Optimising plans using genetic programming

Finding the shortest plan for a given planning problem is extremely hard. We present a domain independent approach for plan optimisation based on Genetic Programming. The algorithm is seeded with correct plans created by hand-encoded heuristic policy sets. The plans are very unlikely to be optimal but are created quickly. The suboptimal plans are then evolved using a generational algorithm towards the optimal plan. We present initial results from Blocks World and found that GP method almost always improved sub-optimal plans, often drastically

Investigation into the use of evolutionary algorithms for fully automated planning

This thesis presents a new approach to the Arti cial Intelligence (AI) problem of fully automated planning. Planning is the act of deliberation before acting that guides rational behaviour and is a core area of AI. Many practical real-world problems can be classed as planning problems, therefore practical and theoretical developments in AI planning are well motivated. Unfortunately, planning for even toy domains is hard, many different search algorithms have been proposed, and new approaches are actively encouraged. The approach taken in this thesis is to adopt ideas from Evolutionary Algorithms (EAs) and apply the techniques to fully automated plan synthesis. EA methods have enjoyed great success in many problem areas of AI. They are a new kind of search technique that have their foundation in evolution. Previous attempts to apply EAs to plan synthesis have promised encouraging results, but have been ad-hoc and piecemeal. This thesis thoroughly investigates the approach of applying evolutionary search to the fully automated planning problem. This is achieved by developing and modifying a proof of concept planner called GENPLAN. Before EA-based systems can be used, a thorough examination of various parameter settings must be explored. Once this was completed, the performance of GENPLAN was evaluated using a selection of benchmark domains and other competition style planners. The dif culties raised by the benchmark domains and the extent to which they cause problems for the approach are highlighted along with problems associated with EA search. Modi cations are proposed and experimented with in an attempt to alleviate some of the identi ed problems. EAs offer a exible framework for fully automated planning, but demonstrate a clear weakness across a range of currently used benchmark domains for plan synthesis

Effect of biofuel- and lube oil-originated sulfur and phosphorus on the performance of Cu-SSZ-13 and V2O5-WO3/TiO2 SCR catalysts

Two different SCR catalysts, V2O5-WO3/TiO2 and Cu-SSZ-13, were exposed to biodiesel exhausts generated by a diesel burner. The effect of phosphorus and sulfur on the SCR performance of these catalysts was investigated by doping the fuel with P-, S-, or P + S-containing compounds. Elemental analyses showed that both catalysts captured phosphorus while only Cu-SSZ-13 captured sulfur. High molar P/V ratios, up to almost 3, were observed for V2O5-WO3/TiO2, while the highest P/Cu ratios observed were slightly above 1 for the Cu-SSZ-13 catalyst. Although the V2O5-WO3/TiO2 catalyst captured more P than did the Cu-SSZ-13 catalyst, a higher degree of deactivation was observed for the latter, especially at low temperatures. For both catalysts, phosphorus exposure resulted in suppression of the SCR performance over the entire temperature range. Sulfur exposure, on the other hand, resulted in deactivation of the Cu-SSZ-13 catalyst mainly at temperatures below 300-350 \ub0C. The use of an oxidation catalyst upstream of the SCR catalyst during the exhaust-exposure protects the SCR catalyst from phosphorus poisoning by capturing phosphorus. The results in this work will improve the understanding of chemical deactivation of SCR catalysts and aid in developing durable aftertreatment systems

Application of a convolutional neural network to the quality control of MRI defacing

Large-scale neuroimaging datasets present unique challenges for automated processing pipelines. Motivated by a large clinical trials dataset with over 235,000 MRI scans, we consider the challenge of defacing — anonymisation to remove identifying facial features. The defacing process must undergo quality control (QC) checks to ensure that the facial features have been removed and that the brain tissue is left intact. Visual QC checks are time-consuming and can cause delays in preparing data. We have developed a convolutional neural network (CNN) that can assist with the QC of the application of MRI defacing; our CNN is able to distinguish between scans that are correctly defaced and can classify defacing failures into three sub-types to facilitate parameter tuning during remedial re-defacing. Since integrating the CNN into our anonymisation pipeline, over 75,000 scans have been processed. Strict thresholds have been applied so that ambiguous classifications are referred for visual QC checks, however all scans still undergo an efficient verification check before being marked as passed. After applying the thresholds, our network is 92% accurate and can classify nearly half of the scans without the need for protracted manual checks. Our model can generalise across MRI modalities and has comparable performance when tested on an independent dataset. Even with the introduction of the verification checks, incorporation of the CNN has reduced the time spent undertaking QC checks by 42% during initial defacing, and by 35% overall. With the help of the CNN, we have been able to successfully deface 96% of the scans in the project whilst maintaining high QC standards. In a similarly sized new project, we would expect the model to reduce the time spent on manual QC checks by 125 h. Our approach is applicable to other projects with the potential to greatly improve the efficiency of imaging anonymisation pipelines

