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arXiv 2024年

作者： Tang, Xiangru Dai, Howard Knight, Elizabeth Wu, Fang Li, Yunyang Li, Tianxiao Gerstein, Mark Department of Computer Science Yale University New HavenCT06520 United States School of Medicine Yale University New HavenCT06520 United States Computer Science Department Stanford University CA94305 United States Program in Computational Biology & Bioinformatics Yale University New HavenCT06520 United States Department of Molecular Biophysics & Biochemistry Yale University New HavenCT06520 United States Department of Statistics & Data Science Yale University New HavenCT06520 United States Department of Biomedical Informatics & Data Science Yale University New HavenCT06520 United States

Artificial intelligence (AI)-driven methods can vastly improve the historically costly drug design process, with various generative models already in widespread use. Generative models for de novo drug design, in particular, focus on the creation of novel biological compounds entirely from scratch, representing a promising future direction. Rapid development in the field, combined with the inherent complexity of the drug design process, creates a difficult landscape for new researchers to enter. In this survey, we organize de novo drug design into two overarching themes: small molecule and protein generation. Within each theme, we identify a variety of subtasks and applications, highlighting important datasets, benchmarks, and model architectures and comparing the performance of top models. We take a broad approach to AI-driven drug design, allowing for both micro-level comparisons of various methods within each subtask and macro-level observations across different fields. We discuss parallel challenges and approaches between the two applications and highlight future directions for AI-driven de novo drug design as a whole. An organized repository of all covered sources is available at https://***/gersteinlab/GenAI4Drug. © 2024, CC BY.

关键词： Proteins

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Surgical Instrument Detection for Laparoscopic Surgery using Deep Learning 19

Surgical Instrument Detection for Laparoscopic Surgery using...

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19th International Conference on Electrical Engineering/Electronics, Computer, Telecommunications and Information Technology, ECTI-CON 2022

作者： Boonkong, Apiwat Hormdee, Daranee Sonsilphong, Suphachoke Khampitak, Kovit Khon Kaen University Embedded System RandD Group Computer Engineering Khon Kaen Thailand Khon Kaen University Data Science and Health Informatics Program Academic Affairs Khon Kaen Thailand Khon Kaen University Faculty of Medicine Department of Obstetrics and Gynecology Khon Kaen Thailand

ISBN: (纸本)9781665485845

Laparoscopic surgery has transformed conventional open surgery. Robot-Assisted laparoscopic surgery which is minimally invasive is effective for operations in limited space. Nevertheless, the robotic system which is utilized in such surgery can inflict impair to the surgical instruments, organs, or tissues as a consequence of the narrow field of view and space available to operate, and insufficient tactile response. In laparoscopy, the surgeon observes what he operates via digital images which are displayed on a monitor. In addition to the surgeon's expertise, the image-guided surgery system could offer him significant support if that system is capable of understanding those images. Computer Vision has been able to proceed due to the emergence of Machine Learning, and especially Deep Learning. This paper applies Deep Learning for surgical instrument detection for laparoscopic surgery. The fastest model, based on results trained on the COCO 2017 dataset on TensorFlow Framework, for each of 4 algorithms-Faster-RCNN, SSD, CenterNet and EfficientDet-from Model Zoo, along with YOLOv4 on Darknet Framework, have been investigated in this work. The evaluation metrics used are Precision, Recall and F1-score. The results reveal that each model plays its part well;however, YOLOv4 seemed to breakthrough this statement by offering grate result for all three accuracy metrics. © 2022 IEEE.

关键词： Laparoscopy

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

Predicting Microsatellite Instability from Histology Images ...

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IEEE Symposium on Bioinformatics and Bioengineering (BIBE)

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

ISBN: (数字)9798331518622

ISBN: (纸本)9798331518639

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.

关键词： Attention mechanisms Histopathology Computational modeling Precision medicine Small satellites Immunotherapy Colorectal cancer Predictive models Transformers Genetics

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Improvement of Jakarta's air quality during large scale social restriction 2

Improvement of Jakarta's air quality during large scale soci...

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2nd International Conference on Biospheric Harmony Advanced Research, ICOBAR 2020

作者： Rahutomo, R. Purwandari, K. Sigalingging, J.W.C. Pardamean, B. Information System Department School of Information Systems Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Master of Computer Science Program Bina Nusantara University Jakarta11480 Indonesia Database Center Division of BMKG Meteorological Climatological and Geophysical Agency Jakarta10720 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia

After Large-Scale Social Restriction (PSBB) established in Jakarta, a change of air quality was indicated by the citizens. Representatives of Indonesia's Agency for Meteorology, Climatology, and Geophysics (BMKG) supported as the fact that mobility of Jakarta's citizen and commuters were reduced. With utilizing Weather data Acquisition System managed by BMKG, this research compared fluctuations of Jakarta's air quality during two periods of time: Pre-PSBB and During-PSBB. This study proved that Jakarta's air quality has positively improved compared to the previous year, although in the lower range of unhealthy level. © Published under licence by IOP Publishing Ltd.

