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Marine Predators Algorithm with Deep Learning-Based Leukemia Cancer Classification on Medical Images

Computer Modeling in Engineering & Sciences 2024年第10期141卷 893-916页

作者： Sonali Das Saroja Kumar Rout Sujit Kumar Panda Pradyumna Kumar Mohapatra Abdulaziz S.Almazyad Muhammed Basheer Jasser Guojiang Xiong Ali Wagdy Mohamed Department of Computer Science&Engineering Gandhi Institute for TechnologyBPUTBhubaneswar752054India Department of Information Technology Vardhaman College of Engineering(Autonomous)Hyderabad501218TelanganaIndia Department of Electronic&Communication Engineering Vedang Institute of TechnologyBhubaneswar752010India Department of Computer Engineering College of Computer and Information SciencesKing Saud UniversityRiyadh11543Saudi Arabia Department of Computing and Information Systems School of Engineering and TechnologySunway UniversityJalan UniversitiBandar SunwaySelangor Darul Ehsan47500Malaysia Research Centre for Human-Machine Collaboration(HUMAC) School of Engineering and TechnologySunway UniversityJalan UniversitiBandar SunwaySelangor Darul Ehsan47500Malaysia Guizhou Key Laboratory of Intelligent Technology in Power System College of Electrical EngineeringGuizhou UniversityGuiyang550025China Operations Research Department Faculty of Graduate Studies for Statistical ResearchCairo UniversityGiza12613Egypt Applied Science Research Center Applied Science Private UniversityAmman11931Jordan

In blood or bone marrow,leukemia is a form of cancer.A person with leukemia has an expansion of white blood cells(WBCs).It primarily affects children and rarely affects *** depends on the type of leukemia and the extent to which cancer has established throughout the *** leukemia in the initial stage is vital to providing timely patient *** image-analysis-related approaches grant safer,quicker,and less costly solutions while ignoring the difficulties of these invasive *** can be simple to generalize Computer vision(CV)-based and image-processing techniques and eradicate human *** researchers have implemented computer-aided diagnosticmethods andmachine learning(ML)for laboratory image analysis,hopefully overcoming the limitations of late leukemia detection and determining its *** study establishes a Marine Predators Algorithm with Deep Learning Leukemia Cancer Classification(MPADL-LCC)algorithm onMedical *** projectedMPADL-LCC system uses a bilateral filtering(BF)technique to pre-process medical *** MPADL-LCC system uses Faster SqueezeNet withMarine Predators Algorithm(MPA)as a hyperparameter optimizer for feature ***,the denoising autoencoder(DAE)methodology can be executed to accurately detect and classify leukemia *** hyperparameter tuning process using MPA helps enhance leukemia cancer classification *** results are compared with other recent approaches concerning various measurements and the MPADL-LCC algorithm exhibits the best results over other recent approaches.

关键词： Leukemia cancer medical imaging image classification deep learning marine predators algorithm

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A Novel Federated Learning Based Intrusion Detection System for IoT Networks

A Novel Federated Learning Based Intrusion Detection System ...

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IEEE International Conference on Communications (ICC)

作者： Rabaie Benameur Amine Dahane Sami Souihi Abdelhamid Mellouk Laboratory of Industrial Computing and Networks (RIIR) University of Oran 1 Oran Algeria Institute of Applied Science and Technology ISTA Oran Algeria Image Signal and Intelligent Systems (LiSSi) Laboratory TincNET Research Team Univ. Paris-Est Cr eteil France

ISBN: (数字)9781728190549

ISBN: (纸本)9781728190556

In the realm of IoT platforms, susceptibility to cyber-attacks is a pressing concern, necessitating the deployment of Intrusion Detection systems (IDS). Constructing a scalable, accurate, and lightweight model without compromising data privacy poses a formidable challenge. This study assesses classical and novel approaches employing federated learning (FL) to train IDS models. Optimization through Knowledge Distillation (KD) techniques aims to enhance computational efficiency. Experimental results reveal the efficacy of federated learning, achieving an 84.5% accuracy for 15 attack types, and an impressive performance for binary network attack classification. Notably, these models exhibit shorter inference times compared to cutting-edge machine learning models trained on the Edge-IIoTset dataset, offering promising advancements in IoT security.

