Towards Building Deep Networks with Bayesian Factor Graphs

We propose a Multi-Layer Network based on the Bayesian framework of the Factor Graphs in Reduced Normal Form (FGrn) applied to a two-dimensional lattice. The Latent Variable Model (LVM) is the basic building block of a quadtree hierarchy built on top of a bottom layer of random variables that represent pixels of an image, a feature map, or more generally a collection of spatially distributed discrete variables. The multi-layer architecture implements a hierarchical data representation that, via belief propagation, can be used for learning and inference. Typical uses are pattern completion, correction and classification. The FGrn paradigm provides great flexibility and modularity and appears as a promising candidate for building deep networks: the system can be easily extended by introducing new and different (in cardinality and in type) variables. Prior knowledge, or supervised information, can be introduced at different scales. The FGrn paradigm provides a handy way for building all kinds of architectures by interconnecting only three types of units: Single Input Single Output (SISO) blocks, Sources and Replicators. The network is designed like a circuit diagram and the belief messages flow bidirectionally in the whole system. The learning algorithms operate only locally within each block. The framework is demonstrated in this paper in a three-layer structure applied to images extracted from a standard data set.Comment: Submitted for journal publicatio

Structural Properties of the Caenorhabditis elegans Neuronal Network

Despite recent interest in reconstructing neuronal networks, complete wiring diagrams on the level of individual synapses remain scarce and the insights into function they can provide remain unclear. Even for Caenorhabditis elegans, whose neuronal network is relatively small and stereotypical from animal to animal, published wiring diagrams are neither accurate nor complete and self-consistent. Using materials from White et al. and new electron micrographs we assemble whole, self-consistent gap junction and chemical synapse networks of hermaphrodite C. elegans. We propose a method to visualize the wiring diagram, which reflects network signal flow. We calculate statistical and topological properties of the network, such as degree distributions, synaptic multiplicities, and small-world properties, that help in understanding network signal propagation. We identify neurons that may play central roles in information processing and network motifs that could serve as functional modules of the network. We explore propagation of neuronal activity in response to sensory or artificial stimulation using linear systems theory and find several activity patterns that could serve as substrates of previously described behaviors. Finally, we analyze the interaction between the gap junction and the chemical synapse networks. Since several statistical properties of the C. elegans network, such as multiplicity and motif distributions are similar to those found in mammalian neocortex, they likely point to general principles of neuronal networks. The wiring diagram reported here can help in understanding the mechanistic basis of behavior by generating predictions about future experiments involving genetic perturbations, laser ablations, or monitoring propagation of neuronal activity in response to stimulation

One-dimensional layout optimization, with applications to graph drawing by axis separation

AbstractIn this paper we discuss a useful family of graph drawing algorithms, characterized by their ability to draw graphs in one dimension. We define the special requirements from such algorithms and show how several graph drawing techniques can be extended to handle this task. In particular, we suggest a novel optimization algorithm that facilitates using the Kamada and Kawai model [Inform. Process. Lett. 31 (1989) 7–15] for producing one-dimensional layouts. The most important application of the algorithms seems to be in achieving graph drawing by axis separation, where each axis of the drawing addresses different aspects of aesthetics

Multifractal Network Generator

We introduce a new approach to constructing networks with realistic features. Our method, in spite of its conceptual simplicity (it has only two parameters) is capable of generating a wide variety of network types with prescribed statistical properties, e.g., with degree- or clustering coefficient distributions of various, very different forms. In turn, these graphs can be used to test hypotheses, or, as models of actual data. The method is based on a mapping between suitably chosen singular measures defined on the unit square and sparse infinite networks. Such a mapping has the great potential of allowing for graph theoretical results for a variety of network topologies. The main idea of our approach is to go to the infinite limit of the singular measure and the size of the corresponding graph simultaneously. A very unique feature of this construction is that the complexity of the generated network is increasing with the size. We present analytic expressions derived from the parameters of the -- to be iterated-- initial generating measure for such major characteristics of graphs as their degree, clustering coefficient and assortativity coefficient distributions. The optimal parameters of the generating measure are determined from a simple simulated annealing process. Thus, the present work provides a tool for researchers from a variety of fields (such as biology, computer science, biology, or complex systems) enabling them to create a versatile model of their network data.Comment: Preprint. Final version appeared in PNAS

05191 Abstracts Collection -- Graph Drawing

From 08.05.05 to 13.05.05, the Dagstuhl Seminar 05191 ``Graph Drawing\u27\u27 was held in the International Conference and Research Center (IBFI), Schloss Dagstuhl. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available

Graph layout for applications in compiler construction

We address graph visualization from the viewpoint of compiler construction. Most data structures in compilers are large, dense graphs such as annotated control flow graph, syntax trees, dependency graphs. Our main focus is the animation and interactive exploration of these graphs. Fast layout heuristics and powerful browsing methods are needed. We give a survey of layout heuristics for general directed and undirected graphs and present the browsing facilities that help to manage large structured graph