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Raphaël Marée - Publications ORBI
Vandaele, R., LALLEMAND, F., MARTINIVE, P., GULYBAN, A., JODOGNE, S., COUCKE, P., Geurts, P., & Marée, R. (in press). Automated multimodal volume registration based on supervised 3D anatomical landmark detection. SCITEPRESS Digital Library.
Peer reviewed
We propose a new method for automatic 3D multimodal registration based on anatomical landmark detection. Landmark detectors are learned independantly in the two imaging modalities using Extremely Randomized ...
Marée, R. (2017). The need for careful data collection for pattern recognition in digital pathology. Journal of Pathology Informatics.
Peer reviewed
Effective pattern recognition requires carefully designed ground-truth datasets. In this technical note, we first summarize potential data collection issues in digital pathology and then propose guidelines to ...
Marée, R., Rollus, L., Stévens, B., Hoyoux, R., Louppe, G., Vandaele, R., Begon, J.-M., Kainz, P., Geurts, P., & Wehenkel, L. (2016, January 10). Collaborative analysis of multi-gigapixel imaging data using Cytomine. Bioinformatics, 7.
Peer reviewed (verified by ORBi)
Motivation: Collaborative analysis of massive imaging datasets is essential to enable scientific discoveries. Results: We developed Cytomine to foster active and distributed collaboration of ...
Marée, R., Geurts, P., & Wehenkel, L. (2016). Towards Generic Image Classification using Tree-based Learning: an Extensive Empirical Study. Pattern Recognition Letters.
Peer reviewed (verified by ORBi)
This paper considers the general problem of image classification without using any prior knowledge about image classes. We study variants of a method based on supervised learning whose common ...
Marée, R., Olivo-Marin, J.-C., & Meas-Yedid, V. (2016). An approach for detection of glomeruli in multisite digital pathology. Proceedings International Symposium on Biomedical Imaging (pp. 4).
Peer reviewed
We present a novel bioimage informatics workflow that combines Icy and Cytomine software and their algorithms to enable large-scale analysis of digital slides from multiple sites. In particular, we apply ...
Marée, R., Jean-Christophe, O.-M., & Vannary, M.-Y. (2015, September 08). Détection automatique de glomérules en pathologie digitale. Paper presented at 25ème colloque GRETSI, Lyon, France.
Dans cet article, nous proposons une méthodologie de détection de glomérules au sein d’images de biopsies rénales. Elle combine des techniques de traitement d’images et d’apprentissage supervisé. Nous évaluons ...
WEEKERS, L., De Tullio, P., BOVY, C., Poma, L., Marée, R., BONVOISIN, C., Defraigne, J.-O., Krzesinski, J.-M., & Jouret, F. (2015). Activation of the calcium-sensing receptor before renal ischemia/reperfusion exacerbates kidney injury. American Journal of Translational Research, 7(1), 128-138.
Peer reviewed
Activation of the calcium-sensing receptor (CaSR) by ischemia/reperfusion (I/R) favours apoptosis in cardiomyocytes, hepatocytes and neurons. Its role in renal I/R is unknown. We investigated the impact of ...
Aceto, J., Nourizadeh-Lillabadi, R., Marée, R., Dardenne, N., Jeanray, N., Wehenkel, L., Aleström, P., van Loon, J., & Muller, M. (2015). Zebrafish bone and general physiology are differently affected by hormones or changes in gravity. PLoS ONE, 10(6), 1-42.
Peer reviewed (verified by ORBi)
Teleost fish such as zebrafish (Danio rerio) are increasingly used for physiological, genetic and developmental studies. Our understanding of the physiological consequences of altered gravity in an entire ...
Boukerroucha, M., Josse, C., El Guendi, S., Boujemla, B., Freres, P., Marée, R., Wenric, S., SEGERS, K., COLLIGNON, J., Jerusalem, G., & Bours, V. (2015). Evaluation of BRCA1-related molecular features and microRNAs as prognostic factors for triple negative breast cancers. BMC cancer, 15(1), 755.