关键词： Data privacy Accuracy Federated learning Computational modeling Image edge detection Intrusion detection Pressing

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IoT Urban River Water Quality System Using Federated Learning via Knowledge Distillation

IoT Urban River Water Quality System Using Federated Learnin...

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IEEE International Conference on Communications (ICC)

作者： Amine Dahane Rabaie Benameur Manel Naloufi Sami Souihi Thiago Abreu Francoise S. Lucas Abdelhamid Mellouk Laboratory of Industrial Computing and Networks (RIIR) University of Oran 1 Oran Algeria Institute of Applied Science and Technology ISTA Oran Algeria Image Signal and Intelligent Systems (LiSSi) Laboratory TincNET Research Team Univ. Paris-Est Créteil France Laboratoire Eau Environnement et Systèmes Urbains (Leesu) Univ. Paris-Est Créteil École des Ponts ParisTech France

ISBN: (数字)9781728190549

ISBN: (纸本)9781728190556

In the past decades, the use of urban rivers for recreational and sporting activities has gained increasing interest. However, bathing in urban surface waters is not without health risks due to short-term pollution of fecal origin, which may have an important impact on the overall population health within a region where bathing in water streams is possible. Therefore, EU member states are required to lower the contamination risk of such areas through active water quality management, as defined by the Bathing Water directory (BWD, 2006/7/EC). This paper develops and evaluates a cost-effective IoT-based water quality monitoring system, based on low-cost water quality sensors coupled with machine-learning approaches. By monitoring spatiotemporal dynamics of several physical and chemical parameters correlated with bacterial indicators, managers can more easily decide if the water quality of a bathing site is enough for usage. To determine the water suitability at particular river sites, the system employs a convolutional neural network (CNN) deep learning classifier, integrating federated learning (FL) with knowledge distillation (FedKD) to streamline model architecture, reduce communication costs, and preserve data privacy. The system is tested on the Seine and the Marne rivers (Paris area, France) and results demonstrate that FedKD outperforms centralized knowledge distillation (KD) and FL algorithms such as FedAvg and UFedAVG. Using the current features, it achieves a satisfactory average accuracy of 90.74% at Marne station.

关键词： Federated learning Surface contamination Water quality Water pollution Rivers Spatiotemporal phenomena Convolutional neural networks

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Quality Optimization of Live Streaming Services over HTTP with Reinforcement Learning

Quality Optimization of Live Streaming Services over HTTP wi...

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2021 IEEE Global Communications Conference (GLOBECOM)

作者： F. Tashtarian R. Falanji A. Bentaleb A. Erfanian P. S. Mashhadi C. Timmerer H. Hellwagner R. Zimmermann Christian Doppler Laboratory ATHENA Institute of Information Technology Alpen-Adria-Universität Klagenfurt Austria Sharif University of Technology Tehran Iran School of Computing National University of Singapore (NUS) Center for Applied Intelligent Systems Research (CAISR) Halmstad University Sweden

ISBN: (纸本)9781728181059

Recent years have seen tremendous growth in HTTP adaptive live video traffic over the Internet. In the presence of highly dynamic network conditions and diverse request patterns, existing yet simple hand-crafted heuristic approaches for serving client requests at the network edge might incur a large overhead and significant increase in time complexity. Therefore, these approaches might fail in delivering acceptable Quality of Experience (QoE) to end users. To bridge this gap, we propose ROPL, a learning-based client request management solution at the edge that leverages the power of the recent breakthroughs in deep reinforcement learning, to serve requests of concurrent users joining various HTTP-based live video channels. ROPL is able to react quickly to any changes in the environment, performing accurate decisions to serve clients requests, which results in achieving satisfactory user QoE. We validate the efficiency of ROPL through trace-driven simulations and a real-world setup. Experimental results from real-world scenarios confirm that ROPL outperforms existing heuristic-based approaches in terms of QoE, with a factor up to $3.7\times$ .

