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In silico prediction of loop-mediated isothermal amplification using a generalized linear model

Synthetic Biology 2025年第1期10卷

作者： Taguchi, Kenshiro Michiyuki, Satoru Tsuji, Takumasa Kotoku, Jun’ichi Graduate Degree Program of Health Data Science Teikyo University 2-11-1 Kaga Itabashi-Ku Tokyo173-8605 Japan Fundamental Research Laboratory Eiken Chemical Co. Ltd Tochigi329-0114 Japan Graduate School of Medical Care and Technology Teikyo University 2-11-1 Kaga Itabashi-Ku Tokyo173-8605 Japan

Loop-mediated isothermal amplification (LAMP), a DNA amplification technique under isothermal conditions, provides the important benefits of high sensitivity, specificity, rapidity, and simplicity. Maximizing LAMP features necessitates the design of a complex LAMP primer set (LPS) consisting of four primers for six regions of a given target DNA. Furthermore, the LPS of a given target DNA is designed with LPS design support software such as Primer Explorer. However, even if the design is completed, we still must do many in vitro experiments and evaluations. Consequently, designing LPS often fails to achieve high performance, including efficient amplification. For this study, we examined in silico LAMP: a generalized linear model to predict DNA amplification from LPS. Using logistic regression with elastic net regularization, we identified factors that strongly affect LPS design. These factors, combined with domain knowledge for LPS design, led to the creation of LAMP kernel variables that are highly essential for high LAMP reaction. In silico LAMP, constructed using logistic regression with LAMP kernel variables, allows classification and performance prediction of LPS with an area under the curve of 0.86. These results suggest that a high LAMP reaction can be predicted using LAMP kernel variables and generalized linear regression model. Moreover, an LPS with high performance can be constructed without in vitro experimentation. © The Author(s) 2025. Published by Oxford University Press.

关键词： Logistic regression

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Cryptotanshinone Suppresses the STAT3/BCL-2 Pathway to Provoke Human Bladder Urothelial Carcinoma Cell Death

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Environmental Toxicology 2025年第4期40卷 624-635页

作者： Tung, Min-Che Chang, Ge-Man Dai, Wen-Chyi Hsu, Chen-Hsuan Chang, Hsiang-Chun Yang, Wei-Ting Ho, Yann-Jen Lu, Chien-Hsing Chen, Yi-Hsin Chang, Chia-Che Division of Urology Department of Surgery Tungs' Taichung MetroHarbor Hospital Taichung Taiwan Graduate Institute of Biomedical Sciences National Chung Hsing University Taichung Taiwan Doctoral Program in Biotechnology Industrial Innovation and Management National Chung Hsing University Taichung Taiwan Department of Life Sciences National Chung Hsing University Taichung Taiwan Department of Obstetrics and Gynecology Taichung Veterans General Hospital Taichung Taiwan Doctoral Program in Translational Medicine National Chung Hsing University Taichung Taiwan Department of Nephrology Taichung Tzu Chi Hospital Buddhist Tzu chi Medical Foundation Taichung Taiwan School of Medicine Tzu Chi University Hualein Taiwan Department of Artificial Intelligence and Data Science National Chung Hsing University Taichung Taiwan Master Program in Precision Health Rong Hsing Research Center for Translational Medicine The iEGG and Animal Biotechnology Research Center National Chung Hsing University Taichung Taiwan Department of Medical Laboratory Science and Biotechnology Asia University Taichung Taiwan Department of Medical Research China Medical University Hospital Taichung Taiwan

Bladder cancer is one of the most common human malignancies worldwide. Aberrant activation of signal transducer and activator of transcription 3 (STAT3) is crucial to driving malignant progression and predicting poor prognosis of multiple human cancers, including bladder cancer, making STAT3 a promising target of cancer therapeutics. Cryptotanshinone (CTS) is an anticancer ingredient of Danshen (Salvia miltiorrhiza), a top-graded Chinese medicinal herb. However, whether CTS targets STAT3 to exert its cytotoxic effect on human bladder cancer remains unknown. Herein, we demonstrated that CTS is cytotoxic to multiple human urinary bladder transitional cell carcinoma (TCC) cell lines while sparing normal human urothelial cells. CTS provoked apoptosis-dependent bladder TCC cytotoxicity, as apoptosis blockage by z-VAD-fmk markedly rescued the clonogenicity of CTS-treated cells. Besides, CTS was found to suppress constitutive and interleukin 6-inducible activation of STAT3, evidenced by the downregulation of STAT3 tyrosine 705 phosphorylation and BCL2, a recognized STAT3 transcriptional target. Notably, ectopic expression of a dominant-active STAT3 mutant (STAT3-C) or BCL-2 alleviated CTS-induced apoptosis and clonogenicity inhibition, thus confirming STAT3 blockade as a pivotal mechanism of CTS's cytotoxic action on bladder TCC cells. Lastly, immunoblotting revealed that CTS lowered the levels of active JAK2, an upstream kinase that mediates STAT3 tyrosine 705 phosphorylation. Altogether, we conclude that the blockade of the JAK2/STAT3/BCL-2 antiapoptotic signaling axis is a vital mechanism whereby CTS provokes bladder cancer cytotoxicity. The current evidence implicates CTS's potential to be translated into a bladder cancer therapeutic agent. © 2024 Wiley Periodicals LLC.

