Raphaël Marée




me    PhD in computer science (since 2005)

   E-mail: Raphael.Maree@ulg.ac.be
   Tél: (+32) 4 366 26 44
   Address:
       Systems and Modeling
       GIGA Research & Montefiore Institute
       Tour GIGA (B34, +1)
       Avenue de l'Hopital 1
       4000 Liège
       Belgique


    From 10/2014 to 10/2015 I'm mainly affiliated with:
    Quantitative Image Analysis unit,
    Pasteur Institute, Paris, France.


Curriculum vitae - Projects & Research Interests - Publications - Software - Conference Calendar - Students - Misc














Projects & Research Interests

Bioimage informatics

My personal research interests lie within the field of "bioimage informatics", ie. the development and application of machine learning, computer vision, and software development methodologies to recognize cells, tissues and other biological or biomedical "objects" in large-scale, imaging datasets, and on the delivery of user-friendly softwares to help biologists/pathologists/etc. to facilitate the exploration of their imaging data, derive new knowledge, and support their findings and diagnoses.

Since October 2010, I am the initiator and scientific coordinator of the open-source (coming early 2015) CYTOMINE software platform, a "Google Maps"-like rich internet application for remote visualization, annotation and automated analysis of high-resolution images.


cytomine applications

Machine learning and computer vision

This research is about the design of generic methods for automatic image classification, retrieval, and semantic segmentation. Indeed, as potential applications of image recognition technologies are multidinous, we seek to develop general-purpose methods for the recognition of various types of images that share some visual regularities, without relying on too strong assumptions about patterns to recognize and acquisition conditions, and without having to rely on domain experts to design specific features.

In 2003, we proposed to combine ensemble of randomized decision trees with random extraction of subwindows (square patches) described by their raw pixel values for image classification/categorization. It was first described in our JDS03 paper (in french) and then in our SGAI-AI-2003 paper. The main contributions are summarized in the CVPR05 paper. See our other publications for details, various applications (in particular on biomedical problems), and latest extensions e.g. for distributed and incremental content-based image retrieval (MIR10) and semantic segmentation (VISAPP09, CVPR09-OTBVS). The java software PiXiT implements the CVPR05 method for image classification and I suggest to use it with its default parameters as a baseline method on new datasets. If results are satisfactory, then you do not need to develop a new method. ;-)

Currently (2011-...), we are conducting large-scale empirical studies on many datasets to better identify influential design choices and draw general guidelines for future use, and to further increase robustness of the approach. On several datasets, results are significantly improved compared to our previous works (paper in preparation).

Bioinformatics

Between January 2005 and October 2014, I was the GIGA Bioinformatics platform manager (scientific head: Prof. L. Wehenkel). In close collaboration with the Bioinformatics and Modeling research unit, this platform offers software development and data analysis services to academic (within the GIGA research center and beyond) as well as to industrial researchers. Its services include classification of biological/biomedical data (SELDI mass spectra, microarrays, clinical databases, ...) obtained from various medical instrumentation based on machine learning methods.
This activity lead to co-authorship of several journal papers (in Journal of Immunology, Proteomics, Annals of the rheumatic diseases, ...) in various application domains (inflammatory diseases, cancer, ...).

Publications

To access all my publications on the institutional repository (ORBI), please go here.

Our citations according to Google Scholar are here.

Most of my publications are directly available, others (with publisher's constraints, symbolized by the padlock) are also available after filling a simple request form:

Software

CYTOMINE is a "Google Maps"-like rich internet application for remote visualization, annotation and automated analysis of high-resolution images. It will be released as open-source early 2015. It will also includes a module in Python with our latest algorithm development for image classification, retrieval, and semantic segmentation.

PiXiT, a Java software which implements the CVPR05 aforementioned image classification method is available upon request for evaluation and non-commercial purpose, in collaboration with PEPITe. Newer extensions and improvments are not included in this version.

Conference Calendar

For years, for personal usage I'm trying to maintain a unofficial, browsable, conference calendar in the fields of machine learning, computer vision, biomedical imaging (or import the .ics iCalendar file in your application).
Tip: click on too see the calendar by month.

In the field of computer vision, the conference listing from USC is far more complete.

Étudiants

Please contact me for final thesis proposals, traineeships, ... in bioimage informatics or machine learning for computer vision.

Misc

I listen very much to music (mostly ambient/electronica/modern classical/fields recordings) like in this selection.
I used to select and play music on a local radio and I co-organized the Panoptica festival with friends.
I also enjoy reading (society essays and "independent" comics), eating (from thaï/indian/lebanese/vietnamese/japanese food to belgian boulet-frites), traveling, taking pictures, thinking, ...

Seoul(Korea) San Diego(San Diego) San Diego(Beijing) Tokyo(Tokyo-Kyoto) Lisbon (Lisbon) Belle-Île(Brittany)





Université de Liège Faculté des Sciences Appliquées GIGA