Estimation of Hidden Markov Models parameters using differential evolution

Hidden Markov Models (HMMs) have been successfully applied to different modelling and classification problems from different areas over the recent years. An important step in using HMMs is the initialisation of the parameters of the model as the subsequent learning of HMM’s parameters will be dependent on these values. This initialisation should take into account the knowledge about the addressed problem and also optimisation techniques to estimate the best initial parameters given a cost function, and consequently, to estimate the best log-likelihood. This paper proposes the initialisation of Hidden Markov Models parameters using the optimisation algorithm Differential Evolution with the aim to obtain the best log-likelihood.

Exploration vs exploitation in differential evolution

Differential Evolution (DE) is a tool for efficient optimisation, and it belongs to the class of evolutionary algorithms, which include Evolution Strategies and Genetic Algorithms. DE algorithms work well when the population covers the entire search space, and they have shown to be effective on a large range of classical optimisation problems. However, an undesirable behaviour was detected when all the members of the population are in a basin of attraction of a local optimum (local minimum or local maximum), because in this situation the population cannot escape from it. This paper proposes a modification of the standard mechanisms in DE algorithm in order to change the exploration vs. exploitation balance to improve its behaviour.

Single-trial event-related potential analysis for brain-computer interfaces

Abstract. Different types of mental activity are utilised as an input in Brain-Computer Interface (BCI) systems. One such activity type is based on Event-Related Potentials (ERPs). The characteristics of ERPs are not visible in single-trials, thus averaging over a number of trials is necessary before the signals become usable. An improvement in ERP-based BCI operation and system usability could be obtained if the use of single-trial ERP data was possible. The method of Independent Component Analysis (ICA) can be utilised to separate single-trial recordings of ERP data into components that correspond to ERP characteristics, background electroencephalogram (EEG) activity and other components with non- cerebral origin. Choice of specific components and their use to reconstruct “denoised” single-trial data could improve the signal quality, thus allowing the successful use of single-trial data without the need for averaging. This paper assesses single-trial ERP signals reconstructed using a selection of estimated components from the application of ICA on the raw ERP data. Signal improvement is measured using Contrast-To-Noise measures. It was found that such analysis improves the signal quality in all single-trials.

Effect of incremental levels of fish oil in the diet on ruminal lipid metabolism in growing steers

Based on the potential benefits to human health, there is interest in developing sustainable nutritional strategies to enhance the concentration of long-chain n-3 fatty acids in ruminant-derived foods. Four Aberdeen Angus steers fitted with rumen and duodenal cannulae were used in a 4 × 4 Latin square experiment with 21 d experimental periods to examine the potential of fish oil (FO) in the diet to enhance the supply of 20 : 5n-3 and 22 : 6n-3 available for absorption in growing cattle. Treatments consisted of total mixed rations based on maize silage fed at a rate of 85 g DM/kg live weight0·75/d containing 0, 8, 16 and 24 g FO/kg diet DM. Supplements of FO reduced linearly (P < 0·01) DM intake and shifted (P < 0·01) rumen fermentation towards propionate at the expense of acetate and butyrate. FO in the diet enhanced linearly (P < 0·05) the flow of trans-16 : 1, trans-18 : 1, trans-18 : 2, 20 : 5n-3 and 22 : 6n-3, and decreased linearly (P < 0·05) 18 : 0 and 18 : 3n-3 at the duodenum. Increases in the flow of trans-18 : 1 were isomer dependent and were determined primarily by higher amounts of trans-11 reaching the duodenum. In conclusion, FO alters ruminal lipid metabolism of growing cattle in a dose-dependent manner consistent with an inhibition of ruminal biohydrogenation, and enhances the amount of long-chain n-3 fatty acids at the duodenum, but the increases are marginal due to extensive biohydrogenation in the rumen.

