A Topological Analysis of the Magnetic Breakout Model for an Eruptive Solar Flare

Maclean, R., Beveridge, C., Longcope, D.W., Brown, D.S. and Priest, E.R., 2005, A topological analysis of the magnetic breakout model for an eruptive solar flare, Proc. Roy. Soc., 461, 2099-2120. Sponsorship: PPARC/STFC

On the structure of quasi-two-dimensional foams

S.J. Cox and E. Janiaud (2008) On the structure of quasi-two-dimensional foams. Phil. Mag. Letts. 88:693-701 Philosophical Magazine Letters Volume 88, Issue 9-10, 2008 Special Issue: Solid and Liquid Foams. In commemoration of Manuel Amaral Fortes The full text will be available 12 months after publication Sponsorship: We thank K. Brakke for his development and maintenance of the Surface Evolver code, I. Cantat, N. Denkov and F. Graner for their insightful comments on this work, and the participants in the Grenoble Foam Mechanics Workshop (2008) for their suggestions. EJ thanks D. Weaire and S. Hutzler for support, and ESA (MAP AO-99-108:C14914/02/NL/SH, MAP AO-99-075:C14308/00/NL/SH) for funding. SJC thanks the British Council Alliance programme, CNRS and EPSRC (EP/D048397/1, EP/D071127/1) for financial support.

Making DSpace your own

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Integration of relational and hierarchical network information for protein function prediction

BACKGROUND:In the current climate of high-throughput computational biology, the inference of a protein's function from related measurements, such as protein-protein interaction relations, has become a canonical task. Most existing technologies pursue this task as a classification problem, on a term-by-term basis, for each term in a database, such as the Gene Ontology (GO) database, a popular rigorous vocabulary for biological functions. However, ontology structures are essentially hierarchies, with certain top to bottom annotation rules which protein function predictions should in principle follow. Currently, the most common approach to imposing these hierarchical constraints on network-based classifiers is through the use of transitive closure to predictions.RESULTS:We propose a probabilistic framework to integrate information in relational data, in the form of a protein-protein interaction network, and a hierarchically structured database of terms, in the form of the GO database, for the purpose of protein function prediction. At the heart of our framework is a factorization of local neighborhood information in the protein-protein interaction network across successive ancestral terms in the GO hierarchy. We introduce a classifier within this framework, with computationally efficient implementation, that produces GO-term predictions that naturally obey a hierarchical 'true-path' consistency from root to leaves, without the need for further post-processing.CONCLUSION:A cross-validation study, using data from the yeast Saccharomyces cerevisiae, shows our method offers substantial improvements over both standard 'guilt-by-association' (i.e., Nearest-Neighbor) and more refined Markov random field methods, whether in their original form or when post-processed to artificially impose 'true-path' consistency. Further analysis of the results indicates that these improvements are associated with increased predictive capabilities (i.e., increased positive predictive value), and that this increase is consistent uniformly with GO-term depth. Additional in silico validation on a collection of new annotations recently added to GO confirms the advantages suggested by the cross-validation study. Taken as a whole, our results show that a hierarchical approach to network-based protein function prediction, that exploits the ontological structure of protein annotation databases in a principled manner, can offer substantial advantages over the successive application of 'flat' network-based methods.

Structural Analysis of Network Traffic Flows

Network traffic arises from the superposition of Origin-Destination (OD) flows. Hence, a thorough understanding of OD flows is essential for modeling network traffic, and for addressing a wide variety of problems including traffic engineering, traffic matrix estimation, capacity planning, forecasting and anomaly detection. However, to date, OD flows have not been closely studied, and there is very little known about their properties. We present the first analysis of complete sets of OD flow timeseries, taken from two different backbone networks (Abilene and Sprint-Europe). Using Principal Component Analysis (PCA), we find that the set of OD flows has small intrinsic dimension. In fact, even in a network with over a hundred OD flows, these flows can be accurately modeled in time using a small number (10 or less) of independent components or dimensions. We also show how to use PCA to systematically decompose the structure of OD flow timeseries into three main constituents: common periodic trends, short-lived bursts, and noise. We provide insight into how the various constituents contribute to the overall structure of OD flows and explore the extent to which this decomposition varies over time.