关键词： Cell death

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Effects of Mobile health Care App "Asmile" on Physical Activity of 80,689 Users in Osaka Prefecture, Japan: Longitudinal Observational Study

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Journal of medical Internet research 2025年 27卷 e65943页

作者： Asuka Oyama Kenshiro Taguchi Hiroe Seto Reiko Kanaya Jun'ichi Kotoku Miyae Yamakawa Hiroshi Toki Ryohei Yamamoto Health and Counseling Center The University of Osaka Toyonaka Japan. Graduate Degree Program of Health Data Science Teikyo University Tokyo Japan. Graduate School of Human Sciences The University of Osaka Suita Japan. Division of Health Sciences Graduate School of Medicine The University of Osaka Suita Japan. Graduate School of Medical Care and Technology Teikyo University Tokyo Japan. Department of Nephrology Graduate School of Medicine The University of Osaka Suita Japan. Laboratory of Behavioral Health Promotion Department of Health Promotion Graduate School of Medicine The University of Osaka Suita Japan. Institute for Sports and Global Health The University of Osaka Suita Japan.

BACKGROUND:Lifestyle-related diseases can be controlled by improving individuals' lifestyles; however, improving and maintaining a healthy lifestyle is difficult. Mobile health (mhealth) applications have recently attracted attention as tools for maintaining and improving health, and their use may also increase physical activity. OBJECTIVE:This study aimed to verify the effect of registration in Asmile, an mhealth application provided by the Osaka Prefectural Government, on step counts using a Causal Impact approach based on the step count data recorded in the Asmile application. METHODS:This observational study included Osaka residents aged 20-79 years, newly registered to Asmile, between the fiscal years 2020 and 2023. Of these, 80,689 participants with step count records for 4 weeks before and after the day they registered to Asmile were included in the analysis. We used daily step counts that were automatically transferred from a standard smartphone health care app into Asmile. We used a Causal Impact model to estimate the increase in step count after registration to Asmile. RESULTS:Of the 80,689 participants analyzed, 38.5% (31,082/80,689) were men, and the mean age was 51.6 (SD 13.2) years. The mean step count before registration was 5923 (SD 4860) steps per day, with the highest proportion of new users registered in spring (38,389/80,689, 47.6%) and in fiscal year 2020 (34,491/80,689, 42.7%). The analysis revealed that the effect of Asmile registration on step counts was 360 steps (95% CI 331-389) per day and 10,041 steps (95% CI 9632-10,450) over 4 weeks. Stratified analysis showed that the impact of increased step count was more pronounced in younger groups and groups with fewer step counts before registration. Conversely, the effect of registration on step count was relatively minor in the groups registered in summer or winter. CONCLUSIONS:This study demonstrates increased physical activity among users registered with the Asmile app. These findings suggest

关键词： Causal Impact Causal Inference Japan Osaka app apps exercise healthy lifestyle lifestyle-related disease mhealth mobile health mobile phone observational study physical activity smartphone step counts

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Implementing electronic health record-based anxiety and depression screening in an epilepsy clinic: Theory-based implementation strategy and pre-post quantitative outcomes using RE-AIM

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Journal of Clinical and Translational science 2025年第1期9卷 e108-e108页

作者： Munger Clary, Heidi M. Alexander, Halley B. Gesell, Sabina Wan, Mingyu Conner, Kelly R. Boggs, Jane Robles, Christian Sam, Maria Christopher, Jerryl Marini, Christina Snively, Beverly M. Department of Neurology Wake Forest University School of Medicine United States Department of Social Sciences and Health Policy Wake Forest University School of Medicine United States Neuroscience Graduate Program Wake Forest University United States Department of Physician Assistant Studies Wake Forest University School of Medicine United States Department of Biostatistics and Data Science Wake Forest University School of Medicine United States Department of Neurology New York University Grossman School of Medicine United States

