Publikationen

Hier finden Sie von Know-Center MitarbeiterInnen verfasste wissenschaftliche Publikationen

2019

Lovric Mario, Žuvela Petar, Kern Roman, Lucic, Bono, J. Jay Liu, Tomasz Bączek

Machine learning methods for cross-column prediction of retention time in reversed-phased liquid chromatography

8th World Conference on Physico Chemical Methods in Drug Discovery and Developmen, IAPC, Split, Croatia, 2019

Konferenz
Quantitative structure-retention relationships (QSRR) were employed to build global models for prediction of chromatographic retention time of synthetic peptides across six RP-LC-MS/MS columns and varied experimental conditions. The global QSRR models were based on only three a priori selected molecular descriptors: sum of gradient retention times of 20 natural amino acids (logSumAA), van der Waals volume (logvdWvol.), and hydrophobicity (clogP) related to the retention mechanism of RP-LC separation of peptides. Three machine learning regression methods were compared: random forests (RF), partial least squares (PLS), and adaptive boosting (ADA). All the models were comprehensively optimized through 3-fold cross-validation (CV) and validated through an external validation set. The chemical domain of applicability was also defined. Percentage root mean square error of prediction (%RMSEP) was used as an external validation metric. Results have shown that RF exhibited a %RMSEP of 14.99 %; PLS exhibited a %RMSEP of 40.561 %; whereas ADA exhibited a %RMSEP of 26.35 %. The ensemble models considerably outperform the conventional PLS-based QSRR model. Novel methods of tree-based model explainability were employed to reveal mechanisms behind black-box global ensemble QSRR models. The models revelead the highest feature importance for sum of gradient retention times (logSumAA), followed by van der Waals volume (logvdWvol.), and hydrophobicity (clogP). The promising results of this study show the potential of machine learning for improved peptide identification, retention time standardization and integration into state-of-the-art LC-MS/MS proteomics workflows.
2018

Lovric Mario, Stipaničev Draženka , Repec Siniša , Malev Olga , Klobučar Göran

Combined toxic unit: Moving towards a multipath risk assessment strategy of organic contaminants in river sediment

The International Water Association, Zagreb, Croatia, 2018

Konferenz
2018

Lovric Mario, Krebs Sarah, Cemernek David, Kern Roman

BIG DATA IN INDUSTRIAL APPLICATION

XII Meeting of Young Chemical Engineers, Zagreb, Croatia, 2018

Konferenz
The use of big data technologies has a deep impact on today’s research (Tetko et al., 2016) and industry (Li et al., n.d.), but also on public health (Khoury and Ioannidis, 2014) and economy (Einav and Levin, 2014). These technologies are particularly important for manufacturing sites, where complex processes are coupled with large amounts of data, for example in chemical and steel industry. This data originates from sensors, processes. and quality-testing. Typical application of these technologies is related to predictive maintenance and optimisation of production processes. Media makes the term “big data” a hot buzzword without going to deep into the topic. We noted a lack in user’s understanding of the technologies and techniques behind it, making the application of such technologies challenging. In practice the data is often unstructured (Gandomi and Haider, 2015) and a lot of resources are devoted to cleaning and preparation, but also to understanding causalities and relevance among features. The latter one requires domain knowledge, making big data projects not only challenging from a technical perspective, but also from a communication perspective. Therefore, there is a need to rethink the big data concept among researchers and manufacturing experts including topics like data quality, knowledge exchange and technology required. The scope of this presentation is to present the main pitfalls in applying big data technologies amongst users from industry, explain scaling principles in big data projects, and demonstrate common challenges in an industrial big data project
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