Analysis of OD Flows (Raw Data)

In a recent paper, Structural Analysis of Network Traffic Flows, we analyzed the set of Origin Destination traffic flows from the Sprint-Europe and Abilene backbone networks. This report presents the complete set of results from analyzing data from both networks. The results in this report are specific to the Sprint-1 and Abilene datasets studied in the above paper. The following results are presented here: 1 Rows of Principal Matrix (V) 2 1.1 Sprint-1 Dataset ................................ 2 1.2 Abilene Dataset.................................. 9 2 Set of Eigenflows 14 2.1 Sprint-1 Dataset.................................. 14 2.2 Abilene Dataset................................... 21 3 Classifying Eigenflows 26 3.1 Sprint-1 Dataset.................................. 26 3.2 Abilene Datase.................................... 44

Graph Wavelets for Spatial Traffic Analysis

A number of problems in network operations and engineering call for new methods of traffic analysis. While most existing traffic analysis methods are fundamentally temporal, there is a clear need for the analysis of traffic across multiple network links — that is, for spatial traffic analysis. In this paper we give examples of problems that can be addressed via spatial traffic analysis. We then propose a formal approach to spatial traffic analysis based on the wavelet transform. Our approach (graph wavelets) generalizes the traditional wavelet transform so that it can be applied to data elements connected via an arbitrary graph topology. We explore the necessary and desirable properties of this approach and consider some of its possible realizations. We then apply graph wavelets to measurements from an operating network. Our results show that graph wavelets are very useful for our motivating problems; for example, they can be used to form highly summarized views of an entire network's traffic load, to gain insight into a network's global traffic response to a link failure, and to localize the extent of a failure event within the network.

Anisotropic Interpolation on Graphs: The Combinatorial Dirichlet Problem

The combinatorial Dirichlet problem is formulated, and an algorithm for solving it is presented. This provides an effective method for interpolating missing data on weighted graphs of arbitrary connectivity. Image processing examples are shown, and the relation to anistropic diffusion is discussed.

Isoperimetric Graph Partitioning for Data Clustering and Image Segmentation

Spectral methods of graph partitioning have been shown to provide a powerful approach to the image segmentation problem. In this paper, we adopt a different approach, based on estimating the isoperimetric constant of an image graph. Our algorithm produces the high quality segmentations and data clustering of spectral methods, but with improved speed and stability.

Isoperimetric Partitioning: A New Algorithm for Graph Partitioning

Temporal structure is skilled, fluent action exists at several nested levels. At the largest scale considered here, short sequences of actions that are planned collectively in prefronatal cortex appear to be queued for performance by a cyclic competitive process that operates in concert with a parallel analog representation that implicitly specifies the relative priority of elements of the sequence. At an intermediate scale, single acts, like reaching to grasp, depend on coordinated scaling of the rates at which many muscles shorten or lengthen in parallel. To ensure success of acts such as catching an approaching ball, such parallel rate scaling, which appears to be one function of the basal ganglia, must be coupled to perceptual variables such as time-to-contact. At a finer scale, within each act, desired rate scaling can be realized only if precisely timed muscle activations first accelerate and then decelerate the limbs, to ensure that muscle length changes do not under- or over- shoot the amounts needed for precise acts. Each context of action may require a different timed muscle activation pattern than similar contexts. Because context differences that require different treatment cannot be known in advance, a formidable adaptive engine-the cerebellum-is needed to amplify differences within, and continuosly search, a vast parallel signal flow, in order to discover contextual "leading indicators" of when to generate distinctive patterns of analog signals. From some parts of the cerebellum, such signals control muscles. But a recent model shows how the lateral cerebellum may serve the competitive queuing system (frontal cortex) as a repository of quickly accessed long-term sequence memories. Thus different parts of the cerebellum may use the same adaptive engine design to serve the lowest and highest of the three levels of temporal structure treated. If so, no one-to-one mapping exists between leveels of temporal structure and major parts of the brain. Finally, recent data cast doubt on network-delay models of cerebellar adaptive timing.

