Colour image coding with wavelets and matching pursuit

This thesis considers sparse approximation of still images as the basis of a lossy compression system. The Matching Pursuit (MP) algorithm is presented as a method particularly suited for application in lossy scalable image coding. Its multichannel extension, capable of exploiting inter-channel correlations, is found to be an efficient way to represent colour data in RGB colour space. Known problems with MP, high computational complexity of encoding and dictionary design, are tackled by finding an appropriate partitioning of an image. The idea of performing MP in the spatio-frequency domain after transform such as Discrete Wavelet Transform (DWT) is explored. The main challenge, though, is to encode the image representation obtained after MP into a bit-stream. Novel approaches for encoding the atomic decomposition of a signal and colour amplitudes quantisation are proposed and evaluated. The image codec that has been built is capable of competing with scalable coders such as JPEG 2000 and SPIHT in terms of compression ratio.

Visual data mining using principled projection algorithms and information visualization techniques

We introduce a flexible visual data mining framework which combines advanced projection algorithms from the machine learning domain and visual techniques developed in the information visualization domain. The advantage of such an interface is that the user is directly involved in the data mining process. We integrate principled projection algorithms, such as generative topographic mapping (GTM) and hierarchical GTM (HGTM), with powerful visual techniques, such as magnification factors, directional curvatures, parallel coordinates and billboarding, to provide a visual data mining framework. Results on a real-life chemoinformatics dataset using GTM are promising and have been analytically compared with the results from the traditional projection methods. It is also shown that the HGTM algorithm provides additional value for large datasets. The computational complexity of these algorithms is discussed to demonstrate their suitability for the visual data mining framework. Copyright 2006 ACM.

Dual-polarization multi-band optical OFDM transmission and transceiver limitations for up to 500 Gb/s uncompensated long-haul links

A number of critical issues for dual-polarization single- and multi-band optical orthogonal-frequency division multiplexing (DPSB/ MB-OFDM) signals are analyzed in dispersion compensation fiber (DCF)-free long-haul links. For the first time, different DP crosstalk removal techniques are compared, the maximum transmission-reach is investigated, and the impact of subcarrier number and high-level modulation formats are explored thoroughly. It is shown, for a bit-error-rate (BER) of 10-3, 2000 km of quaternary phase-shift keying (QPSK) DP-MBOFDM transmission is feasible. At high launched optical powers (LOP), maximum-likelihood decoding can extend the LOP of 40 Gb/s QPSK DPSB- OFDM at 2000 km by 1.5 dB compared to zero-forcing. For a 100 Gb/s DP-MB-OFDM system, a high number of subcarriers contribute to improved BER but at the cost of digital signal processing computational complexity, whilst by adapting the cyclic prefix length the BER can be improved for a low number of subcarriers. In addition, when 16-quadrature amplitude modulation (16QAM) is employed the digital-toanalogue/ analogue-to-digital converter (DAC/ADC) bandwidth is relaxed with a degraded BER; while the 'circular' 8QAM is slightly superior to its 'rectangular' form. Finally, the transmission of wavelength-division multiplexing DP-MB-OFDM and single-carrier DP-QPSK is experimentally compared for up to 500 Gb/s showing great potential and similar performance at 1000 km DCF-free G.652 line. © 2014 Optical Society of America.

Advanced perturbation technique for digital backward propagation in WDM systems

An improved digital backward propagation (DBP) is proposed to compensate inter-nonlinear effects and dispersion jointly in WDM systems based on an advanced perturbation technique (APT). A non-iterative weighted concept is presented to replace the iterative in analytical recursion expression, which can dramatically simplify the complexity and improve accuracy compared to the traditional perturbation technique (TPT). Furthermore, an analytical recursion expression of the output after backward propagation is obtained initially. Numerical simulations are executed for various parameters of the transmission system. The results indicate that the advanced perturbation technique will relax the step size requirements and reduce the oversampling factor when launch power is higher than -2 dBm. We estimate this technique will reduce computational complexity by a factor of around seven with respect to the conventional DBP. © 2013 Optical Society of America.

Message passing for distributed optimisation of power allocation with renewable resources

The increase in renewable energy generators introduced into the electricity grid is putting pressure on its stability and management as predictions of renewable energy sources cannot be accurate or fully controlled. This, with the additional pressure of fluctuations in demand, presents a problem more complex than the current methods of controlling electricity distribution were designed for. A global approximate and distributed optimisation method for power allocation that accommodates uncertainties and volatility is suggested and analysed. It is based on a probabilistic method known as message passing [1], which has deep links to statistical physics methodology. This principled method of optimisation is based on local calculations and inherently accommodates uncertainties; it is of modest computational complexity and provides good approximate solutions.We consider uncertainty and fluctuations drawn from a Gaussian distribution and incorporate them into the message-passing algorithm. We see the effect that increasing uncertainty has on the transmission cost and how the placement of volatile nodes within a grid, such as renewable generators or consumers, effects it.

