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DRAC: Diabetic Retinopathy Analysis Challenge with Ultra-Wide Optical Coherence Tomography Angiography Images

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arXiv 2023年

作者： Qian, Bo Chen, Hao Wang, Xiangning Che, Haoxuan Kwon, Gitaek Kim, Jaeyoung Choi, Sungjin Shin, Seoyoung Krause, Felix Unterdechler, Markus Hou, Junlin Feng, Rui Li, Yihao Daho, Mostafa El Habib Wu, Qiang Zhang, Ping Yang, Xiaokang Cai, Yiyu Li, Huating Jia, Weiping Sheng, Bin Department of Computer Science and Engineering Shanghai Jiao Tong University Shanghai China Department of Computer Science and Engineering The Hong Kong University of Science and Technology Hong Kong Department of Chemical and Biological Engineering The Hong Kong University of Science and Technology Hong Kong Department of Ophthalmology Shanghai Jiao Tong University Affiliated Sixth People’s Hospital Shanghai China VUNO Inc. Seoul Korea Republic of AI/DX Convergence Business Group KT Korea Republic of Johannes Kepler University Linz Linz Austria School of Computer Science Shanghai Key Laboratory of Intelligent Information Processing Fudan University China Academy for Engineering and Technology Fudan University China LaTIM UMR 1101 Inserm Brest France University of Western Brittany Brest France Department of Computer Science and Engineering The Ohio State University Ohio United States Department of Biomedical Informatics The Ohio State University Ohio United States Translational Data Analytics Institute The Ohio State University Ohio United States MoE Key Lab of Artificial Intelligence Artificial Intelligence Institute Shanghai Jiao Tong University Shanghai China School of Mechanical and Aerospace Engineering Nanyang Technological University Singapore Department of Endocrinology and Metabolism Shanghai Jiao Tong University Affiliated Sixth People’s Hospital Shanghai China Shanghai Diabetes Institute Shanghai Clinical Center for Diabetes Shanghai China

computer-assisted automatic analysis of diabetic retinopathy (DR) is of great importance in reducing the risks of vision loss and even blindness. Ultra-wide optical coherence tomography angiography (UW-OCTA) is a non-invasive and safe imaging modality in DR diagnosis system, but there is a lack of publicly available benchmarks for model development and evaluation. To promote further research and scientific benchmarking for diabetic retinopathy analysis using UW-OCTA images, we organized a challenge named "DRAC - Diabetic Retinopathy Analysis Challenge" in conjunction with the 25th International Conference on Medical Image Computing and computer Assisted Intervention (MICCAI 2022). The challenge consists of three tasks: segmentation of DR lesions, image quality assessment and DR grading. The scientific community responded positively to the challenge, with 11, 12, and 13 teams from geographically diverse institutes submitting different solutions in these three tasks, respectively. This paper presents a summary and analysis of the top-performing solutions and results for each task of the challenge. The obtained results from top algorithms indicate the importance of data augmentation, model architecture and ensemble of networks in improving the performance of deep learning models. These findings have the potential to enable new developments in diabetic retinopathy analysis. The challenge remains open for post-challenge registrations and submissions for benchmarking future methodology developments. Copyright © 2023, The Authors. All rights reserved.

关键词： Optical tomography

A Secure Federated data-Driven Evolutionary Multi-objective Optimization Algorithm

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arXiv 2022年

作者： Liu, Qiqi Yan, Yuping Ligeti, Péter Jin, Yaochu Trustworthy and General AI Lab School of Engineering Westlake University China Faculty of Technology Bielefeld University Bielefeld33619 Germany Faculty of Informatics Department of Computeralgebra Eötvös Loránd University Hungary Smart Data Group E-Group ICT Software Zrt Hungary Department of Computer Science University of Surrey Surrey GuildfordGU2 7XH United Kingdom

data-driven evolutionary algorithms usually aim to exploit the information behind a limited amount of data to perform optimization, which have proved to be successful in solving many complex real-world optimization problems. However, most data-driven evolutionary algorithms are centralized, causing privacy and security concerns. Existing federated Bayesian optimization algorithms and data-driven evolutionary algorithms mainly protect the raw data on each client. To address this issue, this paper proposes a secure federated data-driven evolutionary multiobjective optimization algorithm to protect both the raw data and the newly infilled solutions obtained by optimizing the acquisition function conducted on the server. We select the query points on a randomly selected client at each round of surrogate update by calculating the acquisition function values of the unobserved points on this client, thereby reducing the risk of leaking the information about the solution to be sampled. In addition, since the predicted objective values of each client may contain sensitive information, we mask the objective values with Diffie-Hellman-based noise, and then send only the masked objective values of other clients to the selected client via the server. Since the calculation of the acquisition function also requires both the predicted objective value and the uncertainty of the prediction, the predicted mean objective and uncertainty are normalized to reduce the influence of noise. Experimental results on a set of widely used multi-objective optimization benchmarks show that the proposed algorithm can protect privacy and enhance security with only negligible sacrifice in the performance of federated data-driven evolutionary optimization. Copyright © 2022, The Authors. All rights reserved.

