Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement

Recently, the target function for crystallographic refinement has been improved through a maximum likelihood analysis, which makes proper allowance for the effects of data quality, model errors, and incompleteness. The maximum likelihood target reduces the significance of false local minima during the refinement process, but it does not completely eliminate them, necessitating the use of stochastic optimization methods such as simulated annealing for poor initial models. It is shown that the combination of maximum likelihood with cross-validation, which reduces overfitting, and simulated annealing by torsion angle molecular dynamics, which simplifies the conformational search problem, results in a major improvement of the radius of convergence of refinement and the accuracy of the refined structure. Torsion angle molecular dynamics and the maximum likelihood target function interact synergistically, the combination of both methods being significantly more powerful than each method individually. This is demonstrated in realistic test cases at two typical minimum Bragg spacings (dmin = 2.0 and 2.8 Å, respectively), illustrating the broad applicability of the combined method. In an application to the refinement of a new crystal structure, the combined method automatically corrected a mistraced loop in a poor initial model, moving the backbone by 4 Å.

Using rare mutations to estimate population divergence times: A maximum likelihood approach

In this paper we propose a method to estimate by maximum likelihood the divergence time between two populations, specifically designed for the analysis of nonrecurrent rare mutations. Given the rapidly growing amount of data, rare disease mutations affecting humans seem the most suitable candidates for this method. The estimator RD, and its conditional version RDc, were derived, assuming that the population dynamics of rare alleles can be described by using a birth–death process approximation and that each mutation arose before the split of a common ancestral population into the two diverging populations. The RD estimator seems more suitable for large sample sizes and few alleles, whose age can be approximated, whereas the RDc estimator appears preferable when this is not the case. When applied to three cystic fibrosis mutations, the estimator RD could not exclude a very recent time of divergence among three Mediterranean populations. On the other hand, the divergence time between these populations and the Danish population was estimated to be, on the average, 4,500 or 15,000 years, assuming or not a selective advantage for cystic fibrosis carriers, respectively. Confidence intervals are large, however, and can probably be reduced only by analyzing more alleles or loci.

Maximum-likelihood noncoherent lattice decoding of QAM

We present a novel, maximum-likelihood (ML), lattice-decoding algorithm for noncoherent block detection of QAM signals. The computational complexity is polynomial in the block length; making it feasible for implementation compared with the exhaustive search ML detector. The algorithm works by enumerating the nearest neighbor regions for a plane defined by the received vector; in a conceptually similar manner to sphere decoding. Simulations show that the new algorithm significantly outperforms existing approaches

Parallel geostatistics for sparse and dense datasets

Very large spatially-referenced datasets, for example, those derived from satellite-based sensors which sample across the globe or large monitoring networks of individual sensors, are becoming increasingly common and more widely available for use in environmental decision making. In large or dense sensor networks, huge quantities of data can be collected over small time periods. In many applications the generation of maps, or predictions at specific locations, from the data in (near) real-time is crucial. Geostatistical operations such as interpolation are vital in this map-generation process and in emergency situations, the resulting predictions need to be available almost instantly, so that decision makers can make informed decisions and define risk and evacuation zones. It is also helpful when analysing data in less time critical applications, for example when interacting directly with the data for exploratory analysis, that the algorithms are responsive within a reasonable time frame. Performing geostatistical analysis on such large spatial datasets can present a number of problems, particularly in the case where maximum likelihood. Although the storage requirements only scale linearly with the number of observations in the dataset, the computational complexity in terms of memory and speed, scale quadratically and cubically respectively. Most modern commodity hardware has at least 2 processor cores if not more. Other mechanisms for allowing parallel computation such as Grid based systems are also becoming increasingly commonly available. However, currently there seems to be little interest in exploiting this extra processing power within the context of geostatistics. In this paper we review the existing parallel approaches for geostatistics. By recognising that diffeerent natural parallelisms exist and can be exploited depending on whether the dataset is sparsely or densely sampled with respect to the range of variation, we introduce two contrasting novel implementations of parallel algorithms based on approximating the data likelihood extending the methods of Vecchia [1988] and Tresp [2000]. Using parallel maximum likelihood variogram estimation and parallel prediction algorithms we show that computational time can be significantly reduced. We demonstrate this with both sparsely sampled data and densely sampled data on a variety of architectures ranging from the common dual core processor, found in many modern desktop computers, to large multi-node super computers. To highlight the strengths and weaknesses of the diffeerent methods we employ synthetic data sets and go on to show how the methods allow maximum likelihood based inference on the exhaustive Walker Lake data set.

Demonstration of 10 Gbit/s transmission over 900 km SMF with <400 ns adaptation time using full-field EDC

This reported work significantly extends the reach of 10Gbit/s on-off keying singlemode fibre (SMF) transmission using full-field based electronic dispersion compensation (EDC) to 900 km. In addition, the EDC balances the complexity and the adaptation capability by employing a simple dispersive transmission line with static parameters for coarse dispersion compensation and 16-state maximum likelihood sequence estimation with Gaussian approximation based channel training for adaptive impairment trimming. Improved adaptation times of less than 400 ns for a bit error rate target of 10-3 over distances ranging from 0 to 900 km are reported.

