Comparison of Two Methods for Caluculating the Partition Functions of Various Spatial Statistical Models

Likelihood computation in spatial statistics requires accurate and efficient calculation of the normalizing constant (i.e. partition function) of the Gibbs distribution of the model. Two available methods to calculate the normalizing constant by Markov chain Monte Carlo methods are compared by simulation experiments for an Ising model, a Gaussian Markov field model and a pairwise interaction point field model.

Hierarchical semi-markov conditional random fields for recursive sequential data

Inspired by the hierarchical hidden Markov models (HHMM), we present the hierarchical semi-Markov conditional random field (HSCRF), a generalisation of embedded undirected Markov chains to model complex hierarchical, nested Markov processes. It is parameterised in a discriminative framework and has polynomial time algorithms for learning and inference. Importantly, we develop efficient algorithms for learning and constrained inference in a partially-supervised setting, which is important issue in practice where labels can only be obtained sparsely. We demonstrate the HSCRF in two applications: (i) recognising human activities of daily living (ADLs) from indoor surveillance cameras, and (ii) noun-phrase chunking. We show that the HSCRF is capable of learning rich hierarchical models with reasonable accuracy in both fully and partially observed data cases.

Contextually Learnt Detection of Unusual Motion-Based Behaviour in Crowded Public Spaces

In this paper we are interested in analyzing behaviour in crowded publicplaces at the level of holistic motion. Our aim is to learn, without user input, strong scene priors or labelled data, the scope of ‘‘normal behaviour’’ for a particular scene and thus alert to novelty in unseen footage. The first contribution is a low-level motion model based on what we term tracklet primitives, which are scenespecific elementary motions. We propose a clustering-based algorithm for tracklet estimation from local approximations to tracks of appearance features. This is followed by two methods for motion novelty inference from tracklet primitives: (a) an approach based on a non-hierarchial ensemble of Markov chains as a means of capturing behavioural characteristics at different scales, and (b) a more flexible alternative which exhibits a higher generalizing power by accounting for constraints introduced by intentionality and goal-oriented planning of human motion in a particular scene. Evaluated on a 2 h long video of a busy city marketplace, both algorithms are shown to be successful at inferring unusual behaviour, the latter model achieving better performance for novelties at a larger spatial scale.

Inferring activity budgets in wild animals to estimate the consequences of disturbances

Activity budgets can provide a direct link to an animal's bioenergetic budget and is thus a valuable unit of measure when assessing human-induced nonlethal effects on wildlife conservation status. However, activity budget inference can be challenging for species that are difficult to observe and require multiple observational variables. Here, we assessed whether whalewatching boat interactions could affect the activity budgets of minke whales (Balaenoptera acutorostrata). We used a stepwise modeling approach to quantitatively record, identify, and assign activity states to continuous behavioral time series data, to estimate activity budgets. First, we used multiple behavioral variables, recorded from continuous visual observations of individual animals, to quantitatively identify and define behavioral types. Activity states were then assigned to each sampling unit, using a combination of hidden and observed states. Three activity states were identified: nonfeeding, foraging, and surface feeding (SF). From the resulting time series of activity states, transition probability matrices were estimated using first-order Markov chains. We then simulated time series of activity states, using Monte Carlo methods based on the transition probability matrices, to obtain activity budgets, accounting for heterogeneity in state duration. Whalewatching interactions reduced the time whales spend foraging and SF, potentially resulting in an overall decrease in energy intake of 42%. This modeling approach thus provides a means to link short-term behavioral changes resulting from human disturbance to potential long-term bioenergetic consequences in animals. It also provides an analytical framework applicable to other species when direct observations of activity states are not possible.

On the fast Lanczos method for computation of eigenvalues of Hankel matrices using multiprecision arithmetics

The use of the fast Fourier transform (FFT) accelerates Lanczos tridiagonalisation method for Hankel and Toeplitz matrices by reducing the complexity of matrix-vector multiplication. In multiprecision arithmetics, the FFT has overheads that make it less competitive compared with alternative methods when the accuracy is over 10000 decimal places. We studied two alternative Hankel matrix-vector multiplication methods based on multiprecision number decomposition and recursive Karatsuba-like multiplication, respectively. The first method was uncompetitive because of huge precision losses, while the second turned out to be five to 14 times faster than FFT in the ranges of matrix sizes up to n = 8192 and working precision of b = 32768 bits we were interested in. We successfully applied our approach to eigenvalues calculations to studies of spectra of matrices that arise in research on Riemann zeta function. The recursive matrix-vector multiplication significantly outperformed both the FFT and the traditional multiplication in these studies.

