30/03/2020

The HARMONY consortium is recruiting a post-doc fellow with expertise in deep learning for image applications


  • ORGANISATION/COMPANY
    INSERM
  • RESEARCH FIELD
    Computer science
    Engineering
    Medical sciencesMedicine
  • RESEARCHER PROFILE
    Recognised Researcher (R2)
    Established Researcher (R3)
  • APPLICATION DEADLINE
    31/07/2020 14:00 - Europe/Brussels
  • LOCATION
    France › Nantes, Tours
  • TYPE OF CONTRACT
    Temporary
  • JOB STATUS
    Full-time
  • HOURS PER WEEK
    35
  • OFFER STARTING DATE
    03/08/2020

The project

Radiomics denotes the high throughput extraction of numerous quantitative metrics (including shape, intensity or textural features) of medical images with the goal of providing a full macroscopic phenotyping of tissues (tumors, organs, etc.) that could reflect at least in part the underlying pathophysiological processes (such as necrosis, proliferation, etc.), down to the genomic level [1]. Radiomics has shown promising results in identifying tumor subtypes, aggressiveness as well as in predicting response to therapy and outcome of patients in several cancers [2], however, most of these results have been obtained small, retrospective and monocentric cohorts. On the one hand, standardization was identified early on as a major limitation preventing radiomics to enter clinical practice, because of the lack of comparability of the results. No meta-analysis could be carried out, because each research group relied on different methodological workflows, software, nomenclature and implementation choices, and did not provide sufficient details for their work to be reproduced [3]. These issues have been addressed by the Imaging Biomarker Standardization Initiative (IBSI) [4]. On the other hand, it has been shown for PET [5]–[7], CT [8], [9] and MRI [10], [11] that most radiomic features exhibit moderate to high sensitivity to variability in scanner models, acquisition protocols and reconstruction settings, which constitutes the biggest challenge for multicentric studies [12].

Objectives

Our long term goal is to achieve societal impact by improving patients management. This will be achieved thanks to more robust and accurate predictive models that will help identify patients at risk before initiating treatment. In order for these tools to be exploited in the clinical routine a high level of proof is necessary, which in turn requires larger scale, multicentric (ideally prospective) studies regarding the use of radiomics and/or deep learning techniques relying on multimodal medical images, which are currently lacking. Our objectives are thus to develop harmonization techniques in both image and feature domains in order to improve, facilitate or even render feasible otherwise impossible radiomic analyses of large, multicentric, heterogeneous cohorts. In the present project, we aim at validating these methods in several applications across the consortium.

The consortium

Four teams from the West of France will be working together to address that challenge and to validate the methodological developments across six different multicentric datasets and clinical contexts.

The four teams in the consortium have extensive and complementary expertise in radiomics, medical imaging and image processing/analysis, cancer applications, machine/deep learning and statistics.

Access to a high performance computing platform (PLACIS, http://placis.univ-brest.fr/english) which is a hybrid cluster with 800 CPU cores and 50 GPUs dedicated to calculations, with a 150 TB storage facility, will be granted to all participants in the project.

Recruitment

The consortium is recruiting 1 post-doc fellow. The candidate must hold a PhD with expertise in deep learning for imaging applications (computer vision, medical imaging, etc.). Previous experience in radiomics and/or medical image analysis and cancer applications is a plus but is not a requisite. The position will be filled for approximately 2 years. The recruited post-doc fellow will work in two different laboratories of the network (Tours and Nantes) on different datasets and clinical applications, and will also collaborate with the other post-doc already recruited, who will work mostly in the laboratories of Brest and Angers.

Applications containing a CV and a letter of motivation, should be sent to mathieu.hatt@inserm.fr

Candidates that have not yet defended their PhD thesis will be considered as long as they have a defense date already scheduled.

References

[1] E. Segal, C. B. Sirlin, C. Ooi, A. S. Adler, J. Gollub, X. Chen, B. K. Chan, G. R. Matcuk, C. T. Barry, H. Y. Chang, and M. D. Kuo, “Decoding global gene expression programs in liver cancer by noninvasive imaging,” Nat Biotechnol, vol. 25, no. 6, pp. 675–80, Jun. 2007.

[2] M. Hatt, C. C. Le Rest, F. Tixier, B. Badic, U. Schick, and D. Visvikis, “Radiomics: Data Are Also Images,” J. Nucl. Med. Off. Publ. Soc. Nucl. Med., vol. 60, no. Suppl 2, pp. 38S-44S, Sep. 2019.

[3] M. Vallières, A. Zwanenburg, B. Badic, C. Cheze Le Rest, D. Visvikis, and M. Hatt, “Responsible Radiomics Research for Faster Clinical Translation,” J. Nucl. Med. Off. Publ. Soc. Nucl. Med., vol. 59, no. 2, pp. 189–193, 2018.

