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  1. Article ; Online: The FeatureCloud Platform for Federated Learning in Biomedicine: Unified Approach.

    Matschinske, Julian / Späth, Julian / Bakhtiari, Mohammad / Probul, Niklas / Kazemi Majdabadi, Mohammad Mahdi / Nasirigerdeh, Reza / Torkzadehmahani, Reihaneh / Hartebrodt, Anne / Orban, Balazs-Attila / Fejér, Sándor-József / Zolotareva, Olga / Das, Supratim / Baumbach, Linda / Pauling, Josch K / Tomašević, Olivera / Bihari, Béla / Bloice, Marcus / Donner, Nina C / Fdhila, Walid /
    Frisch, Tobias / Hauschild, Anne-Christin / Heider, Dominik / Holzinger, Andreas / Hötzendorfer, Walter / Hospes, Jan / Kacprowski, Tim / Kastelitz, Markus / List, Markus / Mayer, Rudolf / Moga, Mónika / Müller, Heimo / Pustozerova, Anastasia / Röttger, Richard / Saak, Christina C / Saranti, Anna / Schmidt, Harald H H W / Tschohl, Christof / Wenke, Nina K / Baumbach, Jan

    Journal of medical Internet research

    2023  Volume 25, Page(s) e42621

    Abstract: Background: Machine learning and artificial intelligence have shown promising results in many areas and are driven by the increasing amount of available data. However, these data are often distributed across different institutions and cannot be easily ... ...

    Abstract Background: Machine learning and artificial intelligence have shown promising results in many areas and are driven by the increasing amount of available data. However, these data are often distributed across different institutions and cannot be easily shared owing to strict privacy regulations. Federated learning (FL) allows the training of distributed machine learning models without sharing sensitive data. In addition, the implementation is time-consuming and requires advanced programming skills and complex technical infrastructures.
    Objective: Various tools and frameworks have been developed to simplify the development of FL algorithms and provide the necessary technical infrastructure. Although there are many high-quality frameworks, most focus only on a single application case or method. To our knowledge, there are no generic frameworks, meaning that the existing solutions are restricted to a particular type of algorithm or application field. Furthermore, most of these frameworks provide an application programming interface that needs programming knowledge. There is no collection of ready-to-use FL algorithms that are extendable and allow users (eg, researchers) without programming knowledge to apply FL. A central FL platform for both FL algorithm developers and users does not exist. This study aimed to address this gap and make FL available to everyone by developing FeatureCloud, an all-in-one platform for FL in biomedicine and beyond.
    Methods: The FeatureCloud platform consists of 3 main components: a global frontend, a global backend, and a local controller. Our platform uses a Docker to separate the local acting components of the platform from the sensitive data systems. We evaluated our platform using 4 different algorithms on 5 data sets for both accuracy and runtime.
    Results: FeatureCloud removes the complexity of distributed systems for developers and end users by providing a comprehensive platform for executing multi-institutional FL analyses and implementing FL algorithms. Through its integrated artificial intelligence store, federated algorithms can easily be published and reused by the community. To secure sensitive raw data, FeatureCloud supports privacy-enhancing technologies to secure the shared local models and assures high standards in data privacy to comply with the strict General Data Protection Regulation. Our evaluation shows that applications developed in FeatureCloud can produce highly similar results compared with centralized approaches and scale well for an increasing number of participating sites.
    Conclusions: FeatureCloud provides a ready-to-use platform that integrates the development and execution of FL algorithms while reducing the complexity to a minimum and removing the hurdles of federated infrastructure. Thus, we believe that it has the potential to greatly increase the accessibility of privacy-preserving and distributed data analyses in biomedicine and beyond.
    MeSH term(s) Humans ; Artificial Intelligence ; Algorithms ; Health Occupations ; Software ; Computer Communication Networks ; Privacy
    Language English
    Publishing date 2023-07-12
    Publishing country Canada
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2028830-X
    ISSN 1438-8871 ; 1438-8871
    ISSN (online) 1438-8871
    ISSN 1438-8871
    DOI 10.2196/42621
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Genetic newborn screening and digital technologies: A project protocol based on a dual approach to shorten the rare diseases diagnostic path in Europe.