关键词： Air quality

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Deep Learning as a Vector Embedding Model for Customer Churn

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Procedia Computer science 2021年 179卷 624-631页

作者： Tjeng Wawan Cenggoro Raditya Ayu Wirastari Edy Rudianto Mochamad Ilham Mohadi Dinne Ratj Bens Pardamean Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 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

To face the tight competition in the telecommunication industry, it is important to minimize the rate of customers stopping their service subscription, which is known as customer churn. For that goal, an explainable predictive customer churn model is an essential tool to be owned by a telecommunication provider. In this paper, we developed the explainable model by utilizing the concept of vector embedding in Deep Learning. We show that the model can reveal churning customers that can potentially be converted back to use the previous telecommunication service. The generated vectors are also highly discriminative between the churning and loyal customers, which enable the developed models to be highly predictive for determining whether a customer would cease his/her service subscription or not. The best model in our experiment achieved a predictive performance of 81.16%, measured by the F1 Score. Further analysis on the clusters similarity and t-SNE plot also confirmed that the generated vectors are discriminative for churn prediction.

关键词： customer churn customer behavior deep learning vector embedding representation learning

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A Design of Polygenic Risk Model with Deep Learning for Colorectal Cancer in Multiethnic Indonesians

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Procedia Computer science 2021年 179卷 632-639页

作者： Steven Amadeus Tjeng Wawan Cenggoro Arif Budiarto Bens Pardamean Computer Science Department BINUS Graduate Program – Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480

Recently, health management is emerging and attract attention to how to provide better prognostication and health management systems. The challenges in the prognostication are how to develop a model that can self-learn the prognostication features and how to get a high accuracy prediction. Prognostication in health disease involves SNPs which is a genetic marker. In this paper, we propose a polygenic risk model using deep learning: Transformer with self-attention mechanism and DeepLIFT. The use of these deep learning model allows us to predict the risk of colorectal cancer and see the correlation between SNPs.

关键词： Prognostication Polygenic Risk Model Transformer Model DeepLIFT Colorectal Cancer

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Quantum Fourier Transform of Atrial Fibrillation

Quantum Fourier Transform of Atrial Fibrillation

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Quantum Computing and Engineering (QCE), IEEE International Conference on

作者： Yu-Ching Chen Chih-Yu Chen Tsung-Wei Huang Chia-Ho Ou Master Program in Intelligent Computing and Big Data Chung Yuan Christian University Taoyuan Taiwan Quantum Information Center Chung Yuan Christian University Taoyuan Taiwan Department of Computer Science and Information Engineering National Pingtung University Pingtung Taiwan

ISBN: (数字)9798331541378

ISBN: (纸本)9798331541385

Electrocardiograms (ECGs) are crucial for detecting cardiac diseases like atrial fibrillation (AF). Traditional analysis methods like fast Fourier transform (FFT) face challenges with increasing data complexity. This study uses Taipei Veterans General Hospital data to explore quantum Fourier transform (QFT) for ECG analysis. Results show that QFT effectively analyzes ECG signals, matching FFT performance while benefiting from quantum computing's efficiency.

关键词： Heart Quantum computing Fast Fourier transforms Hospitals High performance computing Atrial fibrillation Machine learning Electrocardiography Real-time systems Signal analysis

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Impact of CLAHE-based image enhancement for diabetic retinopathy classification through deep learning

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Procedia Computer science 2023年 216卷 57-66页

作者： Mira Hayati Kahlil Muchtar Roslidar Novi Maulina Irfan Syamsuddin Gregorius Natanael Elwirehardja Bens Pardamean Department of Electrical and Computer Engineering Universitas Syiah Kuala Banda Aceh 23111 Indonesia Telematics Research Center (TRC) Universitas Syiah Kuala Banda Aceh 23111 Indonesia Faculty of Medicine Universitas Syiah Kuala Banda Aceh 23111 Indonesia Department of Computer and Networking Engineering Politeknik Negeri Ujung Pandang Makassar 90245 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta 11480 Indonesia Computer Science Department BINUS Graduate Program – Master of Computer Science Program Bina Nusantara University Jakarta 11480 Indonesia

Diabetic retinopathy (DR) is a type of diabetes mellitus that attacks the retina of the eye. DR will cause patients to experience blindness slowly. Generally, DR can be detected by using a special instrument called an ophthalmoscope to view the inside of the eyeball. However, in conditions where there is a very small difference between the normal image and the DR image, computer-based assistance is needed for maximizing image reading value. In this research, a method of image quality improvement will be carried out which will then be integrated with a classification algorithm based on deep learning. The results of image improvement using Contrast Limited Adaptive Histogram Equalization (CLAHE) shows that the average accuracy of the method on several models is very competitive, 91% for the VGG16 model, 95% for InceptionV3, and 97% for EfficientNet compared to the results original image which only has an accuracy of 87% for VGG16 model, 90% for InceptionV3 model, and 95% for EfficientNet. However, in ResNet34 better accuracy is obtained in the original image with an accuracy of 95% while in the CLAHE image the accuracy value is only 84%. The results of this comprehensive evaluation and recommendation of famous backbone networks can be useful in the computer-aided diagnosis of diabetic retinopathy.

