Comment of Global dynamics of biological systems

In a recent study, (Grigorov, 2006) analyzed temporal gene expression profiles (Arbeitman et al., 2002) generated in a Drosophila experiment using SSA in conjunction with Monte-Carlo SSA. The author (Grigorov, 2006) makes three important claims in his article, namely: Claim1: A new method based on the theory of nonlinear time series analysis is used to capture the global dynamics of the fruit-fly cycle temporal gene expression profiles. Claim 2: Flattening of a significant part of the eigen-spectrum confirms the hypothesis about an underly-ing high-dimensional chaotic generating process. Claim 3: Monte-Carlo SSA can be used to establish whether a given time series is distinguishable from any well-defined process including deterministic chaos. In this report we present fundamental concerns with respect to the above claims (Grigorov, 2006) in a systematic manner with simple examples. The discussion provided especially discourages the choice of SSA for inferring nonlinear dynamical structure form time series obtained in any biological paradigm.Comment: 6 pages, 2 figure

Evidence of crossover phenomena in wind speed data

In this report, a systematic analysis of hourly wind speed data obtained from three potential wind generation sites (in North Dakota) is analyzed. The power spectra of the data exhibited a power-law decay characteristic of $1/f^{\alpha}$ processes with possible long-range correlations. Conventional analysis using Hurst exponent estimators proved to be inconclusive. Subsequent analysis using detrended fluctuation analysis (DFA) revealed a crossover in the scaling exponent ($\alpha$). At short time scales, a scaling exponent of $\alpha \sim 1.4$ indicated that the data resembled Brownian noise, whereas for larger time scales the data exhibited long range correlations ($\alpha \sim 0.7$). The scaling exponents obtained were similar across the three locations. Our findings suggest the possibility of multiple scaling exponents characteristic of multifractal signals

A Multifractal Description of Wind Speed Records

In this paper, a systematic analysis of hourly wind speed data obtained from four potential wind generation sites in North Dakota is conducted. The power spectra of the data exhibited a power law decay characteristic of $1/f^{\alpha}$ processes with possible long range correlations. The temporal scaling properties of the records were studied using multifractal detrended fluctuation analysis {\em MFDFA}. It is seen that the records at all four locations exhibit similar scaling behavior which is also reflected in the multifractal spectrum determined under the assumption of a binomial multiplicative cascade model

Power-law Signatures and Patchiness in Genechip Oligonucleotide Microarrays

. Genechip oligonucleotide microarrays have been used widely for transcriptional profiling of a large number of genes in a given paradigm. Gene expression estimation precedes biological inference and is given as a complex combination of atomic entities on the array called probes. These probe intensities are further classified into perfect-match (PM) and mis-match (MM) probes. While former is a measure of specific binding, the lat-ter is a measure of non-specific binding. The behavior of the MM probes has especially proven to be elusive. The present study investigates qualita-tive similarities in the distributional signatures and local correlation struc-tures/patchiness between the PM and MM probe intensities. These qualita-tive similarities are established on publicly available microarrays generated across laboratories investigating the same paradigm. Persistence of these similarities across raw as well as background subtracted probe intensities is also investigated. The results presented raise fundamental concerns in inter-preting Genechip oligonucleotide microarray data.Comment: 21 Pages, 6 Figure

Reliable scaling exponent estimation of long-range correlated noise in the presence of random spikes

Detrended fluctuation analysis (DFA) has been used widely to determine possible long-range correlations in data obtained from diverse settings. In a recent study [1], uncorrelated random spikes superimposed on the long-range correlated noise (LR noise) were found to affect DFA scaling exponent estimates. In this brief communication, singular-value decomposition (SVD) filter is proposed to minimize the effect random spikes superimposed on LR noise, thus facilitating reliable estimation of the scaling exponents. The effectiveness of the proposed approach is demonstrated on random spikes sampled from normal and uniform distributions.Comment: 36 Pages, 20 Figure

On Identifying Significant Edges in Graphical Models of Molecular Networks

Objective: Modelling the associations from high-throughput experimental molecular data has provided unprecedented insights into biological pathways and signalling mechanisms. Graphical models and networks have especially proven to be useful abstractions in this regard. Ad-hoc thresholds are often used in conjunction with structure learning algorithms to determine significant associations. The present study overcomes this limitation by proposing a statistically-motivated approach for identifying significant associations in a network. Methods and Materials: A new method that identifies significant associations in graphical models by estimating the threshold minimising the $L_{\mathrm{1}}$ norm between the cumulative distribution function (CDF) of the observed edge confidences and those of its asymptotic counterpart is proposed. The effectiveness of the proposed method is demonstrated on popular synthetic data sets as well as publicly available experimental molecular data corresponding to gene and protein expression profiles. Results: The improved performance of the proposed approach is demonstrated across the synthetic data sets using sensitivity, specificity and accuracy as performance metrics. The results are also demonstrated across varying sample sizes and three different structure learning algorithms with widely varying assumptions. In all cases, the proposed approach has specificity and accuracy close to 1, while sensitivity increases linearly in the logarithm of the sample size. The estimated threshold systematically outperforms common ad-hoc ones in terms of sensitivity while maintaining comparable levels of specificity and accuracy. Networks from experimental data sets are reconstructed accurately with respect to the results from the original papers.Comment: 21 pages, 9 figures. Presented at the Conference for Artificial Intelligence in Medicine (AIME '11), Workshop on Probabilistic Problem Solving in Biomedicin