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arXiv 2020年

作者： Zhang, Yuhao Jiang, Hang Miura, Yasuhide Manning, Christopher D. Langlotz, Curtis P. Biomedical Informatics Training Program Stanford University United States Symbolic Systems Program Stanford University United States Computer Science Department Stanford University United States Computer Science and Linguistics Departments Stanford University United States Department of Radiology Stanford University United States

Learning visual representations of medical images (e.g., X-rays) is core to medical image understanding but its progress has been held back by the scarcity of human annotations. Existing work commonly relies on fine-tuning weights transferred from ImageNet pretraining, which is suboptimal due to drastically different image characteristics, or rule-based label extraction from the textual report data paired with medical images, which is inaccurate and hard to generalize. Meanwhile, several recent studies show exciting results from unsupervised contrastive learning from natural images, but we find these methods help little on medical images because of their high inter-class similarity. We propose ConVIRT, an alternative unsupervised strategy to learn medical visual representations by exploiting naturally occurring paired descriptive text. Our new method of pretraining medical image encoders with the paired text data via a bidirectional contrastive objective between the two modalities is domain-agnostic, and requires no additional expert input. We test ConVIRT by transferring our pretrained weights to 4 medical image classification tasks and 2 zero-shot retrieval tasks, and show that it leads to image representations that considerably outperform strong baselines in most settings. Notably, in all 4 classification tasks, our method requires only 10% as much labeled training data as an ImageNet initialized counterpart to achieve better or comparable performance, demonstrating superior data efficiency. Copyright © 2020, The Authors. All rights reserved.

关键词： Zero-shot learning

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Treatment Algorithm for the Resorption of Calcific Tendinitis Using Extracorporeal Shockwave Therapy: A Data Mining Study

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Orthopaedic Journal of Sports Medicine 2024年第3期12卷 23259671241231609页

作者： Chou, Wen-Yi Cheng, Jai-Hong Lien, Yu-Jui Huang, Tian-Hsiang Ho, Wen-Hsien Chou, Paul Pei-Hsi Doctoral Degree Program in Biomedical Engineering College of Medicine Kaohsiung Medical University Kaohsiung Taiwan Department of Orthopedic Surgery Kaohsiung Chang Gung Memorial Hospital Chang Gung University College of Medicine Kaohsiung Taiwan Department of Leisure and Sport Management Cheng Shiu University Kaohsiung Taiwan Center for Shockwave Medicine and Tissue Engineering Department of Medical Research Kaohsiung Chang Gung Memorial Hospital Chang Gung University College of Medicine Kaohsiung Taiwan Department of Healthcare Administration and Medical Informatics Kaohsiung Medical University Kaohsiung Taiwan Department of Computer Science and Information Engineering National Penghu University of Science and Technology Penghu Taiwan College of Professional Studies National Pingtung University of Science and Technology Pingtung Taiwan Department of Sports Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan Division of Sports Medicine Department of Orthopaedic Surgery Kaohsiung Medical University Hospital Kaohsiung Taiwan Department of Orthopaedics School of Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan Department of Orthopaedic Surgery Kaohsiung Municipal Hsiao-Kang Hospital Kaohsiung Taiwan

