Research Explorer

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Researcher

Willem Waegeman

Publications & Research Data

Awards & Distinctions

219 Results

2025

A calibration test for evaluating set-based epistemic uncertainty representations

Mira Kristin JürgensThomas MortierEyke HüllermeierViktor BengsWillem Waegeman

A1 Journal Article in MACHINE LEARNING

A systematic assessment of single-cell language model configurations

Gaetan De WaeleGerben MenschaertWillem Waegeman

Addressing uncertainty in automatic cell type annotation of single-cell transcriptomics data

Lauren TheunissenWillem WaegemanYvan Saeys

Assessment of uncertainty quantification in universal differential equations

Nina SchmidDavid Fernandes del PozoWillem WaegemanJan Hasenauer

A1 Journal Article in PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Conditional validity of heteroskedastic conformal regression

Nicolas DewolfBernard De BaetsWillem Waegeman

A1 Journal Article in INFORMATION AND INFERENCE-A JOURNAL OF THE IMA

Evaluation of out-of-distribution detection methods for data shifts in single-cell transcriptomics

Lauren TheunissenThomas MortierYvan SaeysWillem Waegeman

A1 Journal Article in BRIEFINGS IN BIOINFORMATICS

Harnessing machine learning to predict antibiotic susceptibility in Pseudomonas aeruginosa biofilms

Fauve VergauweGaetan De WaeleAndrea SassCallum HighmoreNiall HanrahanYoshiki CookMads LichtenbergMargo CnockaertPeter VandammeSumeet Mahajan et al.

A1 Journal Article in NPJ BIOFILMS AND MICROBIOMES

Machine learning reveals novel compound for the improved production of chitooligosaccharides in Escherichia coli

Friederike MeyGaetan De WaeleWouter DemeesterChiara GuidiDries DuchiTomek DiederenHanne KochuytKirsten Van HuffelNicola ZamboniWillem Waegeman et al.

A1 Journal Article in NEW BIOTECHNOLOGY

Pre-trained Maldi Transformers improve MALDI-TOF MS-based prediction

Gaetan De WaeleGerben MenschaertPeter VandammeWillem Waegeman

A1 Journal Article in COMPUTERS IN BIOLOGY AND MEDICINE

Self-supervised transformers for biological data modalities

Gaetan De WaeleWillem WaegemanGerben Menschaert

Valid prediction intervals for weather forecasting with conformal prediction

Thomas MortierCas DecancqYusuf SaleAlireza JavanmardiWillem WaegemanEyke HüllermeierDiego Miralles

2024

A comparative study of conformal prediction methods for valid uncertainty quantification in machine learning

Nicolas DewolfBernard De BaetsWillem Waegeman

A comparison of embedding aggregation strategies in drug-target interaction prediction

Dimitrios IliadisBernard De BaetsTapio PahikkalaWillem Waegeman

A1 Journal Article in BMC BIOINFORMATICS

A framework for tracing timber following the Ukraine invasion

Thomas MortierJakub TruszkowskiMarigold NormanMarkus BonerBogdan BuligaCaspar ChaterHenry JenningsJade SaundersRosie SibleyAlexandre Antonelli et al.

A1 Journal Article in NATURE PLANTS

An antimicrobial drug recommender system using MALDI-TOF MS and dual-branch neural networks

Gaetan De WaeleGerben MenschaertWillem Waegeman

A2 Journal Article in ELIFE

Hyperparameter optimization of two-branch neural networks in multi-target prediction

Dimitrios IliadisMarcel WeverBernard De BaetsWillem Waegeman

A1 Journal Article in APPLIED SOFT COMPUTING

Is epistemic uncertainty faithfully represented by evidential deep learning methods?

Mira Kristin JürgensNis MeinertViktor BengsEyke HüllermeierWillem Waegeman

Machine-learning-based prediction of disability progression in multiple sclerosis : an observational, international, multi-center study

Edward De BrouwerThijs BeckerLorin Werthen-BrabantsPieter DewulfDimitrios IliadisCathérine DekeyserGuy LaureysBart Van WijmeerschVeronica PopescuTom Dhaene et al.

A2 Journal Article in PLOS DIGITAL HEALTH

Optimising DNA metabarcoding and machine learning for advanced impact assessments in the North Sea : a case study on sand extraction

Laure Van den BulckeWillem WaegemanSofie DeryckeAnnelies De Backer

Out-of-sample R2 : estimation and inference

Stijn HawinkelWillem WaegemanSteven Maere

A1 Journal Article in AMERICAN STATISTICIAN

Pre-trained Maldi Transformers improve MALDI-TOF MS-based prediction

Gaetan De WaeleGerben MenschaertPeter VandammeWillem Waegeman

Uncertainty-aware single-cell annotation with a hierarchical reject option

Lauren TheunissenThomas MortierYvan SaeysWillem Waegeman

A1 Journal Article in BIOINFORMATICS

2023

Automated multi-target prediction with two-branch neural networks

Dimitrios IliadisBernard De BaetsWillem Waegeman

DeepMTP : a Python-based deep learning framework for multi-target prediction

Dimitrios IliadisBernard De BaetsWillem Waegeman

A1 Journal Article in SOFTWAREX

Efﬁcient algorithms for set-valued prediction in classiﬁcation

Thomas MortierWillem WaegemanKrzysztof Dembczyński

Integration of synthetic biology, systems biology and machine learning for the production of chitooligosaccharides in Escherichia coli

Friederike MeyMarjan De MeyWillem Waegeman

Model reduction and parameter estimation for kinetic models of biochemical reaction networks

