Periodicity Detection Method for Small-Sample Time Series Datasets

Time series of gene expression often exhibit periodic behavior under the influence of multiple signal pathways, and are represented by a model that incorporates multiple harmonics and noise. Most of these data, which are observed using DNA microarrays, consist of few sampling points in time, but most periodicity detection methods require a relatively large number of sampling points. We have previously developed a detection algorithm based on the discrete Fourier transform and Akaike’s information criterion. Here we demonstrate the performance of the algorithm for small-sample time series data through a comparison with conventional and newly proposed periodicity detection methods based on a statistical analysis of the power of harmonics

Self-Similar Anisotropic Texture Analysis: the Hyperbolic Wavelet Transform Contribution

Textures in images can often be well modeled using self-similar processes while they may at the same time display anisotropy. The present contribution thus aims at studying jointly selfsimilarity and anisotropy by focusing on a specific classical class of Gaussian anisotropic selfsimilar processes. It will first be shown that accurate joint estimates of the anisotropy and selfsimilarity parameters are performed by replacing the standard 2D-discrete wavelet transform by the hyperbolic wavelet transform, which permits the use of different dilation factors along the horizontal and vertical axis. Defining anisotropy requires a reference direction that needs not a priori match the horizontal and vertical axes according to which the images are digitized, this discrepancy defines a rotation angle. Second, we show that this rotation angle can be jointly estimated. Third, a non parametric bootstrap based procedure is described, that provides confidence interval in addition to the estimates themselves and enables to construct an isotropy test procedure, that can be applied to a single texture image. Fourth, the robustness and versatility of the proposed analysis is illustrated by being applied to a large variety of different isotropic and anisotropic self-similar fields. As an illustration, we show that a true anisotropy built-in self-similarity can be disentangled from an isotropic self-similarity to which an anisotropic trend has been superimposed

Incorporating covariance estimation uncertainty in spatial sampling design for prediction with trans-Gaussian random fields

Recently, Spock and Pilz [38], demonstratedthat the spatial sampling design problem forthe Bayesian linear kriging predictor can betransformed to an equivalent experimentaldesign problem for a linear regression modelwith stochastic regression coefficients anduncorrelated errors. The stochastic regressioncoefficients derive from the polar spectralapproximation of the residual process. Thus,standard optimal convex experimental designtheory can be used to calculate optimal spatialsampling designs. The design functionals ̈considered in Spock and Pilz [38] did nottake into account the fact that kriging isactually a plug-in predictor which uses theestimated covariance function. The resultingoptimal designs were close to space-fillingconfigurations, because the design criteriondid not consider the uncertainty of thecovariance function.In this paper we also assume that thecovariance function is estimated, e.g., byrestricted maximum likelihood (REML). Wethen develop a design criterion that fully takesaccount of the covariance uncertainty. Theresulting designs are less regular and space-filling compared to those ignoring covarianceuncertainty. The new designs, however, alsorequire some closely spaced samples in orderto improve the estimate of the covariancefunction. We also relax the assumption ofGaussian observations and assume that thedata is transformed to Gaussianity by meansof the Box-Cox transformation. The resultingprediction method is known as trans-Gaussiankriging. We apply the Smith and Zhu [37]approach to this kriging method and show thatresulting optimal designs also depend on theavailable data. We illustrate our results witha data set of monthly rainfall measurementsfrom Upper Austria

Selective routing of spatial information flow from input to output in hippocampal granule cells

Dentate gyrus granule cells (GCs) connect the entorhinal cortex to the hippocampal CA3 region, but how they process spatial information remains enigmatic. To examine the role of GCs in spatial coding, we measured excitatory postsynaptic potentials (EPSPs) and action potentials (APs) in head-fixed mice running on a linear belt. Intracellular recording from morphologically identified GCs revealed that most cells were active, but activity level varied over a wide range. Whereas only ∼5% of GCs showed spatially tuned spiking, ∼50% received spatially tuned input. Thus, the GC population broadly encodes spatial information, but only a subset relays this information to the CA3 network. Fourier analysis indicated that GCs received conjunctive place-grid-like synaptic input, suggesting code conversion in single neurons. GC firing was correlated with dendritic complexity and intrinsic excitability, but not extrinsic excitatory input or dendritic cable properties. Thus, functional maturation may control input-output transformation and spatial code conversion

Topology control and data handling in wireless sensor networks

Our work in this thesis have provided two distinctive contributions to WSNs in the areas of data handling and topology control. In the area of data handling, we have demonstrated a solution to improve the power efficiency whilst preserving the important data features by data compression and the use of an adaptive sampling strategy, which are applicable to the specific application for oceanography monitoring required by the SECOAS project. Our work on oceanographic data analysis is important for the understanding of the data we are dealing with, such that suitable strategies can be deployed and system performance can be analysed. The Basic Adaptive Sampling Scheduler (BASS) algorithm uses the statistics of the data to adjust the sampling behaviour in a sensor node according to the environment in order to conserve energy and minimise detection delay. The motivation of topology control (TC) is to maintain the connectivity of the network, to reduce node degree to ease congestion in a collision-based medium access scheme; and to reduce power consumption in the sensor nodes. We have developed an algorithm Subgraph Topology Control (STC) that is distributed and does not require additional equipment to be implemented on the SECOAS nodes. STC uses a metric called subgraph number, which measures the 2-hops connectivity in the neighbourhood of a node. It is found that STC consistently forms topologies that have lower node degrees and higher probabilities of connectivity, as compared to k-Neighbours, an alternative algorithm that does not rely on special hardware on sensor node. Moreover, STC also gives better results in terms of the minimum degree in the network, which implies that the network structure is more robust to a single point of failure. As STC is an iterative algorithm, it is very scalable and adaptive and is well suited for the SECOAS applications

