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IEEE Symposium on Computers and Communications (ISCC)

作者： Andreia Pinto João Viana Diogo Martinho Vítor Crista José Miguel Diniz Joana Reis João Matos David Greer Goreti Marreiros Alberto Freitas Department of Community Medicine Information and Health Decision Sciences (MEDCIDS) Faculty of Medicine Center for Health Technology and Services Research (CINTESIS) University of Porto Porto Portugal Research Group on Intelligent Engineering and Computing for Advanced Innovation and Development (GECAD) Institute of Engineering Polytechnic of Porto Porto Portugal Health Data Science PhD Program Faculty of Medicine Center for Health Technology and Services Research (CINTESIS) University of Porto Lisboa Portugal CLOO - Behavioral Insights Unit Faculty of Psychology CICPSI - Research Center for Psychological Science University of Lisbon Lisboa Portugal Behavioral Insights Unit CLOO Porto Portugal Behavioral Insights Unit CLOO Lisboa Portugal

ISBN: (数字)9781665497923

ISBN: (纸本)9781665497930

Type 2 diabetes is an increasingly prevalent disease and patients do not always manage the disease properly. Therefore, creating tools that help diabetics self-manage their condition over time is of the utmost importance. Technological tools that include features meeting this population's needs, with an integrated personalized feedback system, in an environment of gamified incentives, may be the way for developing a sustained app's usage. This work aims to present a still in development, novel approach to managing diabetes type 2 with a focus on data analysis from user-inputs, gamification, and personalized coaching, with an accessible user interface. Thus, we will present some functionalities, in particular the theoretical and practical concept that is behind this development, namely the Transtheoretical model of behavior change to create different profiles, to provide customized feedback according to the user's behavioral stage, and also to ascertain if it induces any improvement at the behavioral level.

关键词： Computers data analysis Computational modeling User interfaces Diabetes Behavioral sciences Mobile applications

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Location embedding based pairwise distance learning for fine-grained diagnosis of urinary stones

arXiv

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arXiv 2024年

作者： Jin, Qiangguo Huang, Jiapeng Sun, Changming Cui, Hui Xuan, Ping Su, Ran Wei, Leyi Wu, Yu-Jie Wu, Chia-An Duh, Henry B.L. Lu, Yueh-Hsun School of Software Northwestern Polytechnical University Shaanxi China Yangtze River Delta Research Institute of NPU Suzhou China CSIRO Data61 Sydney Australia Department of Computer Science and Information Technology La Trobe University Melbourne Australia School of Engineering Shantou University Guangdong China College of Intelligence and Computing Tianjin University Tianjin China School of Information Xiamen University Xiamen China AIDD Faculty of Applied Science Macao Polytechnic University China Department of Radiology Shuang-Ho Hospital Taipei Medical University Taipei Taiwan Master of Public Health Program National Yang Ming Chiao Tung University Taipei Taiwan School of Design The Hong Kong Polytechnic University Hong Kong Department of Radiology School of Medicine College of Medicine Taipei Medical University Taipei Taiwan

The precise diagnosis of urinary stones is crucial for devising effective treatment strategies. The diagnostic process, however, is often complicated by the low contrast between stones and surrounding tissues, as well as the variability in stone locations across different patients. To address this issue, we propose a novel location embedding based pairwise distance learning network (LEPD-Net) that leverages low-dose abdominal X-ray imaging combined with location information for the fine-grained diagnosis of urinary stones. LEPD-Net enhances the representation of stone-related features through context-aware region enhancement, incorporates critical location knowledge via stone location embedding, and achieves recognition of fine-grained objects with our innovative fine-grained pairwise distance learning. Additionally, we have established an in-house dataset on urinary tract stones to demonstrate the effectiveness of our proposed approach. Comprehensive experiments conducted on this dataset reveal that our framework significantly surpasses existing state-of-the-art methods. Copyright © 2024, The Authors. All rights reserved.

关键词： Embeddings

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Explainable Biomedical Hypothesis Generation via Retrieval Augmented Generation enabled Large Language Models

arXiv

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arXiv 2024年

作者： Pelletier, Alexander R. Ramirez, Joseph Adam, Irsyad Sankar, Simha Yan, Yu Wang, Ding Steinecke, Dylan Wang, Wei Ping, Peipei Department of Physiology UCLA School of Medicine Suite 1-609 MRL Building 675 Charles E. Young Dr. LACA90095-1760 United States Department of Computer Science UCLA School of Engineering Los AngelesCA90095 United States NIH BRIDGE2AI Center UCLA NHLBI Integrated Cardiovascular Data Science Training Program at UCLA Suite 1-609 MRL Building 675 Charles E. Young Dr. South Los AngelesCA90095-1760 United States CA90095 United States UCLA School of Medicine Suite 1-609 MRL Building 675 Charles E. Young Dr. South Los AngelesCA90095-1760 United States

