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A pretrained transformer model for decoding individual glucose dynamics from continuous glucose monitoring data

National science Review 2025年第5期 362-381页

作者： Yurun Lu Dan Liu Zhongming Liang Rui Liu Pei Chen Yitong Liu Jiachen Li Zhanying Feng Lei M.Li Bin Sheng Weiping Jia Luonan Chen Huating Li Yong Wang Center for Excellence in Mathematical Sciences National Center for Mathematics and Interdisciplinary Sciences Hua Loo-Keng Center for Mathematical Sciences Key Laboratory of Management Decision and Information System Academy of Mathematics and Systems ScienceChinese Academy of Sciences School of Mathematics University of Chinese Academy of SciencesChinese Academy of Sciences Department of Endocrinology and Metabolism Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai Diabetes InstituteShanghai Clinical Center for Diabetes Shanghai Key Laboratory of Diabetes Mellitus Key Laboratory of Systems Health Science of Zhejiang Province School of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of Sciences BGI-Research School of Mathematics South China University of Technology Department of Statistics Department of Biomedical Data Science Bio-X ProgramStanford University Department of Computer Science and Engineering Shanghai Jiao Tong University State Key Laboratory of Cell Biology Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of Sciences Guangdong Institute of Intelligence Science and Technology Pazhou Laboratory (Huangpu)

Continuous glucose monitoring(CGM) technology has grown rapidly to track real-time blood glucose levels and trends with improved sensor accuracy. The ease of use and wide availability of CGM will facilitate safe and effective decision making for diabetes management. Here, we developed an attention-based deep learning model, CGMformer, pretrained on a well-controlled and diverse corpus of CGM data to represent individual's intrinsic metabolic state and enable clinical applications. During pretraining, CGMformer encodes glucose dynamics including glucose level, fluctuation, hyperglycemia, and hypoglycemia into latent space with self-supervised learning. It shows generalizability in imputing glucose value across five external datasets with different populations and metabolic states(MAE = 3.7 mg/d L). We then fine-tuned CGMformer towards a diverse panel of downstream tasks in the screening of diabetes and its complications using task-specific data, which demonstrated a consistently boosted predictive accuracy over direct fine-tuning on a single task(AUROC = 0.914 for type 2 diabetes(T2D) screening and 0.741 for complication screening). By learning an intrinsic representation of an individual's glucose dynamics,CGMformer classifies non-diabetic individuals into six clusters with elevated T2D risks, and identifies a specific cluster with lean body-shape but high risk of glucose metabolism disorders, which is overlooked by traditional glucose measurements. Furthermore, CGMformer achieves high accuracy in predicting an individual's postprandial glucose response with dietary modelling(Pearson correlation coefficient = 0.763)and helps personalized dietary recommendations. Overall, CGMformer pretrains a transformer neural network architecture to learn an intrinsic representation by borrowing information from a large amount of daily glucose profiles, and demonstrates predictive capabilities fine-tuned towards a broad range of downstream applications, holding promise for the ear

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A Cybersecurity Detection Platform Integrating IOTA DLT and IPFS for Vulnerability Management

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Electronics 2025年第10期14卷 1929-1929页

作者： Iuon-Chang Lin Jyun-Yan Ruan Ching-Chun Chang Chin-Chen Chang Chun-Tse Wang Department of Management Information Systems National Chung Hsing University Taichung 40227 Taiwan Information and Communication Security Research Center Feng Chia University Taichung 40724 Taiwan Department of Information Engineering and Computer Science Feng Chia University Taichung 40724 Taiwan Ph.D. Program for Infrastructure Planning and Engineering Feng Chia University Taichung 40724 Taiwan

In response to the Cybersecurity Law, organizations face numerous management and technical requirements. Detection techniques such as vulnerability scanning and penetration testing are employed to identify risks. Addressing these vulnerabilities demands substantial manpower, time, and financial resources. Security concerns also arise during digital file transmission and remediation efforts. This study proposes a security detection platform with step-by-step implementation guidelines, enabling resource-limited units to replicate the setup and address security gaps. It compares detection results between open-source and commercial tools, highlighting key differences and offering remediation strategies. Numerous digital files (e.g., test reports) are generated during testing. To ensure secure storage and sharing, the system integrates IOTA’s distributed ledger and IPFS, generating HASH values and uploading files on-chain to preserve integrity and authenticity. The objective is to deliver a scalable, cost-effective security detection framework that enhances system resilience while minimizing resource consumption.