Amplification schemes and multi-channel DBP for unrepeatered transmission

The performance of unrepeatered transmission of a seven Nyquist-spaced 10 GBd PDM-16QAM superchannel using full signal band coherent detection and multi-channel digital back propagation (MC-DBP) to mitigate nonlinear effects is analysed. For the first time in unrepeatered transmission, the performance of two amplification systems is investigated and directly compared in terms of achievable information rates (AIRs): 1) erbium-doped fibre amplifier (EDFA) and 2) second-order bidirectional Raman pumped amplification. The experiment is performed over different span lengths, demonstrating that, for an AIR of 6.8 bit/s/Hz, the Raman system enables an increase of 93 km (36 %) in span length. Further, at these distances, MC-DBP gives an improvement in AIR of 1 bit/s/Hz (to 7.8 bit/s/Hz) for both amplification schemes. The theoretical AIR gains for Raman and MC-DBP are shown to be preserved when considering low-density parity-check codes. Additionally, MC-DBP algorithms for both amplification schemes are compared in terms of performance and computational complexity. It is shown that to achieve the maximum MC-DBP gain, the Raman system requires approximately four times the computational complexity due to the distributed impact of fibre nonlinearity.

Distributed optimization in transportation and logistics networks

Many important problems in communication networks, transportation networks, and logistics networks are solved by the minimization of cost functions. In general, these can be complex optimization problems involving many variables. However, physicists noted that in a network, a node variable (such as the amount of resources of the nodes) is connected to a set of link variables (such as the flow connecting the node), and similarly each link variable is connected to a number of (usually two) node variables. This enables one to break the problem into local components, often arriving at distributive algorithms to solve the problems. Compared with centralized algorithms, distributed algorithms have the advantages of lower computational complexity, and lower communication overhead. Since they have a faster response to local changes of the environment, they are especially useful for networks with evolving conditions. This review will cover message-passing algorithms in applications such as resource allocation, transportation networks, facility location, traffic routing, and stability of power grids.

Simple approximate MAP inference for Dirichlet processes mixtures

The Dirichlet process mixture model (DPMM) is a ubiquitous, flexible Bayesian nonparametric statistical model. However, full probabilistic inference in this model is analytically intractable, so that computationally intensive techniques such as Gibbs sampling are required. As a result, DPMM-based methods, which have considerable potential, are restricted to applications in which computational resources and time for inference is plentiful. For example, they would not be practical for digital signal processing on embedded hardware, where computational resources are at a serious premium. Here, we develop a simplified yet statistically rigorous approximate maximum a-posteriori (MAP) inference algorithm for DPMMs. This algorithm is as simple as DP-means clustering, solves the MAP problem as well as Gibbs sampling, while requiring only a fraction of the computational effort. (For freely available code that implements the MAP-DP algorithm for Gaussian mixtures see http://www.maxlittle.net/.) Unlike related small variance asymptotics (SVA), our method is non-degenerate and so inherits the “rich get richer” property of the Dirichlet process. It also retains a non-degenerate closed-form likelihood which enables out-of-sample calculations and the use of standard tools such as cross-validation. We illustrate the benefits of our algorithm on a range of examples and contrast it to variational, SVA and sampling approaches from both a computational complexity perspective as well as in terms of clustering performance. We demonstrate the wide applicabiity of our approach by presenting an approximate MAP inference method for the infinite hidden Markov model whose performance contrasts favorably with a recently proposed hybrid SVA approach. Similarly, we show how our algorithm can applied to a semiparametric mixed-effects regression model where the random effects distribution is modelled using an infinite mixture model, as used in longitudinal progression modelling in population health science. Finally, we propose directions for future research on approximate MAP inference in Bayesian nonparametrics.

Complexity and chirality indices for molecular informatics::differential geometry approach

Novel molecular complexity measures are designed based on the quantum molecular kinematics. The Hamiltonian matrix constructed in a quasi-topological approximation describes the temporal evolution of the modelled electronic system and determined the time derivatives for the dynamic quantities. This allows to define the average quantum kinematic characteristics closely related to the curvatures of the electron paths, particularly, the torsion reflecting the chirality of the dynamic system. A special attention has been given to the computational scheme for this chirality measure. The calculations on realistic molecular systems demonstrate reasonable behaviour of the proposed molecular complexity indices.