Integrating network analysis, sensor tags, and observation to understand shark ecology and behavior

Group living in animals is a well-studied phenomenon, having been documented extensively in a wide range of terrestrial, freshwater, and marine species. Although social dynamics are complex across space and time, recent technological and analytical advances enable deeper understanding of their nature and ecological implications. While for some taxa, a great deal of information is known regarding the mechanistic underpinnings of these social processes, knowledge of these mechanisms in elasmobranchs is lacking. Here, we used an integrative and novel combination of direct observation, accelerometer biologgers, and recent advances in network analysis to better understand the mechanistic bases of individual-level differences in sociality (leadership, network attributes) and diel patterns of locomotor activity in a widespread marine predator, the lemon shark (Negaprion brevirostris). We found that dynamic models of interaction based on Markov chains can accurately predict juvenile lemon shark social behavior and that lemon sharks did not occupy consistent positions within their network. Lemon sharks did however preferentially associate with specific group members, by sex as well as by similarity or nonsimilarity for a number of behavioral (nonsimilarity: leadership) and locomotor traits (similarity: proportion of time swimming "fast," mean swim duration; nonsimilarity: proportion of swimming bursts/transitions between activity states). Our study provides some of the first information on the mechanistic bases of group living and personality in sharks and further, a potential experimental approach for studying fine-scale differences in behavior and locomotor patterns in difficult-to-study organisms.

Assuring virtual network reliability and resilience

A framework developed that uses reliability block diagrams and continuous-time Markov chains to model and analyse the reliability and availability of a Virtual Network Environment (VNE). In addition, to minimize the unpredicted failures and reduce the impact of failure on a virtual network, a dynamic solution proposed for detecting a failure before it occurs in the VNE. Moreover, to predict failure and establish a tolerable maintenance plan before failure occurs in the VNE, a failure prediction method for VNE can be used to minimise the unpredicted failures, reduce backup redundancy and maximise system performance.

BacHbpred: support vector machine methods for the prediction of bacterial hemoglobin-like proteins

The recent upsurge in microbial genome data has revealed that hemoglobin-like (HbL) proteins may be widely distributed among bacteria and that some organisms may carry more than one HbL encoding gene. However, the discovery of HbL proteins has been limited to a small number of bacteria only. This study describes the prediction of HbL proteins and their domain classification using a machine learning approach. Support vector machine (SVM) models were developed for predicting HbL proteins based upon amino acid composition (AC), dipeptide composition (DC), hybrid method (AC + DC), and position specific scoring matrix (PSSM). In addition, we introduce for the first time a new prediction method based on max to min amino acid residue (MM) profiles. The average accuracy, standard deviation (SD), false positive rate (FPR), confusion matrix, and receiver operating characteristic (ROC) were analyzed. We also compared the performance of our proposed models in homology detection databases. The performance of the different approaches was estimated using fivefold cross-validation techniques. Prediction accuracy was further investigated through confusion matrix and ROC curve analysis. All experimental results indicate that the proposed BacHbpred can be a perspective predictor for determination of HbL related proteins. BacHbpred, a web tool, has been developed for HbL prediction.

Underdetermined blind source separation based on relaxed sparsity condition of sources

Recently, Aissa-El-Bey et al. have proposed two subspacebased methods for underdetermined blind source separation (UBSS) in time-frequency (TF) domain. These methods allow multiple active sources at TF points so long as the number of active sources at any TF point is strictly less than the number of sensors, and the column vectors of the mixing matrix are pairwise linearly independent. In this correspondence, we first show that the subspace-based methods must also satisfy the condition that any M × M submatrix of the mixing matrix is of full rank. Then we present a new UBSS approach which only requires that the number of active sources at any TF point does not exceed that of sensors. An algorithm is proposed to perform the UBSS.

A novel monotonic fixed-point algorithm for l1-regularized least square vector and matrix problem

Least square problem with l₁ regularization has been proposed as a promising method for sparse signal reconstruction (e.g., basis pursuit de-noising and compressed sensing) and feature selection (e.g., the Lasso algorithm) in signal processing, statistics, and related fields. These problems can be cast as l₁-regularized least-square program (LSP). In this paper, we propose a novel monotonic fixed point method to solve large-scale l₁-regularized LSP. And we also prove the stability and convergence of the proposed method. Furthermore we generalize this method to least square matrix problem and apply it in nonnegative matrix factorization (NMF). The method is illustrated on sparse signal reconstruction, partner recognition and blind source separation problems, and the method tends to convergent faster and sparser than other l₁-regularized algorithms.

A new method for deriving priority weights by extracting consistent numerical-valued matrices from interval-valued fuzzy judgement matrix

It is important to derive priority weights from interval-valued fuzzy preferences when a pairwise comparative mechanism is used. By focusing on the significance of consistency in the pairwise comparison matrix, two numerical-valued consistent comparison matrices are extracted from an interval fuzzy judgement matrix. Both consistent matrices are derived by solving the linear or nonlinear programming models with the aid of assessments from Decision Makers (DMs). An interval priority weight vector from the extracted consistent matrices is generated. In order to retain more information hidden in the intervals, a new probability-based method for comparison of the interval priority weights is introduced. An algorithm for deriving the final priority interval weights for both consistent and inconsistent interval matrices is proposed. The algorithm is also generalized to handle the pairwise comparison matrix with fuzzy numbers. The comparative results from the five examples reveal that the proposed method, as compared with eight existing methods, exhibits a smaller degree of uncertainty pertaining to the priority weights, and is also more reliable based on the similarity measure. © 2014 Elsevier Inc. All rights reserved.