CLARIFY is an innovative, multinational, multi-sectorial, and multidisciplinary research and training programme that links two highly differentiated specialities: engineering and medicine, to produce 12 Early Stage Researchers (ESRs) in artificial intelligence (AI), cloud computing and clinical pathology with the focus on digital pathology.
CLARIFY’s main goal is to develop a robust automated digital diagnostic environment based on artificial intelligence and cloud-oriented data algorithms that facilitates whole-slide-image (WSI) interpretation and diagnosis everywhere with the aim of maximising the benefits of digital pathology and aiding pathologists in their daily work.
CLARIFY gathers relevant scientific staff from academia, industry and leading hospitals ensuring that CLARIFY’s ESRs, as well as, future PhD students following the same tracks, will have outstanding Career Opportunities within the digital pathology sector and beyond.
Specific and challenging cancer types have been selected to test the tools and methods developed through the project reflecting the existing variability in cancer diagnosis: Triple negative breast cancer (TNBC), High-risk non-muscle invasive bladder cancer (HR-NMIBC) and Spitzoid melanocytic lesions (SML).
H2020 -MSCA - ITN - 2019
€ 3 220 753,32
12 Early Stage Researchers
SCIENTIFIC: The main scientific goal of CLARIFY is to create a research infrastructure based on digital image processing, artificial intelligence and cloud computing to enhance knowledge sharing and reach better-informed decisions in pathology. This ambitious goal breaks down as follows:
Advanced image processing techniques and artificial intelligence methods for automatic WSI interpretation with two purposes: diagnosis and image retrieval.
Novel cloud-oriented data infrastructure and algorithms: to securely store, retrieve and share a publicly available WSI database assuring data interoperability and portability
Innovative and user-friendly software: computer-aided diagnosis and content-based image retrieval tools based on artificial intelligence and cloud-computing algorithms to improve workflow efficiency, stimulate collaboration and increase diagnostic confidence at pathology labs no matter their location.
TRAINNING: CLARIFY will provide a high-level personalised multidisciplinary training program. This will include enrolment in a PhD program (in two tracks: engineering and medicine) as well as further education in transferable skills (such as entrepreneurship, project management, ethical issues, IPR, open access). The long-term ambition is evolving scientific leadership – a foundation for ERC starting grants and/or industry leadership – Industry Fellow.
DISSEMINATION AND OUTREACH: Disseminate the digital pathology methods and tools developed by the ITN to a wide spectrum of stakeholders ranging from the scientific community to clinicians and industry; create awareness in the pathology field about the need of using new technologies to reduce their workload; to encourage pathology and computer engineer vocational careers among young students, with special emphasis on women.
CLARIFY is almost two-year-old, read our newsletter to know the last outcomes of the CLARIFY project, including scientific results, ESR project updates, dissemination actions, events, training activities, secondments, etc.
ESR7 starts her secondment in INCLIVA
Laëtitia (ESR7 at UPV) started last month her 2-month on-site secondment at the INCLIVA foundation, where Andrés (ESR12) is doing his Ph.D., under the supervision of Carlos Monteagudo.
Laëtitia is the first ESR to have the opportunity to do an on-site secondment because of the pandemic restrictions, as all other on-going secondments are currently held online.
First CLARIFY secondments secondments started from March 2021. Due to COVID mobility restrictions, most of them were virtual.
All ESRs in place!
All CLARIFY’s ESRs are already enrolled and starting their careers. Welcome to Na Li, Yuandou Wang, Jiahui Geng, Neel Kanwal, Saul Fuster Navarro, Claudio Fernandez, Laëtitia Launet, Arne Schmidt, Zahra TabaTabaei, Farbod Khoraminia, Umay Kiraz, Andrés Mosquera-Zamudio. A great team!
Visit Researchers section to get to know them!
The COVID-19 outbreak had also consequences on CLARIFY project. The incorporation of the ESRs had to be postponed. First ESRs joined CLARIFY network in sep-2020.
Visit Researchers section to get to know them.
CLARIFY – CLoud ARtificial Intelligence For pathologY – starts on 1-nov-2019 and ends 31-oct-2023. The project, coordinated by the Universitat Politècnica de València (Spain), is funded under the programme: H2020-EU.1.3.1. – Fostering new skills by means of excellent initial training of researchers.
The virtual secondment in EMC in Rotterdam consisted in attending to the weekly lab meeting with the bladder cancer group and a course with the uropathologist explaining bladder cancer.
Hi everyone! Today we (Claudio, Laëtitia and Andrés) will talk about the online secondment we did at Roche Diagnostics S.L.U.
Topic: Tools, good practices and use cases for digital pathology
Supervisory Board (SB) and ESR Supervisors (ES)
External Advisory Board
ESR6 and ESR11 at Stavanger Day in Pathology
On September 30, 2021, the Stavanger University Hospital (SUH) organized the seminar “Stavanger Day in Pathology” with more of 50 attendants among members of the SUH Pathology department (included CLARIFY ESR6 and ESR11) and students of Pathology.
ESR8 in MICCAI 2021
On 27Sep – 1Oct 2021, ESR8 presented a paper on the topic of Multiple Instance Learning in the 24th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2021). This work is a successful collaboration between the University of Granada and the Northwestern University.
On Sep 17-22, 2021, ESR10 and ESR11 attended EMPAIA Academy training program where renowned speakers from the fields of IT, artificial intelligence (AI) and pathology talked about their experiences, use cases and the latest developments in digital pathology. Courses: (i) Introduction to Pathology and AI in Pathology, (ii) Introduction to Computational Pathology, (iii) Requirements for Application of AI.
On Sep 17, 2021, the ESR3’s work titled “Optimized Federated Learning on Class-biased Distributed Data Sources” was presented in the 4th Workshop on Parallel, Distributed and #FederatedLearning as part of the ECML-PKDD 2021 conference.