Peer reviewed (verified by ORBi)
BACKGROUND: The BRCA1 gene plays a key role in triple negative breast cancers (TNBCs), in which its expression can be lost by multiple mechanisms: germinal mutation followed by deletion of the second allele ...
Jeanray, N., Marée, R., Pruvot, B., Stern, O., Geurts, P., Wehenkel, L., & Muller, M. (2015). Phenotype Classification of Zebrafish Embryos by Supervised Learning. PLoS ONE, 10(1), 0116989, 1-20.
Peer reviewed (verified by ORBi)
Zebrafish is increasingly used to assess biological properties of chemical substances and thus is becoming a specific tool for toxicological and pharmacological studies. The effects of chemical substances on ...
Leroi, N., Sounni, N. E., Van Overmeire, E., Blacher, S., Marée, R., Van Ginderachter, J., Lallemand, F., LENAERTS, E., COUCKE, P., Noël, A.* , & MARTINIVE, P.* . (2015). The timing of surgery after neoadjuvant radiotherapy influences tumor dissemination in a preclinical model. Oncotarget.
Peer reviewed
Neoadjuvant radiotherapy (neoRT) used in cancer treatments aims at improving local tumor control and patient overall survival. The neoRT schedule and the timing of the surgical treatment (ST) are empirically ...
* These authors have contributed equally to this work.
Marée, R., Geurts, P., & Wehenkel, L. (2014). Towards generic image classification: an extensive empirical study (1). Eprint/Working paper retrieved from http://orbi.ulg.ac.be/handle/2268/175525.
This paper considers the general problem of image classification without using any prior knowledge about image classes. We study variants of a method based on supervised learning whose common ...
Vincke, G., Marée, R., Wehenkel, L., Defaweux, V., QUATRESOOZ, P., d'Haene, N., Salmon, I., Renard, P., Depiereux, E., Snoeck, C., Denis, B., & Verpoorten, D. (2014, December 16). HistoWeb - Toward a new learning ecology for histology. Paper presented at Digital learning round table, Luxembourg, Luxembourg.
HistoWeb targets the transformation of the professional tool Cytomineinto a comprehensive and innovative teaching platform, valuing the notions of learning ecology and new learning dimensions seeking for ...
Marée, R., Rollus, L., Stevens, B., Louppe, G., Caubo, O., Rocks, N., Bekaert, S., Cataldo, D., & Wehenkel, L. (2014). A hybrid human-computer approach for large-scale image-based measurements using web services and machine learning. Proceedings IEEE International Symposium on Biomedical Imaging. IEEE.
Peer reviewed
We present a novel methodology combining web-based software development practices, machine learning, and spatial databases for computer-aided quantification of regions of interest (ROIs) in large-scale ...
Delga, A., GOFFIN, F., Kridelka, F., Marée, R., LAMBERT, C., & Delvenne, P. (2014). Evaluation of CellSolutions BestPrep(R) Automated Thin-Layer Liquid-Based Cytology Papanicolaou Slide Preparation and BestCyte(R) Cell Sorter Imaging System. Acta cytologica.
Peer reviewed (verified by ORBi)
Objective: A double-blind study was conducted to compare the performance of the new BestPrep(R) (CellSolutions) liquid-based thin-layer Papanicolaou (Pap) test with ThinPrep(R) (Hologic). Study Design: Samples ...
Mikut, R., Dickmeis, T., Driever, W., Geurts, P., Hamprecht, F. A., Kausler, B. X., Ledesma-Carbayo, M. J., Maree, R., Mikula, K., Pantazis, P., Ronneberger, O., Santos, A., Stotzka, R., Strahle, U., & Peyrieras, N. (2013). Automated Processing of Zebrafish Imaging Data: A Survey. Zebrafish, 10(3), 401-421.
Peer reviewed
Due to the relative transparency of its embryos and larvae, the zebrafish is an ideal model organism for bioimaging approaches in vertebrates. Novel microscope technologies allow the imaging of developmental ...
Marée, R., Wehenkel, L., & Geurts, P. (2013). Extremely Randomized Trees and Random Subwindows for Image Classification, Annotation, and Retrieval. In A., Criminisi & J., Shotton (Eds.), Decision Forests in Computer Vision and Medical Image Analysis, Advances in Computer Vision and Pattern Recognition (pp. 125-142). Springer.