    Garnier, Nicolas / Berghout, Joanne / Zygmunt, Aldona / Singh, Deependra / Huang, Kui A / Kantz, Waltraud / Blankart, Carl Rudolf / Gillner, Sandra / Zhao, Jiawei / Roettger, Richard / Saier, Christina / Kirschner, Jan / Schenk, Joern / Atkins, Leon / Ryan, Nuala / Zarakowska, Kaja / Zschüntzsch, Jana / Zuccolo, Michela / Müllenborn, Matthias /
    Man, Yuen-Sum / Goodman, Liz / Trad, Marie / Chalandon, Anne Sophie / Sansen, Stefaan / Martinez-Fresno, Maria / Badger, Shirlene / Walther van Olden, Rudolf / Rothmann, Robert / Lehner, Patrick / Tschohl, Christof / Baillon, Ludovic / Gumus, Gulcin / Gross, Edith / Stefanov, Rumen / Iskrov, Georgi / Raycheva, Ralitsa / Kostadinov, Kostadin / Mitova, Elena / Einhorn, Moshe / Einhorn, Yaron / Schepers, Josef / Hübner, Miriam / Alves, Frauke / Iskandar, Rowan / Mayer, Rudolf / Renieri, Alessandra / Piperkova, Aneta / Gut, Ivo / Beltran, Sergi / Matthiesen, Mads Emil / Poetz, Marion / Hansson, Mats / Trollmann, Regina / Agolini, Emanuele / Ottombrino, Silvia / Novelli, Antonio / Bertini, Enrico / Selvatici, Rita / Farnè, Marianna / Fortunato, Fernanda / Ferlini, Alessandra

    PloS one

    2023  Volume 18, Issue 11, Page(s) e0293503

    Abstract: Since 72% of rare diseases are genetic in origin and mostly paediatrics, genetic newborn screening represents a diagnostic "window of opportunity". Therefore, many gNBS initiatives started in different European countries. Screen4Care is a research ... ...

    Abstract Since 72% of rare diseases are genetic in origin and mostly paediatrics, genetic newborn screening represents a diagnostic "window of opportunity". Therefore, many gNBS initiatives started in different European countries. Screen4Care is a research project, which resulted of a joint effort between the European Union Commission and the European Federation of Pharmaceutical Industries and Associations. It focuses on genetic newborn screening and artificial intelligence-based tools which will be applied to a large European population of about 25.000 infants. The neonatal screening strategy will be based on targeted sequencing, while whole genome sequencing will be offered to all enrolled infants who may show early symptoms but have resulted negative at the targeted sequencing-based newborn screening. We will leverage artificial intelligence-based algorithms to identify patients using Electronic Health Records (EHR) and to build a repository "symptom checkers" for patients and healthcare providers. S4C will design an equitable, ethical, and sustainable framework for genetic newborn screening and new digital tools, corroborated by a large workout where legal, ethical, and social complexities will be addressed with the intent of making the framework highly and flexibly translatable into the diverse European health systems.
    MeSH term(s) Infant, Newborn ; Humans ; Child ; Neonatal Screening/methods ; Rare Diseases/diagnosis ; Rare Diseases/epidemiology ; Rare Diseases/genetics ; Artificial Intelligence ; Digital Technology ; Europe
    Language English
    Publishing date 2023-11-22
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0293503
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Book ; Online: Privacy-preserving Artificial Intelligence Techniques in Biomedicine

    Torkzadehmahani, Reihaneh / Nasirigerdeh, Reza / Blumenthal, David B. / Kacprowski, Tim / List, Markus / Matschinske, Julian / Späth, Julian / Wenke, Nina Kerstin / Bihari, Béla / Frisch, Tobias / Hartebrodt, Anne / Hausschild, Anne-Christin / Heider, Dominik / Holzinger, Andreas / Hötzendorfer, Walter / Kastelitz, Markus / Mayer, Rudolf / Nogales, Cristian / Pustozerova, Anastasia /
    Röttger, Richard / Schmidt, Harald H. H. W. / Schwalber, Ameli / Tschohl, Christof / Wohner, Andrea / Baumbach, Jan

    2020  

    Abstract: Artificial intelligence (AI) has been successfully applied in numerous scientific domains. In biomedicine, AI has already shown tremendous potential, e.g. in the interpretation of next-generation sequencing data and in the design of clinical decision ... ...

