KERMIT -- Research Unit Knowledge-based Systems

Journal papers

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2024 (2)
2023 (2)
2022 (4)
2021 (12)
2020 (5)
2019 (7)
2018 (7)
2017 (10)
2016 (2)
2015 (1)
2014 (4)
2013 (7)
2012 (6)
2011 (6)
2010 (4)
2009 (2)
2008 (4)
2007 (1)

(12) Towards harmonization of DNA metabarcoding for monitoring marine macrobenthos: the effect of technical replicates and pooled DNA extractions on species detection
L. Van den Bulcke, A. De Backer, B. Ampe, S. Maes, J. Wittoeck, W. Waegeman, K. Hostens and S. Derycke
(2021) METABARCODING AND METAGENOMICS. 5, 233-247.

(11) Bacterial species identification using MALDI-TOF mass spectrometry and machine learning techniques: a large-scale benchmarking study
T. Mortier, A. Wieme, P. Vandamme and W. Waegeman
(2021) COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL. 19, 6157-6168.

(10) Improving the performance of machine learning models for biotechnology: the quest for deux ex machina
F. Mey, J. Clauwaert, K. Van Huffel, W. Waegeman and M. De Mey
(2021) BIOTECHNOLOGY ADVANCES. 53, 107858.

(9) Pressure injury prediction models for critically-ill patients should consider both the case-mix and local factors
M. Deschepper, S. Labeau, W. Waegeman and S. Blot
(2021) INTENSIVE AND CRITICAL CARE NURSING. 65, 103033.

(8) Explainability in transformer models for functional genomics
J. Clauwaert, G. Menschaert and W. Waegeman
(2021) BRIEFINGS IN BIOINFORMATICS. 22, 1-11.

(7) Predicting the presence and abundance of bacterial taxa in environmental communities through flow cytometric fingerprinting
J. Heyse, F. Schattenberg, P. Rubbens, S. Müller, W. Waegeman, N. Boon and R. Props
(2021) MSYSTEMS. 6, e00551-21.

(6) Ambient temperature and relative humidity-based drift correction in frequency domain electromagnetics using machine learning
D. Hanssens, E. Van De Vijver, W. Waegeman, M. E. Everett, I. Moffat, A. Sarris and P. De Smedt
(2021) NEAR SURFACE GEOPHYSICS . 19, 541-556.

(5) Efficient set-valued prediction in multi-class classification
T. Mortier, M. Wydmuch, K. Dembczynski, E. Hüllermeier and W. Waegeman
(2021) DATA MINING AND KNOWLEDGE DISCOVERY. 35, 1435-1469.

(4) Aleatoric and epistemic uncertainty in machine learning: an introduction to concepts and methods
E. Hüllermeier and W. Waegeman
(2021) MACHINE LEARNING. 110, 457-506.

(3) PhenoGMM: Gaussian mixture modelling of cytometry data quantifies changes in microbial community structure
P. Rubbens, R. Props, F.-M. Kerckhof, N. Boon and W. Waegeman
(2021) MSPHERE. 6, e00530-20.

(2) High-resolution surveying with small-loop frequency domain electromagnetic systems: Efficient survey design and adaptive processing
D. Hanssens, W. Waegeman, Y. Declercq, H. Dierckx, H. Verschelde and P. De Smedt
(2021) IEEE GEOSCIENCE AND REMOTE SENSING MAGAZINE. 9, 167-183.

(1) Cytometric fingerprints of gut microbiota predict Crohn's disease state
P. Rubbens, R. Props, F.-M. Kerckhof, N. Boon and W. Waegeman
(2021) THE ISME JOURNAL. 15, 354-358.

Date	Title
18/08/2014	2015 IEEE CIS Outstanding TFS Paper Award
27/08/2012	Best Paper Award for Willem Waegeman
17/08/2012	Second Winner Award for Willem Waegeman

Name	Title	Date
N. Dewolf	A comparative study of conformal prediction methods for valid uncertainty quantification in machine learning	25/04/2024
D. Iliadis	Automated multi-target prediction with two-branch neural networks	17/11/2023
T. Mortier	Efficient algorithms for set-valued prediction in classification	23/06/2023
M. Gasparyan	Model reduction and parameter estimation for kinetic models of biochemical reaction networks	19/01/2023
F. Mey	Integration of synthetic biology, systems biology and machine learning for the production of chitooligosaccharides in Escherichia coli	18/01/2023
J. Clauwaert	Deep learning techniques for genome processing and annotation tasks in prokaryotes	24/09/2020
P. Rubbens	Machine learning approaches for microbial flow cytometry at the single-cell and community level	24/09/2019
C. Papagiannopoulou	A data-guided insight into global climate-vegetation dynamics	05/10/2018
M. Stock	Exact and efficient algorithms for pairwise learning	21/04/2017