Effect of linseed oil and fish oil alone or as an equal mixture of ruminal fatty acid metabolism in growing steers fed maize silage-based diets

Based on the potential benefits to human health there is interest in increasing 18:3n-3, 20:5n-3, 22:6n-6, and cis-9,trans-11 conjugated linoleic acid (CLA) in ruminant foods. Four Aberdeen Angus steers (406 ± 8.2 kg BW) fitted with rumen and duodenal cannulae were used in a 4 x 4 Latin square experiment with 21 d periods to examine the potential of fish oil (FO) and linseed oil (LO) in the diet to increase ruminal outflow of trans-11 18:1 and total n-3 polyunsaturated fatty acids (PUFA) in growing cattle. Treatments consisted of a control diet (60:40; forage:concentrate ratio, on a DM basis, respectively) based on maize silage, or the same basal ration containing 30 g/kg DM of FO, LO or a mixture (1:1, w/w) of FO and LO (LFO). Diets were offered as total mixed rations and fed at a rate of 85 g DM/kg BW0.75/d. Oils had no effect (P = 0.52) on DM intake. Linseed oil had no effect (P > 0.05) on ruminal pH or VFA concentrations, while FO shifted rumen fermentation towards propionate at the expense of acetate. Compared with the control, LO increased (P < 0.05) 18:0, cis 18:1 (Δ9, 12-15), trans 18:1 (Δ4-9, 11-16), trans 18:2, geometric isomers of ∆9,11, ∆11,13, and ∆13,15 CLA, trans-8,cis-10 CLA, trans-10,trans-12 CLA, trans-12,trans-14 CLA, and 18:3n-3 flow at the duodenum. Inclusion of FO in the diet resulted in higher (P < 0.05) flows of cis-9 16:1, trans 16:1 (Δ6-13), cis 18:1 (Δ9, 11, and 13), trans 18:1 (Δ6-15), trans 18:2, 20:5n-3, 22:5n-3, and 22:6n-3, and lowered (P < 0.001) 18:0 at the duodenum relative to the control. For most fatty acids at the duodenum responses to LFO were intermediate of FO and LO. However, LFO resulted in higher (P = 0.04) flows of total trans 18:1 than LO and increased (P < 0.01) trans-6 16:1 and trans-12 18:1 at the duodenum compared with FO or LO. Biohydrogenation of cis-9 18:1 and 18:2n-6 in the rumen was independent of treatment, but both FO and LO increased (P < 0.001) the extent of 18:3n-3 biohydrogenation compared with the control. Ruminal 18:3n-3 biohydrogenation was higher (P < 0.001) for LO and LFO than FO, while biohydrogenation of 20:5n-3 and 22:6n-3 in the rumen was marginally lower (P = 0.05) for LFO than FO. In conclusion, LO and FO at 30 g/kg DM altered the biohydrogenation of unsaturated fatty acids in the rumen causing an increase in the flow of specific intermediates at the duodenum, but the potential of these oils fed alone or as a mixture to increase n-3 PUFA at the duodenum in cattle appears limited.

A continuum model of a fishing net

A working report for the Department of Agriculture and Fisheries, Scotland, Marine Laboratory Aberdeen

The role of UK retailing in urban regeneration

This research examines the role of retailing in urban regeneration nationally and locally in the UK. The research uses data at a national level and local shopping centre case studies to examine the employment and property impacts of retailing. Focusing on schemes built during the first part of the 1990s it shows that retail can bring employment and economic benefits to town centres, but that the impact on the inner city should not be overlooked. Valuable lessons can be learned from the experience of centres built during this period of recession, and new challenges such as eCommerce now face these centres and others being developed today. The research examines the multiplier effect of retail regeneration schemes nationally using National Accounts data, and the local property and employment impacts of shopping centre schemes in the case study towns of Aberdeen, Bristol, Norwich, Bromley, Worcester and Leicester. The report includes valuable statistical sources, a full literature and policy review and will be of interest to those involved in property investment, regeneration and planning. The research was funded by the Office of Science & Technology and the Harold Samuel Educational Trust.