Manvel GasparyanShodhan RaoArnout Van MessemWillem Waegeman

On second-order scoring rules for epistemic uncertainty quantification

Viktor BengsEyke HüllermeierWillem Waegeman

On the calibration of probabilistic classifier sets

Thomas MortierViktor BengsEyke HüllermeierStijn LucaWillem Waegeman

Valid prediction intervals for regression problems

Nicolas DewolfBernard De BaetsWillem Waegeman

A1 Journal Article in ARTIFICIAL INTELLIGENCE REVIEW

2022

CpG transformer for imputation of single-cell methylomes

Gaetan De WaeleJim ClauwaertGerben MenschaertWillem Waegeman

A1 Journal Article in BIOINFORMATICS

Heterogeneity hampers the identification of general pressure injury risk factors in intensive care populations : a predictive modelling analysis

Mieke DeschepperSonia LabeauWillem WaegemanStijn Blot

A1 Journal Article in INTENSIVE AND CRITICAL CARE NURSING

Machine-learning-based prediction of disability progression in multiple sclerosis : an observational, international, multi-center study

Edward De BrouwerThijs BeckerLorin Werthen-BrabantsPieter DewulfDimitrios IliadisCathérine DekeyserGuy LaureysBart Van WijmeerschVeronica PopescuTom Dhaene et al.

Multi-target prediction for dummies using two-branch neural networks

Dimitrios IliadisBernard De BaetsWillem Waegeman

A1 Journal Article in MACHINE LEARNING

Novel transformer networks for improved sequence labeling in genomics

Jim ClauwaertWillem Waegeman

A1 Journal Article in IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS

Pitfalls of epistemic uncertainty quantification through loss minimisation

Viktor BengsEyke HüllermeierWillem Waegeman

ProD : a tool for predictive design of tailored promoters in Escherichia coli

Friederike MeyJim ClauwaertMaarten Van BremptMichiel StockJo MaertensWillem WaegemanMarjan De Mey

Bookchapter in Prokaryotic gene regulation : methods and protocols

Seasonal prediction of Horn of Africa long rains using machine learning : the pitfalls of preselecting correlated predictors

Victoria DemanAkash KoppaWillem WaegemanDavid A. MacLeodMichael Bliss SingerDiego Miralles

A2 Journal Article in FRONTIERS IN WATER

Set-valued prediction in hierarchical classification with constrained representation complexity

Thomas MortierEyke HüllermeierKrzysztof DembczynskiWillem Waegeman

2021

Aleatoric and epistemic uncertainty in machine learning : an introduction to concepts and methods

Eyke HuellermeierWillem Waegeman

A1 Journal Article in MACHINE LEARNING

Ambient temperature and relative humidity-based drift correction in frequency domain electromagnetics using machine learning

Daan HanssensEllen Van De VijverWillem WaegemanMark E. EverettIan MoffatApostolos SarrisPhilippe De Smedt

A1 Journal Article in NEAR SURFACE GEOPHYSICS

Bacterial species identification using MALDI-TOF mass spectrometry and machine learning techniques : a large-scale benchmarking study

Thomas MortierAnneleen WiemePeter VandammeWillem Waegeman

A1 Journal Article in COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL

Cytometric fingerprints of gut microbiota predict Crohn's disease state

Peter RubbensRuben PropsFrederiek-Maarten KerckhofNico BoonWillem Waegeman

A1 Journal Article in ISME JOURNAL

Efficient set-valued prediction in multi-class classification

Thomas MortierMarek WydmuchKrzysztof DembczynskiEyke HuellermeierWillem Waegeman

A1 Journal Article in DATA MINING AND KNOWLEDGE DISCOVERY

Explainability in transformer models for functional genomics

Jim ClauwaertGerben MenschaertWillem Waegeman

A1 Journal Article in BRIEFINGS IN BIOINFORMATICS

High-resolution surveying with small-loop requency-domain electromagnetic systems : efficient survey design and adaptive processing

Daan HanssensWillem WaegemanYnse DeclercqHans DierckxHenri VerscheldePhilippe De Smedt

A1 Journal Article in IEEE GEOSCIENCE AND REMOTE SENSING MAGAZINE

Improving the performance of machine learning models for biotechnology : the quest for deus ex machina

Friederike MeyJim ClauwaertKirsten Van HuffelWillem WaegemanMarjan De Mey

A1 Journal Article in BIOTECHNOLOGY ADVANCES

PhenoGMM : Gaussian mixture modeling of cytometry data quantifies changes in microbial community structure

Peter RubbensRuben PropsFrederiek-Maarten KerckhofNico BoonWillem Waegeman

A1 Journal Article in MSPHERE

Predicting the presence and abundance of bacterial taxa in environmental communities through flow cytometric fingerprinting

Jasmine HeyseFlorian SchattenbergPeter RubbensSusann MüllerWillem WaegemanNico BoonRuben Props

A1 Journal Article in MSYSTEMS

Pressure injury prediction models for critically-ill patients should consider both the case-mix and local factors

Mieke DeschepperSonia LabeauWillem WaegemanStijn Blot

A1 Journal Article in INTENSIVE AND CRITICAL CARE NURSING

The quest for deus ex machina : harnessing the power of machine learning for synthetic biology

Friederike MeyJim ClauwaertKirsten Van HuffelWillem WaegemanMarjan De Mey

Lecture / Speech

Towards harmonization of DNA metabarcoding for monitoring marine macrobenthos : the effect of technical replicates and pooled DNA extractions on species detection

Laure Van den BulckeAnnelies De BackerBart AmpeSara MaesJan WittoeckWillem WaegemanKris HostensSofie Derycke

