55,251 research outputs found
Random hierarchies that facilitate self-organization
©2002 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE.Since it is widely accepted that self-organization is difficult to achieve using constructive or centrally run algorithms a random hierarchy is proposed that intrinsically facilitates self-organization. The random hierarchy consists of each node in the network independently choosing a rank at random such that a mean 2(\Delta-1)\Delta^{i-1} nodes have rank i, where \Delta is a network wide hierarchy parameter. Each node of rank i chooses the nearest node of rank i-1 as its leader which forms the hierarchy. The mean and variance of the relevant properties is derived, for example it is shown that each leader has a mean \Delta followers. Simulations were used to demonstrate the effectiveness of the proposed hierarchy and a "bare-bones" set of procedures where provided that may be used to implement the hierarchy over a network of autonomous nodes in a robust way.Aaron Harwood, Hong She
Hierarchical coexistence of universality and diversity controls robustness and multi-functionality in intermediate filament protein networks
Proteins constitute the elementary building blocks of a vast variety of biological materials such as cellular protein networks, spider silk or bone, where they create extremely robust, multi-functional materials by self-organization of structures over many length- and time scales, from nano to macro. Some of the structural features are commonly found in a many different tissues, that is, they are highly conserved. Examples of such universal building blocks include alpha-helices, beta-sheets or tropocollagen molecules. In contrast, other features are highly specific to tissue types, such as particular filament assemblies, beta-sheet nanocrystals in spider silk or tendon fascicles. These examples illustrate that the coexistence of universality and diversity – in the following referred to as the universality-diversity paradigm (UDP) – is an overarching feature in protein materials. This paradigm is a paradox: How can a structure be universal and diverse at the same time? In protein materials, the coexistence of universality and diversity is enabled by utilizing hierarchies, which serve as an additional dimension beyond the 3D or 4D physical space. This may be crucial to understand how their structure and properties are linked, and how these materials are capable of combining seemingly disparate properties such as strength and robustness. Here we illustrate how the UDP enables to unify universal building blocks and highly diversified patterns through formation of hierarchical structures that lead to multi-functional, robust yet highly adapted structures. We illustrate these concepts in an analysis of three types of intermediate filament proteins, including vimentin, lamin and keratin
Hierarchical mutual information for the comparison of hierarchical community structures in complex networks
The quest for a quantitative characterization of community and modular
structure of complex networks produced a variety of methods and algorithms to
classify different networks. However, it is not clear if such methods provide
consistent, robust and meaningful results when considering hierarchies as a
whole. Part of the problem is the lack of a similarity measure for the
comparison of hierarchical community structures. In this work we give a
contribution by introducing the {\it hierarchical mutual information}, which is
a generalization of the traditional mutual information, and allows to compare
hierarchical partitions and hierarchical community structures. The {\it
normalized} version of the hierarchical mutual information should behave
analogously to the traditional normalized mutual information. Here, the correct
behavior of the hierarchical mutual information is corroborated on an extensive
battery of numerical experiments. The experiments are performed on artificial
hierarchies, and on the hierarchical community structure of artificial and
empirical networks. Furthermore, the experiments illustrate some of the
practical applications of the hierarchical mutual information. Namely, the
comparison of different community detection methods, and the study of the
consistency, robustness and temporal evolution of the hierarchical modular
structure of networks.Comment: 14 pages and 12 figure
Information Horizons in Networks
We investigate and quantify the interplay between topology and ability to
send specific signals in complex networks. We find that in a majority of
investigated real-world networks the ability to communicate is favored by the
network topology on small distances, but disfavored at larger distances. We
further discuss how the ability to locate specific nodes can be improved if
information associated to the overall traffic in the network is available.Comment: Submitted top PR
Self-organization of action hierarchy and compositionality by reinforcement learning with recurrent neural networks
Recurrent neural networks (RNNs) for reinforcement learning (RL) have shown
distinct advantages, e.g., solving memory-dependent tasks and meta-learning.
However, little effort has been spent on improving RNN architectures and on
understanding the underlying neural mechanisms for performance gain. In this
paper, we propose a novel, multiple-timescale, stochastic RNN for RL. Empirical
results show that the network can autonomously learn to abstract sub-goals and
can self-develop an action hierarchy using internal dynamics in a challenging
continuous control task. Furthermore, we show that the self-developed
compositionality of the network enhances faster re-learning when adapting to a
new task that is a re-composition of previously learned sub-goals, than when
starting from scratch. We also found that improved performance can be achieved
when neural activities are subject to stochastic rather than deterministic
dynamics
An ontology to standardize research output of nutritional epidemiology : from paper-based standards to linked content
Background: The use of linked data in the Semantic Web is a promising approach to add value to nutrition research. An ontology, which defines the logical relationships between well-defined taxonomic terms, enables linking and harmonizing research output. To enable the description of domain-specific output in nutritional epidemiology, we propose the Ontology for Nutritional Epidemiology (ONE) according to authoritative guidance for nutritional epidemiology.
Methods: Firstly, a scoping review was conducted to identify existing ontology terms for reuse in ONE. Secondly, existing data standards and reporting guidelines for nutritional epidemiology were converted into an ontology. The terms used in the standards were summarized and listed separately in a taxonomic hierarchy. Thirdly, the ontologies of the nutritional epidemiologic standards, reporting guidelines, and the core concepts were gathered in ONE. Three case studies were included to illustrate potential applications: (i) annotation of existing manuscripts and data, (ii) ontology-based inference, and (iii) estimation of reporting completeness in a sample of nine manuscripts.
Results: Ontologies for food and nutrition (n = 37), disease and specific population (n = 100), data description (n = 21), research description (n = 35), and supplementary (meta) data description (n = 44) were reviewed and listed. ONE consists of 339 classes: 79 new classes to describe data and 24 new classes to describe the content of manuscripts.
Conclusion: ONE is a resource to automate data integration, searching, and browsing, and can be used to assess reporting completeness in nutritional epidemiology
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