关键词： blockchain information security IOTA IPFS

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EXPPO: EXecution Performance Profiling and Optimization for CPS Co-simulation-as-a-Service

EXPPO: EXecution Performance Profiling and Optimization for ...

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International Symposium on Object-Oriented Real-Time Distributed Computing

作者： Yogesh D. Barve Himanshu Neema Zhuangwei Kang Hongyang Sun Aniruddha Gokhale Thomas Roth Department of Electrical Engineering and Computer Science Vanderbilt University Nashville TN USA Smart Grid and Cyber-Physical Systems Program Office Engineering Laboratory National Institute of Standards and Technology Gaithersburg MD USA

ISBN: (数字)9781728169583

ISBN: (纸本)9781728169590

A co-simulation may comprise several heterogeneous federates with diverse spatial and temporal execution characteristics. In an iterative time-stepped simulation, a federation exhibits the Bulk Synchronous Parallel (BSP) computation paradigm in which all federates perform local operations and synchronize with their peers before proceeding to the next round of computation. In this context, the lowest performing (i.e., slowest) federate dictates the progression of the federation logical time. One challenge in co-simulation is performance profiling for individual federates and entire federations. The computational resource assignment to the federates can have a large impact on federation performance. Furthermore, a federation may comprise federates located on different physical machines as is the case for cloud and edge computing environments. As such, distributed profiling and resource assignment to the federation is a major challenge for operationalizing the co-simulation execution at scale. This paper presents the Execution Performance Profiling and Optimization (EXPPO) methodology, which addresses these challenges by using execution performance profiling at each simulation execution step and for every federate in a federation. EXPPO uses profiling to learn performance models for each federate, and uses these models in its federation resource recommendation tool to solve an optimization problem that improves the execution performance of the co-simulation. Using an experimental testbed, the efficacy of EXPPO is validated to show the benefits of performance profiling and resource assignment in improving the execution runtimes of co-simulations while also minimizing the execution cost.

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Development of hydroxyapatite-enhanced membrane for nanoplastics removal: Multiple scenarios and mechanism exploration

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Journal of hazardous materials 2025年 495卷 138781页

作者： Mengna Li Guohe Huang Shuguang Wang Jing Huang Zeyuan Xu Environmental Systems Engineering Program University of Regina Regina Saskatchewan S4S 0A2 Canada China-Canada Center of Energy Environment and Sustainability Research UR-SDU School of Environmental Science and Engineering Shandong University Qingdao 266237 China. China-Canada Center of Energy Environment and Sustainability Research UR-SDU School of Environmental Science and Engineering Shandong University Qingdao 266237 China. Electronic address: huangg@uregina.ca. Shandong Key Laboratory of Water Pollution Control and Resource Reuse School of Environmental Science and Engineering Shandong University Qingdao 266237 China. Environmental Systems Engineering Program University of Regina Regina Saskatchewan S4S 0A2 Canada. Department of Electrical Computer and Biomedical Engineering University of Pavia Pavia 27100 Italy.