Introduction: Anxiety and depression in epilepsy are common and impactful. Screening with validated measures at every epilepsy visit is a quality measure, yet screening remains limited due to time constraints. Methods: This study aimed to develop an implementation strategy for anxiety and depression screening at an epilepsy center and evaluate it in a pre-post design with RE-AIM(Reach, Effectiveness, Adoption, Implementation, Maintenance). Guided by the Capability, Opportunity, Motivation-Behavior(COM-B) behavior change wheel framework, the strategy incorporated electronic health record(EHR) tools and support staff activation of electronic screeners during visit check-in. Outcomes were evaluated over five months post-implementation and compared with two 3-month pre-implementation timeframes. Results: Post-implementation, 29.2% of 943 visits met the anxiety and depression screening quality measure, a significant increase from 12.6% immediately pre-implementation(p<0.0001) and 6.28% before any screening interventions(p<0.0001). Patients who completed electronic screeners post-implementation were younger than non-completers(mean 39.3 vs. 43.4 years, p=0.001) and more likely to be white than other race/ethnicity categories(p=0.002). There was substantial variability in screening rates among clinic staff(0-80% for support staff, 10.1-55.3% for providers), with higher screening among neurology support staff than temporary staff. Only 0.23% of post-implementation visits had screeners initiated but left incomplete. A shift to virtual visits during COVID-19 complicated Maintenance. Conclusions: This framework-based implementation strategy effectively increased screening rates by epilepsy specialists, though challenges remain, including variability across clinic team members and lower reach among older and non-white patients. This study describes a feasible strategy for epilepsy centers to use for improved performance on an AAN quality measure(depression and anxiety screening

关键词： epilepsy quality measures mental health psychiatric comorbidity quality of life seizures

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Performance prediction in major league baseball by long short-term memory networks

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International Journal of data science and Analytics 2023年第1期15卷 93-104页

作者： Sun, Hsuan-Cheng Lin, Tse-Yu Tsai, Yen-Lung Center for Information Systems and Technology Claremont Graduate University Claremont United States Data Science Degree Program National Taiwan University Taipei Taiwan Department of Mathematical Sciences National Chengchi University Taipei Taiwan

Player performance prediction is a serious problem in every sport since it brings valuable future information for managers to make important decisions. In baseball industries, there already existed variable prediction systems and many types of researches that attempt to provide accurate predictions and help domain users. However, it is a lack of studies about the predicting method or systems based on deep learning. Deep learning models had proven to be the greatest solutions in different fields nowadays, so we believe they could be tried and applied to the prediction problem in baseball. Hence, the predicting abilities of deep learning models are set to be our research problem in this paper. As a beginning, we select numbers of home runs as the target because it is one of the most critical indexes to understand the power and the talent of baseball hitters. Moreover, we use the sequential model Long Short-Term Memory as our main method to solve the home run prediction problem in Major League Baseball. We compare models’ ability with several machine learning models and a widely used baseball projection system, sZymborski Projection System. Our results show that Long Short-Term Memory has better performance than others and has the ability to make more exact predictions. We conclude that Long Short-Term Memory is a feasible way for performance prediction problems in baseball and could bring valuable information to fit users’ needs. © 2022, The Author(s), under exclusive licence to Springer Nature Switzerland AG.

关键词： Baseball

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Biomedical data and AI

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science China Life sciences 2025年第5期68卷 1536-1540页