A2 Journal Article in METABARCODING AND METAGENOMICS

2020

Algebraic shortcuts for leave-one-out cross-validation in supervised network inference

Michiel StockTapio PahikkalaAntti AirolaWillem WaegemanBernard De Baets

A1 Journal Article in BRIEFINGS IN BIOINFORMATICS

An in-depth evaluation of annotated transcription start sites in E. coli using deep learning

Jim ClauwaertWillem Waegeman

Deep learning techniques for genome processing and annotation tasks in prokaryotes

Jim ClauwaertWillem WaegemanMarjan De MeyGerben Menschaert

Discriminating bacterial phenotypes at the population and single‐cell level : a comparison of flow cytometry and Raman spectroscopy fingerprinting

Cristina García TimermansPeter RubbensJasmine HeyseFrederiek-Maarten KerckhofRuben PropsAndre SkirtachWillem WaegemanNico Boon

A1 Journal Article in CYTOMETRY PART A

Fast pathogen identification using single-cell matrix-assisted laser desorption/ionization-aerosol time-of-flight mass spectrometry data and deep learning methods

Christina PapagiannopoulouRené ParchenPeter RubbensWillem Waegeman

A1 Journal Article in ANALYTICAL CHEMISTRY

Investigating time series classification techniques for rapid pathogen identification with single-cell MALDI-TOF mass spectrum data

Christina PapagiannopoulouRené ParchenWillem Waegeman

Predictive design of sigma factor-specific promoters

Maarten Van BremptJim ClauwaertFriederike MeyMichiel StockJo MaertensWillem WaegemanMarjan De Mey

A1 Journal Article in NATURE COMMUNICATIONS

The quest for deus ex machina : harnessing the power of machine learning for synthetic biology

Friederike MeyJim ClauwaertKirsten Van HuffelWillem WaegemanMarjan De Mey

Using structured pathology data to predict hospital-wide mortality at admission

Mieke DeschepperWillem WaegemanDirk VogelaersKristof Eeckloo

A1 Journal Article in PLOS ONE

2019

A hospital wide predictive model for unplanned readmission using hierarchical ICD data

Mieke DeschepperKristof EecklooDirk VogelaersWillem Waegeman

A1 Journal Article in COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

A protocol for automated timber species identification using metabolome profiling

Victor DeklerckThomas MortierNathalie GoedersRB CodyWillem WaegemanE EspinozaJoris Van AckerJan Van den BulckeH Beeckman

A1 Journal Article in WOOD SCIENCE AND TECHNOLOGY

Coculturing bacteria leads to reduced phenotypic heterogeneities

Jasmine HeyseBenjamin BuysschaertRuben PropsPeter RubbensAndre SkirtachWillem WaegemanNico Boon

A1 Journal Article in APPLIED AND ENVIRONMENTAL MICROBIOLOGY

DeepRibo : a neural network for precise gene annotation of prokaryotes by combining ribosome profiling signal and binding site patterns

Jim ClauwaertGerben MenschaertWillem Waegeman

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Fingerprinting microbial communities through flow cytometry and Raman spectroscopy

Cristina García TimermansPeter RubbensFrederiek-Maarten KerckhofRuben PropsWillem WaegemanNico Boon

Fingerprinting microbial communities through flow cytometry and Raman spectroscopy

Cristina García TimermansPeter RubbensFrederiek-Maarten KerckhofRuben PropsWillem WaegemanNico Boon

Learning single‐cell distances from cytometry data

Bac Nguyen CongPeter RubbensFrederiek-Maarten KerckhofNico BoonBernard De BaetsWillem Waegeman

A1 Journal Article in CYTOMETRY PART A

Machine learning approaches for microbial flow cytometry at the single-cell and community level

Peter RubbensWillem WaegemanNico Boon

Multi-target prediction : a unifying view on problems and methods

Willem WaegemanKrzysztof DembczyńskiEyke Hüllermeier

A1 Journal Article in DATA MINING AND KNOWLEDGE DISCOVERY

Predicting microbial biodiversity using flow cytometry and 16S rRNA gene amplicon sequencing

Peter RubbensRuben PropsFrederiek-Maarten KerckhofNico BoonWillem Waegeman

Randomized lasso links microbial taxa with aquatic functional groups inferred from flow cytometry

Peter RubbensMarian L SchmidtRuben PropsBopaiah A BiddandaNico BoonWillem WaegemanVincent J Denef

A1 Journal Article in MSYSTEMS

Set-Valued Prediction in Multi-Class Classification

Thomas MortierMarek WydmuchKrzysztof DembczyńskiEyke HüllermeierWillem Waegeman

2018

A comparative study of pairwise learning methods based on kernel ridge regression

Michiel StockTapio PahikkalaAntti AirolaBernard De BaetsWillem Waegeman

A1 Journal Article in NEURAL COMPUTATION

A data-driven search for functional bacterial populations in aquatic systems using flow cytometry, 16S rRNA gene amplicon sequencing and the Randomized Lasso

Peter RubbensMarian SchmidtRuben PropsNico BoonVincent DenefWillem Waegeman

A data-guided insight into global climate-vegetation dynamics

Christina PapagiannopoulouWillem WaegemanDiego Miralles

Deep F-measure maximization in multi-label classification : a comparative study

Stijn DecubberThomas MortierKrzysztof DembczyńskiWillem Waegeman

DeepRibo : precise gene annotation of prokaryotes using deep learning and ribosome profiling data

Jim ClauwaertGerben MenschaertWillem Waegeman

DeepRibo : precise gene annotation of prokaryotes using deep learning and ribosome profiling data