The Graph Analysis Toolbox: Image Processing on Arbitrary Graphs

Office of Naval Research (N00014-01-1-0624)

Estimating Sensor Motion from Wide-Field Optical Flow on a Log-Dipolar Sensor

Log-polar image architectures, motivated by the structure of the human visual field, have long been investigated in computer vision for use in estimating motion parameters from an optical flow vector field. Practical problems with this approach have been: (i) dependence on assumed alignment of the visual and motion axes; (ii) sensitivity to occlusion form moving and stationary objects in the central visual field, where much of the numerical sensitivity is concentrated; and (iii) inaccuracy of the log-polar architecture (which is an approximation to the central 20°) for wide-field biological vision. In the present paper, we show that an algorithm based on generalization of the log-polar architecture; termed the log-dipolar sensor, provides a large improvement in performance relative to the usual log-polar sampling. Specifically, our algorithm: (i) is tolerant of large misalignmnet of the optical and motion axes; (ii) is insensitive to significant occlusion by objects of unknown motion; and (iii) represents a more correct analogy to the wide-field structure of human vision. Using the Helmholtz-Hodge decomposition to estimate the optical flow vector field on a log-dipolar sensor, we demonstrate these advantages, using synthetic optical flow maps as well as natural image sequences.

Intersubject Regularity in the Intrinsic Shape of Human V1

Previous studies have reported considerable intersubject variability in the three-dimensional geometry of the human primary visual cortex (V1). Here we demonstrate that much of this variability is due to extrinsic geometric features of the cortical folds, and that the intrinsic shape of V1 is similar across individuals. V1 was imaged in ten ex vivo human hemispheres using high-resolution (200 μm) structural magnetic resonance imaging at high field strength (7 T). Manual tracings of the stria of Gennari were used to construct a surface representation, which was computationally flattened into the plane with minimal metric distortion. The instrinsic shape of V1 was determined from the boundary of the planar representation of the stria. An ellipse provided a simple parametric shape model that was a good approximation to the boundary of flattened V1. The aspect ration of the best-fitting ellipse was found to be consistent across subject, with a mean of 1.85 and standard deviation of 0.12. Optimal rigid alignment of size-normalized V1 produced greater overlap than that achieved by previous studies using different registration methods. A shape analysis of published macaque data indicated that the intrinsic shape of macaque V1 is also stereotyped, and similar to the human V1 shape. Previoud measurements of the functional boundary of V1 in human and macaque are in close agreement with these results.

Adaptation of Dopamine Neurons' Mismatch Sensitivity Is not Compatible With Reinforcement Learning Theory

Recent electrophysical data inspired the claim that dopaminergic neurons adapt their mismatch sensitivities to reflect variances of expected rewards. This contradicts reward prediction error theory and most basal ganglia models. Application of learning principles points to a testable alternative interpretation-of the same data-that is compatible with existing theory.

Exact Geosedics and Shortest Paths on Polyhedral Surface

We present two algorithms for computing distances along a non-convex polyhedral surface. The first algorithm computes exact minimal-geodesic distances and the second algorithm combines these distances to compute exact shortest-path distances along the surface. Both algorithms have been extended to compute the exact minimalgeodesic paths and shortest paths. These algorithms have been implemented and validated on surfaces for which the correct solutions are known, in order to verify the accuracy and to measure the run-time performance, which is cubic or less for each algorithm. The exact-distance computations carried out by these algorithms are feasible for large-scale surfaces containing tens of thousands of vertices, and are a necessary component of near-isometric surface flattening methods that accurately transform curved manifolds into flat representations.