作者： Hao Xu Shibo Zhou Zefeng Zhu Vincenzo Vitelli Liangyi Chen Ziwei Dai Ning Yang Luhua Lai Shengyong Yang Sergey Ovchinnikov Zhuoran Qiao Sirui Liu Chen Song Jianfeng Pei Han Wen Jianfeng Feng Yaoyao Zhang Zhengwei Xie Yang-Yu Liu Zhiyuan Li Fulai Jin Hao Li Mohammad Lotfollahi Xuegong Zhang Ge Yang Shihua Zhang Ge Gao Pulin Li Qi Liu Jing-Dong Jackie Han Peking-Tsinghua Center for Life Sciences (CLS) Academy for Advanced Interdisciplinary StudiesPeking University Center for Quantitative Biology (CQB) Academy for Advanced Interdisciplinary StudiesPeking University Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program Academy for Advanced Interdisciplinary StudiesPeking University Department of Physics University of Chicago School of Life Sciences Southern University of Science and Technology Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies College of Chemistry and Molecular Engineering Peking University Department of Biotherapy Cancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan University Department of Biology Massachusetts Institute of Technology Lambic Therapeutics Inc. Changping Laboratory Al for Science Institute Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence Fudan University Department of Obstetrics and Gynecology West China Second University HospitalSichuan University Peking University International Cancer Institute and Peking University-Yunnan Baiyao International Medical Institute and State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular PharmacologySchool of Pharmaceutical SciencesPeking University Health Science CenterPeking University Channing Division of Network Medicine Department of MedicineBrigham and Women's Hospital and Harvard Medical School Center for Artificial Intelligence and Modeling the Carl R.Woese Institute for Genomic BiologyUniversity of Illinois Urbana-Champaign Department of Genetics and Genome Sciences School of Medicine and Department of Computer and Data Sciences and Department of Population and Quantitative Health SciencesCase Western Reserve University Department of Biochemistry and Biophysics University of California Sanger Institute Department of Automation Tsinghua University State Key Laboratory of Multimodal Artificial Intelligence Systems I

The development of artificial intelligence(AI) and the mining of biomedical data complement each other. From the direct use of computer vision results to analyze medical images for disease screening, to now integrating biological knowledge into models and even accelerating the development of new AI based on biological discoveries, the boundaries of both are constantly expanding, and their connections are becoming closer.

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Performance of multimodal prediction models for intracerebral hemorrhage outcomes using real-world data

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International Journal of Medical Informatics 2025年 202卷 105989-105989页

作者： Matsumoto, Koutarou Suzuki, Masahiro Ishihara, Kazuaki Tokunaga, Koki Matsuda, Katsuhiko Chen, Jenhui Yamashiro, Shigeo Soejima, Hidehisa Nakashima, Naoki Kamouchi, Masahiro Department of Health Care Administration and Management Graduate School of Medical Sciences Kyushu University Fukuoka Japan Institute for Medical Information Research and Analysis Saiseikai Kumamoto Hospital Kumamoto Japan Graduate Degree Program of Applied Data Sciences Sophia University Tokyo Japan Department of Computer Science and Information Engineering Chang Gung University Taoyuan Taiwan Department of Pharmacy Saiseikai Kumamoto Hospital Kumamoto Japan Department of Radiology Saiseikai Kumamoto Hospital Kumamoto Japan Division of Neurosurgery Saiseikai Kumamoto Hospital Kumamoto Japan Medical Information Center Kyushu University Hospital Fukuoka Japan Department of Medical Informatics Graduate School of Medical Sciences Kyushu University Fukuoka Japan Center for Cohort Studies Graduate School of Medical Sciences Kyushu University Fukuoka Japan

Graphical abstract

关键词： Multimodal model Deep learning Machine learning Intracerebral hemorrhage

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Using Multi-task Deep Neural Network to Explore Person Interaction from Social Media

Using Multi-task Deep Neural Network to Explore Person Inter...

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2022 IEEE/WIC/ACM International Joint Conference on Web Intelligence and Intelligent Agent Technology (WI-IAT)

作者： Yung-Chun Chang Tzu-Ying Chen Ting-Yu Lin Yu-Lun Hsieh Graduate Institute of Data Science Taipei Medical University Taipei Taiwan Data Science Degree Program National Taiwan University Taipei Taiwan

This work sought to identify the interactions between persons mentioned in social media to help readers construct background knowledge of a certain topic. We propose using a rich interactive tree structure to represent syntactic, contextual, and semantic information, and adopt a tree-based convolution kernel to identify segments that carry clues about personal interactions, which are then used to construct person-interaction networks. Empirical evaluations demonstrate that the proposed method is effective in detecting and extracting the interactions between persons in textual data, outperforming other existing extraction approaches. Furthermore, readers will be able to easily navigate through the network of the interactions between persons of interest that is constructed by the proposed method, and efficiently obtain insights from a massive corpus.