[4] A. Zwanenburg, M. Vallières, M. A. Abdalah, H. J. W. L. Aerts, V. Andrearczyk, A. Apte, S. Ashrafinia, S. Bakas, R. J. Beukinga, R. Boellaard, M. Bogowicz, L. Boldrini, I. Buvat, G. J. R. Cook, C. Davatzikos, A. Depeursinge, M.-C. Desseroit, N. Dinapoli, C. V. Dinh, S. Echegaray, I. El Naqa, A. Y. Fedorov, R. Gatta, R. J. Gillies, V. Goh, M. Götz, M. Guckenberger, S. M. Ha, M. Hatt, F. Isensee, P. Lambin, S. Leger, R. T. H. Leijenaar, J. Lenkowicz, F. Lippert, A. Losnegård, K. H. Maier-Hein, O. Morin, H. Müller, S. Napel, C. Nioche, F. Orlhac, S. Pati, E. A. G. Pfaehler, A. Rahmim, A. U. K. Rao, J. Scherer, M. M. Siddique, N. M. Sijtsema, J. Socarras Fernandez, E. Spezi, R. J. H. M. Steenbakkers, S. Tanadini-Lang, D. Thorwarth, E. G. C. Troost, T. Upadhaya, V. Valentini, L. V. van Dijk, J. van Griethuysen, F. H. P. van Velden, P. Whybra, C. Richter, and S. Löck, “The Image Biomarker Standardization Initiative: Standardized Quantitative Radiomics for High-Throughput Image-based Phenotyping,” Radiology, p. 191145, Mar. 2020.

[5] P. E. Galavis, C. Hollensen, N. Jallow, B. Paliwal, and R. Jeraj, “Variability of textural features in FDG PET images due to different acquisition modes and reconstruction parameters,” Acta Oncol, vol. 49, no. 7, pp. 1012–6, Oct. 2010.

[6] J. Yan, J. L. Chu-Shern, H. Y. Loi, L. K. Khor, A. K. Sinha, S. T. Quek, I. W. K. Tham, and D. Townsend, “Impact of Image Reconstruction Settings on Texture Features in 18F-FDG PET,” J Nucl Med, vol. 56, no. 11, pp. 1667–1673, Nov. 2015.

[7] E. Pfaehler, R. J. Beukinga, J. R. de Jong, R. H. J. A. Slart, C. H. Slump, R. A. J. O. Dierckx, and R. Boellaard, “Repeatability of 18 F-FDG PET radiomic features: A phantom study to explore sensitivity to image reconstruction settings, noise, and delineation method,” Med. Phys., vol. 46, no. 2, pp. 665–678, Feb. 2019.

[8] D. Mackin, X. Fave, L. Zhang, D. Fried, J. Yang, B. Taylor, E. Rodriguez-Rivera, C. Dodge, A. K. Jones, and L. Court, “Measuring Computed Tomography Scanner Variability of Radiomics Features,” Invest. Radiol., vol. 50, no. 11, pp. 757–765, Nov. 2015.

[9] R. Berenguer, M. D. R. Pastor-Juan, J. Canales-Vázquez, M. Castro-García, M. V. Villas, F. Mansilla Legorburo, and S. Sabater, “Radiomics of CT Features May Be Nonreproducible and Redundant: Influence of CT Acquisition Parameters,” Radiology, vol. 288, no. 2, pp. 407–415, 2018.

[10] F. Yang, N. Dogan, R. Stoyanova, and J. C. Ford, “Evaluation of radiomic texture feature error due to MRI acquisition and reconstruction: A simulation study utilizing ground truth,” Phys. Medica PM Int. J. Devoted Appl. Phys. Med. Biol. Off. J. Ital. Assoc. Biomed. Phys. AIFB, vol. 50, pp. 26–36, Jun. 2018.

[11] H. Um, F. Tixier, D. Bermudez, J. O. Deasy, R. J. Young, and H. Veeraraghavan, “Impact of image preprocessing on the scanner dependence of multi-parametric MRI radiomic features and covariate shift in multi-institutional glioblastoma datasets,” Phys. Med. Biol., vol. 64, no. 16, p. 165011, Aug. 2019.

[12] M. Hatt, F. Lucia, U. Schick, and D. Visvikis, “Multicentric validation of radiomics findings: challenges and opportunities,” EBioMedicine, Aug. 2019.

 

 

Eligibility criteria

Candidates that have not yet defended their PhD thesis will be considered as long as they have a defense date already scheduled.

Selection process

Applications will be ranked and selected for interviews with all four P.I. of the consortium.

The interviews will be carried out through visioconference.

Offer Requirements

  • REQUIRED EDUCATION LEVEL
    Computer science: PhD or equivalent
    Engineering: PhD or equivalent
    Medical sciences: PhD or equivalent
  • REQUIRED LANGUAGES
    ENGLISH: Excellent

Skills/Qualifications

The candidate must hold a PhD with expertise in deep learning for imaging applications (computer visio, medical imaging, etc.). Previous experience in radiomics and/or medical image analysis and cancer applications is a plus but not a requisite. The position will be filled for approximately 1 year.

Specific Requirements

The recruited post-doc fellows will work in two different laboratories of the network on different datasets and clinical applications.

Map Information

Job Work Location Personal Assistance locations
Work location(s)
1 position(s) available at
INSERM (Tours, Nantes)
France
Nantes, Tours

Open, Transparent, Merit based Recruitment procedures of Researchers (OTM-R)

Know more about it at INSERM

Know more about OTM-R

EURAXESS offer ID: 509409

Disclaimer:

The responsibility for the jobs published on this website, including the job description, lies entirely with the publishing institutions. The application is handled uniquely by the employer, who is also fully responsible for the recruitment and selection processes.

 

Please contact support@euraxess.org if you wish to download all jobs in XML.