关键词： Scalability Conferences Reinforcement learning Streaming media Internet Quality of experience Servers

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Effect of endogenous and anthropogenic factors on the alkalinisation and salinisation of freshwater in United States by using explainable machine learning

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Case Studies in Chemical and Environmental Engineering 2024年 10卷

作者： Wimalagunarathna, N.D. Dharmarathne, Gangani Ekanayake, I.U. Rathanayake, Upaka Alwatugoda, Janaka Meddage, D.P.P. Department of Zoology Faculty of Applied Sciences University of Sri Jayewardenepura Gangodawila Nugegoda Sri Lanka Australian Laboratory Services Global Water and Hydrographic Hume 2620 ACT Australia School of Computing Technologies Royal Melbourne Institute of Technology Melbourne VIC Australia Ceylon Institute for Artificial Intelligence Research (CIAIR) Colombo Sri Lanka Department of Civil Engineering and Construction Faculty of Engineering and Design Atlantic Technological University Sligo Ireland Research and Innovations Centers Division Rabdan Academy Abu Dhabi United Arab Emirates Institute for Integrated and Intelligent Systems Griffith University Nathan QLD Australia School of Engineering and Technology The University of New South Wales Canberra 2600 ACT Australia

Freshwater salinisation and alkalinisation strongly depend on human and natural factors. We used an explainable machine learning approach to investigate the impact of natural and human factors on the salinity and alkalinity in rivers in the United States. The model achieved coefficient of determination of 0.89 for salinity predictions and 0.92 for alkalinity predictions. Shapley additive explanations revealed salinisation is driven mainly by human factors like population density (18 %) and impervious surface percentage (13 %) and natural factors like run-off (14 %). The alkalinisation is mainly influenced by natural processes such as runoff (36 %) and soil-pH (20 %). © 2024 The Authors

关键词： Alkalinity Ecosystem Machine learning Rivers Salinity

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An Early Stage researcher's Primer on systems Medicine Terminology

Network and Systems Medicine

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Network and systems Medicine 2021年第1期4卷 2-50页

作者： Zanin, Massimiliano Aitya, Nadim A.A. Basilio, José Baumbach, Jan Benis, Arriel Behera, Chandan K. Bucholc, Magda Castiglione, Filippo Chouvarda, Ioanna Comte, Blandine Dao, Tien-Tuan Ding, Xuemei Pujos-Guillot, Estelle Filipovic, Nenad Finn, David P. Glass, David H. Harel, Nissim Iesmantas, Tomas Ivanoska, Ilinka Joshi, Alok Boudjeltia, Karim Zouaoui Kaoui, Badr Kaur, Daman Maguire, Liam P. McClean, Paula L. McCombe, Niamh De Miranda, João Luís Moisescu, Mihnea Alexandru Pappalardo, Francesco Polster, Annikka Prasad, Girijesh Rozman, Damjana Sacala, Ioan Sanchez-Bornot, Jose M. Schmid, Johannes A. Sharp, Trevor Solé-Casals, Jordi Spiwok, Vojtěch Spyrou, George M. Stalidzans, Egils Stres, Blaa Sustersic, Tijana Symeonidis, Ioannis Tieri, Paolo Todd, Stephen Van Steen, Kristel Veneva, Milena Wang, Da-Hui Wang, Haiying Wang, Hui Watterson, Steven Wong-Lin, Kongfatt Yang, Su Zou, Xin Schmidt, Harald H.H.W. Centro de Tecnología Biomédica Universidad Politécnica de Madrid Madrid Spain Intelligent Systems Research Centre School of Computing Engineering and Intelligent Systems Ulster University Ulster United Kingdom Center for Physiology and Pharmacology Institute of Vascular Biology and Thrombosis Research Medical University of Vienna Vienna Austria TUM School of Life Sciences Weihenstephan Technical University of Munich Freising Germany Holon Israel CNR National Research Council IAC Institute for Applied Computing Rome Italy Lab of Computing Medical Informatics and Biomedical Imaging Technologies School of Medicine Aristotle University of Thessaloniki Thessaloniki Greece Université Clermont Auvergne INRAE UNH Plateforme d'Exploration du Métabolisme MetaboHUB Clermont Clermont-Ferrand France Université de Technologie de Compiègne Compiègne France Labex MS2T Control of Technological Systems-of-Systems CNRS and Université de Technologie de Compiègne Compiègne France Faculty of Engineering University of Kragujevac Kragujevac Serbia Kragujevac Serbia Steinbeis Advanced Risk Technologies Institute Doo Kragujevac Kragujevac Serbia Pharmacology and Therapeutics School of Medicine Galway Neuroscience Centre National University of Ireland Galway Ireland School of Computing Ulster University Ulster United Kingdom Holon Israel Department of Mathematics and Natural Sciences Kaunas University of Technology Kaunas Lithuania Faculty of Computer Science and Engineering Ss. Cyril and Methodius University Skopje Macedonia Medicine Faculty Université Libre de Bruxelles CHU de Charleroi Charleroi Belgium Northern Ireland Centre for Stratified Medicine Biomedical Sciences Research Institute Ulster University Ulster United Kingdom Escola Superior de Tecnologia e Gestão Instituto Politécnico de Portalegre Portalegre Portugal Instituto Superior Técnico Universidade de Lisboa Lisboa Portugal Faculty of Automatic Control and Computers University Politehnica of B