Channel estimation and compensation in chromatic dispersion limited optical fast OFDM systems

We experimentally investigate the channel estimation and compensation in a chromatic dispersion (CD) limited 20Gbit/s optical fast orthogonal frequency division multiplexing (F-OFDM) system with up to 840km transmission. It is shown that symmetric extension based guard interval (GI) is required to enable CD compensation using one-tap equalizers. As few as one optical F-OFDM symbol with four and six pilot tones per symbol can achieve near-optimal channel estimation and compensation performance for 600km and 840km respectively.

Channel estimation and compensation in chromatic dispersion limited optical fast OFDM systems

We experimentally investigate the channel estimation and compensation in a chromatic dispersion (CD) limited 20Gbit/s optical fast orthogonal frequency division multiplexing (F-OFDM) system with up to 840km transmission. It is shown that symmetric extension based guard interval (GI) is required to enable CD compensation using one-tap equalizers. As few as one optical F-OFDM symbol with four and six pilot tones per symbol can achieve near-optimal channel estimation and compensation performance for 600km and 840km respectively.

Demonstration of 10 Gbit/s transmission over 900 km SMF with <400 ns adaptation time using full-field EDC

This reported work significantly extends the reach of 10Gbit/s on-off keying singlemode fibre (SMF) transmission using full-field based electronic dispersion compensation (EDC) to 900 km. In addition, the EDC balances the complexity and the adaptation capability by employing a simple dispersive transmission line with static parameters for coarse dispersion compensation and 16-state maximum likelihood sequence estimation with Gaussian approximation based channel training for adaptive impairment trimming. Improved adaptation times of less than 400 ns for a bit error rate target of 10-3 over distances ranging from 0 to 900 km are reported.

Em Estimation of the Offspring Distribution in Mutitype Branching Processes - a Model in Cell Kinetics

2000 Mathematics Subject Classification: 60J80, 60J85, 62P10, 92D25.

Optical fibre limits:an approach using ASE channel estimation

In this talk we investigate the usage of spectrally shaped amplified spontaneous emission (ASE) in order to emulate highly dispersed wavelength division multiplexed (WDM) signals in an optical transmission system. Such a technique offers various simplifications to large scale WDM experiments. Not only does it offer a reduction in transmitter complexity, removing the need for multiple source lasers, it potentially reduces the test and measurement complexity by requiring only the centre channel of a WDM system to be measured in order to estimate WDM worst case performance. The use of ASE as a test and measurement tool is well established in optical communication systems and several measurement techniques will be discussed [1, 2]. One of the most prevalent uses of ASE is in the measurement of receiver sensitivity where ASE is introduced in order to degrade the optical signal to noise ratio (OSNR) and measure the resulting bit error rate (BER) at the receiver. From an analytical point of view noise has been used to emulate system performance, the Gaussian Noise model is used as an estimate of highly dispersed signals and has had consider- able interest [3]. The work to be presented here extends the use of ASE by using it as a metric to emulate highly dispersed WDM signals and in the process reduce WDM transmitter complexity and receiver measurement time in a lab environment. Results thus far have indicated [2] that such a transmitter configuration is consistent with an AWGN model for transmission, with modulation format complexity and nonlinearities playing a key role in estimating the performance of systems utilising the ASE channel emulation technique. We conclude this work by investigating techniques capable of characterising the nonlinear and damage limits of optical fibres and the resultant information capacity limits. REFERENCES McCarthy, M. E., N. Mac Suibhne, S. T. Le, P. Harper, and A. D. Ellis, “High spectral efficiency transmission emulation for non-linear transmission performance estimation for high order modulation formats," 2014 European Conference on IEEE Optical Communication (ECOC), 2014. 2. Ellis, A., N. Mac Suibhne, F. Gunning, and S. Sygletos, “Expressions for the nonlinear trans- mission performance of multi-mode optical fiber," Opt. Express, Vol. 21, 22834{22846, 2013. Vacondio, F., O. Rival, C. Simonneau, E. Grellier, A. Bononi, L. Lorcy, J. Antona, and S. Bigo, “On nonlinear distortions of highly dispersive optical coherent systems," Opt. Express, Vol. 20, 1022-1032, 2012.

On the Existence and Uniqueness of the Maximum Likelihood Estimators of Normal and Lognormal Population Parameters with Grouped Data

Lognormal distribution has abundant applications in various fields. In literature, most inferences on the two parameters of the lognormal distribution are based on Type-I censored sample data. However, exact measurements are not always attainable especially when the observation is below or above the detection limits, and only the numbers of measurements falling into predetermined intervals can be recorded instead. This is the so-called grouped data. In this paper, we will show the existence and uniqueness of the maximum likelihood estimators of the two parameters of the underlying lognormal distribution with Type-I censored data and grouped data. The proof was first established under the case of normal distribution and extended to the lognormal distribution through invariance property. The results are applied to estimate the median and mean of the lognormal population.