关键词： Evolutionary algorithms

Towards Faster Fully Homomorphic Encryption Implementation with Integer and Floating-point Computing Power of GPUs

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Towards Faster Fully Homomorphic Encryption Implementation w...

International Symposium on Parallel and Distributed Processing (IPDPS)

作者： Guang Fan Fangyu Zheng Lipeng Wan Lili Gao Yuan Zhao Jiankuo Dong Yixuan Song Yuewu Wang Jingqiang Lin State Key Laboratory of Information Security Institute of Information Engineering Chinese Academy of Sciences Beijing China School of Cyber Security University of Chinese Academy of Sciences Beijing China Data Assurance and Communication Security Research Center Chinese Academy of Sciences Beijing China School of Cryptography University of Chinese Academy of Sciences Beijing China Department of Computer and Software Nanjing University of Information Science and Technology Nanjing China Ant Group Hangzhou China School of Computer Science Nanjing University of Posts and Telecommunications Nanjing China School of Cyber Security University of Science and Technology of China Hefei China

Fully Homomorphic Encryption (FHE) allows computations on encrypted data without knowledge of the plaintext message and currently has been the focus of both academia and industry. However, the performance issue hinders its large-scale application, highlighting the urgent requirements of high-performance FHE *** noticing the tremendous potential of GPUs in the field of cryptographic acceleration, this paper comprehensively investigates how to convert the available computing resources residing in GPUs into FHE workhorses, and implement a full set of low-level and middle-level FHE primitives based on two arithmetic units (i.e., INT32 and FP64 units) with three types of data precision (i.e., INT32, INT64 and FP64). This paper gives a comprehensive evaluation and comparison based on each road-map. Our implementations of fundamental functions outperform the implementations on the same platform by 1.7× to 16.7×. Taking CKKS FHE schemes as a case study, our implementation of homomorphic multiplication achieves 3.2× speedup over the state-of-the-art GPU-based implementation, even considering the difference of platforms. The detailed evaluation and comparison of this paper would offer a vital reference for the follow-up work to choose appropriate underlying arithmetic units and important primitive optimizations in GPU-based FHE implementations.

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Adaptive Information Bottleneck Guided Joint Source and Channel Coding for Image Transmission

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arXiv 2022年

作者： Sun, Lunan Yang, Yang Chen, Mingzhe Guo, Caili Saad, Walid Poor, H. Vincent The Beijing Key Laboratory of Network System Architecture and Convergence School of Information and Communication Engineering Beijing University of Posts and Telecommunications Beijing100876 China The Department of Electrical and Computer Engineering Institute for Data Science and Computing University of Miami Coral GablesFL33146 United States The Beijing Laboratory of Advanced Information Net works School of Information and Communication Engineering Beijing University of Posts and Telecommunications Beijing100876 China The Wireless@VT Group Bradley Department of Electrical and Computer Engineering Virginia Tech ArlingtonVA United States The Department of Electrical and Computer Engineering Princeton University PrincetonNJ08544 United States

Joint source and channel coding (JSCC) for image transmission has attracted increasing attention due to its robustness and high efficiency. However, the existing deep JSCC research mainly focuses on minimizing the distortion between the transmitted and received information under a fixed number of available channels. Therefore, the transmitted rate may be far more than its required minimum value. In this paper, an adaptive information bottleneck (IB) guided joint source and channel coding (AIB-JSCC) method is proposed for image transmission. The goal of AIB-JSCC is to reduce the transmission rate while improving the image reconstruction quality. In particular, a new IB objective for image transmission is proposed so as to minimize the distortion and the transmission rate. A mathematically tractable lower bound on the proposed objective is derived, and then, adopted as the loss function of AIB-JSCC. To trade off compression and reconstruction quality, an adaptive algorithm is proposed to adjust the hyperparameter of the proposed loss function dynamically according to the distortion during the training. Experimental results show that AIB-JSCC can significantly reduce the required amount of transmitted data and improve the reconstruction quality and downstream task accuracy. Copyright © 2022, The Authors. All rights reserved.

关键词： Economic and social effects

Superpixel and Density Based Region Segmentation Algorithm for Lung Nodule Detection

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Superpixel and Density Based Region Segmentation Algorithm f...