Jim ClauwaertsGerben MenschaertWillem Waegeman

DeepRibo : precise gene annotation of prokaryotes using deep learning and ribosome profiling data, validated with mass spectrometry data

Jim ClauwaertGerben MenschaertWillem Waegeman

Detection of microbial disturbances in a drinking water microbial community through continuous acquisition and advanced analysis of flow cytometry data

Ruben PropsPeter RubbensMichael BesmerBenjamin BuysschaertJurg SigristHansueli WeilenmannWillem WaegemanNico BoonFrederik Hammes

A1 Journal Article in WATER RESEARCH

Effects of chlorhexidine gluconate oral care on hospital mortality : a hospital-wide, observational cohort study

Mieke DeschepperWillem WaegemanKristof EecklooDirk VogelaersStijn Blot

A1 Journal Article in INTENSIVE CARE MEDICINE

Global hydro-climatic biomes identified via multitask learning

Christina PapagiannopoulouDiego MirallesMatthias DemuzereNiko VerhoestWillem Waegeman

A1 Journal Article in GEOSCIENTIFIC MODEL DEVELOPMENT

Interpretation and visualisation of data from dairy herds

Kristof HermansGeert OpsomerWillem WaegemanSander MoermanJenne De KosterMieke Van EetveldeBonifacius Van RanstMiel Hostens

A1 Journal Article in IN PRACTICE

Label-free Raman characterization of bacteria calls for standardized procedures

Cristina García TimermansPeter RubbensFrederiek-Maarten KerckhofBenjamin BuysschaertDmitry KhalenkowWillem WaegemanAndre SkirtachNico Boon

A1 Journal Article in JOURNAL OF MICROBIOLOGICAL METHODS

Single-cell bacterial characterization using flow cytometry and Raman spectroscopy

Cristina García TimermansPeter RubbensFrederiek-Maarten KerckhofRuben PropsWillem WaegemanNico Boon

Terrestrial evaporation response to modes of climate variability

Brecht MartensWillem WaegemanWouter A DorigoNiko VerhoestDiego Miralles

A1 Journal Article in NPJ CLIMATE AND ATMOSPHERIC SCIENCE

2017

A non-linear data-driven approach to reveal global vegetation sensitivity to climate

Diego MirallesMatthias DemuzereNiko VerhoestChristina PapagiannopoulouStijn DecubberWillem WaegemanWouter A. Dorigo

A non-linear Granger-causality framework to investigate climate-vegetation dynamics

Christina PapagiannopoulouDiego MirallesStijn DecubberMatthias DemuzereNiko VerhoestWouter A DorigoWillem Waegeman

A1 Journal Article in GEOSCIENTIFIC MODEL DEVELOPMENT

Absolute quantification of microbial taxon abundances

Ruben PropsFrederiek-Maarten KerckhofPeter RubbensJo De VriezeEmma Hernandez SanabriaWillem WaegemanPieter MonsieursFrederik HammesNico Boon

A1 Journal Article in ISME JOURNAL

Analyzing Granger causality in climate data with time series classification methods

Christina PapagiannopoulouStijn DecubberDiego MirallesMatthias DemuzereNiko VerhoestWillem Waegeman

Comparison of statistical regression and data-mining techniques in estimating soil water retention of tropical delta soils

Phuong NguyenAmir HaghverdiJan De PueYves-Dady Botula ManyalaWillem WaegemanWim Cornelis

A1 Journal Article in BIOSYSTEMS ENGINEERING

Exact and efficient algorithms for pairwise learning

Michiel StockBernard De BaetsWillem Waegeman

Flow cytometric single-cell identification of populations in synthetic bacterial communities

Peter RubbensRuben PropsNico BoonWillem Waegeman

A1 Journal Article in PLOS ONE

Identifying synthetic communities using flow cytometry and machine learning

Peter RubbensCristina García TimermansRuben PropsNico BoonWillem Waegeman

Investigating the control of ocean-atmospheric oscillations over global terrestrial evaporation using a simple supervised learning method

Brecht MartensDiego MirallesWouter A DorigoWillem WaegemanNiko Verhoest

Linear filtering reveals false negatives in species interaction data

Michiel StockTimothée PoisotWillem WaegemanBernard De Baets

A1 Journal Article in SCIENTIFIC REPORTS

miSTAR : miRNA target prediction through modeling quantitative and qualitative miRNA binding site information in a stacked model structure

Gert Van PeerAyla De PaepeMichiel StockJasper AnckaertPieter-Jan VoldersJo VandesompeleBernard De BaetsWillem Waegeman

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Novel approaches to assess the quality of fertility data stored in dairy herd management software

Kristof HermansWillem WaegemanGeert OpsomerBonifacius Van RanstJenne De KosterMieke Van EetveldeMiel Hostens

A1 Journal Article in JOURNAL OF DAIRY SCIENCE

Potentials and limitations of existing forecasting models for Alternaria on potatoes : challenges for model improvement

Sofie LandschootJolien De ReuKris AudenaertPieter VanhaverbekeGeert HaesaertBernard De BaetsWillem Waegeman

A1 Journal Article in POTATO RESEARCH

Stripping flow cytometry : how many detectors do we need for bacterial identification?