The vast amount of biomedical information available today presents a significant challenge for investigators seeking to digest, process, and understand these findings effectively. Large Language Models (LLMs) have emerged as powerful tools to navigate this complex and challenging data landscape. However, LLMs may lead to hallucinatory responses, making Retrieval Augmented Generation (RAG) crucial for achieving accurate information. In this protocol, we present RUGGED (Retrieval Under Graph-Guided Explainable disease Distinction), a comprehensive workflow designed to support investigators with knowledge integration and hypothesis generation, identifying validated paths forward. Relevant biomedical information from publications and knowledge bases are reviewed, integrated, and extracted via text-mining association analysis and explainable graph prediction models on disease nodes, forecasting potential links among drugs and diseases. These analyses, along with biomedical texts, are integrated into a framework that facilitates user-directed mechanism elucidation as well as hypothesis exploration through RAG-enabled LLMs. A clinical use-case demonstrates RUGGED's ability to evaluate and recommend therapeutics for Arrhythmogenic Cardiomyopathy (ACM) and Dilated Cardiomyopathy (DCM), analyzing prescribed drugs for molecular interactions and unexplored uses. The platform minimizes LLM hallucinations, offers actionable insights, and improves the investigation of novel therapeutics. © 2024, CC BY.

关键词： Bioinformatics

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Application of expert system for oil palm smallholder-owned plantations

引用

AIP Conference Proceedings 2023年第1期2594卷

作者： A. Umami H. G. Mawandha D. D. Puruhito Purwadi T. Suparyanto D. Sudigyo B. Pardamean Department of Agrotechnology Institute of Agriculture STIPER Yogyakarta Indonesia 55281 Departement of Agricultural Economics Institute of Agriculture STIPER Yogyakarta Indonesia 55281 Departement of Agriculture Engineering Institute of Agriculture STIPER Yogyakarta Indonesia 55281 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

Most of the oil palm smallholders operate independently. As a result of this lack of support and assistance, oil palm owned by independent smallholders has the lowest productivity compared to large private (corporation) plantations and large state plantations. In addition, smallholder-owned plantations often operate without paying attention to sustainability aspects. There is a need for an effective, efficient, and user-friendly mentoring tool for oil palm farmers that are accessed independently. The Android-based platform was developed by applying an expert system to support increased production of oil palm cultivation for smallholders. Several stages of the expert system implementation, including the identification of planters and land profiles, were carried out using the direct interview method. The expert system includes land preparation management, planting material selection, seeding, weeds control, pests and diseases, fertilization, harvesting and transport, plantation administration, chat platforms, and data scrapping from data providers. The type of expert system is a data-driven Decision Support System (DSS).

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Weakly Supervised AI for Efficient Analysis of 3D Pathology Samples

arXiv

引用

arXiv 2023年

作者： Song, Andrew H. Williams, Mane Williamson, Drew F.K. Jaume, Guillaume Zhang, Andrew Chen, Bowen Serafin, Robert Liu, Jonathan T.C. Baras, Alex Parwani, Anil V. Mahmood, Faisal Department of Pathology Brigham and Women’s Hospital Harvard Medical School BostonMA United States Department of Pathology Massachusetts General Hospital Harvard Medical School BostonMA United States Cancer Program Broad Institute of Harvard and MIT CambridgeMA United States Data Science Program Dana-Farber Cancer Institute BostonMA United States Department of Biomedical Informatics Harvard Medical School BostonMA United States Harvard-MIT Division of Health Sciences and Technology Massachusetts Institute of Technology CambridgeMA United States Department of Mechanical Engineering Bioengineering Laboratory Medicine & Pathology University of Washington SeattleWA United States Department of Pathology Johns Hopkins Hospital BaltimoreMD United States Department of Biomedical Engineering Johns Hopkins Hospital BaltimoreMD United States Department of Pathology The Ohio State University ColumbusOH United States