Peer reviewed
We present a unified framework involving the extraction of random subwindows within images and the induction of ensembles of extremely randomized trees. We discuss the specialization of this framework for ...
Levels, J. H., Geurts, P., Karlsson, H., Marée, R., Ljunggren, S., Fornander, L., Wehenkel, L., Lindahl, M., Stroes, E. S., Kuivenhoven, J. A., & Meijers, J. C. (2011). High-density lipoprotein proteome dynamics in human endotoxemia. Proteome science, 9(1), 34.
Peer reviewed (verified by ORBi)
BACKGROUND: A large variety of proteins involved in inflammation, coagulation, lipid-oxidation and lipid metabolism have been associated with high-density lipoprotein (HDL) and it is anticipated that changes ...
Stern, O., Marée, R., Aceto, J., Jeanray, N., Muller, M., Wehenkel, L., & Geurts, P. (2011, May 20). Zebrafish Skeleton Measurements using Image Analysis and Machine Learning Methods. Poster session presented at Belgian Dutch Conference on Machine learning (Benelearn).
Peer reviewed
The zebrafish is a model organism for biological studies on development and gene function. Our work aims at automating the detection of the cartilage skeleton and measuring several distances and angles to ...
DE SENY, D., Sharif, M., Fillet, M., COBRAIVILLE, G., Meuwis, M.-A., Marée, R., HAUZEUR, J.-P., Wehenkel, L., Louis, E., Merville, M.-P., Kirwan, J., Ribbens, C., & Malaise, M. (2011). Discovery and biochemical characterisation of four novel biomarkers for osteoarthritis. Annals of the Rheumatic Diseases, 70(6), 1144-52.
Peer reviewed (verified by ORBi)
OBJECTIVE: Knee osteoarthritis (OA) is a heterogeneous, complex joint pathology of unknown aetiology. Biomarkers have been widely used to investigate OA but currently available biomarkers lack specificity and ...
Stern, O., Marée, R., Aceto, J., Jeanray, N., Muller, M., Wehenkel, L., & Geurts, P. (2011). Automatic localization of interest points in zebrafish images with tree-based methods. Proceedings of the 6th IAPR International Conference on Pattern Recognition in Bioinformatics. Springer.
Peer reviewed
In many biological studies, scientists assess effects of experimental conditions by visual inspection of microscopy images. They are able to observe whether a protein is expressed or not, if cells are going ...
Pisane, J., Marée, R., Wehenkel, L., & Verly, J. (2010, May 24). Radar Classification based on Extra-Trees.
Peer reviewed
In this paper, we describe a new automatic target recognition algorithm for classifying SAR images based on the PiXiT im- age classifier. It uses randomized sub-windows extraction and extremely randomized ...
Marée, R., Denis, P., Wehenkel, L., & Geurts, P. (2010). Incremental Indexing and Distributed Image Search using Shared Randomized Vocabularies. ACM Proceedings MIR 2010.
Peer reviewed
We present a cooperative framework for content-based image retrieval for the realistic setting where images are distributed across multiple cooperating servers. The proposed method is in line ...
Marée, R., Stern, O., & Geurts, P. (2010). Biomedical Imaging Modality Classification Using Bags of Visual and Textual Terms with Extremely Randomized Trees: Report of ImageCLEF 2010 Experiments. CLEF Notebook Papers/LABs/Workshops.
In this paper we describe our experiments related to the ImageCLEF 2010 medical modality classification task using extremely randomized trees. Our best run combines bags of textual and visual features ...
Pisane, J., Marée, R., Wehenkel, L., & Verly, J. (2010). Robust Automatic Target Recognition Using Extra-trees. In J., Pisane (Ed.), Robust Automatic Target Recognition Using Extra-trees. IEEE.
Peer reviewed
In this paper, we describe a new automatic target recognition algorithm for classifying SAR images based on the PiXiT image classifier. It uses randomized sub-windows extraction and extremely randomized trees ...