Computational mechanics reveals nanosecond time correlations in molecular dynamics of liquid systems

Statistical complexity, a measure introduced in computational mechanics has been applied to MD simulated liquid water and other molecular systems. It has been found that statistical complexity does not converge in these systems but grows logarithmically without a limit. The coefficient of the growth has been introduced as a new molecular parameter which is invariant for a given liquid system. Using this new parameter extremely long time correlations in the system undetectable by traditional methods are elucidated. The existence of hundreds of picosecond and even nanosecond long correlations in bulk water has been demonstrated. © 2008 Elsevier B.V. All rights reserved.

The dawn of the RNA World:toward functional complexity through ligation of random RNA oligomers

A main unsolved problem in the RNA World scenario for the origin of life is how a template-dependent RNA polymerase ribozyme emerged from short RNA oligomers obtained by random polymerization on mineral surfaces. A number of computational studies have shown that the structural repertoire yielded by that process is dominated by topologically simple structures, notably hairpin-like ones. A fraction of these could display RNA ligase activity and catalyze the assembly of larger, eventually functional RNA molecules retaining their previous modular structure: molecular complexity increases but template replication is absent. This allows us to build up a stepwise model of ligation- based, modular evolution that could pave the way to the emergence of a ribozyme with RNA replicase activity, step at which information-driven Darwinian evolution would be triggered. Copyright © 2009 RNA Society.

Dynamic complexity of chaotic transitions in high-dimensional classical dynamics:Leu-Enkephalin folding

Leu-Enkephalin in explicit water is simulated using classical molecular dynamics. A ß-turn transition is investigated by calculating the topological complexity (in the "computational mechanics" framework [J. P. Crutchfield and K. Young, Phys. Rev. Lett., 63, 105 (1989)]) of the dynamics of both the peptide and the neighbouring water molecules. The complexity of the atomic trajectories of the (relatively short) simulations used in this study reflect the degree of phase space mixing in the system. It is demonstrated that the dynamic complexity of the hydrogen atoms of the peptide and almost all of the hydrogens of the neighbouring waters exhibit a minimum precisely at the moment of the ß-turn transition. This indicates the appearance of simplified periodic patterns in the atomic motion, which could correspond to high-dimensional tori in the phase space. It is hypothesized that this behaviour is the manifestation of the effect described in the approach to molecular transitions by Komatsuzaki and Berry [T. Komatsuzaki and R.S. Berry, Adv. Chem. Phys., 123, 79 (2002)], where a "quasi-regular" dynamics at the transition is suggested. Therefore, for the first time, the less chaotic character of the folding transition in a realistic molecular system is demonstrated. © Springer-Verlag Berlin Heidelberg 2006.

Complexity of classical dynamics of molecular systems. I. Methodology

Methods for the calculation of complexity have been investigated as a possible alternative for the analysis of the dynamics of molecular systems. “Computational mechanics” is the approach chosen to describe emergent behavior in molecular systems that evolve in time. A novel algorithm has been developed for symbolization of a continuous physical trajectory of a dynamic system. A method for calculating statistical complexity has been implemented and tested on representative systems. It is shown that the computational mechanics approach is suitable for analyzing the dynamic complexity of molecular systems and offers new insight into the process.

Complexity of classical dynamics of molecular systems. II. Finite statistical complexity of a water-Na+ system

The computational mechanics approach has been applied to the orientational behavior of water molecules in a molecular dynamics simulated water–Na + system. The distinctively different statistical complexity of water molecules in the bulk and in the first solvation shell of the ion is demonstrated. It is shown that the molecules undergo more complex orientational motion when surrounded by other water molecules compared to those constrained by the electric field of the ion. However the spatial coordinates of the oxygen atom shows the opposite complexity behavior in that complexity is higher for the solvation shell molecules. New information about the dynamics of water molecules in the solvation shell is provided that is additional to that given by traditional methods of analysis.

Computational modelling approaches to vaccinology

Excepting the Peripheral and Central Nervous Systems, the Immune System is the most complex of somatic systems in higher animals. This complexity manifests itself at many levels from the molecular to that of the whole organism. Much insight into this confounding complexity can be gained through computational simulation. Such simulations range in application from epitope prediction through to the modelling of vaccination strategies. In this review, we evaluate selectively various key applications relevant to computational vaccinology: these include technique that operates at different scale that is, from molecular to organisms and even to population level.