Human tissue consists of complex structures that display a diversity of morphologies, forming a tissue microenvironment that is, by nature, three-dimensional (3D). However, the current standard-of-care involves slicing 3D tissue specimens into two-dimensional (2D) sections and selecting a few for microscopic evaluation1,2, with concomitant risks of sampling bias and misdiagnosis3–6. To this end, there have been intense efforts to capture 3D tissue morphology and transition to 3D pathology, with the development of multiple high-resolution 3D imaging modalities7–18. However, these tools have had little translation to clinical practice as manual evaluation of such large data by pathologists is impractical and there is a lack of computational platforms that can efficiently process the 3D images and provide patient-level clinical insights. Here we present Modality-Agnostic Multiple instance learning for volumetric Block Analysis (MAMBA), a deep-learning-based platform for processing 3D tissue images from diverse imaging modalities and predicting patient outcomes. Archived prostate cancer specimens were imaged with open-top light-sheet microscopy12–14 or microcomputed tomography15,16 and the resulting 3D datasets were used to train risk-stratification networks based on 5-year biochemical recurrence outcomes via MAMBA. With the 3D block-based approach, MAMBA achieves an area under the receiver operating characteristic curve (AUC) of 0.86 and 0.74, superior to 2D traditional single-slice-based prognostication (AUC of 0.79 and 0.57), suggesting superior prognostication with 3D morphological features. Further analyses reveal that the incorporation of greater tissue volume improves prognostic performance and mitigates risk prediction variability from sampling bias, suggesting that there is value in capturing larger extents of spatially heterogeneous 3D morphology. With the rapid growth and adoption of 3D spatial biology and pathology techniques by researchers and clinicians, M

关键词： Pathology

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Learning management system for oil palm smallholder-owned plantations

引用

AIP Conference Proceedings 2023年第1期2594卷

作者： E. Firmansyah D. Nurjannah S. I. Dinarti D. Sudigyo T. Suparyanto B. Pardamean Department of Agrotechnology Institute of Agriculture STIPER Yogyakarta Indonesia 55281 Departement of Agricultural Economics Institute of Agriculture STIPER Yogyakarta Indonesia 55281 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Departement of Agriculture Engineering Institute of Agriculture STIPER Yogyakarta Indonesia 55281 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

The production gap between oil palm smallholder-owned plantations and corporations shows a real problem in the national palm oil industry. To reduce the gap, user-friendly assistance for smallholder-owned plantations is needed for the cultivation of sustainable palm oil production. Android-based software can be a platform for bridging the transfer of knowledge and technology, transfer of problems, and transfer of solutions between planters and experts. The platform development was formulated in five stages which began with Learning Management System (LMS) application development, identification of Good Agricultural Practices (GAP) and Best Management Practices (BMP) materials, development of digital contents, uploading the digital content to the LMS server, and dissemination. The curriculum in the application platform was prepared based on the needs of the growers according to the identification results of the farmers' profiles. The curriculum consists of GAP and BMP material blocks. Each block was divided into discussion topics. The digital contents related to GAP and BMP were set in the LMS, which was built using Moodle platform.

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3D Liver and Tumor Segmentation in CT Scans with Robust Self-Paced Learning

3D Liver and Tumor Segmentation in CT Scans with Robust Self...

引用

International Conference on Information science and Control engineering (ICISCE)

作者： Obed Tettey Nartey Guowu Yang Sarpong Kwadwo Asare Jinzhao Wu Dorothy Araba Yakoba Agyapong Lady Nadia Frempong Big Data Research Center School of Computer Science and Engineering University of Electronic Science and Technology of China Chengdu China School of Electronic Science and Engineering University of Electronic Science and Technology of China Chengdu China School of Mathematics and Physics Guangxi University for Nationalities Nanning China Biomedical Engineering Program Kwame Nkrumah University of Science and Technology Kumasi Ghana

Liver segmentation is a challenging problem where fully supervised deep learning models require large amounts of voxel-wise labels, which are usually laborious, expensive, and time consuming to obtain. However, massive non-annotated 3D CT volumes are usually easily accessible. Most deep learning based works to address semi-supervised CT medical image segmentation problems have mostly been graph-based or adversarial-based. In sharp contrast, this work investigates the potential of a semi-supervised learning method; novel self-training framework utilizing self-paced learning strategy to generate and select pseudo-labels from easy-to-transfer(well represented classes) to hard-to-transfer(less represented classes) samples. The proposed scheme introduces an effective pseudo-label generation and selection algorithm to generate highly confident pseudo-labels, jointly learn and optimize a model which can be solved by alternatively generating pseudo labels on unlabeled target data and re-training the model with the generated labels. Further, we also propose a novel class balancing framework to avoid the gradual eminence of easy-to-transfer discriminative features on pseudo-label generation utilizing class-wise normalization of confidence scores. Comprehensive experiments conducted on publicly available datasets show that the proposed method outperformed other state-of-the-art semi-supervised and some fully supervised methods on the segmentation results of tumors and achieved very competitive performance for liver segmentation.