IEEE Calcutta Conference (CALCON)

作者： Amitava Halder Saptarshi Chatterjee Debangshu Dey Computer Science and Engineering Department Supreme Knowledge Foundation Group of Institutions Hooghly India Electrical Engineering Department Jadavpur University Kolkata India

ISBN: (数字)9781728142838

ISBN: (纸本)9781728153629

Lung nodule detection and segmentation plays an important role in early cancer diagnosis. It is a challenging task owing to the shape and intensity variations of a lung nodule. This paper reports an efficient nodule detection framework in High- Resolution Computed Tomography (HRCT) images. Here, an automated computer-aided lung nodule detection scheme is proposed, combining the concept of superpixel generation and density-based region segmentation algorithm, Superpixel Density-Based Region segmentation (SPDBR). A set of morphological features are extracted from each of the extracted nodule regions. The nodule candidate regions have been classified into the nodule and non-nodule decision using a nonlinear support vector machine (SVM) classifier with an average detection accuracy of 84.75% with 82.86% sensitivity and 86.62% specificity.

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GaNDLF-Synth: A Framework to Democratize Generative AI for (Bio)Medical Imaging

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arXiv 2024年

作者： Pati, Sarthak Mazurek, Szymon Bakas, Spyridon Division of Computational Pathology Department of Pathology and Laboratory Medicine Indiana University School of Medicine IndianapolisIN United States Center for Federated Learning Indiana University School of Medicine IndianapolisIN United States Medical Working Group MLCommons San FranciscoCA United States AGH University of Krakow Academic Computer Centre Cyfronet Krakow Poland Indiana University Melvin and Bren Simon Comprehensive Cancer Center IndianapolisIN United States Department of Radiology & Imaging Sciences Indiana University School of Medicine IndianapolisIN United States Department of Biostatistics & Health Data Science Indiana University School of Medicine IndianapolisIN United States Department of Neurological Surgery Indiana University School of Medicine IndianapolisIN United States Department of Computer Science Luddy School of Informatics Computing and Engineering Indiana University IndianapolisIN United States

Generative Artificial Intelligence (GenAI) is a field of AI that creates new data samples from existing ones. It utilizing deep learning to overcome the scarcity and regulatory constraints of healthcare data by generating new data points that integrate seamlessly with original datasets. This paper explores the background and motivation for GenAI, and introduces the Generally Nuanced Deep Learning Framework for Synthesis (GaNDLF-Synth) to address a significant gap in the literature and move towards democratizing the implementation and assessment of image synthesis tasks in healthcare. GaNDLF-Synth describes a unified abstraction for various synthesis algorithms, including autoencoders, generative adversarial networks, and diffusion models. Leveraging the GANDLF-core framework, it supports diverse data modalities and distributed computing, ensuring scalability and reproducibility through extensive unit testing. The aim of GaNDLF-Synth is to lower the entry barrier for GenAI, and make it more accessible and extensible by the wider scientific community. © 2024, CC BY.

关键词： Generative adversarial networks

A hybrid model for post-treatment mortality rate classification of patients with breast cancer

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Healthcare Analytics 2023年 4卷 100254-100254页

作者： Folorunso, Sakinat Oluwabukonla Awotunde, Joseph Bamidele Adigun, Adepeju Abeke Prasad, L.V. Narasimha Lalitha, Vuyyuru Lakshmi Department of Mathematical Sciences Olabisi Onabanjo University Ogun State Ago-Iwoye Nigeria Artificial Intelligent Systems Research Group (ArISRG) Department of Mathematical Sciences Olabisi Onabanjo University Ago-iwoye Nigeria Department of Computer Science Faculty of Information and Communication Sciences University of Ilorin Ilorin 240003 Nigeria Department of Information and Communication Technology Osun State University Osogbo Nigeria Department of CSE Institute of Aeronautical Engineering Hyderabad India Department of Artificial Intelligence and Data Science Koneru Lakshmaiah Education Foundation India

Terminal cancer is not curable and eventually results in death. Breast cancer (BC) is a prevalent malignancy affecting women. Although there are prognostic indicators, BC prognosis is still challenging because of the intricate connections between various survival factors and influencing factors. This study proposes an ensemble classifier for predicting BC survivability using a new BC post-treatment dataset for the number of survivals. However, the classes survival cases dataset for BC is skewed, which caused a sub-optimal classification performance. Hence, a hybrid sampling scheme of Synthetic Minority Over-Sampling TEchnique (SMOTE) and Wilson's Edited Nearest Neighbor (ENN) is employed to treat the class imbalance in the dataset. Random Forest (RF) ensemble classifier is for classifying the dataset. The proposed framework performs well in terms of accuracy, recall of the two classes, Receiver Operating Characteristics (ROC) and Kappa Statistic (KS) metric on the dataset. The results demonstrated that the RF, with 97.0% accuracy on the holdout sample, is the best predictor. This prediction accuracy is superior to any noted in the literature, compared with Logistic Regression (LR) and Bagging classifiers. © 2023 The Authors