Nanoplastics (NPs) are widespread in wastewater systems and more toxic than microplastics (MPs), necessitating effective removal techniques. Although membranes can effectively remove MPs, their efficiency and mechanisms for NPs removal require further study. A novel hydroxyapatite functionalized PVDF (HAPF) membrane was developed for NPs removal. The optimized HAPF membrane was prepared via a one-step method with 800 mg/L HAP at pH 7.3 for 8 hours. It achieved a water flux of 4376.44 LMH, 3.4 times higher than that of the pristine PVDF membrane, while maintaining a polystyrene (PS) NPs rejection above 99.5 %. The HAPF membrane maintained 95 % of its pure water flux when treating wastewater with only PS NPs, but exhibited severe flux decline under varying conditions, such as surface-functionalized PS NPs, pH changes, or coexisting contaminants. Among these, the presence of MgSO alongside PS NPs caused the most severe water flux reduction, with the HAPF membrane undergoing complete blocking, followed by the formation of a cake layer. XDLVO results revealed that there is an attractive interaction between the HAPF membrane and PS NPs, primarily driven by acid-base interaction. The HAPF membrane exhibited significantly lower R and R values than the PVDF membrane and achieved a flux recovery rate of 92.94 % over multiple fouling-cleaning cycles. Its water flux was 18.9 times that of the PVDF membrane during long-term filtration. The developed HAPF membrane holds significant potential for advanced water treatment and fouling resistance .

关键词： Coexisting pollutants Hermia theory Hydroxyapatite functionalized PVDF (HAPF) membrane Nanoplastic removal XDLVO theory

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A Consensus Privacy Metrics Framework for Synthetic Data

arXiv

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arXiv 2025年

作者： Pilgram, Lisa Dankar, Fida K. Drechsler, Jörg Elliot, Mark Domingo-Ferrer, Josep Francis, Paul Kantarcioglu, Murat Kong, Linglong Malin, Bradley Muralidhar, Krishnamurty Myles, Puja Prasser, Fabian Raisaro, Jean Louis Yan, Chao El Emam, Khaled School of Epidemiology and Public Health University of Ottawa ON Canada CHEO Research Institute ON Canada Department of Nephrology and Medical Intensive Care Charité – Universitätsmedizin Berlin Berlin Germany Department for Statistical Methods Institute for Employment Research Nuernberg Germany Institute for Statistics Ludwig-Maximilians-Universität Munich Germany Joint Program in Survey Methodology University of Maryland United States The Cathie Marsh Institute Research School of Social Sciences University of Manchester Manchester United Kingdom Department of Computer Engineering and Mathematics Universitat Rovira i Virgili Catalonia Tarragona Spain Max Planck Institute for Software Systems Germany Department of Computer Science Virginia Tech United States Department of Mathematical and Statistical Sciences University of Alberta Alberta Canada Department of Biomedical Informatics Vanderbilt University Medical Center NashvilleTN United States Department of Biostatistics Vanderbilt University Medical Center NashvilleTN United States Department of Computer Science Vanderbilt University NashvilleTN United States Department of Marketing and Supply Chain Management University of Oklahoma Oklahoma United States Medicines and Healthcare products Regulatory Agency London United Kingdom Berlin Institute of Health at Charité Universitätsmedizin Berlin Medical Informatics Group Berlin Germany Biomedical Data Science Center University Hospital Lausanne Lausanne Switzerland

Synthetic data generation is one approach for sharing individual-level data. However, to meet legislative requirements, it is necessary to demonstrate that the individuals’ privacy is adequately protected. There is no consolidated standard for measuring privacy in synthetic data. Through an expert panel and consensus process, we developed a framework for evaluating privacy in synthetic data. Our findings indicate that current similarity metrics fail to measure identity disclosure, and their use is discouraged. For differentially private synthetic data, a privacy budget other than close to zero was not considered interpretable. There was consensus on the importance of membership and attribute disclosure, both of which involve inferring personal information about an individual without necessarily revealing their identity. The resultant framework provides precise recommendations for metrics that address these types of disclosures effectively. Our findings further present specific opportunities for future research that can help with widespread adoption of synthetic data. © 2025, CC BY.