Name	Title	Date
N. Tourne	Two-branch neural networks for predicting protein-DNA interaction	2022 - 2023
J.-H. Nowé	Countering illegal timbering by using multimodal machine learning	2022 - 2023
Y. Van Laere	Detection of 5mC modification in Nanopore sequencing data using deep learning	2021 - 2022
E. Lorrez	Quantifying the environmental controls on African tropical forest dynamics through using a Granger causality framework	2020 - 2021
K. Zhang	Drug-target interaction prediction using multi-target prediction methods	2020 - 2021
L. Theunissen	A comparison of flat and hierarchical classification for automatic annotation of single-cell transcriptomics data	2020 - 2021
T. Willaert	Improving classification by rejection of high epistemic uncertainty points	2020 - 2021
L. Pollaris	Protein secondary structure prediction using transformer networks	2019 - 2020
B. De Saedeleer	Combatting illegal timber trade using chemical fingerprints: the power of mathematics and mass spectrometry	2019 - 2020
B. Verfaillie	Pattern recognition in raman spectroscopy data for a faster labelling of subjects in multiple domains	2019 - 2020
L. Davey	Using artificial neural networks to uncover features in promoter sequences responsible for nonorthogonality in E. Coli	2019 - 2020
G. Tjon	Automative drinking water monitoring using flow cytometry data	2019 - 2020
S. Top	Vertical farming of lettuce: the influence of rhizosphere bacteria and substrates	2018 - 2019
K. D'haeyer	Towards a data-driven identification of the microbial "Rammanome"	2018 - 2019
G. De Clercq	Deep learning for classification of DNA functional sequences	2018 - 2019
N. Goeders	Fight the illegal wood trade through chemical fingerprints : The power of mathematics and mass spectrometry	2018 - 2019
B. De Clercq	Forecasting tidal surge in the Lower Sea Scheldt using machine learning techniques	2018 - 2019
M. Van Haeverbeke	Detection of m6a modifications in native RNA using Oxford Nanopore Technology	2018 - 2019
M. Misonne	Prediction of RNA polymerase-DNA interactions in Escherichia Coli	2017 - 2018
R. Ingels	Understanding vegetation anomalies with machine learning methods	2017 - 2018
A. De Graeve	Detecting climate drivers for vegetation extremes	2017 - 2018
T. Vanlerberghe	Hierarchical multi-label classification of food products	2017 - 2018
T. Mortier	Modeling of climate-vegetation dynamics using machine learning techniques in a non-linear Granger causality framework	2016 - 2017
X. Yin	Discovering relationships in climate-vegetation dynamics using dynamic feature selection techniques	2016 - 2017
D. Schaumont	Een integratieve benadering gebaseerd op random forest voor de verbeterde predictie van exon-intron juncties	2016 - 2017
C. Zhang	Visualization and unsupervised learning of flow cytometry data for bacterial identication	2016 - 2017
S. Decubber	Spatiotemporal optimization of Granger causality methods for climate change attribution	2016 - 2017
J. Heyse	Development and application of single-cell analysis tools for the study of sympatric bacterial populations	2016 - 2017
L. Bodyn	Exploration of deep autoencoders for collaborative filtering on cooking recipes	2016 - 2017
L. Tilleman	In silico engineering van cytochroom P450 via machine learning technieken	2015 - 2016
F. Ramon	A data-driven analysis of ingredients in cooking recipes	2015 - 2016
W.K. Tsang	Assessing pathogen invasion based on community evenness and metabolic similarity	2014 - 2015
J. De Reu	Analyse van voorspellingsmodellen voor aardappelziekten en hun toepasbaarheid in Vlaanderen	2014 - 2015
M. De Clercq	Prediction of ingredient combinations using machine learning techniques	2013 - 2014
A. De Paepe	The prediction of interaction between mRNA and miRNA using machine learning techniques	2012 - 2013
M. Stock	Learning pairwise relations in bioinformatics: three case studies	2011 - 2012
J. Vandepitte	Voorspellen van Fusarium spp. aanwezigheid en DON concentraties in wintertarwe met machine learning technieken	2009 - 2010

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