关键词： Breast cancer Class imbalance Ensemble learners Machine learning Random forest Sampling

Recording provenance of workflow runs with RO-Crate

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arXiv 2023年

作者： Leo, Simone Crusoe, Michael R. Rodríguez-Navas, Laura Sirvent, Raül Kanitz, Alexander De Geest, Paul Wittner, Rudolf Pireddu, Luca Garijo, Daniel Fernández, José M. Colonnelli, Iacopo Gallo, Matej Ohta, Tazro Suetake, Hirotaka Capella-Gutierrez, Salvador de Wit, Renske Kinoshita, Bruno P. Soiland-Reyes, Stian CA Pula Italy Vrije Universiteit Amsterdam Amsterdam Netherlands DTL Projects Netherlands Forschungszentrum Jülich Germany Barcelona Supercomputing Center Barcelona Spain Biozentrum University of Basel Basel Switzerland Swiss Institute of Bioinformatics Lausanne Switzerland VIB Data Core Gent Belgium Faculty of Informatics Masaryk University Brno Czech Republic Institute of Computer Science Masaryk University Brno Czech Republic BBMRI-ERIC Graz Austria Ontology Engineering Group Universidad Politécnica de Madrid Madrid Spain Computer Science Department Università degli Studi di Torino Torino Italy Database Center for Life Science Joint Support-Center for Data Science Research Research Organization of Information and Systems Shizuoka Japan Institute for Advanced Academic Research Chiba University Chiba Japan Sator Incorporated Tokyo Japan Department of Computer Science The University of Manchester Manchester United Kingdom Informatics Institute University of Amsterdam Amsterdam Netherlands

Recording the provenance of scientific computation results is key to the support of traceability, reproducibility and quality assessment of data products. Several data models have been explored to address this need, providing representations of workflow plans and their executions as well as means of packaging the resulting information for archiving and sharing. However, existing approaches tend to lack interoperable adoption across workflow management systems. In this work we present Workflow Run RO-Crate, an extension of RO-Crate (Research Object Crate) and *** to capture the provenance of the execution of computational workflows at different levels of granularity and bundle together all their associated objects (inputs, outputs, code, etc.). The model is supported by a diverse, open community that runs regular meetings, discussing development, maintenance and adoption aspects. Workflow Run RO-Crate is already implemented by several workflow management systems, allowing interoperable comparisons between workflow runs from heterogeneous systems. We describe the model, its alignment to standards such as W3C PROV, and its implementation in six workflow systems. Finally, we illustrate the application of Workflow Run RO-Crate in two use cases of machine learning in the digital image analysis domain. © 2023, CC BY.

关键词： Workflow management

CloudBrain-NMR: An Intelligent Cloud Computing Platform for NMR Spectroscopy Processing, Reconstruction and Analysis

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arXiv 2023年

作者： Guo, Di Li, Sijin Liu, Jun Tu, Zhangren Qiu, Tianyu Xu, Jingjing Feng, Liubin Lin, Donghai Hong, Qing Lin, Meijin Lin, Yanqin Qu, Xiaobo School of Computer and Information Engineering Fujian Engineering Research Center for Medical Data Mining and Application Xiamen University of Technology Xiamen361024 China Department of Electronic Science Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance Xiamen University Xiamen361005 China The Key Laboratory for Chemical Biology of Fujian Province MOE Key Laboratory of Spectrochemical Analysis & Instrumentation College of Chemistry and Chemical Engineering Xiamen University Xiamen361005 China Department of Applied Marine Physics and Engineering College of Ocean and Earth Sciences Xiamen University Xiamen361102 China The China Mobile Group Xiamen361005 China

Nuclear Magnetic Resonance (NMR) spectroscopy has served as a powerful analytical tool for studying molecular structure and dynamics in chemistry and biology. However, the processing of raw data acquired from NMR spectrometers and subsequent quantitative analysis involves various specialized tools, which necessitates comprehensive knowledge in programming and NMR. Particularly, the emerging deep learning tools is hard to be widely used in NMR due to the sophisticated setup of computation. Thus, NMR processing is not an easy task for chemist and biologists. In this work, we present CloudBrain-NMR, an intelligent online cloud computing platform designed for NMR data reading, processing, reconstruction, and quantitative analysis. The platform is conveniently accessed through a web browser, eliminating the need for any program installation on the user side. CloudBrain-NMR uses parallel computing with graphics processing units and central processing units, resulting in significantly shortened computation time. Furthermore, it incorporates state-of-the-art deep learning-based algorithms offering comprehensive functionalities that allow users to complete the entire processing procedure without relying on additional software. This platform has empowered NMR applications with advanced artificial intelligence processing. CloudBrain-NMR is openly accessible for free usage at https://***/***. © 2023, CC BY.

关键词： Deep learning