关键词： Differential privacy

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Unifying femtosecond and picosecond single-pulse magnetic switching in Gd-Fe-Co

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Physical Review B 2021年第10期103卷 104422-104422页

作者： F. Jakobs T. A. Ostler C.-H. Lambert Y. Yang S. Salahuddin R. B. Wilson J. Gorchon J. Bokor U. Atxitia Dahlem Center for Complex Quantum Systems and Fachbereich Physik Freie Universität Berlin 14195 Berlin Germany Département de Physique Universitè de Liége (B5) B-4000 Liége Belgium College of Business Technology and Engineering Sheffield Hallam University Howard Street Sheffield S1 1WB United Kingdom Department of Electrical Engineering and Computer Sciences University of California Berkeley California 94720 USA Department of Materials Science and Engineering University of California Berkeley California 94720 USA Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley California 94720 USA Department of Mechanical Engineering and Materials Science and Engineering Program University of California Riverside California 92521 USA

Many questions are still open regarding the physical mechanisms behind the magnetic switching in Gd-Fe-Co alloys by single optical pulses. Phenomenological models suggest a femtosecond scale exchange relaxation between sublattice magnetization as the driving mechanism for switching. The recent observation of thermally induced switching in Gd-Fe-Co by using both several picosecond optical laser pulse as well as electric current pulses has questioned this previous understanding. This has raised the question of whether or not the same switching mechanics are acting at the femtosecond and picosecond scales. In this work, we aim at filling this gap in the understanding of the switching mechanisms behind thermal single-pulse switching. To that end, we have studied experimentally thermal single-pulse switching in Gd-Fe-Co alloys, for a wide range of system parameters, such as composition, laser power, and pulse duration. We provide a quantitative description of the switching dynamics using atomistic spin dynamics methods with excellent agreement between the model and our experiments across a wide range of parameters and timescales, ranging from femtoseconds to picoseconds. Furthermore, we find distinct element-specific damping parameters as a key ingredient for switching with long picosecond pulses and argue that switching with pulse durations as long as 15 ps is possible due to a low damping constant of Gd. Our findings can be easily extended to speed up dynamics in other contexts where ferrimagnetic Gd-Fe-Co alloys have been already demonstrated to show fast and energy-efficient processes, e.g., domain-wall motion in a track and spin-orbit torque switching in spintronics devices.

关键词： Demagnetization Magnetic interactions Magnetic order Magnetism Spin dynamics Ultrafast magnetic effects

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Charge and Energy Transfer Dynamics of Hybridized Exciton-Polaritons in 2D Halide Perovskites

arXiv

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arXiv 2023年

作者： Anantharaman, Surendra B. Lynch, Jason Stevens, Christopher E. Munley, Christopher Li, Chentao Hou, Jin Zhang, Hao Torma, Andrew Darlington, Thomas Coen, Francis Li, Kevin Majumdar, Arka Schuck, P. James Mohite, Aditya Harutyunyan, Hayk Hendrickson, Joshua R. Jariwala, Deep Department of Electrical and Systems Engineering University of Pennsylvania PhiladelphiaPA19104 United States KBR Inc. BeavercreekOH45431 United States Air Force Research Laboratory Sensors Directorate Wright-Patterson Air Force Base OH45433 United States Department of Physics University of Washington SeattleWA98195 United States Department of Physics Emory University AtlantaGA30322 United States Department of Chemical and Biomolecular Engineering Rice University HoustonTX77005 United States Department of Materials Science and Nanoengineering Rice University HoustonTX77005 United States Applied Physics Program Smalley‐Curl Institute Rice University HoustonTX77005 United States Department of Mechanical Engineering Columbia University New YorkNY10027 United States Department of Electrical and Computer Engineering University of Washington SeattleWA98195 United States

Excitons, bound electron-hole pairs, in Two-Dimensional Hybrid Organic Inorganic Perovskites (2D HOIPs) are capable of forming hybrid light-matter states known as exciton-polaritons (E-Ps) when the excitonic medium is confined in an optical cavity. In the case of 2D HOIPs, they can self-hybridize into E-Ps at specific thicknesses of the HOIP crystals that form a resonant optical cavity with the excitons. However, the fundamental properties of these self-hybridized E-Ps in 2D HOIPs, including their role in ultrafast energy and/or charge transfer at interfaces, remain unclear. Here, we demonstrate that > 0.5 µm thick 2D HOIP crystals on Au substrates are capable of supporting multiple-orders of self-hybridized E-P modes. These E-Ps have high Q factors (> 100) and modulate the optical dispersion for the crystal to enhance sub-gap absorption and emission. Through varying excitation energy and ultrafast measurements, we also confirm energy transfer from higher energy upper E-Ps to lower energy, lower E-Ps. Finally, we also demonstrate that E-Ps are capable of charge transport and transfer at interfaces. Our findings provide new insights into charge and energy transfer in E-Ps opening new opportunities towards their manipulation for polaritonic devices. © 2023, CC BY.