Background: Although evidence indicates that extracorporeal shockwave therapy (ESWT) is effective in treating calcifying shoulder tendinitis, incomplete resorption and dissatisfactory results are still reported in many cases. Data mining techniques have been applied in health care in the past decade to predict outcomes of disease and treatment. Purpose: To identify the ideal data mining technique for the prediction of ESWT-induced shoulder calcification resorption and the most accurate algorithm for use in the clinical setting. Study Design: Case-control study. Methods: Patients with painful calcified shoulder tendinitis treated by ESWT were enrolled. Seven clinical factors related to shoulder calcification were adopted as the input attributes: sex, age, side affected, symptom duration, pretreatment Constant-Murley score, and calcification size and type. The 5 data mining techniques assessed were multilayer perceptron (neural network), naïve Bayes, sequential minimal optimization, logistic regression, and the J48 decision tree classifier. Results: A total of 248 patients with calcified shoulder tendinitis were enrolled in this study. Shorter symptom duration yielded the highest gain ratio (0.374), followed by smaller calcification size (0.336) and calcification type (0.253). With the J48 decision tree method, the accuracy of 3 input attributes was 89.5% by 10-fold cross-validation, indicating satisfactory accuracy. A treatment algorithm using the J48 decision tree indicated that a symptom duration of ≤10 months was the most positive indicator of calcification resorption, followed by a calcification size of ≤10.82 mm. Conclusion: The J48 decision tree method demonstrated the highest precision and accuracy in the prediction of shoulder calcification resorption by ESWT. A symptom duration of ≤10 months or calcification size of ≤10.82 mm represented the clinical scenarios most likely to show resorption after ESWT. © The Author(s) 2024.

关键词： calcific tendinitis data mining extracorporeal shockwave therapy J48 decision tree shoulder

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Mind the Performance Gap: Examining Dataset Shift During Prospective Validation 6

Mind the Performance Gap: Examining Dataset Shift During Pro...

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6th Machine Learning for Healthcare Conference, MLHC 2021

作者： Ötleş, Erkin Oh, Jeeheh Li, Benjamin Bochinski, Michelle Joo, Hyeon Ortwine, Justin Shenoy, Erica Washer, Laraine Young, Vincent B. Rao, Krishna Wiens, Jenna Department of Industrial & Operations Engineering University of Michigan United States Medical Scientist Training Program University of Michigan Medical School United States Division of Computer Science & Engineering University of Michigan United States Nursing Informatics Michigan Medicine United States Department of Anesthesiology University of Michigan Medical School United States Department of Learning Health Sciences University of Michigan Medical School United States Infection Control Unit Division of Infectious Diseases Massachusetts General Hospital Harvard Medical School United States Department of Internal Medicine Division of Infectious Diseases University of Michigan Medical School United States Department of Microbiology & Immunology University of Michigan Medical School United States

Once integrated into clinical care, patient risk stratification models may perform worse compared to their retrospective performance. To date, it is widely accepted that performance will degrade over time due to changes in care processes and patient populations. However, the extent to which this occurs is poorly understood, in part because few researchers report prospective validation performance. In this study, we compare the 2020-2021 (’20-’21) prospective performance of a patient risk stratification model for predicting healthcare-associated infections to a 2019-2020 (’19-’20) retrospective validation of the same model. We define the difference in retrospective and prospective performance as the performance gap. We estimate how i) "temporal shift", i.e., changes in clinical workflows and patient populations, and ii) "infrastructure shift", i.e., changes in access, extraction and transformation of data, both contribute to the performance gap. Applied prospectively to 26,864 hospital encounters during a twelve-month period from July 2020 to June 2021, the model achieved an area under the receiver operating characteristic curve (AUROC) of 0.767 (95% confidence interval (CI): 0.737, 0.801) and a Brier score of 0.189 (95% CI: 0.186, 0.191). Prospective performance decreased slightly compared to’19-’20 retrospective performance, in which the model achieved an AUROC of 0.778 (95% CI: 0.744, 0.815) and a Brier score of 0.163 (95% CI: 0.161, 0.165). The resulting performance gap was primarily due to infrastructure shift and not temporal shift. So long as we continue to develop and validate models using data stored in large research data warehouses, we must consider differences in how and when data are accessed, measure how these differences may negatively affect prospective performance, and work to mitigate those differences. © 2021 E. Ötleş & J. Oh et al.