关键词： Diabetic retinopathy Deep Learning CNN Image Enhancement CLAHE

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Female sex hormones and the oral contraceptive pill modulate asthma severity through GLUT-1

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Mucosal Immunology 2025年第3期18卷 656-667页

作者： Brown, Alexandra C. Carroll, Olivia R. Mayall, Jemma R. Zounemat-Kermani, Nazanin Vinzenz, Samantha L.E. Gomez, Henry M. Mills, Ed F. Kim, Richard Y. Donovan, Chantal Baines, Katherine J. Williams, Evan J. Berthon, Bronwyn S. Wynne, Katie Scott, Hayley A. Pinkerton, James W. Guo, Yike Hansbro, Philip M. Foster, Paul S. Wark, Peter A.B. Dahlen, Sven-Erik Adcock, Ian M. Wood, Lisa G. Horvat, Jay C. The University of Newcastle and Immune Health Program Hunter Medical Research Institute Newcastle NSW Australia The Data Science Institute Department of Computing Imperial College London United Kingdom School of Life Sciences Faculty of Science University of Technology Sydney Sydney NSW Australia Respiratory Pharmacology & Toxicology Group National Heart & Lung Institute Imperial College London London United Kingdom Centre for Inflammation Centenary Institute and Faculty of Science University of Technology Sydney Sydney NSW Australia Clinical Lung and Allergy Research Unit Department of Medicine Huddinge Karolinska Institutet and Department of Respiratory Medicine and Allergy Karolinska University Hospital Huddinge and Unit of Integrative Metabolomics Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden The Airway Disease Section National Heart & Lung Institute Imperial College London London United Kingdom Woolcock Institute of Medical Research Sydney NSW Australia School of Translational Medicine Monash University Melbourne VIC Australia Woolcock Institute of Medical Research and Faculty of Medicine Health and Human Sciences Macquarie University Sydney NSW Australia Hong Kong University of Science and Technology Hong Kong

Females are disproportionately affected by asthma. An increased understanding of how female sex hormones influence key pathophysiological processes that underpin asthma may identify new, more effective asthma therapies, particularly for females with severe, poorly controlled asthma. We assessed the effects of oral ethinylestradiol/levonorgestrel (representing OCP use) and depot-medroxyprogesterone acetate (DMPA) and estradiol injections on key features of experimental asthma, and determined their effects on glucose transporter-1 (GLUT-1). The effects of OCP use on clinical asthma outcomes, and the relationships between estrogen receptors and type 2 (T2), non-T2, and GLUT-1 responses, in clinical asthma were also determined. OCP and DMPA reduce T2 responses, disease features, and lung expression of GLUT-1, whereas estradiol increases lung expression of GLUT-1, and results in severe, corticosteroid-insensitive, neutrophil-enriched disease, in experimental asthma. OCP use is associated with reduced T2 cytokine and GLUT-1 responses in clinical asthma. GLUT-1 expression is increased in sputum of severe asthmatics, and positively correlates with estrogen receptor expression and both T2 and non-T2 inflammatory responses. Significantly, OCP or GLUT-1 inhibition protects against obesity-associated or estradiol-induced, severe, experimental asthma, respectively. Together, these data show how female sex hormones and the OCP likely modulate asthma severity by modifying GLUT-1 responses in the airways. © 2025 The Authors

关键词： Asthma Estrogen GLUT-1 oral contraceptive pill (OCP) Progesterone

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Entity-level Factual Adaptiveness of Fine-tuning based Abstractive Summarization Models

arXiv

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arXiv 2024年

作者： Song, Jongyoon Park, Nohil Hwang, Bongkyu Yun, Jaewoong Joe, Seongho Gwon, Youngjune L. Yoon, Sungroh Data Science & AI Laboratory Seoul National University Korea Republic of Samsung SDS Korea Republic of Deptment of ECE and Interdisciplinary Program in AI Seoul National University Korea Republic of ASRI INMC AIIS Seoul National University Korea Republic of

Abstractive summarization models often generate factually inconsistent content particularly when the parametric knowledge of the model conflicts with the knowledge in the input document. In this paper, we analyze the robustness of fine-tuning based summarization models to the knowledge conflict, which we call factual adaptiveness. We utilize pre-trained language models to construct evaluation sets and find that factual adaptiveness is not strongly correlated with factual consistency on original datasets. Furthermore, we introduce a controllable counterfactual data augmentation method where the degree of knowledge conflict within the augmented data can be adjustable. Our experimental results on two pre-trained language models (PEGASUS and BART) and two fine-tuning datasets (XSum and CNN/DailyMail) demonstrate that our method enhances factual adaptiveness while achieving factual consistency on original datasets on par with the contrastive learning baseline. Copyright © 2024, The Authors. All rights reserved.

关键词： Machine learning

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