On May 26, Andres ESR12 attended to the Online Course “Spitzoid Melanocytic Tumors: Histological-Genetic Correlations: Expert Analysis of 70 Spitzoid Melanocytic Proliferations With Known Genetic Changes” directed by Dr.Artur Zembowicz and Pedram Gerami. By Dermpedia.org.
ESR3 and ESR4 presented their paper (DID-eFed: Facilitating Federated Learning as a Service with Decentralized Identities) at EASE 2021 Trondheim Norway, held virtually on June 24, 2021, within the 2nd Blockchain Software Engineering Workshop.
2nd CLARIFY Virtual Fieldtrip
On June 22, 2021, ESRs had the pleasure to attend the 2nd CLARIFY Virtual Fieldtrip titled “Anatomic pathology instruments and reagents” led by ROCHE, one of our partner organizations. ROCHE showed a virtual demo of some of their solutions for the Anatomic Pathology Lab.
ESR4 at DPA Webinar
On April 22, 2021, Neel, ESR4 at UiS, attended a webinar on “Enabling Interoperability for Digital and Computational Pathology in the Age of Artificial Intelligence: Current Status and Future Directions” by the Digital Pathology Association (DPA).
First annual meeting
On 14-16 Apr 2021, after closing the CLARIFY training school, the first CLARIFY annual meeting started, in which all CLARIFY ESRs presented themselves, their background, their individual research projects and the work performed until then. A meeting with the distinguished members of the CLARIFY External Advisory Board was held and the different CLARIFY committees were joined. Finally, the first CLARIFY annual meeting concluded with the Mid-term check by the REA – European Research Executive Agency – to assess the project at that point.
First online training school
On 13-14 Apr 2021, the first CLARIFY training school was held. The event was composed of 3 technical courses lectured by some of the CLARIFY supervisors and 3 master classes by some distinguished members of our External Advisory Board. Besides, we had also a workshop and two seminars to cover relevant transferable skills issues.
ESR2 at the HPCS 2020
On 23-27 March 2021, ESR2 has attended the 2020 international conference on high performance Computing & Simulation (HPCS 2020) online event, Under the theme of “HPC and Modeling & Simulation for 21st Century”, HPCS 2020 focused on a wide range of the state-of-the-art as well as emerging topics pertaining to high performance and large-scale computing systems at both the client and backend levels.
ESR11 at Molecular diagnostics and genomics in breast cancer event
On 1-5 March 2021, ESR11 attended the Molecular diagnostics and genomics in breast cancer event organized by Onco Corner, the e-learning platform from Sharing Progress in Cancer Care (SPCC).
ESR6 and ESR7 at the IEEE EMBS Forum
Claudio Fernandez and Laëtitia Launet, respectively ESR6 and ESR7 at the UPV, attended the IEEE EMBS Grand Challenge Forum on Data Science and Engineering in Healthcare, held virtually on Feb 10-13, 2021.
ESR12 at SEAP-IAP Annual Meeting
From the 4th to the 5th of February 2021, ESR12 attended the XLIV Annual Meeting of the Sociedad Española de Anatomía Patológica, the Spanish Division of the International Academy of Pathology.
1st Virtual Fieldtrip
On Jan 26, 2021, took place the first on-line networking training session of CLARIFY. Supervisors, co-supervisors and ESRs introduced themselves as an introduction to partner’s expertise and disciplines. This training was hosted by UPV.
ESR2 at DAWHI 2020
Yuandou Wang, ESR2 from UvA, gave a short virtual talk about “Decentralized workflow management on software defined infrastructure” at the 1st Workshop On Data-Centric Workflows On Heterogeneous Infrastructures: Challenges And Directions (DAWHI), in the context of IEEE Services Congress, 2020.
On 7th and 8th November, CLARIFY’s kick-off meeting took place in Valencia (Spain).
2020 IEEE Services: IEEE World Congress on Services (19-24 Oct-2020; Online)
Wang, Y., Zhao, Z., Decentralized workflow management on software defined infrastructure, 1st Workshop On Data-Centric Workflows On Heterogeneous Infrastructures: Challenges And Directions (DAWHI) in the context of IEEE Services Congress, 2020. http://doi.org/10.1109/SERVICES48979.2020.00059
HPCS 2020: International Conference on High Performance Computing & Simulation (22-27 March-2021; Online)
Kruijer W., Wang Y., Koulouzis S., Li N., Bianchi R., Zhao, Z.: FAIR-Cells: an interactive tool for enabling the FAIRness of code fragments in Jupyter notebooks, in the proceedings of international conference of High Performance Computing and Simulation (HPCS) (2020), Spain [to appear]
ECML-PKDD 2021: European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (13-17
September 2021; Online)
Yongli Mou, Jiahui Geng, Sascha Welten, Chunming Rong, Stefan Decker, and Oya Beyan, Optimized Federated Learning on Class-biased Distributed Data Sources. 4th Workshop on Parallel, Distributed and Federated Learning at ECML-PKDD 2021.
MICCAI 2021: MICCAI 2021: International Conference on Medical Image Computingand Computer Assisted Intervention (27 Sep – 1 Oct 2021; Online)
Yunan Wu, Arne Schmidt, Enrique Hernández Sánchez, Rafael Molina, and Aggelos K. Katsaggelos, Combining Attention-based Multiple Instance Learning and Gaussian Processes for CT Hemorrhage Detection. 24th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2021).
Sandra Morales, Kjersti Engan, Valery Naranjo, Artificial intelligence in computational pathology – challenges and future directions, Digital Signal Processing, 2021, 103196, ISSN 1051-2004, https://doi.org/10.1016/j.dsp.2021.103196.