关键词： Text mining Deep learning Social networking (online) Navigation Semantics Neural networks Syntactics

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Changing life expectancy in European countries 1990–2021: a subanalysis of causes and risk factors from the Global Burden of Disease Study 2021

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The Lancet Public health 2025年第3期10卷 e172-e188页

作者： Steel, Nicholas Bauer-Staeb, Clarissa Maria Mercedes Ford, John A. Abbafati, Cristiana Abdalla, Mohammed Altigani Abdelkader, Atef Abdi, Parsa Zuñiga, Roberto Ariel Abeldaño Abiodun, Olugbenga Olusola Abolhassani, Hassan Abu-Gharbieh, Eman Abukhadijah, Hana J. Abu-Zaid, Ahmed Addo, Isaac Yeboah Addolorato, Giovanni Adekanmbi, Victor Adetunji, Juliana Bunmi Adeyeoluwa, Temitayo Esther Agardh, Emilie E. Agyemang-Duah, Williams Ahmad, Danish Ahmed, Ayman Ahmed, Syed Anees Akinosoglou, Karolina Akkaif, Mohammed Ahmed Al Awaidy, Salah Al Hasan, Syed Mahfuz Al Zaabi, Omar Ali Mohammed Aldridge, Robert W. Algammal, Abdelazeem M. Al-Gheethi, Adel Ali Saeed Ali, Abid Ali, Mohammed Usman Ali, Syed Shujait Ali, Waad Alicandro, Gianfranco Alif, Sheikh Mohammad Al-Jumaily, Adel Allebeck, Peter Alrawashdeh, Ahmad Al-Rifai, Rami H. Alsabri, Mohammed A. Alshahrani, Najim Z. Aluh, Deborah Oyine Al-Wardat, Mohammad Al-Zyoud, Walid A. Amiri, Sohrab Anderlini, Deanna Andrei, Catalina Liliana Anil, Abhishek Anvari, Saeid Anyasodor, Anayochukwu Edward Appiah, Seth Christopher Yaw Aquilano, Michele Arabloo, Jalal Arafat, Mosab Areda, Demelash Aremu, Abdulfatai Armani, Keivan Armocida, Benedetta Ärnlöv, Johan Asaduzzaman, Muhammad Astell-Burt, Thomas Aujayeb, Avinash Ausloos, Marcel Azadnajafabad, Sina Aziz, Shahkaar Azzam, Ahmed Y. Babu, Giridhara Rathnaiah Badache, Andreea Corina Badiye, Ashish D. Bahramian, Saeed Baig, Atif Amin Baker, Jennifer L. Bansal, Hansi Bärnighausen, Till Winfried Barone, Mark Thomaz Ugliara Barrow, Amadou Barteit, Sandra Bashir, Shahid Bashiru, Hameed Akande Basso, João Diogo Bastan, Mohammad-Mahdi Basu, Sanjay Batra, Kavita Bauckneht, Matteo Baune, Bernhard T. Beghi, Massimiliano Beiranvand, Maryam Béjot, Yannick Bell, Michelle L. Bello, Olorunjuwon Omolaja Belo, Luis Beloukas, Apostolos Beneke, Alice A. Bettencourt, Paulo J.G. Bhagavathula, Akshaya Srikanth Bhala, Neeraj Bhaskar, Sonu Bisulli, Francesca Bjørge, Tone Bodunrin, Aadam Olalekan Carvajal, Alejandro Botero Bouaoud, Souad Brayne, Carol Brenner, H Department of Primary Care and Public Health University of East Anglia Norwich United Kingdom Office for Health Improvement and Disparities Department of Health and Social Care London United Kingdom Department of Legal and Economic Studies La Sapienza University Rome Italy Rome Italy Hull York Medical School University of Hull Hull United Kingdom Department of Mathematics and Sciences Ajman University Ajman United Arab Emirates Department of Medicine Memorial University St. John's NL Canada Postgraduate Department University of Sierra Sur Miahuatlan de Porfirio Diaz Mexico Yhteiskuntadatatieteen keskus (Centre for Social Data Science) Helsinki Finland Department of Internal Medicine Federal Medical Centre Abuja Nigeria Research Center for Immunodeficiencies Tehran University of Medical Sciences Tehran Iran Department of Medical Biochemistry and Biophysics Karolinska Institutet (Karolinska Institute) Stockholm Sweden Department of Clinical Sciences University of Sharjah Sharjah United Arab Emirates Department of Biopharmaceutics and Clinical Pharmacy University of Jordan Amman Jordan Medical Research Center Hamad Medical Corporation Doha Qatar Department of Biochemistry and Molecular Medicine Alfaisal University Riyadh Saudi Arabia College of Graduate Health Sciences University of Tennessee Memphis TN United States School of Medicine Sydney NSW Australia Centre for Social Research in Health University of New South Wales Sydney NSW Australia Internal Medicine and Alcohol Related Disease Unit Fondazione Policlinico Universitario A. Gemelli IRCCS Rome Italy Department of Medical and Surgical Sciences Università Cattolica di Roma (Catholic University of Rome) Rome Italy Department of Obstetrics and Gynecology University of Texas Medical Branch Galveston TX United States Department of Biochemistry Osun State University Osogbo Nigeria Department of Pharmacology and Therapeutics University of Medical Sciences Ondo Ondo Nigeria Department of Veteri

