Population-based local search for protein folding simulation in the MJ energy model and cubic lattices

We present experimental results on benchmark problems in 3D cubic lattice structures with the Miyazawa-Jernigan energy function for two local search procedures that utilise the pull-move set: (i) population-based local search (PLS) that traverses the energy landscape with greedy steps towards (potential) local minima followed by upward steps up to a certain level of the objective function; (ii) simulated annealing with a logarithmic cooling schedule (LSA). The parameter settings for PLS are derived from short LSA-runs executed in pre-processing and the procedure utilises tabu lists generated for each member of the population. In terms of the total number of energy function evaluations both methods perform equally well, however. PLS has the potential of being parallelised with an expected speed-up in the region of the population size. Furthermore, both methods require a significant smaller number of function evaluations when compared to Monte Carlo simulations with kink-jump moves. (C) 2009 Elsevier Ltd. All rights reserved.

A disparity energy model improved by line, edge and keypoint correspondences

Disparity energy models (DEMs) estimate local depth information on the basis ofVl complex cells. Our recent DEM (Martins et al, 2011 ISSPlT261-266) employs a population code. Once the population's cells have been trained with randorn-dot stereograms, it is applied at all retinotopic positions in the visual field. Despite producing good results in textured regions, the model needs to be made more precise, especially at depth transitions.

Towards an Application-Specific Thermal Energy Model of Current Processors

Recent developments of high-end processors recognize temperature monitoring and tuning as one of the main challenges towards achieving higher performance given the growing power and temperature constraints. To address this challenge, one needs both suitable thermal energy abstraction and corresponding instrumentation. Our model is based on application-specific parameters such as power consumption, execution time, and asymptotic temperature as well as hardware-specific parameters such as half time for thermal rise or fall. As observed with our out-of-band instrumentation and monitoring infrastructure, the temperature changes follow a relatively slow capacitor-style charge-discharge process. Therefore, we use the lumped thermal model that initiates an exponential process whenever there is a change in processor’s power consumption. Initial experiments with two codes – Firestarter and Nekbone – validate our thermal energy model and demonstrate its use for analyzing and potentially improving the application-specific balance between temperature, power, and performance.

Antiferromagnetic spherical spin-glass model

We study the thermodynamic properties and the phase diagrams of a multi-spin antiferromagnetic spherical spin-glass model using the replica method. It is a two-sublattice version of the ferromagnetic spherical p-spin glass model. We consider both the replica-symmetric and the one-step replica-symmetry-breaking solutions, the latter being the most general solution for this model. We find paramagnetic, spin-glass, antiferromagnetic and mixed or glassy antiferromagnetic phases. The phase transitions are always of second order in the thermodynamic sense, but the spin-glass order parameter may undergo a discontinuous change.

Investigating Facebook groups through a random graph model

Facebook disseminates messages for billions of users everyday. Though there are log files stored on central servers, law enforcement agencies outside of the U.S. cannot easily acquire server log files from Facebook. This work models Facebook user groups by using a random graph model. Our aim is to facilitate detectives quickly estimating the size of a Facebook group with which a suspect is involved. We estimate this group size according to the number of immediate friends and the number of extended friends which are usually accessible by the public. We plot and examine UML diagrams to describe Facebook functions. Our experimental results show that asymmetric Facebook friendship fulfills the assumption of applying random graph models.

Detection on application layer DDoS using random walk model

Application Layer Distributed Denial of Service (ALDDoS) attacks have been increasing rapidly with the growth of Botnets and Ubiquitous computing. Differentiate to the former DDoS attacks, ALDDoS attacks cannot be efficiently detected, as attackers always adopt legitimate requests with real IP address, and the traffic has high similarity to legitimate traffic. In spite of that, we think, the attackers' browsing behavior will have great disparity from that of the legitimate users'. In this paper, we put forward a novel user behavior-based method to detect the application layer asymmetric DDoS attack. We introduce an extended random walk model to describe user browsing behavior and establish the legitimate pattern of browsing sequences. For each incoming browser, we observe his page request sequence and predict subsequent page request sequence based on random walk model. The similarity between the predicted and the observed page request sequence is used as a criterion to measure the legality of the user, and then attacker would be detected based on it. Evaluation results based on real collected data set has demonstrated that our method is very effective in detecting asymmetric ALDDoS attacks. © 2014 IEEE.

Milk yield persistency in Brazilian Gyr cattle based on a random regression model

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

A Markov random field model for combining optimum-path forest classifiers using decision graphs and game strategy approach

The research on multiple classifiers systems includes the creation of an ensemble of classifiers and the proper combination of the decisions. In order to combine the decisions given by classifiers, methods related to fixed rules and decision templates are often used. Therefore, the influence and relationship between classifier decisions are often not considered in the combination schemes. In this paper we propose a framework to combine classifiers using a decision graph under a random field model and a game strategy approach to obtain the final decision. The results of combining Optimum-Path Forest (OPF) classifiers using the proposed model are reported, obtaining good performance in experiments using simulated and real data sets. The results encourage the combination of OPF ensembles and the framework to design multiple classifier systems. © 2011 Springer-Verlag.

Genetic parameters for production traits of dairy Gyr (Bos indicus) x Holstein cattle estimated with a random regression model

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Alzheimer random walk model: Two previously overlooked diffusion regimes

A non-Markovian one-dimensional random walk model is studied with emphasis on the phase-diagram, showing all the diffusion regimes, along with the exactly determined critical lines. The model, known as the Alzheimer walk, is endowed with memory-controlled diffusion, responsible for the model's long-range correlations, and is characterized by a rich variety of diffusive regimes. The importance of this model is that superdiffusion arises due not to memory per se, but rather also due to loss of memory. The recently reported numerically and analytically estimated values for the Hurst exponent are hereby reviewed. We report the finding of two, previously overlooked, phases, namely, evanescent log-periodic diffusion and log-periodic diffusion with escape, both with Hurst exponent H = 1/2. In the former, the log-periodicity gets damped, whereas in the latter the first moment diverges. These phases further enrich the already intricate phase diagram. The results are discussed in the context of phase transitions, aging phenomena, and symmetry breaking.

Superdiffusion in a non-Markovian random walk model with a Gaussian memory profile

Most superdiffusive Non-Markovian random walk models assume that correlations are maintained at all time scales, e. g., fractional Brownian motion, Levy walks, the Elephant walk and Alzheimer walk models. In the latter two models the random walker can always "remember" the initial times near t = 0. Assuming jump size distributions with finite variance, the question naturally arises: is superdiffusion possible if the walker is unable to recall the initial times? We give a conclusive answer to this general question, by studying a non-Markovian model in which the walker's memory of the past is weighted by a Gaussian centered at time t/2, at which time the walker had one half the present age, and with a standard deviation sigma t which grows linearly as the walker ages. For large widths we find that the model behaves similarly to the Elephant model, but for small widths this Gaussian memory profile model behaves like the Alzheimer walk model. We also report that the phenomenon of amnestically induced persistence, known to occur in the Alzheimer walk model, arises in the Gaussian memory profile model. We conclude that memory of the initial times is not a necessary condition for generating (log-periodic) superdiffusion. We show that the phenomenon of amnestically induced persistence extends to the case of a Gaussian memory profile.