introduced by Grothendieck in the context of algebraic geometry. We exemplify the symmetry fibrations in gene regulatory networks and then show that they universally apply across species and domains from biology to social and infrastructure networks. The building blocks are classified into topological classes of input trees characterized by integer branching ratios and fractal golden ratios of Fibonacci sequences representing cycles of information. Thus, symmetry fibrations describe how complex networks are built from the bottom up to process information through the synchronization of their constitutive building blocks

Estimating PageRank deviations in crawled graphs

Most real-world graphs collected from the Web like Web graphs and social network graphs are partially discovered or crawled. This leads to inaccurate estimates of graph properties based on link analysis such as PageRank. In this paper we focus on studying such deviations in ordering/ranking imposed by PageRank over crawled graphs. We first show that deviations in rankings induced by PageRank are indeed possible. We measure how much a ranking, induced by PageRank, on an input graph could deviate from the original unseen graph. More importantly, we are interested in conceiving a measure that approximates the rank correlation among them without any knowledge of the original graph. To this extent we formulate the HAK measure that is based on computing the impact redistribution of PageRank according to the local graph structure. We further propose an algorithm that identifies connected subgraphs over the input graph for which the relative ordering is preserved. Finally, we perform extensive experiments on both real-world Web and social network graphs with more than 100M vertices and 10B edges as well as synthetic graphs to showcase the utility of HAK and our High-fidelity Component Selection approach

Neighborhood Structure Configuration Models

We develop a new method to efficiently sample synthetic networks that preserve the d-hop neighborhood structure of a given network for any given d. The proposed algorithm trades off the diversity in network samples against the depth of the neighborhood structure that is preserved. Our key innovation is to employ a colored Configuration Model with colors derived from iterations of the so-called Color Refinement algorithm. We prove that with increasing iterations the preserved structural information increases: the generated synthetic networks and the original network become more and more similar, and are eventually indistinguishable in terms of centrality measures such as PageRank, HITS, Katz centrality and eigenvector centrality. Our work enables to efficiently generate samples with a precisely controlled similarity to the original network, especially for large networks

States and sequences of paired subspace ideals and their relationship to patterned brain function

It is found here that the state of a network of coupled ordinary differential equations is partially localizable through a pair of contractive ideal subspaces, chosen from dual complete lattices related to the synchrony and synchronization of cells within the network. The first lattice is comprised of polydiagonal subspaces, corresponding to synchronous activity patterns that arise from functional equivalences of cell receptive fields. This lattice is dual to a transdiagonal subspace lattice ordering subspaces transverse to these network-compatible synchronies. Combinatorial consideration of contracting polydiagonal and transdiagonal subspace pairs yields a rich array of dynamical possibilities for structured networks. After proving that contraction commutes with the lattice ordering, it is shown that subpopulations of cells are left at fixed potentials when pairs of contracting subspaces span the cells' local coordinates - a phenomenon named glyph formation here. Treatment of mappings between paired states then leads to a theory of network-compatible sequence generation. The theory's utility is illustrated with examples ranging from the construction of a minimal circuit for encoding a simple phoneme to a model of the primary visual cortex including high-dimensional environmental inputs, laminar speficicity, spiking discontinuities, and time delays. In this model, glyph formation and dissolution provide one account for an unexplained anomaly in electroencephalographic recordings under periodic flicker, where stimulus frequencies differing by as little as 1 Hz generate responses varying by an order of magnitude in alpha-band spectral power. Further links between coupled-cell systems and neural dynamics are drawn through a review of synchronization in the brain and its relationship to aggregate observables, focusing again on electroencephalography. Given previous theoretical work relating the geometry of visual hallucinations to symmetries in visual cortex, periodic perturbation of the visual system along a putative symmetry axis is hypothesized to lead to a greater concentration of harmonic spectral energy than asymmetric perturbations; preliminary experimental evidence affirms this hypothesis. To conclude, connections drawn between dynamics, sensation, and behavior are distilled to seven hypotheses, and the potential medical uses of the theory are illustrated with a lattice depiction of ketamine xylazine anaesthesia and a reinterpretation of hemifield neglect

Graphical Models and Symmetries : Loopy Belief Propagation Approaches

Whenever a person or an automated system has to reason in uncertain domains, probability theory is necessary. Probabilistic graphical models allow us to build statistical models that capture complex dependencies between random variables. Inference in these models, however, can easily become intractable. Typical ways to address this scaling issue are inference by approximate message-passing, stochastic gradients, and MapReduce, among others. Exploiting the symmetries of graphical models, however, has not yet been considered for scaling statistical machine learning applications. One instance of graphical models that are inherently symmetric are statistical relational models. These have recently gained attraction within the machine learning and AI communities and combine probability theory with first-order logic, thereby allowing for an efficient representation of structured relational domains. The provided formalisms to compactly represent complex real-world domains enable us to effectively describe large problem instances. Inference within and training of graphical models, however, have not been able to keep pace with the increased representational power. This thesis tackles two major aspects of graphical models and shows that both inference and training can indeed benefit from exploiting symmetries. It first deals with efficient inference exploiting symmetries in graphical models for various query types. We introduce lifted loopy belief propagation (lifted LBP), the first lifted parallel inference approach for relational as well as propositional graphical models. Lifted LBP can effectively speed up marginal inference, but cannot straightforwardly be applied to other types of queries. Thus we also demonstrate efficient lifted algorithms for MAP inference and higher order marginals, as well as the efficient handling of multiple inference tasks. Then we turn to the training of graphical models and introduce the first lifted online training for relational models. Our training procedure and the MapReduce lifting for loopy belief propagation combine lifting with the traditional statistical approaches to scaling, thereby bridging the gap between statistical relational learning and traditional statistical machine learning

Graph fibrations, graph isomorphism, and PageRank

PageRank is a ranking method that assigns scores to web pages using the limit distribution of a random walk on the web graph. A fibration of graphs is a morphism that is a local isomorphism of in-neighbourhoods, much in the same way a covering projection is a local isomorphism of neighbourhoods. We show that a deep connection relates fibrations and Markov chains with restart, a particular kind of Markov chains that include the PageRank one as a special case. This fact provides constraints on the values that PageRank can assume. Using our results, we show that a recently defined class of graphs that admit a polynomial-time isomorphism algorithm based on the computation of PageRank is really a subclass of fibration-prime graphs, which possess simple, entirely discrete polynomial-time isomorphism algorithms based on classical techniques for graph isomorphism. We discuss efficiency issues in the implementation of such algorithms for the particular case of web graphs, in which O(n) space occupancy (where n is the number of nodes) may be acceptable, but O(m) is not (where m is the number of arcs)

Graph fibrations, graph isomorphism, and PageRank

PageRank is a ranking method that assigns scores to web pages using the limit distribution of a random walk on the web graph. A fibration of graphs is a morphism that is a local isomorphism of in-neighbourhoods, much in the same way a covering projection is a local isomorphism of neighbourhoods. We show that a deep connection relates fibrations and Markov chains with restart, a particular kind of Markov chains that include the PageRank one as a special case. This fact provides constraints on the values that PageRank can assume. Using our results, we show that a recently defined class of graphs that admit a polynomial-time isomorphism algorithm based on the computation of PageRank is really a subclass of fibration-prime graphs, which possess simple, entirely discrete polynomial-time isomorphism algorithms based on classical techniques for graph isomorphism. We discuss efficiency issues in the implementation of such algorithms for the particular case of web graphs, in which O(n) space occupancy (where n is the number of nodes) may be acceptable, but O(m) is not (where m is the number of arcs).