Identifying affinity classes of inorganic materials binding sequences via a graph-based model

Rapid advances in bionanotechnology have recently generated growing interest in identifying peptides that bind to inorganic materials and classifying them based on their inorganic material affinities. However, there are some distinct characteristics of inorganic materials binding sequence data that limit the performance of many widely-used classification methods when applied to this problem. In this paper, we propose a novel framework to predict the affinity classes of peptide sequences with respect to an associated inorganic material. We first generate a large set of simulated peptide sequences based on an amino acid transition matrix tailored for the specific inorganic material. Then the probability of test sequences belonging to a specific affinity class is calculated by minimizing an objective function. In addition, the objective function is minimized through iterative propagation of probability estimates among sequences and sequence clusters. Results of computational experiments on two real inorganic material binding sequence data sets show that the proposed framework is highly effective for identifying the affinity classes of inorganic material binding sequences. Moreover, the experiments on the structural classification of proteins (SCOP) data set shows that the proposed framework is general and can be applied to traditional protein sequences.

A non-stationary panel data investigation of the unemployment–crime relationship

Many empirical studies of the economics of crime focus solely on the determinants thereof, and do not consider the dynamic and cross-sectional properties of their data. As a response to this, the current paper offers an in-depth analysis of this issue using data covering 21 Swedish counties from 1975 to 2010. The results suggest that the crimes considered are non-stationary, and that this cannot be attributed to county-specific disparities alone, but that there are also a small number of common stochastic trends to which groups of counties tend to revert. In an attempt to explain these common stochastic trends, we look for a long-run cointegrated relationship between unemployment and crime. Overall, the results do not support cointegration, and suggest that previous findings of a significant unemployment–crime relationship might be spurious.

Nonparametric rank tests for non-stationary panels

We develop a set of nonparametric rank tests for non-stationary panels based on multivariate variance ratios which use untruncated kernels. As such, the tests do not require the choice of tuning parameters associated with bandwidth or lag length and also do not require choices with respect to numbers of common factors. The tests allow for unrestricted cross-sectional dependence and dynamic heterogeneity among the units of the panel, provided simply that a joint functional central limit theorem holds for the panel of differenced series. We provide a discussion of the relationships between our setting and the settings for which first- and second generation panel unit root tests are designed. In Monte Carlo simulations we illustrate the small-sample performance of our tests when they are used as panel unit root tests under the more restrictive DGPs for which panel unit root tests are typically designed, and for more general DGPs we also compare the small-sample performance of our nonparametric tests to parametric rank tests. Finally, we provide an empirical illustration by testing for income convergence among countries.

A stochastic time-domain model for burst data aggregation in IEEE 802.15.4 wireless sensor networks

In many network applications, the nature of traffic is of burst type. Often, the transient response of network to such traffics is the result of a series of interdependant events whose occurrence prediction is not a trivial task. The previous efforts in IEEE 802.15.4 networks often followed top-down approaches to model those sequences of events, i.e., through making top-view models of the whole network, they tried to track the transient response of network to burst packet arrivals. The problem with such approaches was that they were unable to give station-level views of network response and were usually complex. In this paper, we propose a non-stationary analytical model for the IEEE 802.15.4 slotted CSMA/CA medium access control (MAC) protocol under burst traffic arrival assumption and without the optional acknowledgements. We develop a station-level stochastic time-domain method from which the network-level metrics are extracted. Our bottom-up approach makes finding station-level details such as delay, collision and failure distributions possible. Moreover, network-level metrics like the average packet loss or transmission success rate can be extracted from the model. Compared to the previous models, our model is proven to be of lower memory and computational complexity order and also supports contention window sizes of greater than one. We have carried out extensive and comparative simulations to show the high accuracy of our model.

The adaptable buffer algorithm for high quantile estimation in non-stationary data streams

The need to estimate a particular quantile of a distribution is an important problem which frequently arises in many computer vision and signal processing applications. For example, our work was motivated by the requirements of many semi-automatic surveillance analytics systems which detect abnormalities in close-circuit television (CCTV) footage using statistical models of low-level motion features. In this paper we specifically address the problem of estimating the running quantile of a data stream with non-stationary stochasticity when the memory for storing observations is limited. We make several major contributions: (i) we derive an important theoretical result which shows that the change in the quantile of a stream is constrained regardless of the stochastic properties of data, (ii) we describe a set of high-level design goals for an effective estimation algorithm that emerge as a consequence of our theoretical findings, (iii) we introduce a novel algorithm which implements the aforementioned design goals by retaining a sample of data values in a manner adaptive to changes in the distribution of data and progressively narrowing down its focus in the periods of quasi-stationary stochasticity, and (iv) we present a comprehensive evaluation of the proposed algorithm and compare it with the existing methods in the literature on both synthetic data sets and three large 'real-world' streams acquired in the course of operation of an existing commercial surveillance system. Our findings convincingly demonstrate that the proposed method is highly successful and vastly outperforms the existing alternatives, especially when the target quantile is high valued and the available buffer capacity severely limited.