Multivariate Markov networks for fitness modelling in an estimation of distribution algorithm.

A well-known paradigm for optimisation is the evolutionary algorithm (EA). An EA maintains a population of possible solutions to a problem which converges on a global optimum using biologically-inspired selection and reproduction operators. These algorithms have been shown to perform well on a variety of hard optimisation and search problems. A recent development in evolutionary computation is the Estimation of Distribution Algorithm (EDA) which replaces the traditional genetic reproduction operators (crossover and mutation) with the construction and sampling of a probabilistic model. While this can often represent a significant computational expense, the benefit is that the model contains explicit information about the fitness function. This thesis expands on recent work using a Markov network to model fitness in an EDA, resulting in what we call the Markov Fitness Model (MFM). The work has explored the theoretical foundations of the MFM approach which are grounded in Walsh analysis of fitness functions. This has allowed us to demonstrate a clear relationship between the fitness model and the underlying dynamics of the problem. A key achievement is that we have been able to show how the model can be used to predict fitness and have devised a measure of fitness modelling capability called the fitness prediction correlation (FPC). We have performed a series of experiments which use the FPC to investigate the effect of population size and selection operator on the fitness modelling capability. The results and analysis of these experiments are an important addition to other work on diversity and fitness distribution within populations. With this improved understanding of fitness modelling we have been able to extend the framework Distribution Estimation Using Markov networks (DEUM) to use a multivariate probabilistic model. We have proposed and demonstrated the performance of a number of algorithms based on this framework which lever the MFM for optimisation, which can now be added to the EA toolbox. As part of this we have investigated existing techniques for learning the structure of the MFM; a further contribution which results from this is the introduction of precision and recall as measures of structure quality. We have also proposed a number of possible directions that future work could take

Research article - Comet 81P/Wild 2 under a microscope

The Stardust spacecraft collected thousands of particles from comet 81P/Wild 2 and returned them to Earth for laboratory study. The preliminary examination of these samples shows that the nonvolatile portion of the comet is an unequilibrated assortment of materials that have both presolar and solar system origin. The comet contains an abundance of silicate grains that are much larger than predictions of interstellar grain models, and many of these are high-temperature minerals that appear to have formed in the inner regions of the solar nebula. Their presence in a comet proves that the formation of the solar system included mixing on the grandest scales

Risk of COVID-19 after natural infection or vaccinationResearch in context

Summary: Background: While vaccines have established utility against COVID-19, phase 3 efficacy studies have generally not comprehensively evaluated protection provided by previous infection or hybrid immunity (previous infection plus vaccination). Individual patient data from US government-supported harmonized vaccine trials provide an unprecedented sample population to address this issue. We characterized the protective efficacy of previous SARS-CoV-2 infection and hybrid immunity against COVID-19 early in the pandemic over three-to six-month follow-up and compared with vaccine-associated protection. Methods: In this post-hoc cross-protocol analysis of the Moderna, AstraZeneca, Janssen, and Novavax COVID-19 vaccine clinical trials, we allocated participants into four groups based on previous-infection status at enrolment and treatment: no previous infection/placebo; previous infection/placebo; no previous infection/vaccine; and previous infection/vaccine. The main outcome was RT-PCR-confirmed COVID-19 >7–15 days (per original protocols) after final study injection. We calculated crude and adjusted efficacy measures. Findings: Previous infection/placebo participants had a 92% decreased risk of future COVID-19 compared to no previous infection/placebo participants (overall hazard ratio [HR] ratio: 0.08; 95% CI: 0.05–0.13). Among single-dose Janssen participants, hybrid immunity conferred greater protection than vaccine alone (HR: 0.03; 95% CI: 0.01–0.10). Too few infections were observed to draw statistical inferences comparing hybrid immunity to vaccine alone for other trials. Vaccination, previous infection, and hybrid immunity all provided near-complete protection against severe disease. Interpretation: Previous infection, any hybrid immunity, and two-dose vaccination all provided substantial protection against symptomatic and severe COVID-19 through the early Delta period. Thus, as a surrogate for natural infection, vaccination remains the safest approach to protection. Funding: National Institutes of Health