Peter RubbensRuben PropsCristina García TimermansNico BoonWillem Waegeman

A1 Journal Article in CYTOMETRY PART A

The use of shallow convolutional neural networks in predicting promotor strength in Eschericha coli

Jim ClauwaertMichiel StockMarjan De MeyWillem Waegeman

Vegetation anomalies caused by antecedent precipitation in most of the world

Christina PapagiannopoulouDiego MirallesWouter A DorigoNiko VerhoestMathieu DepoorterWillem Waegeman

A1 Journal Article in ENVIRONMENTAL RESEARCH LETTERS

2016

Clustering environmental flow cytometry data by searching density peaks

Peter RubbensWillem WaegemanRuben PropsNico Boon

Consistency of probabilistic classifier trees

Krzysztof DembczyńskiWojciech KotłowskiWillem WaegemanRóbert Busa-FeketeEyke Hüllermeier

Data-driven recipe completion using machine learning methods

Marlies De ClercqMichiel StockBernard De BaetsWillem Waegeman

A1 Journal Article in TRENDS IN FOOD SCIENCE & TECHNOLOGY

Discovering relationships in climate-vegetation dynamics using satellite data

Christina PapagiannopoulouDiego MirallesMathieu DepoorterNiko VerhoestWouter DorigoWillem Waegeman

Exact and efficient top-K inference for multi-target prediction by querying separable linear relational models

Michiel StockKrzysztof DembczynskiBernard De BaetsWillem Waegeman

A1 Journal Article in DATA MINING AND KNOWLEDGE DISCOVERY

Identifying synthetic microbial communities by learning in silico communities using flow cytometry

Peter RubbensWillem WaegemanRuben PropsNico Boon

Learning in silico communities to perform flow cytometric identification of synthetic bacterial communities

Peter RubbensRuben PropsNico BoonWillem Waegeman

2015

Prediction of subacute ruminal acidosis based on milk fatty acids: a comparison of linear discriminant and support vector machine approaches for model development

Ellen ColmanWillem WaegemanBernard De BaetsVeerle Fievez

A1 Journal Article in COMPUTERS AND ELECTRONICS IN AGRICULTURE

Recipe completion using machine learning techniques

Marlies De ClercqMichiel StockBernard De BaetsWillem Waegeman

2014

A community effort to assess and improve drug sensitivity prediction algorithms

James C CostelloLaura M HeiserElisabeth GeorgiiMehmet GönenMichael P MendenNicholas J WangMukesh BansalMuhammad Ammad-ud-dinPetteri HintsanenSuleiman A Khan et al.

A1 Journal Article in NATURE BIOTECHNOLOGY

A two-step learning approach for solving full and almost full cold start problems in dyadic prediction

Tapio PahikkalaMichiel StockAntti AirolaTero AittokallioBernard De BaetsWillem Waegeman

Identification of functionally related enzymes by learning-to-rank methods

Michiel StockThomas FoberEyke HüllermeierSerghei GlincaGerhard KlebeTapio PahikkalaAntti AirolaBernard De BaetsWillem Waegeman

A1 Journal Article in IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS

On the Bayes-optimality of F-measure maximizers

Willem WaegemanKrzysztof DembczyńskiArkadiusz JachnikWeiwei ChengEyke Hüllermeier

A1 Journal Article in JOURNAL OF MACHINE LEARNING RESEARCH

Predicting spatio-temporal Culicoides imicola distributions in Spain based on environmental habitat characteristics and species dispersal

Jan PetersWillem WaegemanJasper Van doninckE DucheyneC CalveteJ LucientesNiko VerhoestBernard De Baets

A1 Journal Article in ECOLOGICAL INFORMATICS

2013

A field-specific web tool for the prediction of Fusarium head blight and deoxynivalenol content in Belgium

Sofie LandschootWillem WaegemanKris AudenaertP Van DammeJudith VandepitteBernard De BaetsGeert Haesaert

A1 Journal Article in COMPUTERS AND ELECTRONICS IN AGRICULTURE

Combined exposure to cyanobacteria and carbaryl results in antagonistic effects on the reproduction of Daphnia pulex

Jana AsselmanJoris MeysWillem WaegemanBernard De BaetsKarel De Schamphelaere

A1 Journal Article in ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Does risk assessment of harmful algal blooms need to consider combined and interactive effects with pesticides (and vice versa)?

Jana AsselmanMichael PfrenderJacqueline LopezJoseph ShawWillem WaegemanBernard De BaetsKarel De Schamphelaere

Efficient regularized least-squares algorithms for conditional ranking on relational data

Tapio PahikkalaAntti AirolaMichiel StockBernard De BaetsWillem Waegeman

A1 Journal Article in MACHINE LEARNING

Exploration and prediction of interactions between methanotrophs and heterotrophs

Michiel StockSven HoefmanFrederiek-Maarten KerckhofNico BoonPaul De VosBernard De BaetsKim HeylenWillem Waegeman

A1 Journal Article in RESEARCH IN MICROBIOLOGY

Habitat prediction and knowledge extraction for spawning European grayling (Thymallus thymallus L.) using a broad range of species distribution models

Shinji FukudaBernard De BaetsWillem WaegemanJan VerwaerenAns Mouton

A1 Journal Article in ENVIRONMENTAL MODELLING & SOFTWARE

Influence of maize-wheat rotation systems on Fusarium head blight infection and deoxynivalenol content in wheat under low versus high disease pressure

Sofie LandschootKris AudenaertWillem WaegemanBernard De BaetsGeert Haesaert

A1 Journal Article in CROP PROTECTION

Optimizing the F-measure in multi-label classification : plug-in rule approach versus structured loss minimization

Krzysztof DembczyńskiArkadiusz JachnikWojciech KotłowskiWillem WaegemanEyke Hüllermeier

