Protracted speciation revitalizes the neutral theory of biodiversity.

Understanding the maintenance and origin of biodiversity is a formidable task, yet many ubiquitous ecological patterns are predicted by a surprisingly simple and widely studied neutral model that ignores functional differences between species. However, this model assumes that new species arise instantaneously as singletons and consequently makes unrealistic predictions about species lifetimes, speciation rates and number of rare species. Here, we resolve these anomalies - without compromising any of the original models existing achievements and retaining computational and analytical tractability - by modelling speciation as a gradual, protracted, process rather than an instantaneous event. Our model also makes new predictions about the diversity of incipient species and rare species in the metacommunity. We show that it is both necessary and straightforward to incorporate protracted speciation in future studies of neutral models, and argue that non-neutral models should also model speciation as a gradual process rather than an instantaneous one

Electromagnetic models for ultrasound image processing

Speckle noise appears when coherent illumination is employed, as for example Laser, Synthetic Aperture Radar (SAR), Sonar, Magnetic Resonance, X-ray and Ultrasound imagery. Backscattered echoes from the randomly distributed scatterers in the microscopic structure of the medium are the origin of speckle phenomenon, which characterizes coherent imaging with a granular appearance. It can be shown that speckle noise is of multiplicative nature, strongly correlated and more importantly, with non-Gaussian statistics. These characteristics differ greatly from the traditional assumption of white additive Gaussian noise, often taken in image segmentation, filtering, and in general, image processing; which leads to reduction of the methods effectiveness for final image information extraction; therefore, this kind of noise severely impairs human and machine ability to image interpretation. Statistical modeling is of particular relevance when dealing with speckled data in order to obtain efficient image processing algorithms; but, additionally, clinical ultrasound imaging systems employ nonlinear signal processing to reduce the dynamic range of the input echo signal to match the smaller dynamic range of the display device and to emphasize objects with weak backscatter. This reduction in dynamic range is normally achieved through a logarithmic amplifier i.e. logarithmic compression, which selectively compresses large input signals. This kind of nonlinear compression totally changes the statistics of the input envelope signal; and, a closed form expression for the density function of the logarithmic transformed data is usually hard to derive. This thesis is concerned with the statistical distributions of the Log-compressed amplitude signal in coherent imagery, and its main objective is to develop a general statistical model for log-compressed ultrasound B-scan images. The developed model is adapted, making the pertinent physical analogies, from the multiplicative model in Synthetic Aperture Radar (SAR) context. It is shown that the proposed model can successfully describe log-compressed data generated from different models proposed in the specialized ultrasound image processing literature. Also, the model is successfully applied to model in-vivo echo-cardiographic (ultrasound) B-scan images. Necessary theorems are established to account for a rigorous mathematical proof of the validity and generality of the model. Additionally, a physical interpretation of the parameters is given, and the connections between the generalized central limit theorems, the multiplicative model and the compound representations approaches for the different models proposed up-to-date, are established. It is shown that the log-amplifier parameters are included as model parameters and all the model parameters are estimated using moments and maximum likelihood methods. Finally, three applications are developed: speckle noise identification and filtering; segmentation of in vivo echo-cardiographic (ultrasound) B-scan images and a novel approach for heart ejection fraction evaluationEl ruido Speckle aparece cuando se utilizan sistemas de iluminación coherente, como por ejemplo Láser, Radar de Apertura Sintética (SAR), Sonar, Resonancia Magnética, rayos X y ultrasonidos. Los ecos dispersados por los centros dispersores distribuidos al azar en la estructura microscópica del medio son el origen de este fenómeno, que caracteriza las imágenes coherentes con un aspecto granular. Se puede demostrar que el ruido Speckle es de carácter multiplicativo, fuertemente correlacionados y lo más importante, con estadística no Gaussiana. Estas características son muy diferentes de la suposición tradicional de ruido aditivo gaussiano blanco, a menudo asumida en la segmentación de imágenes, filtrado, y en general, en el procesamiento de imágenes; lo cual se traduce en la reducción de la eficacia de los métodos para la extracción de información de la imagen final. La modelización estadística es de particular relevancia cuando se trata con datos Speckle, a fin de obtener algoritmos de procesamiento de imágenes eficientes. Además, el procesamiento no lineal de señales empleado en sistemas clínicos de imágenes por ultrasonido para reducir el rango dinámico de la señal de eco de entrada de manera que coincida con el rango dinámico más pequeño del dispositivo de visualización y resaltar así los objetos con dispersión más débil, modifica radicalmente la estadística de los datos. Esta reducción en el rango dinámico se logra normalmente a través de un amplificador logarítmico es decir, la compresión logarítmica, que comprime selectivamente las señales de entrada y una forma analítica para la expresión de la función de densidad de los datos transformados logarítmicamente es por lo general difícil de derivar. Esta tesis se centra en las distribuciones estadísticas de la amplitud de la señal comprimida logarítmicamente en las imágenes coherentes, y su principal objetivo es el desarrollo de un modelo estadístico general para las imágenes por ultrasonido comprimidas logarítmicamente en modo-B. El modelo desarrollado se adaptó, realizando las analogías físicas relevantes, del modelo multiplicativo en radares de apertura sintética (SAR). El Modelo propuesto puede describir correctamente los datos comprimidos logarítmicamente a partir datos generados con los diferentes modelos propuestos en la literatura especializada en procesamiento de imágenes por ultrasonido. Además, el modelo se aplica con éxito para modelar ecocardiografías en vivo. Se enuncian y demuestran los teoremas necesarios para dar cuenta de una demostración matemática rigurosa de la validez y generalidad del modelo. Además, se da una interpretación física de los parámetros y se establecen las conexiones entre el teorema central del límite generalizado, el modelo multiplicativo y la composición de distribuciones para los diferentes modelos propuestos hasta a la fecha. Se demuestra además que los parámetros del amplificador logarítmico se incluyen dentro de los parámetros del modelo y se estiman usando los métodos estándar de momentos y máxima verosimilitud. Por último, tres aplicaciones se desarrollan: filtrado de ruido Speckle, segmentación de ecocardiografías y un nuevo enfoque para la evaluación de la fracción de eyección cardiaca.Postprint (published version