Schoemans, R., Aigrot, M.-S., Wu, C., Marée, R., Hong, P., Belachew, S., Josse, C., Lubetzki, C., & Bours, V. (2010). Oligodendrocyte development and myelinogenesis are not impaired by high concentrations of phenylalanine or its metabolites. Journal of Inherited Metabolic Disease, 33(2), 113-20.
Peer reviewed (verified by ORBi)
Phenylketonuria (PKU) is a metabolic genetic disease characterized by deficient phenylalanine hydroxylase (PAH) enzymatic activity. Brain hypomyelination has been reported in untreated patients, but its ...
Dumont, M., Marée, R., Wehenkel, L., & Geurts, P. (2009). Fast Multi-Class Image Annotation with Random Subwindows and Multiple Output Randomized Trees. Proc. International Conference on Computer Vision Theory and Applications (VISAPP) (pp. 196-203).
Peer reviewed
This paper addresses image annotation, i.e. labelling pixels of an image with a class among a finite set of predefined classes. We propose a new method which extracts a sample of subwindows from a set of ...
Marée, R., Geurts, P., & Wehenkel, L. (2009). Content-based Image Retrieval by Indexing Random Subwindows with Randomized Trees. IPSJ Transactions on Computer Vision and Applications, 1.
Peer reviewed
We propose a new method for content-based image retrieval which exploits the similarity measure and indexing structure of totally randomized tree ensembles induced from a set of subwindows randomly extracted ...
De Seny, D., Ribbens, C., Cobraiville, G., Meuwis, M.-A., Marée, R., Geurts, P., Wehenkel, L., Louis, E., Merville, M.-P., Fillet, M., & Malaise, M. (2009). Protéomique par SELDI-TOF-MS des maladies inflammatoires articulaires: identification des protéines S100 comme protéines d'intérêt. Revue Médicale de Liège, 64(Spec No), 29-35.
Peer reviewed (verified by ORBi)
Clinical proteomics is a technical approach studying the entire proteome expressed by cells, tissues or organs. It describes the dynamics of cell regulation by detecting molecular events related ...
Lecut, C., Frederix, K., Johnson, D. M., Deroanne, C., Thiry, M., Faccinetto, C., Marée, R., Evans, R. J., Volders, P. G., Bours, V., & Oury, C. (2009). P2X1 Ion Channels Promote Neutrophil Chemotaxis through Rho Kinase Activation. Journal of Immunology.
Peer reviewed (verified by ORBi)
This study shows that activation of P2X1 ion channels by ATP promotes neutrophil chemotaxis, a process involving Rho kinase-dependent actomyosin-mediated contraction at the cell rear. These ion channels may ...
Marée, R., Stevens, B., Geurts, P., Guern, Y., & Mack, P. (2009). A Machine Learning Approach for Material Detection in Hyperspectral Images. Proc. 6th IEEE Workshop on Object Tracking and Classification Beyond and in the Visible Spectrum (OTCBVS-CVPR09). IEEE.
Peer reviewed
In this paper we propose a machine learning approach for the detection of gaseous traces in thermal infra red hyperspectral images. It exploits both spectral and spatial information by extracting subcubes ...
Quesada Calvo, F., Fillet, M., De Seny, D., Meuwis, M.-A., Marée, R., Crahay, C., Paulissen, G., Rocks, N., Guéders, M., Wehenkel, L., Merville, M.-P., Louis, R., Foidart, J.-M., Noël, A., & Cataldo, D. (2009). Biomarker discovery in asthma-related inflammation and remodeling. Proteomics, 9(8), 2163-2170.
Peer reviewed (verified by ORBi)
Asthma is a complex inflammatory disease of airways. A network of reciprocal interactions between inflammatory cells, peptidic mediators, extracellular matrix components, and proteases is thought to be ...
De Seny, D., Fillet, M., Ribbens, C., Marée, R., Meuwis, M.-A., Lutteri, L., Chapelle, J.-P., Wehenkel, L., Louis, E., Merville, M.-P., & Malaise, M. (2008). Monomeric calgranulins measured by SELDI-TOF mass spectrometry and calprotectin measured by ELISA as biomarkers in arthritis. Clinical Chemistry, 54, 1066-1075.