Ordinal regression models for predicting deoxynivalenol in winter wheat

Sofie LandschootWillem WaegemanKris AudenaertGeert HaesaertBernard De Baets

A1 Journal Article in PLANT PATHOLOGY

Plant disease prediction using data mining and machine learning: a case study on Fusarium head blight and deoxynivalenol content in winter wheat

Sofie LandschootKris AudenaertWillem WaegemanBernard De BaetsGeert Haesaert

2012

A field-specific webtool for the prediction of Fusarium head blight and DON content in Belgium

Sofie LandschootWillem WaegemanKris AudenaertJ VandepittePatrick Van DammeBernard De BaetsGeert Haesaert

A kernel-based framework for learning graded relations from data

Willem WaegemanTapio PahikkalaAntti AirolaTapio SalakoskiMichiel StockBernard De Baets

A1 Journal Article in IEEE TRANSACTIONS ON FUZZY SYSTEMS

A machine learning approach to predict Fusarium head blight

Sofie LandschootWillem WaegemanKris AudenaertJudith VandepittePatrick Van DammeBernard De BaetsGeert Haesaert

An analysis of chaining in multi-label classification

Krzysztof DembczyńskiWillem WaegemanEyke Hüllermeier

An empirical analysis of explanatory variables affecting Fusarium head blight infection and deoxynivalenol content in wheat

Sofie LandschootWillem WaegemanKris AudenaertJan VandepitteJan BaetensBernard De BaetsGeert Haesaert

A1 Journal Article in JOURNAL OF PLANT PATHOLOGY

Applying morphological changes during the evolution of quadruped robots results in robust gaits

Jonas DegraveFrancis wyffelsTim WaegemanPieter-Jan KindermansBenjamin Schrauwen

BeneLearn 2012 : proceedings of the 21st Belgian-Dutch conference on machine learning

Conditional ranking algorithms for efﬁcient object retrieval and object querying on relational data

Willem WaegemanMichiel StockBernard De BaetsTapio PahikkalaAntti AirolaTapio Salakoski

Determination of trade-offs in ecosystem service delivery using Bayesian belief networks

Rob D'hondtDries LanduytKatrien Van der BiestSander Jacobs

Distance dependent extensions of the Chinese restaurant process

Willem WyboCamille CollePieter-Jan KindermansBenjamin Schrauwen

F-Measure maximization in topical classification

Weiwei ChengKrzysztof DembczyńskiEyke HüllermeierAdrian JaroszewiczWillem Waegeman

Inferring gene regulatory network topologies using ensembles of feature selection techniques

Joeri RuyssinckTom DhaeneYvan Saeys

Label ranking with partial abstention based on thresholded probabilistic models

Weiwei ChengEyke HüllermeierWillem WaegemanVolkmar Welker

Learning monadic and dyadic relations : three case studies in systems biology

Michiel StockTapio PahikkalaAntti AirolaTapio SalakoskiBernard De BaetsWillem Waegeman

Learning partial ordinal class memberships with kernel-based proportional odds models

Jan VerwaerenWillem WaegemanBernard De Baets

A1 Journal Article in COMPUTATIONAL STATISTICS & DATA ANALYSIS

On label dependence and loss minimization in multi-label classification

Krzystzof DembczyńskiWillem WaegemanWeiwei ChengEyke Hüllermeier

A1 Journal Article in MACHINE LEARNING

Predicting long term behavior of genetic regulatory networks with answer set programming

Gustavo Adolfo Torres TorresKathleen MarchalYves Van de PeerMartine De Cock

System modeling for active noise control with reservoir computing

Jens NymanKen CaluwaertsTim WaegemanBenjamin Schrauwen

The logistic curve as a tool to describe the daily ruminal pH pattern and its link with milk fatty acids

Ellen ColmanBM TasWillem WaegemanBernard De BaetsVeerle Fievez

A1 Journal Article in JOURNAL OF DAIRY SCIENCE

Toward a reliable evaluation of forecasting systems for plant diseases : a case study using fusarium head blight of wheat

Sofie LandschootWillem WaegemanKris AudenaertJ. VandepitteGeert HaesaertBernard De Baets

A1 Journal Article in PLANT DISEASE

Towards incorporation of hierarchical Bayesian models into evolution strategies for quadruped gait generation

Pieter-Jan KindermansFrancis wyffelsKen CaluwaertsBert GunsBenjamin Schrauwen

2011

A discussion on the accuracy-complexity relationship in modelling fish habitat preference using genetic Takagi-Sugeno fuzzy systems

Shinji FukudaJun NakajimaBernard De BaetsWillem WaegemanTakahiko MukaiAns MoutonNorio Orikura

A kernel framework for learning relations from paired-comparison data

Willem WaegemanTapio PahikkalaAntti AirolaTapio SalakoskiBernard De Baets

An analysis of explanatory variables affecting Fusarium infection and DON content in wheat

Sofie LandschootWillem WaegemanKris AudenaertJ VandepitteJ BaetenBernard De BaetsGeert Haesaert

An exact algorithm for F-measure maximization

Krzysztof DembczyńskiWillem WaegemanWeiwei ChengEyke Hüllermeier

An exact algorithm for F-measure maximization

Krzysztof DembczyńskiWillem WaegemanWeiwei ChengEyke Hüllermeier

An experimental comparison of cross-validation techniques for estimating the area under the ROC curve

Antti AirolaTapio PahikkalaWillem WaegemanBernard De BaetsTapio Salakoski

A1 Journal Article in COMPUTATIONAL STATISTICS & DATA ANALYSIS

Bacterial species identification from MALDI-TOF mass spectra through data analysis and machine learning

Katrien De BruyneBram SlabbinckWillem WaegemanPaul VauterinBernard De BaetsPeter Vandamme