Background: systems Medicine is a novel approach to medicine, that is, an interdisciplinary field that considers the human body as a system, composed of multiple parts and of complex relationships at multiple levels, and further integrated into an environment. Exploring systems Medicine implies understanding and combining concepts coming from diametral different fields, including medicine, biology, statistics, modeling and simulation, and data science. Such heterogeneity leads to semantic issues, which may slow down implementation and fruitful interaction between these highly diverse fields. Methods: In this review, we collect and explain more than100 terms related to systems Medicine. These include both modeling and data science terms and basic systems medicine terms, along with some synthetic definitions, examples of applications, and lists of relevant references. Results: This glossary aims at being a first aid kit for the systems Medicine researcher facing an unfamiliar term, where he/she can get a first understanding of them, and, more importantly, examples and references for digging into the topic. © Massimiliano Zanin et al., 2021;Published by Mary Ann Liebert, Inc. 2021.

关键词： Semantics

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Understanding metric-related pitfalls in image analysis validation

arXiv

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arXiv 2023年

作者： Reinke, Annika Tizabi, Minu D. Baumgartner, Michael Eisenmann, Matthias Heckmann-Nötzel, Doreen Kavur, A. Emre Rädsch, Tim Sudre, Carole H. Acion, Laura Antonelli, Michela Arbel, Tal Bakas, Spyridon Benis, Arriel Blaschko, Matthew B. Buettner, Florian Cardoso, M. Jorge Cheplygina, Veronika Chen, Jianxu Christodoulou, Evangelia Cimini, Beth A. Collins, Gary S. Farahani, Keyvan Ferrer, Luciana Galdran, Adrian van Ginneken, Bram Glocker, Ben Godau, Patrick Haase, Robert Hashimoto, Daniel A. Hoffman, Michael M. Huisman, Merel Isensee, Fabian Jannin, Pierre Kahn, Charles E. Kainmueller, Dagmar Kainz, Bernhard Karargyris, Alexandros Karthikesalingam, Alan Kenngott, Hannes Kleesiek, Jens Kofler, Florian Kooi, Thijs Kopp-Schneider, Annette Kozubek, Michal Kreshuk, Anna Kurc, Tahsin Landman, Bennett A. Litjens, Geert Madani, Amin Maier-Hein, Klaus Martel, Anne L. Mattson, Peter Meijering, Erik Menze, Bjoern Moons, Karel G.M. Müller, Henning Nichyporuk, Brennan Nickel, Felix Petersen, Jens Rafelski, Susanne M. Rajpoot, Nasir Reyes, Mauricio Riegler, Michael A. Rieke, Nicola Saez-Rodriguez, Julio Sánchez, Clara I. Shetty, Shravya Summers, Ronald M. Taha, Abdel A. Tiulpin, Aleksei Tsaftaris, Sotirios A. van Calster, Ben Varoquaux, Gaël Yaniv, Ziv R. Jäger, Paul F. Maier-Hein, Lena Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Heidelberg Division of Intelligent Medical Systems Germany NCT Heidelberg A Partnership Between DKFZ University Medical Center Heidelberg Germany Heidelberg Division of Medical Image Computing Germany Heidelberg Division of Intelligent Medical Systems Germany MRC Unit for Lifelong Health and Ageing UCL Centre for Medical Image Computing Department of Computer Science University College London London United Kingdom School of Biomedical Engineering and Imaging Science King’s College London London United Kingdom Instituto de Cálculo CONICET – Universidad de Buenos Aires Buenos Aires Argentina Centre for Medical Image Computing University College London London United Kingdom McGill University Montreal Canada Division of Computational Pathology Dept of Pathology & Laboratory Medicine Indiana University School of Medicine IU Health Information and Translational Sciences Building Indianapolis United States University of Pennsylvania Richards Medical Research Laboratories FL7 PhiladelphiaPA United States Department of Digital Medical Technologies Holon Institute of Technology Holon Israel European Federation for Medical Informatics Le Mont-sur-Lausanne Switzerland Center for Processing Speech and Images Department of Electrical Engineering KU Leuven Leuven Belgium partner site Frankfurt/Mainz a partnership between DKFZ and UCT Frankfurt Marburg Germany Heidelberg Germany Goethe University Frankfurt Department of Medicine Germany Goethe University Frankfurt Department of Informatics Germany and Frankfurt Cancer Insititute Germany Department of Computer Science IT University of Copenhagen Copenhagen Denmark Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V. Dortmund Germany Imaging Platform Broad Institute of MIT and Harvard CambridgeMA United States Centre for Statistics in Medicine University of Oxford Oxford United Kingdom Center for Biomedical In