Peer reviewed (verified by ORBi)
BACKGROUND: SELDI-TOF mass spectrometry (MS) is a high-throughput proteomic approach with potential for identifying novel forms of serum biomarkers of arthritis. METHODS: We used SELDI-TOF MS to ...
Meuwis, M.-A., Fillet, M., Lutteri, L., Marée, R., Geurts, P., De Seny, D., Malaise, M., Chapelle, J.-P., Wehenkel, L., Belaiche, J., Merville, M.-P., & Louis, E. (2008). Proteomics for prediction and characterization of response to infliximab in Crohn's disease: a pilot study. Clinical Biochemistry, 41(12), 960-7.
Peer reviewed (verified by ORBi)
OBJECTIVES: Infliximab is the first anti-TNFalpha accepted by the Food and Drug Administration for use in inflammatory bowel disease treatment. Few clinical, biological and genetic factors tend to predict ...
Hiard, S., Rigali, S., Colson, S., Marée, R., & Wehenkel, L. (2007, November 12). PREDetector : Prokaryotic Regulatory Element Detector. Poster session presented at Benelux Bioinformatics Conference 2007, Leuven, Belgium.
Background: In the post-genomic area, in silico predictions of regulatory networks are considered as a powerful approach to decipher and understand biological pathways within prokaryotic cells. The emergence ...
Hiard, S., Marée, R., Colson, S., Hoskisson, P. A., Titgemeyer, F., van Wezel, G. P., Joris, B., Wehenkel, L., & Rigali, S. (2007). PREDetector: A new tool to identify regulatory elements in bacterial genomes. Biochemical and Biophysical Research Communications, 357(4), 861-864.
Peer reviewed (verified by ORBi)
In the post-genomic area, the prediction of transcription factor regulons by position weight matrix-based programmes is a powerful approach to decipher biological pathways and to modelize regulatory networks ...
Hiard, S., Rigali, S., Colson, S., Marée, R., & Wehenkel, L. (2007, February 15). PREDetector : Prokaryotic Regulatory Element Detector. Poster session presented at Bioinformatics and Modeling : From genomes to network, Liège, Belgium.
Background: In the post-genomic area, in silico predictions of regulatory networks are considered as a powerful approach to decipher and understand biological pathways within prokaryotic cells. The emergence ...
Chandrika, K., Dellot, P., Frippiat, F., Giot, J.-B., Leonard, P., Marée, R., Mayasi, N., Meuris, C., Mukeba Tshialala, D., Rahmouni, S., Uurlings, F., Vaira, D., Wehenkel, L., Demonty, J., & Moutschen, M. (2007). Nouvelles approches dans la prise en charge de l'infection a VIH. Revue Médicale de Liège, 62 Spec No, 47-50.
Peer reviewed (verified by ORBi)
HIV infection remains a major problem of public health in Belgium as well as globally. The number of new diagnosies of HIV infection in Belgium remains between two and three daily. Given the dramatic effect of ...
Marée, R., Geurts, P., & Wehenkel, L. (2007). Content-based Image Retrieval by Indexing Random Subwindows with Randomized Trees. Proc. 8th Asian Conference on Computer Vision (ACCV), LNCS (pp. 611-620). Springer-Verlag.
Peer reviewed
We propose a new method for content-based image retrieval which exploits the similarity measure and indexing structure of totally randomized tree ensembles induced from a set of subwindows randomly ...
Marée, R., Geurts, P., & Wehenkel, L. (2007). Random subwindows and extremely randomized trees for image classification in cell biology. BMC Cell Biology, 8(Suppl. 1).
Peer reviewed (verified by ORBi)
Background: With the improvements in biosensors and high-throughput image acquisition technologies, life science laboratories are able to perform an increasing number of experiments that involve the generation ...
Hiard, S., Rigali, S., Colson, S., Marée, R., & Wehenkel, L. (2006, May 17). PreDetector : Prokaryotic Regulatory Element Detector. Poster session presented at 10th Bioforum, Liège, Belgium.
