Factorization in the Cloud: Integer Factorization Using F# and Windows Azure

Implementations are presented of two common algorithms for integer factorization, Pollard’s “p – 1” method and the SQUFOF method. The algorithms are implemented in the F# language, a functional programming language developed by Microsoft and officially released for the first time in 2010. The algorithms are thoroughly tested on a set of large integers (up to 64 bits in size), running both on a physical machine and a Windows Azure machine instance. Analysis of the relative performance between the two environments indicates comparable performance when taking into account the difference in computing power. Further analysis reveals that the relative performance of the Azure implementation tends to improve as the magnitudes of the integers increase, indicating that such an approach may be suitable for larger, more complex factorization tasks. Finally, several questions are presented for future research, including the performance of F# and related languages for more efficient, parallelizable algorithms, and the relative cost and performance of factorization algorithms in various environments, including physical hardware and commercial cloud computing offerings from the various vendors in the industry.

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.

Surface Reconstruction from Multiple Views using Rational B-Splines

A method for reconstructing 3D rational B-spline surfaces from multiple views is proposed. The method takes advantage of the projective invariance properties of rational B-splines. Given feature correspondences in multiple views, the 3D surface is reconstructed via a four step framework. First, corresponding features in each view are given an initial surface parameter value (s; t), and a 2D B-spline is fitted in each view. After this initialization, an iterative minimization procedure alternates between updating the 2D B-spline control points and re-estimating each feature's (s; t). Next, a non-linear minimization method is used to upgrade the 2D B-splines to 2D rational B-splines, and obtain a better fit. Finally, a factorization method is used to reconstruct the 3D B-spline surface given 2D B-splines in each view. This surface recovery method can be applied in both the perspective and orthographic case. The orthographic case allows the use of additional constraints in the recovery. Experiments with real and synthetic imagery demonstrate the efficacy of the approach for the orthographic case.

Surface Reconstruction from Multiple Views using Rational B-Splines and Knot Insertion

A method for reconstruction of 3D rational B-spline surfaces from multiple views is proposed. Given corresponding features in multiple views, though not necessarily visible in all views, the surface is reconstructed. First 2D B-spline patches are fitted to each view. The 3D B-splines and projection matricies can then be extracted from the 2D B-splines using factorization methods. The surface fit is then further refined via an iterative procedure. Finally, a hierarchal fitting scheme is proposed to allow modeling of complex surfaces by means of knot insertion. Experiments with real imagery demonstrate the efficacy of the approach.

Adaptive Neural Networks for Control of Movement Trajectories Invariant under Speed and Force Rescaling

This article describes two neural network modules that form part of an emerging theory of how adaptive control of goal-directed sensory-motor skills is achieved by humans and other animals. The Vector-Integration-To-Endpoint (VITE) model suggests how synchronous multi-joint trajectories are generated and performed at variable speeds. The Factorization-of-LEngth-and-TEnsion (FLETE) model suggests how outflow movement commands from a VITE model may be performed at variable force levels without a loss of positional accuracy. The invariance of positional control under speed and force rescaling sheds new light upon a familiar strategy of motor skill development: Skill learning begins with performance at low speed and low limb compliance and proceeds to higher speeds and compliances. The VITE model helps to explain many neural and behavioral data about trajectory formation, including data about neural coding within the posterior parietal cortex, motor cortex, and globus pallidus, and behavioral properties such as Woodworth's Law, Fitts Law, peak acceleration as a function of movement amplitude and duration, isotonic arm movement properties before and after arm-deafferentation, central error correction properties of isometric contractions, motor priming without overt action, velocity amplification during target switching, velocity profile invariance across different movement distances, changes in velocity profile asymmetry across different movement durations, staggered onset times for controlling linear trajectories with synchronous offset times, changes in the ratio of maximum to average velocity during discrete versus serial movements, and shared properties of arm and speech articulator movements. The FLETE model provides new insights into how spina-muscular circuits process variable forces without a loss of positional control. These results explicate the size principle of motor neuron recruitment, descending co-contractive compliance signals, Renshaw cells, Ia interneurons, fast automatic reactive control by ascending feedback from muscle spindles, slow adaptive predictive control via cerebellar learning using muscle spindle error signals to train adaptive movement gains, fractured somatotopy in the opponent organization of cerebellar learning, adaptive compensation for variable moment-arms, and force feedback from Golgi tendon organs. More generally, the models provide a computational rationale for the use of nonspecific control signals in volitional control, or "acts of will", and of efference copies and opponent processing in both reactive and adaptive motor control tasks.

How Spinal Neural Networks Reduce Discrepancies between Motor Intention and Motor Realization

This paper attempts a rational, step-by-step reconstruction of many aspects of the mammalian neural circuitry known to be involved in the spinal cord's regulation of opposing muscles acting on skeletal segments. Mathematical analyses and local circuit simulations based on neural membrane equations are used to clarify the behavioral function of five fundamental cell types, their complex connectivities, and their physiological actions. These cell types are: α-MNs, γ-MNs, IaINs, IbINs, and Renshaw cells. It is shown that many of the complexities of spinal circuitry are necessary to ensure near invariant realization of motor intentions when descending signals of two basic types independently vary over large ranges of magnitude and rate of change. Because these two types of signal afford independent control, or Factorization, of muscle LEngth and muscle TEnsion, our construction was named the FLETE model (Bullock and Grossberg, 1988b, 1989). The present paper significantly extends the range of experimental data encompassed by this evolving model.