AutoML adoption in ML software

Algorithms and the Foundations of Software technolog

Sparkle: toward accessible meta-algorithmics for improving the state of the art in solving challenging problems

Many fields of computational science advance through improvements in the algorithms used for solving key problems. These advancements are often facilitated by benchmarks and competitions that enable performance comparisons and rankings of solvers. Simultaneously, meta-algorithmic techniques, such as automated algorithm selection and configuration, enable performance improvements by utilizing the complementary strengths of different algorithms or configurable algorithm components. In fact, meta-algorithms have become major drivers in advancing the state of the art in solving many prominent computational problems. However, meta-algorithmic techniques are complex and difficult to use correctly, while their incorrect use may reduce their efficiency, or in extreme cases, even lead to performance losses. Here, we introduce the Sparkle platform, which aims to make meta-algorithmic techniques more accessible to nonexpert users, and to make these techniques more broadly available in the context of competitions, to further enable the assessment and advancement of the true state of the art in solving challenging computational problems. To achieve this, Sparkle implements standard protocols for algorithm selection and configuration that support easy and correct use of these techniques. Following an experiment, Sparkle generates a report containing results, problem instances, algorithms, and other relevant information, for convenient use in scientific publications.Algorithms and the Foundations of Software technolog

Untargeted metabolomics-based screening method for inborn errors of metabolism using semi-automatic sample preparation with an UHPLC-orbitrap-MS platform

Routine diagnostic screening of inborn errors of metabolism (IEM) is currently performed by different targeted analyses of known biomarkers. This approach is time-consuming, targets a limited number of biomarkers and will not identify new biomarkers. Untargeted metabolomics generates a global metabolic phenotype and has the potential to overcome these issues. We describe a novel, single platform, untargeted metabolomics method for screening IEM, combining semi-automatic sample preparation with pentafluorophenylpropyl phase (PFPP)-based UHPLC-Orbitrap-MS. We evaluated analytical performance and diagnostic capability of the method by analysing plasma samples of 260 controls and 53 patients with 33 distinct IEM. Analytical reproducibility was excellent, with peak area variation coefficients below 20% for the majority of the metabolites. We illustrate that PFPP-based chromatography enhances identification of isomeric compounds. Ranked z-score plots of metabolites annotated in IEM samples were reviewed by two laboratory specialists experienced in biochemical genetics, resulting in the correct diagnosis in 90% of cases. Thus, our untargeted metabolomics platform is robust and differentiates metabolite patterns of different IEMs from those of controls. We envision that the current approach to diagnose IEM, using numerous tests, will eventually be replaced by untargeted metabolomics methods, which also have the potential to discover novel biomarkers and assist in interpretation of genetic data

EuroFlow Standardized Approach to Diagnostic Immunopheneotyping of Severe PID in Newborns and Young Children

The EuroFlow PID consortium developed a set of flow cytometry tests for evaluation of patients with suspicion of primary immunodeficiency (PID). In this technical report we evaluate the performance of the SCID-RTE tube that explores the presence of recent thymic emigrants (RTE) together with T-cell activation status and maturation stages and discuss its applicability in the context of the broader EuroFlow PID flow cytometry testing algorithm for diagnostic orientation of PID of the lymphoid system. We have analyzed peripheral blood cells of 26 patients diagnosed between birth and 2 years of age with a genetically defined primary immunodeficiency disorder: 1