A1 Journal Article in SYSTEMATIC AND APPLIED MICROBIOLOGY

Connection between primary Fusarium inoculum on gramineous weeds, crop residues and soil samples and the final population on wheat ears in Flanders, Belgium

Sofie LandschootKris AudenaertWillem WaegemanBart PyckeBoris BekaertBernard De BaetsGeert Haesaert

A1 Journal Article in CROP PROTECTION

Effect of model formulation on the optimization of a genetic Takagi-Sugeno fuzzy system for fish habitat suitability evaluation

Shinji FukudaBernard De BaetsAns MoutonWillem WaegemanJun NakajimaTakahiro MukaiKazuaki HiramatsuNorio Onikura

A1 Journal Article in ECOLOGICAL MODELLING

ERA ranking representability: the missing link between ordinal regression and multi-class classification

Willem WaegemanBernard De Baets

Impact of fungicide timing on the composition of the Fusarium head blight disease complex and the presence of deoxynivalenol (DON) in wheat

Kris AudenaertSofie LandschootAdriaan VanheuleWillem WaegemanBernard De BaetsGeert Haesaert

Bookchapter in Fungicides : beneficial and harmful aspects

Incorporating prior knowledge in multiple output regression with application to chemometrics

Jan VerwaerenWillem WaegemanBernard De Baets

Joint mode estimation in multi-label classification by chaining

Krzysztof DembczyńskiWillem WaegemanEyke Hüllermeier

Learning valued relations from data

Willem WaegemanTapio PahikkalaAntti AirolaTapio SalakoskiBernard De Baets

Modelling fish habitat preference with a genetic algorithm-optimized Takagi-Sugeno model based on pairwise comparisons

Shinji FukudaWillem WaegemanAns MoutonBernard De Baets

Modelling spawning habitat for European grayling (Thymallus thymallus L.) using a support vector machine and a genetic Takagi-Sugeno fuzzy model

Shinji FukudaWillem WaegemanAns MoutonBernard De Baets

On the ERA ranking representability of pairwise bipartite ranking functions

Willem WaegemanBernard De Baets

A1 Journal Article in ARTIFICIAL INTELLIGENCE

Supervised learning algorithms for multi-class classification problems with partial class memberships

Willem WaegemanJan VerwaerenBram SlabbinckBernard De Baets

A1 Journal Article in FUZZY SETS AND SYSTEMS

2010

A comparison of AUC estimators in small-sample studies

Antti AirolaTapio PahikkalaWillem WaegemanBernard De BaetsTapio Salakoski

A genetic Takagi-Sugeno system for fish habitat preference modelling

Shinji FukudaNorio OnikuraBernard De BaetsWillem WaegemanAns MoutonJun NakajimaTakahiko Mukai

A machine learning approach to predict Fusarium head blight in winter wheat

Sofie LandschootKris AudenaertWillem WaegemanBernard De BaetsGeert Haesaert

A survey on ROC-based ordinal regression learning

Willem WaegemanBernard De Baets

Bookchapter in Preference learning

A transitivity analysis of bipartite rankings in pairwise multi-class classification

Willem WaegemanBernard De Baets

A1 Journal Article in INFORMATION SCIENCES

An empirical analysis of explanatory variables affecting Fusarium and deoxynivalenol in wheat for feed production

Sofie LandschootKris AudenaertWillem WaegemanJan VandepitteGeert HaesaertBernard De Baets

Composition of primary Fusarium head blight (FHB) inoculums and the final population on wheat ears

Sofie LandschootKris AudenaertWillem WaegemanBernard De BaetsBart PyckeBoris Bekaert

Composition of primary Fusarium inoculum and the final population on wheat ears

Sofie LandschootKris AudenaertWillem WaegemanBart PyckeBieke BekaertBernard De BaetsGeert Haesaert

Conditional ranking on relational data

Willem WaegemanTapio PahikkalaAntti AirolaTapio SalakoskiBernard De Baets

Conditional ranking on relational data

Tapio PahikkalaWillem WaegemanAntti AirolaTapio SalakoskiBernard De Baets

Directional predictions for 4-class BCI data

Dieter DevlaminckWillem WaegemanBruno BauwensBart WynsGeorges OtteLuc BoullartPatrick Santens

Ensemble methods for multi-label learning of compositional data

Jan VerwaerenWillem WaegemanBernard De Baets

From circular ordinal regression to multilabel classification

Dieter DevlaminckWillem WaegemanBruno BauwensBart WynsPatrick SantensGeorges Otte

From learning taxonomies to phylogenetic learning: integration of 16S rRNA gene data into FAME-based bacterial classification

Bram SlabbinckWillem WaegemanPeter DawyndtPaul De VosBernard De Baets

A1 Journal Article in BMC BIOINFORMATICS

Learning intransitive reciprocal relations with kernel methods

Tapio PahikkalaWillem WaegemanEvgeni TsivtsivadzeTapio SalakoskiBernard De Baets

A1 Journal Article in EUROPEAN JOURNAL OF OPERATIONAL RESEARCH

Learning partial ordinal class memberships in a proportional odds setting

Jan VerwaerenWillem WaegemanBernard De Baets

On label dependence in multilabel classification

Krzysztof DembszynskiWillem WaegemanWeiwei ChengEyke Hüllermeier

On the role of cost-sensitive learning in multi-class brain-computer interfaces

Dieter DevlaminckWillem WaegemanBart WynsGeorges OttePatrick Santens

A1 Journal Article in BIOMEDIZINISCHE TECHNIK

Regret analysis for performance metrics in multi-label classification: the case of Hamming and subset zero-one loss

