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1.
Toward learning the principles of plant gene regulation
Jan Zrimec, Aleksej Zelezniak, Kristina Gruden, 2022, drugi znanstveni članki

Povzetek: Advanced machine learning (ML) algorithms produce highly accurate models of gene expression, uncovering novel regulatory features in nucleotide sequences involving multiple cis-regulatory regions across whole genes and structural properties. These broaden our understanding of gene regulation and point to new principles to test and adopt in the field of plant science.
Ključne besede: gene expression prediction, bioinformatics, deep learning, regulatory genomics
Objavljeno v DiRROS: 06.08.2024; Ogledov: 196; Prenosov: 82
.pdf Celotno besedilo (403,50 KB)
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2.
On the potential of ensemble forecasting for the prediction of meteotsunamis in the Balearic Islands : sensitivity to atmospheric model parameterizations
Baptiste Mourre, A. Santana, A. Buils, L. Gautreau, Matjaž Ličer, Agusti Jansá, B. Casas, B. Amengual, Joaquín Tintoré, 2021, izvirni znanstveni članek

Povzetek: This study investigates the potential of ensemble forecasting using full realistic high-resolution nested atmosphere–ocean models for the prediction of meteotsunamis in Ciutadella (Menorca, Spain). The sensitivity of model results to the parameterizations of the atmospheric model is assessed considering the ten most significant recent meteotsunami events for which observations are available. Different schemes adapted to high-resolution Weather Research and Forecasting model simulations were used for the representation of cumulus, microphysics, planetary boundary layer and longwave and shortwave radiations. Results indicate a large spread of the ensemble simulations in terms of the final magnitude of the meteotsunamis. While the modeling system is shown to be able to realistically trigger tsunamigenic atmospheric disturbances in more than 90% of the situations, the small-scale characteristics of these disturbances are significantly modified with the change of parameterizations, leading to significant differences in the magnitude of the simulated sea-level response. No preferred set of parameterizations can be identified that leads to either the largest or the most realistic magnitudes in the majority of situations. Instead, the performance of a given set of parameterizations is found to change with the meteotsunami event under consideration. Importantly, the observed magnitude of the extreme sea-level oscillations lies within the range of a nine-member ensemble in 70% of the cases. This ensemble approach would then allow to generate a realistic range of possibilities in the majority of events, thus improving the realism of meteotsunami predictions compared to single deterministic forecasts.
Ključne besede: meteotsunamis prediction, atmosphere, ocean modeling, ensemble forecasting, atmospheric model parameterizations
Objavljeno v DiRROS: 19.07.2024; Ogledov: 207; Prenosov: 151
.pdf Celotno besedilo (4,16 MB)
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Breast cancer risk prediction using Tyrer-Cuzick algorithm with an 18-SNPs polygenic risk score in a European population with below-average breast cancer incidence
Tjaša Oblak, Petra Škerl, Benjamin J. Narang, Rok Blagus, Mateja Krajc, Srdjan Novaković, Janez Žgajnar, 2023, izvirni znanstveni članek

Povzetek: Goals: To determine whether an 18 single nucleotide polymorphisms (SNPs) polygenic risk score (PRS18) improves breast cancer (BC) risk prediction for women at above-average risk of BC, aged 40-49, in a Central European population with BC incidence below EU average. Methods: 502 women aged 40-49 years at the time of BC diagnosis completed a questionnaire on BC risk factors (as per Tyrer-Cuzick algorithm) with data known at age 40 and before BC diagnosis. Blood samples were collected for DNA isolation. 250 DNA samples from healthy women aged 50 served as a control cohort. 18 BC-associated SNPs were genotyped in both groups and PRS18 was calculated. The predictive power of PRS18 to detect BC was evaluated using a ROC curve. 10-year BC risk was calculated using the Tyrer-Cuzick algorithm adapted to the Slovenian incidence rate (S-IBIS): first based on questionnaire-based risk factors and, second, including PRS18. Results: The AUC for PRS18 was 0.613 (95 % CI 0.570-0.657). 83.3 % of women were classified at above-average risk for BC with S-IBIS without PRS18 and 80.7 % when PRS18 was included. Conclusion: BC risk prediction models and SNPs panels should not be automatically used in clinical practice in different populations without prior population-based validation. In our population the addition of an 18SNPs PRS to questionnaire-based risk factors in the Tyrer-Cuzick algorithm in general did not improve BC risk stratification, however, some improvements were observed at higher BC risk scores and could be valuable in distinguishing women at intermediate and high risk of BC.
Ključne besede: early breast cancer, polygenic risk score, risk prediction
Objavljeno v DiRROS: 21.03.2024; Ogledov: 404; Prenosov: 114
.pdf Celotno besedilo (1,54 MB)

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Sensitivity analysis of RF+clust for leave-one-problem-out performance prediction
Ana Nikolikj, Michal Pluhacek, Carola Doerr, Peter Korošec, Tome Eftimov, 2023, objavljeni znanstveni prispevek na konferenci