关键词： Data warehouses

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Negative prognostic factors and clinical improvement prediction modeling for extracorporeal shockwave therapy in calcific shoulder tendinitis using artificial intelligence techniques

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Journal of Shoulder and Elbow Surgery 2025年

作者： Chou, Wen-Yi Huang, Tian-Hsiang Cheng, Jai-Hong Lien, Yu-Jui Ho, Wen-Hsien Chou, Paul Pei-Hsi Ph.D. Program in Biomedical Engineering College of Medicine Kaohsiung Medical University Kaohsiung Taiwan Department of Orthopedic Surgery Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine Kaohsiung Taiwan Department of Leisure and Sport Management Cheng Shiu University Kaohsiung Taiwan Department of Computer Science and Information Engineering National Penghu University of Science and Technology Penghu Taiwan Department of Medical Research Center for Shockwave Medicine and Tissue Engineering Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine Kaohsiung Taiwan Department of Healthcare Administration and Medical Informatics Kaohsiung Medical University Kaohsiung Taiwan Department of Medical Research Kaohsiung Medical University Hospital Kaohsiung Taiwan College of Professional Studies National Pingtung University of Science and Technology Pingtung Taiwan Precision Sports Medicine and Health Promotion Center Kaohsiung Medical University Kaohsiung Taiwan Department of Sports Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan Division of Sports Medicine Department of Orthopaedic Surgery Kaohsiung Medical University Hospital Kaohsiung Taiwan Department of Orthopaedics School of Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan

Background: The efficacy of extracorporeal shockwave therapy (ESWT) for treating shoulder calcific tendinitis can be influenced by various prognostic factors. This study aimed to identify prognostic factors associated with the failure of ESWT for symptom relief and to evaluate the predictive capability of the eXtreme Gradient Boosting (XGBoost) algorithm of artificial intelligence techniques in this context. Methods: This retrospective study enrolled patients with persistent shoulder pain attributed to calcific tendinitis who underwent ESWT after failed conservative treatment between January 1998 and December 2022. Age, sex, duration of symptoms, calcification classification and size, pre-ESWT visual analog scale (VAS), and pre-ESWT Constant-Murley score (CMS) served as potential input attributes. The difference in VAS and CMS were defined as the output attributes. The XGBoost model was used to predict treatment outcomes based on these factors. The dataset was balanced using the synthetic minority oversampling technique, and the model's performance was assessed using 10-fold cross-validation. Spearman's rank correlation coefficient analysis was adopted to explore the relationships between significant continuous input attributes and post-ESWT VAS and CMS scores. Results: A total of 296 patients with calcific tendinitis were enrolled and completed the 1-year follow-up. The findings revealed that a prolonged symptom duration (>10 months), severe pain (pre-ESWT VAS >5), and higher pre-ESWT CMS (>55) were significant prognostic factors for the failure of ESWT for symptom relief. Using these factors as inputs, the XGBoost model demonstrated high accuracy, precision, recall, and F1 score. By reducing the input attributes to age, calcification size, pre-ESWT CMS, and symptom duration, the model maintained a high prediction rate, suggesting that these factors are sufficient for effective prediction. Discussion: The present study identified significant prognostic factors asso

关键词： Artificial intelligence Basic science Study calcific tendinitis CMS Development of Predictive computer Modeling Using AI/Machine Learning ESWT shoulder VAS XGBoost

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Scientific discovery in the age of artificial intelligence

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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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Autoencoders as Weight Initialization of Deep Classification Networks for Cancer versus Cancer Studies

arXiv

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arXiv 2020年

作者： Ferreira, Mafalda Falcão Camacho, Rui Teixeira, Luís F. Doctoral Program in Informatics Engineering Faculty of Engineering University of Porto INESC TEC - Institute for Systems and Computer Engineering Technology and Science Porto Portugal Department of Informatics Engineering Faculty of Engineering University of Porto Porto - Portugal

Cancer is still one of the most devastating diseases of our time. One way of automatically classifying tumor samples is by analyzing its derived molecular information (i.e., its genes expression signatures). In this work, we aim to distinguish three different types of cancer: thyroid, skin, and stomach. For that, we compare the performance of a Denoising Autoencoder (DAE) used as weight initialization of a deep neural network. Although we address a different domain problem in this work, we have adopted the same methodology of Ferreira et al.. In our experiments, we assess two different approaches when training the classification model: (a) fixing the weights, after pre-training the DAE, and (b) allowing fine-tuning of the entire classification network. Additionally, we apply two different strategies for embedding the DAE into the classification network: (1) by only importing the encoding layers, and (2) by inserting the complete autoencoder. Our best result was the combination of unsupervised feature learning through a DAE, followed by its full import into the classification network, and subsequent fine-tuning through supervised training, achieving an F1 score of 98.04% ± 1.09 when identifying cancerous thyroid samples. Copyright © 2020, The Authors. All rights reserved.

