Advancing microbiome research with machine learning : key findings from the ML4Microbiome COST action

The rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed to exploit the benefits of ML in this field fully. In particular, there is a need to establish "gold standard" protocols for conducting ML analysis experiments and improve interactions between microbiome researchers and ML experts. The Machine Learning Techniques in Human Microbiome Studies (ML4Microbiome) COST Action CA18131 is a European network established in 2019 to promote collaboration between discovery-oriented microbiome researchers and data-driven ML experts to optimize and standardize ML approaches for microbiome analysis. This perspective paper presents the key achievements of ML4Microbiome, which include identifying predictive and discriminatory 'omics' features, improving repeatability and comparability, developing automation procedures, and defining priority areas for the novel development of ML methods targeting the microbiome. The insights gained from ML4Microbiome will help to maximize the potential of ML in microbiome research and pave the way for new and improved healthcare practices

Report: State-of-the-Art DE-ghosting Algorithms for High Dynamic Range Imaging

High Dynamic Range Imaging (HDRI) may be generated by combining multiple low dynamic range (LDR) images of the same scene with different exposures. However, this technique of generating HDR images is limited to static scenes. During capturing of LDR images, any changes in the scene between different captures caused by either camera shake or object motion results in ghost artifacts in the produced HDR image. These ghost artifacts make the same object appear more than once in the generated HDR image. As a result, deghosting algorithms have been developed over the past years in an attempt to remove any ghosting present in HDR images.This article is a report of  „State-of-the-art deghosting algorithms for generating HDR images“(Karađuzović-Hadžiabdić K., and Hasić Telalović J., 2013)

Assessment of multi-exposure HDR image deghosting methods

© 2017 Elsevier LtdTo avoid motion artefacts when merging multiple exposures into a high dynamic range image, a number of HDR deghosting algorithms have been proposed. However, these algorithms do not work equally well on all types of scenes, and some may even introduce additional artefacts. As the number of proposed deghosting methods is increasing rapidly, there is an immediate need to evaluate them and compare their results. Even though subjective methods of evaluation provide reliable means of testing, they are often cumbersome and need to be repeated for each new proposed method or even its slight modification. Because of that, there is a need for objective quality metrics that will provide automatic means of evaluation of HDR deghosting algorithms. In this work, we explore several computational approaches of quantitative evaluation of multi-exposure HDR deghosting algorithms and demonstrate their results on five state-of-the-art algorithms. In order to perform a comprehensive evaluation, a new dataset consisting of 36 scenes has been created, where each scene provides a different challenge for a deghosting algorithm. The quality of HDR images produced by deghosting method is measured in a subjective experiment and then evaluated using objective metrics. As this paper is an extension of our conference paper, we add one more objective quality metric, UDQM, as an additional metric in the evaluation. Furthermore, analysis of objective and subjective experiments is performed and explained more extensively in this work. By testing correlation between objective metric and subjective scores, the results show that from the tested metrics, that HDR-VDP-2 is the most reliable metric for evaluating HDR deghosting algorithms. The results also show that for most of the tested scenes, Sen et al.'s deghosting method outperforms other evaluated deghosting methods. The observations based on the obtained results can be used as a vital guide in the development of new HDR deghosting algorithms, which would be robust to a variety of scenes and could produce high quality results

Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action

Peer reviewed: TrueAcknowledgements: The authors are grateful to all COST Action CA18131 “Statistical and machine learning techniques in human microbiome studies” members for their contribution to the COST Action objectives, and to COST (European Cooperation in Science and Technology) for the economic support, www.cost.eu. WG2 and WG3 thank Emmanuelle Le Chatelier and Pauline Barbet (Université Paris-Saclay, INRAE, MetaGenoPolis, 78350, Jouy-en-Josas, France) for preparing the shotgun CRC benchmark dataset.The rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed to exploit the benefits of ML in this field fully. In particular, there is a need to establish “gold standard” protocols for conducting ML analysis experiments and improve interactions between microbiome researchers and ML experts. The Machine Learning Techniques in Human Microbiome Studies (ML4Microbiome) COST Action CA18131 is a European network established in 2019 to promote collaboration between discovery-oriented microbiome researchers and data-driven ML experts to optimize and standardize ML approaches for microbiome analysis. This perspective paper presents the key achievements of ML4Microbiome, which include identifying predictive and discriminatory ‘omics’ features, improving repeatability and comparability, developing automation procedures, and defining priority areas for the novel development of ML methods targeting the microbiome. The insights gained from ML4Microbiome will help to maximize the potential of ML in microbiome research and pave the way for new and improved healthcare practices

Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action

The rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed to exploit the benefits of ML in this field fully. In particular, there is a need to establish “gold standard” protocols for conducting ML analysis experiments and improve interactions between microbiome researchers and ML experts. The Machine Learning Techniques in Human Microbiome Studies (ML4Microbiome) COST Action CA18131 is a European network established in 2019 to promote collaboration between discovery-oriented microbiome researchers and data-driven ML experts to optimize and standardize ML approaches for microbiome analysis. This perspective paper presents the key achievements of ML4Microbiome, which include identifying predictive and discriminatory ‘omics’ features, improving repeatability and comparability, developing automation procedures, and defining priority areas for the novel development of ML methods targeting the microbiome. The insights gained from ML4Microbiome will help to maximize the potential of ML in microbiome research and pave the way for new and improved healthcare practices