Validation metrics are key for tracking scientific progress and bridging the current chasm between artificial intelligence (AI) research and its translation into practice. However, increasing evidence shows that particularly in image analysis, metrics are often chosen inadequately. While taking into account the individual strengths, weaknesses, and limitations of validation metrics is a critical prerequisite to making educated choices, the relevant knowledge is currently scattered and poorly accessible to individual researchers. Based on a multi-stage Delphi process conducted by a multidisciplinary expert consortium as well as extensive community feedback, the present work provides the first reliable and comprehensive common point of access to information on pitfalls related to validation metrics in image analysis. While focused on biomedical image analysis, the addressed pitfalls generalize across application domains and are categorized according to a newly created, domain-agnostic taxonomy. The work serves to enhance global comprehension of a key topic in image analysis validation. © 2023, CC BY.

关键词： Computer vision

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Why is the Winner the Best?

Why is the Winner the Best?

引用

Conference on Computer Vision and Pattern Recognition (CVPR)

作者： M. Eisenmann A. Reinke V. Weru M. D. Tizabi F. Isensee T. J. Adler S. Ali V. Andrearczyk M. Aubreville U. Baid S. Bakas N. Balu S. Bano J. Bernal S. Bodenstedt A. Casella V. Cheplygina M. Daum M. De Bruijne A. Depeursinge R. Dorent J. Egger D. G. Ellis S. Engelhardt M. Ganz N. Ghatwary G. Girard P. Godau A. Gupta L. Hansen K. Harada M. Heinrich N. Heller A. Hering A. Huaulmé P. Jannin A. E. Kavur O. Kodym M. Kozubek J. Li H. Li J. Ma C. Martín-Isla B. Menze A. Noble V. Oreiller N. Padoy S. Pati K. Payette T. Rädsch J. Rafael-Patiño V. Singh Bawa S. Speidel C. H. Sudre K. Van Wijnen M. Wagner D. Wei A. Yamlahi M. H. Yap C. Yuan M. Zenk A. Zia D. Zimmerer D. Aydogan B. Bhattarai L. Bloch R. Brüngel J. Cho C. Choi Q. Dou I. Ezhov C. M. Friedrich C. Fuller R. R. Gaire A. Galdran Á. García Faura M. Grammatikopoulou S. Hong M. Jahanifar I. Jang A. Kadkhodamohammadi I. Kang F. Kofler S. Kondo H. Kuijf M. Li M. Luu T. Martinčič P. Morais M. A. Naser B. Oliveira D. Owen S. Pang J. Park S. Park S. Płotka E. Puybareau N. Rajpoot K. Ryu N. Saeed A. Shephard P. Shi D. Štepec R. Subedi G. Tochon H. R. Torres H. Urien J. L. Vilaça K. A. Wahid H. Wang J. Wang L. Wang X. Wang B. Wiestler M. Wodzinski F. Xia J. Xie Z. Xiong S. Yang Y. Yang Z. Zhao K. Maier-Hein P. F. Jäger A. Kopp-Schneider L. Maier-Hein Division of Intelligent Medical Systems German Cancer Research Center (DKFZ) Heidelberg Germany Helmholtz Imaging German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Division of Biostatistics German Cancer Research Center (DKFZ) Heidelberg Germany Division of Medical Image Computing German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Engineering and Physical Sciences School of Computing University of Leeds Leeds UK Institute of Informatics School of Management HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland Sierre Switzerland Department of Nuclear Medicine and Molecular Imaging Lausanne University Hospital Lausanne Switzerland Technische Hochschule Ingolstadt Ingolstadt Germany Center for Artificial Intelligence and Data Science for Integrated Diagnostics (AI2D) and Center for Biomedical Image Computing and Analytics (CBICA) University of Pennsylvania Philadelphia PA USA Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Department of Radiology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Department of Radiology University of Washington Seattle WA USA Department of Computer Science Wellcome/EPSRC Centre for Interventional and Surgical Sciences (WEISS) University College London London UK Universitat Autònoma de Barcelona & Computer Vision Center Barcelona Spain Division of Translational Surgical Oncology National Center for Tumor Diseases (NCT/UCC) Dresden Dresden Germany Department of Advanced Robotics Istituto Italiano di Tecnologia Italy Department of Electronics Information and Bioengineering Politecnico di Milano Milan Italy IT University of Copenhagen Copenhagen Denmark Department of General Visceral and Transplantation Surgery Heidelberg University Hospital Heidelberg Germany Department of Radiology and Nuc