Background: Decades of steady improvements in life expectancy in Europe slowed down from around 2011, well before the COVID-19 pandemic, for reasons which remain disputed. We aimed to assess how changes in risk factors and cause-specific death rates in different European countries related to changes in life expectancy in those countries before and during the COVID-19 pandemic. Methods: We used data and methods from the Global Burden of Diseases, Injuries, and Risk Factors Study 2021 to compare changes in life expectancy at birth, causes of death, and population exposure to risk factors in 16 European Economic Area countries (Austria, Belgium, Denmark, Finland, France, Germany, Greece, Iceland, Ireland, Italy, Luxembourg, the Netherlands, Norway, Portugal, Spain, and Sweden) and the four UK nations (England, Northern Ireland, Scotland, and Wales) for three time periods: 1990–2011, 2011–19, and 2019–21. Changes in life expectancy and causes of death were estimated with an established life expectancy cause-specific decomposition method, and compared with summary exposure values of risk factors for the major causes of death influencing life expectancy. Findings: All countries showed mean annual improvements in life expectancy in both 1990–2011 (overall mean 0·23 years [95% uncertainty interval [UI] 0·23 to 0·24]) and 2011–19 (overall mean 0·15 years [0·13 to 0·16]). The rate of improvement was lower in 2011–19 than in 1990–2011 in all countries except for Norway, where the mean annual increase in life expectancy rose from 0·21 years (95% UI 0·20 to 0·22) in 1990–2011 to 0·23 years (0·21 to 0·26) in 2011–19 (difference of 0·03 years). In other countries, the difference in mean annual improvement between these periods ranged from –0·01 years in Iceland (0·19 years [95% UI 0·16 to 0·21] vs 0·18 years [0·09 to 0·26]), to –0·18 years in England (0·25 years [0·24 to 0·25] vs 0·07 years [0·06 to 0·08]). In 2019–21, there was an overall decrease in mean annual life expectancy a

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Predicting Microsatellite Instability from Histology Images with Dilated Neighborhood Attention Transformer in Colorectal Cancer 24

Predicting Microsatellite Instability from Histology Images ...

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24th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2024

作者： Chen, Yun-Chi Chao, Tung Phandita, Wimaya Nitya Sun, Tzu-Yu Wang, Huai-Zhi Hsieh, Yi-Hsien Hsu, Le-Yin Lin, Che Taipei Taiwan College of Bioresources and Agriculture NTU Taipei Taiwan National Taiwan University of Science and Technology Department of Computer Science and Information Engineering Taipei Taiwan Graduate Institute of Communication Engineering NTU Taipei Taiwan NTU Data Science Degree Program Taipei Taiwan NTU Department of Electrical Engineering Taipei Taiwan Center for Advanced Computing and Imaging in Biomedicine NTU Taipei Taiwan NTU Smart Medicine and Health Informatics Program Taipei Taiwan

ISBN: (纸本)9798331518622

Microsatellite instability (MSI) is a pivotal genetic marker influencing the efficacy of immunotherapy in colorectal cancer. Traditional MSI examination often requires additional genetic or immunohistochemical tests, whereas histology images, widely available in colorectal cancer diagnosis, offer a valuable alternative for MSI prediction. Although Transformer-based models have demonstrated promising outcomes in predicting MSI from histology images, they are hampered by traditional local attention mechanisms that struggle to capture long-range interdependencies and establish a comprehensive global receptive field. In this study, we introduce DiNAT-MSI, a novel framework for histology-based MSI prediction that incorporates the Dilated Neighborhood Attention Transformer (DiNAT). This model enhances global context recognition and substantially expands receptive fields, all without additional computational burden. Our results demonstrate that DiNAT-MSI achieves a superior patientwise AUROC compared to ResNet18 and Swin Transformer, along with commendable explainability. Our work not only illustrates a more accessible diagnostic tool for leveraging histological data but also underscores the potential of Transformerbased models with sophisticated attention designs in advancing precision medicine for colorectal cancer patients. © 2024 IEEE.

关键词： Diseases

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