关键词： Training Deep learning Image segmentation Information science Three-dimensional displays Computed tomography Liver

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Correction: Extremely boosted neural network for more accurate multi-stage Cyber attack prediction in cloud computing environment

引用

Journal of Cloud Computing 2023年第1期12卷 1-1页

作者： Dalal, Surjeet Manoharan, Poongodi Kumar, Lilhore Umesh Seth, Bijeta alsekait, Deema Mohammed Simaiya, Sarita Hamdi, Mounir Raahemifar, Kaamran Department of Computer Science and Engineering Amity University Haryana Gurugram India Division of Information and Computing Technology College of Science and Engineering Hamad Bin Khalifa University Qatar Foundation Doha Qatar School of Computing University of Louisiana Lafayette USA Department of Computer Science and Engineering Chandigarh University Mohali India Department of Computer Science and Engineering B. M. Institute of Engineering & Technology Sonipat India Department of Computer Science and Information Technology Applied College Princess Nourah Bint Abdulrahman University Riyadh Saudi Arabia College of Information Sciences and Technology Data Science and Artificial Intelligence Program State College USA School of Optometry and Vision Science Faculty of Science University of Waterloo Waterloo Canada Faculty of Engineering University of Waterloo Waterloo Canada

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Biases in Inverse Ising Estimates of Near-Critical Behaviour

arXiv

引用

arXiv 2023年

作者： Kloucek, Maximilian B. Machon, Thomas Kajimura, Shogo Royall, C. Patrick Masuda, Naoki Turci, Francesco H.H. Wills Laboratory School of Physics University of Bristol Bristol United Kingdom Bristol Centre for Functional Nanomaterials University of Bristol Bristol United Kingdom Faculty of Information and Human Sciences Kyoto Institute of Technology Kyoto606-8585 Japan Gulliver UMR CNRS 7083 ESPCI Paris Université PSL Paris75005 France Department of Mathematics State University of New York BuffaloNY14260-2900 United States Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo BuffaloNY14260-5030 United States

Inverse Ising inference allows pairwise interactions of complex binary systems to be reconstructed from empirical correlations. Typical estimators used for this inference, such as Pseudo-likelihood maximization (PLM), are biased. Using the Sherrington-Kirkpatrick (SK) model as a benchmark, we show that these biases are large in critical regimes close to phase boundaries, and may alter the qualitative interpretation of the inferred model. In particular, we show that the small-sample bias causes models inferred through PLM to appear closer-to-criticality than one would expect from the data. data-driven methods to correct this bias are explored and applied to a functional magnetic resonance imaging (fMRI) dataset from neuroscience. Our results indicate that additional care should be taken when attributing criticality to real-world datasets. Copyright © 2023, The Authors. All rights reserved.

关键词： Criticality (nuclear fission)

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Scientific discovery in the age of artificial intelligence

引用

NATURE 2023年第7978期621卷 E33-E33页

作者： Wang, Hanchen Fu, Tianfan Du, Yuanqi Gao, Wenhao Huang, Kexin Liu, Ziming Chandak, Payal Liu, Shengchao Van Katwyk, Peter Deac, Andreea Anandkumar, Anima Bergen, Karianne Gomes, Carla P. Ho, Shirley Kohli, Pushmeet Lasenby, Joan Leskovec, Jure Liu, Tie-Yan Manrai, Arjun Marks, Debora Ramsundar, Bharath Song, Le Sun, Jimeng Tang, Jian Velickovic, Petar Welling, Max Zhang, Linfeng Coley, Connor W. Bengio, Yoshua Zitnik, Marinka Department of Engineering University of Cambridge Cambridge UK Department of Computing and Mathematical Sciences California Institute of Technology Pasadena CA USA NVIDIA Santa Clara CA USA Department of Computational Science and Engineering Georgia Institute of Technology Atlanta GA USA Department of Computer Science Cornell University Ithaca NY USA Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA USA Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA USA Department of Computer Science Stanford University Stanford CA USA Department of Physics Massachusetts Institute of Technology Cambridge MA USA Harvard-MIT Program in Health Sciences and Technology Cambridge MA USA Mila – Quebec AI Institute Montreal Quebec Canada Université de Montréal Montreal Quebec Canada HEC Montréal Montreal Quebec Canada CIFAR AI Chair Toronto Ontario Canada Department of Earth Environmental and Planetary Sciences Brown University Providence RI USA Data Science Institute Brown University Providence RI USA Center for Computational Astrophysics Flatiron Institute New York NY USA Department of Astrophysical Sciences Princeton University Princeton NJ USA Department of Physics Carnegie Mellon University Pittsburgh PA USA Department of Physics and Center for Data Science New York University New York NY USA Google DeepMind London UK Department of Computer Science and Technology University of Cambridge Cambridge UK Microsoft Research Beijing China Department of Biomedical Informatics Harvard Medical School Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA Harvard Data Science Initiative Cambridge MA USA Kempner Institute for the Study of Natural and Artificial Intelligence Harvard University Cambridge MA USA Department of Systems Biology Harvard Medical School Boston MA USA Deep Forest Sciences Palo Alto CA USA BioMap Beijing China Mo

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