The Kohlrausch function: properties and applications

In a wide variety of applications, including the modelling of the glassy state of dense matter, non-exponential correlation functions in nuclear magnetic resonance, polymer dynamics, and bone and muscle rheology, Kohlrausch functions have proved to be more appropriate in modelling the associated relaxation and decay processes than the standard exponential function. However, mathematical results about this function, important for both computational and modelling endeavours, are spread over publications in several quite different areas of mathematics and science. The purpose of this paper is to review the key properties of Kohlrausch functions in a unified manner, which motivates its use in the modelling of molecular processes. Some representative applications and related computational issues are discussed

Convolution operations arising from Vandermonde matrices

Different types of convolution operations involving large Vandermonde matrices are considered. The convolutions parallel those of large Gaussian matrices and additive and multiplicative free convolution. First additive and multiplicative convolution of Vandermonde matrices and deterministic diagonal matrices are considered. After this, several cases of additive and multiplicative convolution of two independent Vandermonde matrices are considered. It is also shown that the convergence of any combination of Vandermonde matrices is almost sure. We will divide the considered convolutions into two types: those which depend on the phase distribution of the Vandermonde matrices, and those which depend only on the spectra of the matrices. A general criterion is presented to find which type applies for any given convolution. A simulation is presented, verifying the results. Implementations of all considered convolutions are provided and discussed, together with the challenges in making these implementations efficient. The implementation is based on the technique of Fourier-Motzkin elimination, and is quite general as it can be applied to virtually any combination of Vandermonde matrices. Generalizations to related random matrices, such as Toeplitz and Hankel matrices, are also discussed.Comment: Submitted to IEEE Transactions on Information Theory. 16 pages, 1 figur

Dynamic Spectrum Sharing in Cognitive Radio and Device-to-Device Systems

abstract: Cognitive radio (CR) and device-to-device (D2D) systems are two promising dynamic spectrum access schemes in wireless communication systems to provide improved quality-of-service, and efficient spectrum utilization. This dissertation shows that both CR and D2D systems benefit from properly designed cooperation scheme. In underlay CR systems, where secondary users (SUs) transmit simultaneously with primary users (PUs), reliable communication is by all means guaranteed for PUs, which likely deteriorates SUs’ performance. To overcome this issue, cooperation exclusively among SUs is achieved through multi-user diversity (MUD), where each SU is subject to an instantaneous interference constraint at the primary receiver. Therefore, the active number of SUs satisfying this constraint is random. Under different user distributions with the same mean number of SUs, the stochastic ordering of SU performance metrics including bit error rate (BER), outage probability, and ergodic capacity are made possible even without observing closed form expressions. Furthermore, a cooperation is assumed between primary and secondary networks, where those SUs exceeding the interference constraint facilitate PU’s transmission by relaying its signal. A fundamental performance trade-off between primary and secondary networks is observed, and it is illustrated that the proposed scheme outperforms non-cooperative underlay CR systems in the sense of system overall BER and sum achievable rate. Similar to conventional cellular networks, CR systems suffer from an overloaded receiver having to manage signals from a large number of users. To address this issue, D2D communications has been proposed, where direct transmission links are established between users in close proximity to offload the system traffic. Several new cooperative spectrum access policies are proposed allowing coexistence of multiple D2D pairs in order to improve the spectral efficiency. Despite the additional interference, it is shown that both the cellular user’s (CU) and the individual D2D user's achievable rates can be improved simultaneously when the number of D2D pairs is below a certain threshold, resulting in a significant multiplexing gain in the sense of D2D sum rate. This threshold is quantified for different policies using second order approximations for the average achievable rates for both the CU and the individual D2D user.Dissertation/ThesisDoctoral Dissertation Electrical Engineering 201