Krzysztof DembszynskiWillem WaegemanWeiwei ChengEyke Hüllermeier

Relationship between primary Fusarium inoculum and the final population on wheat ears

Sofie LandschootKris AudenaertWillem WaegemanBernard De BaetsGeert Haesaert

2009

A transitivity analysis of bipartite rankings in a pairwise multi-class setting

Willem WaegemanBernard De Baets

From ranking to intranstivie preference learning : rock-paper-scissors and beyond

Tapio PahikkalaWillem WaegemanEvgeni TsivtsivadzeTapio SalakoskiBernard De Baets

Kernel-based learning methods for preference aggregation

Willem WaegemanBernard De BaetsLuc Boullart

A1 Journal Article in 4OR-A QUARTERLY JOURNAL OF OPERATIONS RESEARCH

Learning intransitive reciprocal relations with regularized least-squares

Tapio PahikkalaWillem WaegemanEvgeni TsivtsivadzeTapio SalakoskiBernard De Baets

Learning intransitive reciprocal relations with regularized least-squares

Willem WaegemanTapio PahikkalaEvgeni TsivtsivadzeTapio SalakoskiBernard De Baets

Learning ordinal partial class memberships with kernel-based proportional odds models

Willem WaegemanJan VerwaerenBernard De Baets

Learning to rank: a ROC-based graph-theoretic approach

Willem Waegeman

A1 Journal Article in 4OR-A QUARTERLY JOURNAL OF OPERATIONS RESEARCH

Machine learning algorithms for coupling FAME and 16S rRNA data in bacterial species identification

Dries Van AudenhoveWillem WaegemanBram SlabbinckPeter DawyndtBernard De Baets

Machine learning algorithms for disease prediction in winter wheat

Dorien ColmanWillem WaegemanKris AudenaertBernard De BaetsGeert Haesaert

MMN: emotional dimension of distractor task in a simple duration mismatch paradigm

Georges OtteG De BrueckerWillem WaegemanPieter-Jan GeertsBart Wyns

Modelling partial class memberships in multi-class classification: a probabilistic approach

Willem WaegemanBernard De Baets

On the use of ordinal regression and cost-sensitive classification in 3-class brain-computer interfaces

Dieter DevlaminckWillem WaegemanBart WynsGeorges OttePatrick Santes

Ordinal regression for a 3-class brain-computer interface

Dieter DevlaminckWillem WaegemanBart WynsLuc BoullartGeorges OttePatrick Santens

2008

A Graph-theoretic Approach for Reducing One-versus-one Multi-class Classification to Ranking. International Workshop on Mining and Learning with Graphs

Willem WaegemanBernard De BaetsLuc Boullart

Classifying carpets based on laser scanner data

Willem WaegemanJohannes CottynBart WynsLuc BoullartBernard De BaetsLieva Van LangenhoveJan Detand

A1 Journal Article in ENGINEERING APPLICATIONS OF ARTIFICIAL INTELLIGENCE

Integrating Expert Knowledge into Kernel-based Preference Models

Willem WaegemanBernard De BaetsLuc Boullart

Kernel-based learning methods for preference aggregation

Willem WaegemanBernard De BaetsLuc Boullart

Learning layered ranking functions with structured support vector machines

Willem WaegemanBernard De BaetsLuc Boullart

A1 Journal Article in NEURAL NETWORKS

Learning to rank: a ROC-based graph-theoretic approach

Willem WaegemanLuc BoullartBernard De Baets

On the scalability of ordered multi-class ROC analysis

Willem WaegemanBernard De BaetsLuc Boullart

A1 Journal Article in COMPUTATIONAL STATISTICS & DATA ANALYSIS

ROC analysis in ordinal regression learning

Willem WaegemanBernard De BaetsLuc Boullart

A1 Journal Article in PATTERN RECOGNITION LETTERS

When can we simplify a one-versus-one multi-class classifier to a single ranking

Willem WaegemanBernard De BaetsLuc Boullart

2007

Kernel-based aggregation of fuzzy and probabilistic preference relations

Willem WaegemanBernard De BaetsLuc Boullart

Learning a Layered Graph with a Maximal Number of Paths Connecting Source and Sink

Willem WaegemanBernard De BaetsLuc Boullart

Learning a Layered Graph with a Maximal Number of Paths Connecting Source and Sink

Willem WaegemanBernard De BaetsLuc Boullart

Machine learning algorithms for carpets classification

Rares DamianRobain De KeyserLuc BoullartWillem WaegemanLieva Van LangenhoveCorneliu Lazar

Polymorphisms in the ficolin 1 gene (FCN1) are associated with susceptibility to the development of rheumatoid arthritis

Bert Vander CruyssenLieve NuytinckLuc BoullartDirk ElewautWillem WaegemanMira Van ThielenE. DE MEESTERK. LEBEERR. ROSSAUFilip De Keyser

A1 Journal Article in RHEUMATOLOGY

Ranking by learning layered graphs

Willem WaegemanBernard De BaetsLuc Boullart

ROC-based ordinal regression learning: an overview

Willem WaegemanBernard De BaetsLuc Boullart

2006

A comparison of different ROC measures for ordinal regression

Willem WaegemanBernard De BaetsLuc Boullart

An ensemble of weighted support vector machines for ordinal regression

Willem WaegemanLuc Boullart

The volume under the ROC surface as evaluation criterion for ordinal regression models

Willem WaegemanBernard De BaetsLuc Boullart

2004

Ordinal classification with support vector machines for automatic assessment of carpet wear

Willem WaegemanBernard De BaetsLuc Boullart