关键词： Charge transfer

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Interpretable Symbolic Regression for Data science: Analysis of the 2022 Competition

arXiv

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arXiv 2023年

作者： de Franca, F.O. Virgolin, M. Kommenda, M. Majumder, M.S. Cranmer, M. Espada, G. Ingelse, L. Fonseca, A. Landajuela, M. Petersen, B. Glatt, R. Mundhenk, N. Lee, C.S. Hochhalter, J.D. Randall, D.L. Kamienny, P. Zhang, H. Dick, G. Simon, A. Burlacu, B. Kasak, Jaan Machado, Meera Wilstrup, Casper La Cava, W.G. Federal University of ABC Santo Andre Brazil Evolutionary Intelligence Group Centrum Wiskunde & Informatica Science Park 123 Amsterdam Netherlands Computational Health Informatics Program Boston Children's Hospital Harvard Medical School Boston United States University of Applied Sciences Upper Austria Hagenberg Austria Center for Computational Astrophysics Flatiron Institute Department of Astrophysical Sciences Princeton University United States LASIGE Faculdade de Ciências Universidade de Lisboa Lisboa Portugal Computational Engineering Division Lawrence Livermore National Laboratory Livermore United States University of Utah Department of Mechanical Engineering Utah United States Meta FAIR France Victoria University of Wellington School of Engineering and Computer Science New Zealand University of otago Department of Information Science New Zealand Institut für Angewandte Physik Universität Tübingen Max Planck Institute for Intelligent Systems Tübingen Germany Abzu AI Orient Plads 1 Nordhavn 2150 Denmark

Symbolic regression searches for analytic expressions that accurately describe studied phenomena. The main attraction of this approach is that it returns an interpretable model that can be insightful to users. Historically, the majority of algorithms for symbolic regression have been based on evolutionary algorithms. However, there has been a recent surge of new proposals that instead utilize approaches such as enumeration algorithms, mixed linear integer programming, neural networks, and Bayesian optimization. In order to assess how well these new approaches behave on a set of common challenges often faced in real-world data, we hosted a competition at the 2022 Genetic and Evolutionary Computation Conference consisting of different synthetic and real-world datasets which were blind to entrants. For the real-world track, we assessed interpretability in a realistic way by using a domain expert to judge the trustworthiness of candidate models. We present an in-depth analysis of the results obtained in this competition, discuss current challenges of symbolic regression algorithms and highlight possible improvements for future competitions. Copyright © 2023, The Authors. All rights reserved.

关键词： Machine learning

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Technical debt and agile software development practices and processes: An industry practitioner survey

arXiv

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arXiv 2021年

作者： Holvitie, Johannes Licorish, Sherlock A. Spínola, Rodrigo O. Hyrynsalmi, Sami MacDonell, Stephen G. Mendes, Thiago S. Buchan, Jim Leppänen, Ville Turku Centre for Computer Science Software Development Laboratory Turku Finland University of Turku Department of Information Technology Turku Finland University of Otago Department of Information Science Otago Dunedin New Zealand Salvador University Graduate Program in Systems and Computer Bahia Salvador Brazil Federal University of Bahia Fraunhofer Project Center for Software and System Engineering Salvador Brazil Tampere University of Technology Pori Campus Pori Finland Federal Institute of Bahia Information Technology Department Bahia Santo Amaro Brazil Auckland University of Technology School of Engineering Computer and Mathematical Sciences Auckland New Zealand