    Abstract Artificial intelligence (AI) has been successfully applied in numerous scientific domains. In biomedicine, AI has already shown tremendous potential, e.g. in the interpretation of next-generation sequencing data and in the design of clinical decision support systems. However, training an AI model on sensitive data raises concerns about the privacy of individual participants. For example, summary statistics of a genome-wide association study can be used to determine the presence or absence of an individual in a given dataset. This considerable privacy risk has led to restrictions in accessing genomic and other biomedical data, which is detrimental for collaborative research and impedes scientific progress. Hence, there has been a substantial effort to develop AI methods that can learn from sensitive data while protecting individuals' privacy. This paper provides a structured overview of recent advances in privacy-preserving AI techniques in biomedicine. It places the most important state-of-the-art approaches within a unified taxonomy and discusses their strengths, limitations, and open problems. As the most promising direction, we suggest combining federated machine learning as a more scalable approach with other additional privacy preserving techniques. This would allow to merge the advantages to provide privacy guarantees in a distributed way for biomedical applications. Nonetheless, more research is necessary as hybrid approaches pose new challenges such as additional network or computation overhead.

    Comment: 17 pages, 3 figures, 3 tables
    Keywords Computer Science - Cryptography and Security ; Computer Science - Artificial Intelligence
    Subject code 303
    Publishing date 2020-07-22
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Book ; Online: The FeatureCloud AI Store for Federated Learning in Biomedicine and Beyond

    Matschinske, Julian / Späth, Julian / Nasirigerdeh, Reza / Torkzadehmahani, Reihaneh / Hartebrodt, Anne / Orbán, Balázs / Fejér, Sándor / Zolotareva, Olga / Bakhtiari, Mohammad / Bihari, Béla / Bloice, Marcus / Donner, Nina C / Fdhila, Walid / Frisch, Tobias / Hauschild, Anne-Christin / Heider, Dominik / Holzinger, Andreas / Hötzendorfer, Walter / Hospes, Jan /
    Kacprowski, Tim / Kastelitz, Markus / List, Markus / Mayer, Rudolf / Moga, Mónika / Müller, Heimo / Pustozerova, Anastasia / Röttger, Richard / Saranti, Anna / Schmidt, Harald HHW / Tschohl, Christof / Wenke, Nina K / Baumbach, Jan

    2021  

    Abstract: Machine Learning (ML) and Artificial Intelligence (AI) have shown promising results in many areas and are driven by the increasing amount of available data. However, this data is often distributed across different institutions and cannot be shared due to ...

    Abstract Machine Learning (ML) and Artificial Intelligence (AI) have shown promising results in many areas and are driven by the increasing amount of available data. However, this data is often distributed across different institutions and cannot be shared due to privacy concerns. Privacy-preserving methods, such as Federated Learning (FL), allow for training ML models without sharing sensitive data, but their implementation is time-consuming and requires advanced programming skills. Here, we present the FeatureCloud AI Store for FL as an all-in-one platform for biomedical research and other applications. It removes large parts of this complexity for developers and end-users by providing an extensible AI Store with a collection of ready-to-use apps. We show that the federated apps produce similar results to centralized ML, scale well for a typical number of collaborators and can be combined with Secure Multiparty Computation (SMPC), thereby making FL algorithms safely and easily applicable in biomedical and clinical environments.
    Keywords Computer Science - Machine Learning ; Computer Science - Cryptography and Security ; Computer Science - Distributed ; Parallel ; and Cluster Computing
    Subject code 006
    Publishing date 2021-05-12
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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