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multicenter study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), image preprocessing (97%), data curation (79%), and post-processing (66%). The “typical” lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work.

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Metrics Reloaded: Recommendations for image analysis validation

arXiv

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arXiv 2022年

作者： Maier-Hein, Lena Reinke, Annika Godau, Patrick Tizabi, Minu D. Buettner, Florian Christodoulou, Evangelia Glocker, Ben Isensee, Fabian Kleesiek, Jens Kozubek, Michal Reyes, Mauricio Riegler, Michael A. Wiesenfarth, Manuel Emre Kavur, A. Sudre, Carole H. Baumgartner, Michael Eisenmann, Matthias Heckmann-Nötzel, Doreen Rädsch, Tim Acion, Laura Antonelli, Michela Arbel, Tal Bakas, Spyridon Benis, Arriel Blaschko, Matthew B. Jorge Cardoso, M. Cheplygina, Veronika Cimini, Beth A. Collins, Gary S. Farahani, Keyvan Ferrer, Luciana Galdran, Adrian Ginneken, Bram Van Haase, Robert Hashimoto, Daniel A. Hoffman, Michael M. Huisman, Merel Jannin, Pierre Kahn, Charles E. Kainmueller, Dagmar Kainz, Bernhard Karargyris, Alexandros Karthikesalingam, Alan Kenngott, Hannes Kofler, Florian Kopp-Schneider, Annette Kreshuk, Anna Kurc, Tahsin Landman, Bennett A. Litjens, Geert Madani, Amin Maier-Hein, Klaus Martel, Anne L. Mattson, Peter Meijering, Erik Menze, Bjoern Moons, Karel G.M. Müller, Henning Nichyporuk, Brennan Nickel, Felix Petersen, Jens Rajpoot, Nasir Rieke, Nicola Saez-Rodriguez, Julio Sánchez, Clara I. Shetty, Shravya Smeden, Maarten Van Summers, Ronald M. Taha, Abdel A. Tiulpin, Aleksei Tsaftaris, Sotirios A. Calster, Ben Van Varoquaux, Gaël Jäger, Paul F. Heidelberg Division of Intelligent Medical Systems and HI Helmholtz Imaging Germany Faculty of Mathematics and Computer Science and Medical Faculty Heidelberg University Heidelberg Germany NCT Heidelberg a partnership between DKFZ University Medical Center Heidelberg Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Heidelberg Division of Intelligent Medical Systems Germany partner site Frankfurt/Mainz a partnership between DKFZ and UCT Frankfurt-Marburg Germany Heidelberg Goethe University Frankfurt Germany Department of Medicine Goethe University Frankfurt Germany Department of Informatics Frankfurt Cancer Insititute Germany Department of Computing Imperial College London London United Kingdom Heidelberg Division of Medical Image Computing and HI Applied Computer Vision Lab Germany Institute for AI in Medicine University Medicine Essen Essen Germany Centre for Biomedical Image Analysis Faculty of Informatics Masaryk University Brno Czech Republic ARTORG Center for Biomedical Engineering Research University of Bern Bern Switzerland Department of Radiation Oncology University Hospital Bern University of Bern Bern Switzerland Simula Metropolitan Center for Digital Engineering Oslo Norway UiT The Arctic University of Norway Romsø Norway Heidelberg Division of Biostatistics Germany Heidelberg Division of Intelligent Medical Systems Division of Medical Image Computing HI Applied Computer Vision Lab Germany MRC Unit for Lifelong Health and Ageing UCL Centre for Medical Image Computing Department of Computer Science University College London London United Kingdom School of Biomedical Engineering and Imaging Science King’s College London London United Kingdom Heidelberg Division of Medical Image Computing Germany Instituto de Cálculo CONICET – Universidad de Buenos Aires Buenos Aires Argentina Centre for Medical Image Computing University College London London United Kingdom McGill University Montréal