关键词： Classification (of information)

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Flame and smoke detection using Kafka on edge devices

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Internet of Things 2024年 27卷

作者： Yu-Wei Chan Jung-Chun Liu Endah Kristiani Kai-Yu Lien Chao-Tung Yang Bachelor Degree Program of Artificial Intelligence National Taichung University of Science and Technology Taichung City Taiwan ROC Department of Computer Science Tunghai University Taichung City 407224 Taiwan ROC Department of Informatics Krida Wacana Christian University Jakarta 11470 Indonesia Research Center for Smart Sustainable Circular Economy Tunghai University Taichung City 407224 Taiwan ROC

This paper presents object detection methods to accurately identify the sources of flame and smoke in vast circumstances. Aerial drones collected the data, analyzed the recognition outputs in real time on an edge device, and then transferred them to the back-end for data processing and warnings using Kafka. To detect flame and smoke occurrences, the models were compared using various convolutional neural networks (CNN). Several factors considered include streaming speed, accuracy, portability, efficiency, and power consumption on edge devices. This work conducted training comparisons of YOLOV4, YOLOV5, YOLOV7, YOLOV8, and Faster RCNN. The inference performance was then evaluated on an edge computing device. The findings showed an accuracy of 0.91 and 0.87, while maintaining a processing speed of roughly 1 frame per second on the Nvidia Jetson NX without acceleration.

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LC-MS analysis: Mini review frequently used open source softwares 6

LC-MS analysis: Mini review frequently used open source soft...

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6th International Conference on Information Technology, computer and Electrical Engineering, ICITACEE 2019

作者： Binanto, Iwan Warnars, Harco Leslie Hendric Spits Sianipar, Nesti Fronika Abbas, Bahtiar Saleh Sanata Dharma University Informatics Department Yogyakarta Indonesia Bina Nusantara University BINUS Graduate Program Doctor Computer Science Computer Science Department Jakarta11480 Indonesia Research Interest Group Biotechnology Bina Nusantara University Jakarta11480 Indonesia

ISBN: (纸本)9781728126890

This paper provides information about open source softwares that most often used as a tool to analyze data generated from the Liquid chromatography-mass spectrometer (LC-MS) instrument and including a little discussion about how LC-MS works. LC-MS consists of Liquid Chromatography and Mass Spectrometer analytical instruments. This device extensively used in Metabolomics, because it provides more comprehensive information about the metabolites. It also shows the breadth of the diversity of chemical compounds in metabolites that make difficult and time-consuming to identification of metabolite's structures. This is an obstacle in efficient and accurate identification. So, many open source softwares developed to simplify and speed up the analysis and interpretation of LC-MS result. There are popular open source softwares. We compiling mini review of this open source softwares. The conclusion is open source softwares quite helpful in terms of data analysis and interpretation of compounds contained, but no one has provided a single interpretation, still need experts for reliable interpretation. © 2019 IEEE.

关键词： Liquid chromatography

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Question-Answering System Extracts Information on Injection Drug Use from Clinical Notes

arXiv

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arXiv 2023年

作者： Mahbub, Maria Goethert, Ian Danciu, Ioana Knight, Kathryn Srinivasan, Sudarshan Tamang, Suzanne Rozenberg-Ben-Dror, Karine Solares, Hugo Martins, Susana Trafton, Jodie Begoli, Edmon Peterson, Gregory D. Cyber Resilience and Intelligence Division Oak Ridge National Laboratory Oak RidgeTN United States Information Technology Services Division Oak Ridge National Laboratory Oak RidgeTN United States Computational Sciences and Engineering Division Oak Ridge National Laboratory Oak RidgeTN United States Department of Biomedical Informatics Vanderbilt University NashvilleTN United States Program Evaluation and Resource Center Office of Mental Health and Suicide Prevention Department of Veterans Affairs United States Department of Medicine Stanford University School of Medicine StanfordCA United States Veterans Affairs Great Lakes Health Care System WestchesterIL United States Department of Electrical Engineering and Computer Science University of Tennessee Knoxville KnoxvilleTN United States