PreDetector is a stand-alone software, written in java. Its final aim is to predict regulatory sites for prokaryotic species. It comprises two functionalities. The first one is very similar to Target ...
Ernst, D., Marée, R., & Wehenkel, L. (2006). Reinforcement learning with raw image pixels as input state. Advances in machine vision, image processing & pattern analysis (Lecture notes in computer science, Vol. 4153). Berlin: Springer-Verlag Berlin.
Peer reviewed
We report in this paper some positive simulation results obtained when image pixels are directly used as input state of a reinforcement learning algorithm. The reinforcement learning algorithm chosen to carry ...
Geurts, P., Marée, R., & Wehenkel, L. (2006). Segment and combine: a generic approach for supervised learning of invariant classifiers from topologically structured data. Proceedings of the Machine Learning Conference of Belgium and The Netherlands (Benelearn) (pp. 15-23).
Peer reviewed
A generic method for supervised classification of structured objects is presented. The approach induces a classifier by (i) deriving a surrogate dataset from a pre-classified dataset of structured objects ...
Marée, R., Geurts, P., & Wehenkel, L. (2006). Biological Image Classification with Random Subwindows and Extra-Trees. Paper presented at Bio-Image Informatics (Workshop on Multiscale Biological Imaging, Data Mining & Informatics), Santa Barbara, USA.
Peer reviewed
We illustrate the potential of our image classification method on three datasets of images at different imaging modalities/scales, from subcellular locations up to human body regions. The method is based on ...
Marée, R. (2005). Classification automatique d'images par arbres de d́ecision. Unpublished doctoral thesis, University of Lìege - Electrical Engineering and Computer Science.
The work presented in this thesis is motivated by the problem of automatic image classification. Image classification methods seek to automatically classify previously unseen images using databases of labeled ...
Marée, R., Geurts, P., Piater, J., & Wehenkel, L. (2005). Biomedical image classification with random subwindows and decision trees. Computer Vision for Biomedical Image Applications (pp. 220-229). Berlin: Springer-Verlag Berlin.
Peer reviewed
In this paper, we address a problem of biomedical image classification that involves the automatic classification of x-ray images in 57 predefined classes with large intra-class variability. To achieve that ...
Marée, R., Geurts, P., Piater, J., & Wehenkel, L. (2005). Decision Trees and Random Subwindows for Object Recognition. ICML workshop on Machine Learning Techniques for Processing Multimedia Content (MLMM2005).
Peer reviewed
In this paper, we compare five tree-based machine learning methods within a recent generic image classification framework based on random extraction and classification of subwindows. We evaluate them on three ...
Marée, R., Geurts, P., Piater, J., Wehenkel, L., Schmid, C. (Ed.), Soatto, S. (Ed.), & Tomasi, C. (Ed.). (2005). Random Subwindows for Robust Image Classification. Proceedings of the IEEE International Conference on Computer Vision and Pattern Recognition (CVPR 2005) (pp. 34--40).
Peer reviewed
We present a novel, generic image classification method based on a recent machine learning algorithm (ensembles of extremely randomized decision trees). Images are classified using randomly extracted ...
Marée, R., Geurts, P., Piater, J., Wehenkel, L., Hong, K.-S. (Ed.), & Zhang, Z. (Ed.). (2004). A generic approach for image classification based on decision tree ensembles and local sub-windows. Proceedings of the 6th Asian Conference on Computer Vision (pp. 860-865). Asian Federation of Computer Vision Societies (AFCV).
Peer reviewed
A novel and generic approach for image classification is presented. The method operates directly on pixel values and does not require feature extraction. It combines a simple local sub-window extraction ...
Marée, R., Geurts, P., & Wehenkel, L. (2003). Une méthode générique pour la classification automatique d'images à partir des pixels. Revue des Nouvelles Technologies de l'Information, 1, 227-238.
Peer reviewed
Dans cet article, nous évaluons une approche générique de classification automatique d'images. Elle repose sur une méthode d'apprentissage récente qui construit des ensembles d'arbres de décision par sélection ...