Ključne besede: automated performance prediction, autoML, single-objective black-box optimization, zero-shot learning
Objavljeno v DiRROS: 13.11.2023; Ogledov: 610; Prenosov: 391
.pdf Celotno besedilo (4,94 MB)
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7.
MsGEN : measuring generalization of nutrient value prediction across different recipe datasets
Gordana Ispirova, Tome Eftimov, Sašo Džeroski, Barbara Koroušić-Seljak, 2023, izvirni znanstveni članek

Povzetek: In this study, we estimate the generalization of the performance of previously proposed predictive models for nutrient value prediction across different recipe datasets. For this purpose, we introduce a quantitative indicator that determines the level of generalization of using the developed predictive model for new unseen data not presented in the training process. On a predefined corpus of recipe embeddings from six publicly available recipe datasets (i.e., projecting them in the same meta-feature vector space), we train predictive models on one of the six recipe datasets and test the models on the rest of the datasets. In parallel, we define and calculate generalizability indexes which are numbers that indicate how generalizable a predictive model is i.e., how well will a predictive model learned on one dataset perform on another one not involved in the training. The evaluation results prove the validity of these indexes – their relation with the accuracy of the predictions. Further, we define three sampling techniques for selecting representative data instances that will cover all parts from the feature space uniformly (involving data from all datasets) and further will improve the generalization of a predictive model. We train predictive models with these generalized datasets and test them on instances from the six recipe datasets that are not selected and included in the generalized datasets. The results from the evaluation of these predictive models show improvement compared to the results from the predictive models trained on one recipe dataset and tested on the others separately.
Ključne besede: ML pipeline, predictive modeling, nutrient prediction, recipe datasets
Objavljeno v DiRROS: 25.09.2023; Ogledov: 637; Prenosov: 313
.pdf Celotno besedilo (3,27 MB)
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8.
RF+clust for leave-one-problem-out performance prediction
Ana Nikolikj, Carola Doerr, Tome Eftimov, 2023, objavljeni znanstveni prispevek na konferenci

Ključne besede: algorithm performance prediction, automated machine learning, zero-shot learning, black-box optimization
Objavljeno v DiRROS: 30.08.2023; Ogledov: 605; Prenosov: 257
.pdf Celotno besedilo (4,47 MB)
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9.
Impact of leaching on chloride ingress profiles in concrete
Alisa Machner, Marie Helene Bjørndal, Aljoša Šajna, Nikola Mikanovic, Klaartje De Weerdt, 2022, izvirni znanstveni članek

Povzetek: To investigate the effect of leaching on chloride ingress profiles in concrete and mortar, we exposed concrete and mortar specimens for 90 and 180 days to two different exposure solutions: 3% NaCl, and 3% NaCl with KOH added to limit leaching. The solutions were replaced weekly. After exposure, we determined total chloride profiles to investigate the chloride ingress, and portlandite profiles to assess the extent of leaching. The results showed that leaching during exposure greatly affects the chloride ingress profiles in mortar and concrete. We found that leaching leads to considerably higher maximum total chloride content and deeper chloride penetration into the concrete than in the specimens where leaching was limited. We recommend therefore that leaching should be taken into account in standard laboratory testing and that more mechanistic service life models should be used to take into account the impact of leaching.
Ključne besede: chloride ingress, service life prediction, leaching, concrete, portlandite, open access
Objavljeno v DiRROS: 04.05.2023; Ogledov: 533; Prenosov: 386
.pdf Celotno besedilo (1,17 MB)
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10.
Leaching and geochemical modelling of an electric arc furnace (EAF) and ladle slag heap
Mojca Loncnar, Ana Mladenovič, Vesna Zalar Serjun, Marija Zupančič, Hans A. van der Sloot, 2022, izvirni znanstveni članek

Povzetek: Old metallurgical dumps across Europe represent a loss of valuable land and a potential threat to the environment, especially to groundwater (GW). The Javornik electric arc furnace (EAF) and ladle slag heap, situated in Slovenia, was investigated in this study. The environmental impact of the slag heap was evaluated by combining leaching characterization tests of landfill samples and geochemical modelling. It was shown that throughout the landfill the same minerals and sorptive phases control the leaching of elements of potential concern, despite variations in chemical composi- tion. Although carbonation of the disposed steel slags occurred (molar ratio CO3/(Ca+Mg) = 0.53) relative to fresh slag, it had a limited effect on the leaching behaviour of elements of potential concern. The leaching from the slag heaps had also a limited effect on the quality of the GW. A site-specific case, however, was that leachates from the slag heap were strongly diluted, since a rapid flow of GW fed from the nearby Sava River was observed in the landfill area. The sampling and testing approach applied provides a basis for assessing the long-term impact of release and is a good starting point for evaluating future management options, including beneficial uses for this type of slag.
Ključne besede: EAF slag, field verification, geochemical modelling, ladle slag, leaching, release prediction, steel slag heap
Objavljeno v DiRROS: 28.04.2023; Ogledov: 748; Prenosov: 338
.pdf Celotno besedilo (4,37 MB)
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