A mouse informatics platform for phenotypic and translational discovery

The International Mouse Phenotyping Consortium (IMPC) is providing the world’s first functional catalogue of a mammalian genome by characterising a knockout mouse strain for every gene. A robust and highly structured informatics platform has been developed to systematically collate, analyse and disseminate the data produced by the IMPC. As the first phase of the project, in which 5000 new knockout strains are being broadly phenotyped, nears completion, the informatics platform is extending and adapting to support the increasing volume and complexity of the data produced as well as addressing a large volume of users and emerging user groups. An intuitive interface helps researchers explore IMPC data by giving overviews and the ability to find and visualise data that support a phenotype assertion. Dedicated disease pages allow researchers to find new mouse models of human diseases, and novel viewers provide high-resolution images of embryonic and adult dysmorphologies. With each monthly release, the informatics platform will continue to evolve to support the increased data volume and to maintain its position as the primary route of access to IMPC data and as an invaluable resource for clinical and non-clinical researchers

A bioimage informatics platform for high-throughput embryo phenotyping

High-throughput phenotyping is a cornerstone of numerous functional genomics projects. In recent years, imaging screens have become increasingly important in understanding gene–phenotype relationships in studies of cells, tissues and whole organisms. Three-dimensional (3D) imaging has risen to prominence in the field of developmental biology for its ability to capture whole embryo morphology and gene expression, as exemplified by the International Mouse Phenotyping Consortium (IMPC). Large volumes of image data are being acquired by multiple institutions around the world that encompass a range of modalities, proprietary software and metadata. To facilitate robust downstream analysis, images and metadata must be standardized to account for these differences. As an open scientific enterprise, making the data readily accessible is essential so that members of biomedical and clinical research communities can study the images for themselves without the need for highly specialized software or technical expertise. In this article, we present a platform of software tools that facilitate the upload, analysis and dissemination of 3D images for the IMPC. Over 750 reconstructions from 80 embryonic lethal and subviable lines have been captured to date, all of which are openly accessible at mousephenotype.org. Although designed for the IMPC, all software is available under an open-source licence for others to use and develop further. Ongoing developments aim to increase throughput and improve the analysis and dissemination of image data. Furthermore, we aim to ensure that images are searchable so that users can locate relevant images associated with genes, phenotypes or human diseases of interest

LAMA: automated image analysis for the developmental phenotyping of mouse embryos

Advanced 3D imaging modalities, such as micro-computed tomography (micro-CT), have been incorporated into the high-throughput embryo pipeline of the International Mouse Phenotyping Consortium (IMPC). This project generates large volumes of raw data that cannot be immediately exploited without significant resources of personnel and expertise. Thus, rapid automated annotation is crucial to ensure that 3D imaging data can be integrated with other multi-dimensional phenotyping data. We present an automated computational mouse embryo phenotyping pipeline that harnesses the large amount of wild-type control data available in the IMPC embryo pipeline in order to address issues of low mutant sample number as well as incomplete penetrance and variable expressivity. We also investigate the effect of developmental substage on automated phenotyping results. Designed primarily for developmental biologists, our software performs image pre-processing, registration, statistical analysis and segmentation of embryo images. We also present a novel anatomical E14.5 embryo atlas average and, using it with LAMA, show that we can uncover known and novel dysmorphology from two IMPC knockout lines

Genome-wide screening reveals the genetic basis of mammalian embryonic eye development.

BACKGROUND: Microphthalmia, anophthalmia, and coloboma (MAC) spectrum disease encompasses a group of eye malformations which play a role in childhood visual impairment. Although the predominant cause of eye malformations is known to be heritable in nature, with 80% of cases displaying loss-of-function mutations in the ocular developmental genes OTX2 or SOX2, the genetic abnormalities underlying the remaining cases of MAC are incompletely understood. This study intended to identify the novel genes and pathways required for early eye development. Additionally, pathways involved in eye formation during embryogenesis are also incompletely understood. This study aims to identify the novel genes and pathways required for early eye development through systematic forward screening of the mammalian genome. RESULTS: Query of the International Mouse Phenotyping Consortium (IMPC) database (data release 17.0, August 01, 2022) identified 74 unique knockout lines (genes) with genetically associated eye defects in mouse embryos. The vast majority of eye abnormalities were small or absent eyes, findings most relevant to MAC spectrum disease in humans. A literature search showed that 27 of the 74 lines had previously published knockout mouse models, of which only 15 had ocular defects identified in the original publications. These 12 previously published gene knockouts with no reported ocular abnormalities and the 47 unpublished knockouts with ocular abnormalities identified by the IMPC represent 59 genes not previously associated with early eye development in mice. Of these 59, we identified 19 genes with a reported human eye phenotype. Overall, mining of the IMPC data yielded 40 previously unimplicated genes linked to mammalian eye development. Bioinformatic analysis showed that several of the IMPC genes colocalized to several protein anabolic and pluripotency pathways in early eye development. Of note, our analysis suggests that the serine-glycine pathway producing glycine, a mitochondrial one-carbon donator to folate one-carbon metabolism (FOCM), is essential for eye formation. CONCLUSIONS: Using genome-wide phenotype screening of single-gene knockout mouse lines, STRING analysis, and bioinformatic methods, this study identified genes heretofore unassociated with MAC phenotypes providing models to research novel molecular and cellular mechanisms involved in eye development. These findings have the potential to hasten the diagnosis and treatment of this congenital blinding disease