Increasing evidence shows that flaws in machine learning (ML) algorithm validation are an underestimated global problem. Particularly in automatic biomedical image analysis, chosen performance metrics often do not reflect the domain interest, thus failing to adequately measure scientific progress and hindering translation of ML techniques into practice. To overcome this, we created Metrics Reloaded, a comprehensive framework guiding researchers in the problem-aware selection of metrics. It was developed by a large international consortium in a multi-stage Delphi process and is based on the novel concept of a problem fingerprint – a structured representation of the given problem that captures all aspects that are relevant for metric selection, from the domain interest to the properties of the target structure(s), data set and algorithm output. Based on the problem fingerprint, users are guided through the process of choosing and applying appropriate validation metrics while being made aware of potential pitfalls. Metrics Reloaded targets image analysis problems that can be interpreted as a classification task at image, object or pixel level, namely image-level classification, object detection, semantic segmentation, and instance segmentation tasks. To improve the user experience, we implemented the framework in the Metrics Reloaded online tool. Following the convergence of ML methodology across application domains, Metrics Reloaded fosters the convergence of validation methodology. Its applicability is demonstrated for various biomedical use cases. © 2022, CC BY.

关键词： Semantic Segmentation

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Functional Synthetic Biology

arXiv

引用

arXiv 2022年

作者： Aldulijan, Ibrahim Beal, Jacob Billerbeck, Sonja Bouffard, Jeff Chambonnier, Gaël Delkis, Nikolaos Guerreiro, Isaac Holub, Martin Ross, Paul Selvarajah, Vinoo Sprent, Noah Vidal, Gonzalo Vignoni, Alejandro Systems Engineering Stevens Institute of Technology 1 Castle Point Terrace HobokenNJ07030 United States Intelligent Software & Systems Raytheon BBN Technologies 10 Moulton Street CambridgeMA02138 United States Molecular Microbiology Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 7 Groningen9747 AG Netherlands Centre for Applied Synthetic Biology Department of Biology Concordia University 7141 Sherbrooke Street West MontréalQCH4B 1R6 Canada Department of Biological Engineering Massachusetts Institute of Technology CambridgeMA02139 United States Plant and Environmental Biotechnology Laboratory Department of Biochemistry and Biotechnology University of Thessaly Viopolis Mezourlo Larissa41500 Greece iGEM Foundation 45 Prospect Street CambridgeMA02139 United States Delft University of Technology Van der Maasweg 9 2629 HZ Netherlands BioStrat Marketing 9965 Harbour Lake Circle Boynton BeachFL33437 United States Department of Chemical Engineering Imperial College London South Kensington Campus Exhibition Road SW7 2AZ United Kingdom Research Group School of Computing Newcastle University Devonshire Building Devonshire Terrace Newcastle Upon TyneNE1 7RU United Kingdom Synthetic Biology and Biosystems Control Lab Instituto de Automatica e Informatica Industrial Universitat Politecnica de Valencia Camino de Vera s/n Valencia46022 Spain

Synthetic biologists have made great progress over the past decade in developing methods for modular assembly of genetic sequences and in engineering biological systems with a wide variety of functions in various contexts and organisms. However, current paradigms in the field entangle sequence and functionality in a manner that makes abstraction difficult, reduces engineering flexibility, and impairs predictability and design reuse. Functional Synthetic Biology aims to overcome these impediments by focusing the design of biological systems on function, rather than on sequence. This reorientation will decouple the engineering of biological devices from the specifics of how those devices are put to use, requiring both conceptual and organizational change, as well as supporting software tooling. Realizing this vision of Functional Synthetic Biology will allow more flexibility in how devices are used, more opportunity for reuse of devices and data, improvements in predictability, and reductions in technical risk and cost. © 2022, CC BY.

关键词： Biological systems

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