Microbes central to human reproduction

As studies uncover the breadth of microbes associated with human life, opportunities will emerge to manipulate and augment their functions in ways that improve health and longevity. From involvement in the complexities of reproduction and fetal/infant development, to delaying the onset of disease, and indeed countering many maladies, microbes offer hope for human well-being. Evidence is emerging to suggest that microbes may play a beneficial role in body sites traditionally viewed as being sterile. Although further evidence is required, we propose that much of medical dogma is about to change significantly through recognition and understanding of these hitherto unrecognized microbe–host interactions. A meeting of the International Scientific Association for Probiotics and Prebiotics held in Aberdeen, Scotland (June 2014), presented new views and challenged established concepts on the role of microbes in reproduction and health of the mother and infant. This article summarizes some of the main aspects of these discussions.

Handling Mitigating Circumstances for Electronic Contracts

Electronic contracts are a means of representing agreed responsibilities and expected behaviour of autonomous agents acting on behalf of businesses. They can be used to regulate behaviour by providing negative consequences, penalties, where the responsibilities and expectations are not met, i.e. the contract is violated. However, long-term business relationships require some flexibility in the face of circumstances that do not conform to the assumptions of the contract, that is, mitigating circumstances. In this paper, we describe how contract parties can represent and enact policies on mitigating circumstances. As part of this, we require records of what has occurred within the system leading up to a violation: the provenance of the violation. We therefore bring together contract-based and provenance systems to solve the issue of mitigating circumstances.

Modelling and Administration of Contract-Based Systems

Mirroring the paper versions exchanged between businesses today, electronic contracts offer the possibility of dynamic, automatic creation and enforcement of restrictions and compulsions on agent behaviour that are designed to ensure business objectives are met. However, where there are many contracts within a particular application, it can be difficult to determine whether the system can reliably fulfil them all; computer-parsable electronic contracts may allow such verification to be automated. In this paper, we describe a conceptual framework and architecture specification in which normative business contracts can be electronically represented, verified, established, renewed, etc. In particular, we aim to allow systems containing multiple contracts to be checked for conflicts and violations of business objectives. We illustrate the framework and architecture with an aerospace example.

Affine and curvature collineations in space-time

Graham Hall

Performance and carcass characteristics of beef cattle fed with ammoniated marandugrass hay

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Gastrointestinal nematode infection in beef cattle of different genetic groups in Brazil

Resistance to natural infection by gastrointestinal nematodes was compared in 67 female calves of the following genetic groups: Nelore (NX); 1/2 Senepol + 1/2 Nelore (SN); and 1/2 Aberdeen Angus + 1/2 Nelore (AN). The NX (n = 26), SN (n = 23) and AN (n = 18) animals were monitored for 14 months, during which they remained without treatment, allowed to graze in a tropical environment. Eggs per gram of feces (EPG), coprocultures and packed cell volume (PCV) were carried out monthly. No significant effects of the interaction between the genetic groups and month/year of collection and the genetic group on the EPG were found, but there was a significant influence of the month of collection (P < 0.01). The monthly PCV measurements did not differ for the animals of the three genetic groups and there was no association found between the EPG and PCV. The animals of the SN and NX groups showed similar numbers of EPG with results zero, while for the AN group these numbers were significantly lower (P < 0.05). Although the NX group had a large number of EPG with results zero, it also contained many animals with high counts, meaning this group had higher averages during the entire study period. The following nematode genera were found in the coprocultures: Haemonchus, Cooperia, Oesophagostomum and Trichostrongylus, the latter in smallest proportion. There was no significant difference between the genetic groups for averages of all parasites identified, except Cooperia, which were present in higher numbers in the animals of the NX group (P < 0.05). The results obtained in this experiment suggest that the use of Bos taurus x Bos indicus crossbreeds can be a good strategy to reduce the use of chemical control in Brazil. (C) 2009 Elsevier B.V. All rights reserved.

Avaliação de características de crescimento pós-desmama de animais Nelore puros e cruzados no estado do Mato Grosso do Sul

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Avaliação do desempenho ao primeiro parto de fêmeas Nelore e F1

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)