Background: Injection drug use (IDU) is a dangerous health behavior that increases mortality and morbidity. Identifying IDU early and initiating harm reduction interventions can benefit individuals at risk. However, extracting IDU behaviors from patients’ electronic health records (EHR) is difficult because there is no International Classification of Disease (ICD) code and the only place IDU information can be indicated is unstructured free-text clinical notes. Although natural language processing can efficiently extract this information from unstructured data, there are no validated tools. Methods: To address this gap in clinical information, we design and demonstrate a question-answering (QA) framework to extract information on IDU from clinical notes. Our framework involves two main steps: (1) generating a gold-standard QA dataset and (2) developing and testing the QA model. We utilize 2323 clinical notes of 1145 patients sourced from the VA Corporate Data Warehouse to construct the gold-standard dataset for developing and evaluating the QA model. We also demonstrate the QA model’s ability to extract IDU-related information on temporally out-of-distribution data. Results: Here we show that for a strict match between gold-standard and predicted answers, the QA model achieves 51.65% F1 score. For a relaxed match between the gold-standard and predicted answers, the QA model obtains 78.03% F1 score, along with 85.38% Precision and 79.02% Recall scores. Moreover, the QA model demonstrates consistent performance when subjected to temporally out-of-distribution data. Conclusions: Our study introduces a QA framework designed to extract IDU information from clinical notes, aiming to enhance the accurate and efficient detection of people who inject drugs, extract relevant information, and ultimately facilitate informed patient care. © 2023, CC BY-NC-ND.

关键词： Data warehouses

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Comprehensive investigation of proteoglycan gene expression in breast cancer: Discovery of a unique proteoglycan gene signature linked to the malignant phenotype

Proteoglycan research

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Proteoglycan research 2025年第1期3卷 e70014页

作者： Simone Buraschi Gabriel Pascal Federico Liberatore Renato V Iozzo Department of Pathology and Genomic Medicine and the Translational Cellular Oncology Program Sidney Kimmel Cancer Center Sidney Kimmel Medical College at Thomas Jefferson University Philadelphia PA 19107 USA. School of Computer Science and Informatics Cardiff University Cardiff CF24 4AG UK.

Solid tumors present a formidable challenge in oncology, necessitating innovative approaches to improve therapeutic outcomes. Proteoglycans, multifaceted molecules within the tumor microenvironment, have garnered attention due to their diverse roles in cancer progression. Their unique ability to interact with specific membrane receptors, growth factors, and cytokines provides a promising avenue for the development of recombinant proteoglycan-based therapies that could enhance the precision and efficacy of cancer treatment. In this study, we performed a comprehensive analysis of the proteoglycan gene landscape in human breast carcinomas. Leveraging the available wealth of genomic and clinical data regarding gene expression in breast carcinoma and using a machine learning model, we identified a unique gene expression signature composed of five proteoglycans differentially modulated in the tumor tissue: Syndecan-1 and asporin (upregulated) and decorin, PRELP and podocan (downregulated). Additional query of the breast carcinoma data revealed that serglycin, previously shown to be increased in breast carcinoma patients and mouse models and to correlate with a poor prognosis, was indeed decreased in the vast majority of breast cancer patients and its levels inversely correlated with tumor progression and invasion. This proteoglycan gene signature could provide novel diagnostic capabilities in breast cancer biology and highlights the need for further utilization of publicly available datasets for the clinical validation of preclinical experimental results.

关键词： PRELP Proteoglycan gene signature asporin decorin podocan syndecan-1

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