Context: Contemporary software development is typically conducted in dynamic, resource-scarce environments that are prone to the accumulation of technical debt. While this general phenomenon is acknowledged, what remains unknown is how technical debt specifically manifests in and affects software processes, and how the software development techniques employed accommodate or mitigate the presence of this debt. Objectives: We sought to draw on practitioner insights and experiences in order to classify the effects of agile method use on technical debt management, given the popularity and perceived success of agile methods. We explore the breadth of practitioners' knowledge about technical debt;how technical debt is manifested across the software process;and the perceived effects of common agile software development practices and processes on technical debt. In doing so, we address a research gap in technical debt knowledge and provide novel and actionable managerial recommendations. Method: We designed, tested and executed a multi-national survey questionnaire to address our objectives, receiving 184 responses from practitioners in Brazil, Finland, and New Zealand. Results: Our findings indicate that: 1) Practitioners are aware of technical debt, although, there was under utilization of the concept, 2) Technical debt commonly resides in legacy systems, however, concrete instances of technical debt are hard to conceptualize which makes it problematic to manage, 3) Queried agile practices and processes help to reduce technical debt;in particular, techniques that verify and maintain the structure and clarity of implemented artifacts (e.g., Coding standards and Refactoring) positively affect technical debt management. Conclusions: The fact that technical debt instances tend to have characteristics in common means that a systematic approach to its management is feasible. However, notwithstanding the positive effects of some agile practices on technical debt management, comp

关键词： Legacy systems

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Multimodal Whole Slide Foundation Model for Pathology

arXiv

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arXiv 2024年

作者： Ding, Tong Wagner, Sophia J. Song, Andrew H. Chen, Richard J. Lu, Ming Y. Zhang, Andrew Vaidya, Anurag J. Jaume, Guillaume Shaban, Muhammad Kim, Ahrong Williamson, Drew F.K. Chen, Bowen Almagro-Perez, Cristina Doucet, Paul Sahai, Sharifa Chen, Chengkuan Komura, Daisuke Kawabe, Akihiro Ishikawa, Shumpei Gerber, Georg Peng, Tingying Le, Long Phi Mahmood, Faisal Department of Pathology Mass General Brigham Harvard Medical School BostonMA United States Data Science Program Dana-Farber Cancer Institute BostonMA United States Cancer Program Broad Institute of Harvard and MIT CambridgeMA United States John A. Paulson School of Engineering and Applied Sciences Harvard University CambridgeMA United States Helmholtz Munich German Research Center for Environment and Health Munich Germany School of Computation Information and Technology Technical University of Munich Munich Germany Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology CambridgeMA United States Harvard-MIT Division of Health Sciences and Technology Massachusetts Institute of Technology CambridgeMA United States Department of Pathology Pusan National University Busan Korea Republic of Department of Pathology and Laboratory Medicine Emory University School of Medicine AtlantaGA United States Harvard Data Science Initiative Harvard University CambridgeMA United States Department of Systems Biology Harvard Medical School BostonMA United States Department of Preventive Medicine Graduate School of Medicine The University of Tokyo Tokyo Japan Division of Pathology National Cancer Center Exploratory Oncology Research & Clinical Trial Center Chiba Japan

The field of computational pathology has been transformed with recent advances in foundation models that encode histopathology region-of-interests (ROIs) into versatile and transferable feature representations via self-supervised learning (SSL). However, translating these advancements to address complex clinical challenges at the patient and slide level remains constrained by limited clinical data in disease-specific cohorts, especially for rare clinical conditions. We propose TITAN, a multimodal whole slide foundation model pretrained using 335,645 WSIs via visual self-supervised learning and vision-language alignment with corresponding pathology reports and 423,122 synthetic captions generated from a multimodal generative AI copilot for pathology. Without any finetuning or requiring clinical labels, TITAN can extract general-purpose slide representations and generate pathology reports that generalize to resource-limited clinical scenarios such as rare disease retrieval and cancer prognosis. We evaluate TITAN on diverse clinical tasks and find that TITAN outperforms both ROI and slide foundation models across machine learning settings such as linear probing, few-shot and zero-shot classification, rare cancer retrieval and cross-modal retrieval, and pathology report generation. The model is publicly accessible at https://***/mahmoodlab/TITAN © 2024, CC BY-NC-ND.

关键词： Self-supervised learning

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