Depth and Depth-Based Classification with R Package ddalpha

Following the seminal idea of Tukey (1975), data depth is a function that measures how close an arbitrary point of the space is located to an implicitly defined center of a data cloud. Having undergone theoretical and computational developments, it is now employed in numerous applications with classification being the most popular one. The R package ddalpha is a software directed to fuse experience of the applicant with recent achievements in the area of data depth and depth-based classification. ddalpha provides an implementation for exact and approximate computation of most reasonable and widely applied notions of data depth. These can be further used in the depth-based multivariate and functional classifiers implemented in the package, where the DDα-procedure is in the main focus. The package is expandable with user-defined custom depth methods and separators. The implemented functions for depth visualization and the built-in benchmark procedures may also serve to provide insights into the geometry of the data and the quality of pattern recognition

Effort in gestural interactions with imaginary objects in Hindustani Dhrupad vocal music

Physical effort has often been regarded as a key factor of expressivity in music performance. Nevertheless, systematic experimental approaches to the subject have been rare. In North Indian classical (Hindustani) vocal music, singers often engage with melodic ideas during improvisation by manipulating intangible, imaginary objects with their hands, such as through stretching, pulling, pushing, throwing etc. The above observation suggests that some patterns of change in acoustic features allude to interactions that real objects through their physical properties can afford. The present study reports on the exploration of the relationships between movement and sound by accounting for the physical effort that such interactions require in the Dhrupad genre of Hindustani vocal improvisation. The work follows a mixed methodological approach, combining qualitative and quantitative methods to analyse interviews, audio-visual material and movement data. Findings indicate that despite the flexibility in the way a Dhrupad vocalist might use his/her hands while singing, there is a certain degree of consistency by which performers associate effort levels with melody and types of gestural interactions with imaginary objects. However, different schemes of cross-modal associations are revealed for the vocalists analysed, that depend on the pitch space organisation of each particular melodic mode (rāga), the mechanical requirements of voice production, the macro-structure of the ālāp improvisation and morphological cross-domain analogies. Results further suggest that a good part of the variance in both physical effort and gesture type can be explained through a small set of sound and movement features. Based on the findings, I argue that gesturing in Dhrupad singing is guided by: the know-how of humans in interacting with and exerting effort on real objects of the environment, the movement–sound relationships transmitted from teacher to student in the oral music training context and the mechanical demands of vocalisation

Automatic chord transcription from audio using computational models of musical context

PhDThis thesis is concerned with the automatic transcription of chords from audio, with an emphasis on modern popular music. Musical context such as the key and the structural segmentation aid the interpretation of chords in human beings. In this thesis we propose computational models that integrate such musical context into the automatic chord estimation process. We present a novel dynamic Bayesian network (DBN) which integrates models of metric position, key, chord, bass note and two beat-synchronous audio features (bass and treble chroma) into a single high-level musical context model. We simultaneously infer the most probable sequence of metric positions, keys, chords and bass notes via Viterbi inference. Several experiments with real world data show that adding context parameters results in a significant increase in chord recognition accuracy and faithfulness of chord segmentation. The proposed, most complex method transcribes chords with a state-of-the-art accuracy of 73% on the song collection used for the 2009 MIREX Chord Detection tasks. This method is used as a baseline method for two further enhancements. Firstly, we aim to improve chord confusion behaviour by modifying the audio front end processing. We compare the effect of learning chord profiles as Gaussian mixtures to the effect of using chromagrams generated from an approximate pitch transcription method. We show that using chromagrams from approximate transcription results in the most substantial increase in accuracy. The best method achieves 79% accuracy and significantly outperforms the state of the art. Secondly, we propose a method by which chromagram information is shared between repeated structural segments (such as verses) in a song. This can be done fully automatically using a novel structural segmentation algorithm tailored to this task. We show that the technique leads to a significant increase in accuracy and readability. The segmentation algorithm itself also obtains state-of-the-art results. A method that combines both of the above enhancements reaches an accuracy of 81%, a statistically significant improvement over the best result (74%) in the 2009 MIREX Chord Detection tasks.Engineering and Physical Research Council U

THE EFFECT OF SUMMER STORM EVENTS AS A DISTURBANCE ON THE MOVEMENT BEHAVIORS OF BLACK SEA BASS IN THE SOUTHERN MID-ATLANTIC BIGHT

Storm events are a key disturbance in the Middle Atlantic Bight (MAB), driving thermal, hydrodynamic, and acoustic perturbations on demersal fish communities. Black sea bass are a model MAB species as their sedentary behavior exposes them to storm disturbances. I coupled biotelemetry with an oceanographic model, monitoring black sea bass movement behaviors during the summer-fall of 2016-2018. Storm-driven changes in bottom temperature (associated with rapid destratification) had the greatest effects on fish movement and evacuation rates, while the cumulative effects of consecutive storms had little to no observed effect. Storms also generate substantial noise, but the hearing frequencies of black sea bass are currently unknown. I conducted a quantitative literature analysis on fish hearing based on swim bladder elaboration, successfully classifying detected sound frequency ranges among fishes, including black sea bass. Climate change will likely alter the intensity of MAB storms, prioritizing research on their impacts to fish communities