PRIMAGE - PRedictive In-silico Multiscale Analytics to support cancer personalized diaGnosis and prognosis, Empowered by imaging biomarkers

Beschreibung

pPRIMAGE proposes a cloud-based platform to support decision making in the clinical management of malignant solid tumours, offering predictive tools to assist diagnosis, prognosis, therapies choice and treatment follow up, based on the use of novel imaging biomarkers, in-silico tumour growth simulation, advanced visualisation of predictions with weighted confidence scores and machine-learning based translation of this knowledge into predictors for the most relevant, disease-specific, Clinical End Points.br PRIMAGE implements a hybrid cloud model, comprising the of use of open public cloud (based on EOSC services) and private clouds, enabling use by the scientific community (facilitating reuse of de-identified clinical curated data in Open Science) and also suitable for future commercial exploitation.br The proposed data infrastructures, imaging biomarkers and models for in-silico medicine research will be validated in the application context of two paediatric cancers, Neuroblastoma (NB, the most frequent solid cancer of early childhood) and the Diffuse Intrinsic Pontine Glioma (DIPG, the leading cause of brain tumour-related death in children). These two paediatric cancers are relevant validation cases given their representativeness of cancer disease, and their high societal impact, as they affect the most vulnerable and loved family members.br The European Society for Paediatric Oncology, two Imaging Biobanks and three of the most prominent European Paediatric oncology units are partners in this project, making retrospective clinical data (imaging, clinical, molecular and genetics) registries accessible to PRIMAGE, for training of machine learning algorithms and testing of the in-silico tools´ performance. Solutions to streamline and secure the data pseudonymisation, extraction, structuring, quality control and storage processes, will be implemented and validated also for use on prospective data, contributing European shared data infrastructures.

Institutionen
  • AG Keim (Data Analysis and Visualization)
Publikationen
    Jentner, Wolfgang; Lindholz, Giuliana; Schäfer, Hanna; El-Assady, Mennatallah; Ma, Kwan-Liu; Keim, Daniel A. (2023): Visual Analytics of Co-Occurrences to Discover Subspaces in Structured Data ACM Transactions on Interactive Intelligent Systems. ACM. 2023, 13(2), 10. ISSN 2160-6455. eISSN 2160-6463. Available under: doi: 10.1145/3579031

Visual Analytics of Co-Occurrences to Discover Subspaces in Structured Data

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We present an approach that shows all relevant subspaces of categorical data condensed in a single picture. We model the categorical values of the attributes as co-occurrences with data partitions generated from structured data using pattern mining. We show that these co-occurrences are a-priori allowing us to greatly reduce the search space effectively generating the condensed picture where conventional approaches filter out several subspaces as these are deemed insignificant. The task of identifying interesting subspaces is common but difficult due to exponential search spaces and the curse of dimensionality. One application of such a task might be identifying a cohort of patients defined by attributes such as gender, age, and diabetes type that share a common patient history, which is modeled as event sequences. Filtering the data by these attributes is common but cumbersome and often does not allow a comparison of subspaces. We contribute a powerful multi-dimensional pattern exploration approach (MDPE-approach) agnostic to the structured data type that models multiple attributes and their characteristics as co-occurrences, allowing the user to identify and compare thousands of subspaces of interest in a single picture. In our MDPE-approach, we introduce two methods to dramatically reduce the search space, outputting only the boundaries of the search space in the form of two tables. We implement the MDPE-approach in an interactive visual interface (MDPE-vis) that provides a scalable, pixel-based visualization design allowing the identification, comparison, and sense-making of subspaces in structured data. Our case studies using a gold-standard dataset and external domain experts confirm our approach’s and implementation’s applicability. A third use case sheds light on the scalability of our approach and a user study with 15 participants underlines its usefulness and power.

Forschungszusammenhang (Projekte)

  Nieto, Adela Cañete; Ladenstein, Ruth; Hero, Barbara; Taschner-Mandl, Sabine; Pötschger, Ulrike; Düster, Vanessa; Martinez De Las Heras, Blanca; Fischer, Maximilian T.; Metz, Yannick; Keim, Daniel A. (2022): PRIMAGE - An Artifical Intelligence-based Clinical Decision Support System for Optimized Cancer Diagnosis and Risk Assessment : A Progress Update SIOPEN Annual General Meeting 2022

PRIMAGE - An Artifical Intelligence-based Clinical Decision Support System for Optimized Cancer Diagnosis and Risk Assessment : A Progress Update

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dc.contributor.author: Nieto, Adela Cañete; Ladenstein, Ruth; Hero, Barbara; Taschner-Mandl, Sabine; Pötschger, Ulrike; Düster, Vanessa; Martinez De Las Heras, Blanca; Fischer, Maximilian T.; Metz, Yannick; Keim, Daniel A.

Forschungszusammenhang (Projekte)

    Martí-Bonmatí, Luis; Alberich-Bayarri, Ángel; Ladenstein, Ruth; Blanquer, Ignacio; Segrelles, J. Damian; Cerdá-Alberich, Leonor; Gkontra, Polyxeni; Hero, Barbara; Keim, Daniel A.; Jentner, Wolfgang (2020): PRIMAGE project : predictive in silico multiscale analytics to support childhood cancer personalised evaluation empowered by imaging biomarkers European Radiology Experimental. SpringerOpen. 2020, 4(1), 22. eISSN 2509-9280. Available under: doi: 10.1186/s41747-020-00150-9

PRIMAGE project : predictive in silico multiscale analytics to support childhood cancer personalised evaluation empowered by imaging biomarkers

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PRIMAGE is one of the largest and more ambitious research projects dealing with medical imaging, artificial intelligence and cancer treatment in children. It is a 4-year European Commission-financed project that has 16 European partners in the consortium, including the European Society for Paediatric Oncology, two imaging biobanks, and three prominent European paediatric oncology units. The project is constructed as an observational in silico study involving high-quality anonymised datasets (imaging, clinical, molecular, and genetics) for the training and validation of machine learning and multiscale algorithms. The open cloud-based platform will offer precise clinical assistance for phenotyping (diagnosis), treatment allocation (prediction), and patient endpoints (prognosis), based on the use of imaging biomarkers, tumour growth simulation, advanced visualisation of confidence scores, and machine-learning approaches. The decision support prototype will be constructed and validated on two paediatric cancers: neuroblastoma and diffuse intrinsic pontine glioma. External validation will be performed on data recruited from independent collaborative centres. Final results will be available for the scientific community at the end of the project, and ready for translation to other malignant solid tumours.

Forschungszusammenhang (Projekte)

Mittelgeber
Name Finanzierungstyp Kategorie Kennziffer
Europäische Union Drittmittel Forschungsförderprogramm 779/18
Weitere Informationen
Laufzeit: 01.12.2018 – 30.11.2022