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KNU-DTI: KNowledge United Drug-Target Interaction prediction

computers in Biology and Medicine 2025年 189卷 109927-109927页

作者： Heo, Ryong Lee, Dahyeon Kim, Byung Ju Seo, Sangmin Park, Sanghyun Park, Chihyun Interdisciplinary Graduate Program in Medical Bigdata Convergence Kangwon National University Gangwon-do Chuncheon-si24341 Korea Republic of Department of Data Science Kangwon National University Korea Republic of UBLBio Corporation Yeongtong-ro 237 Gyeonggi-do Suwon16679 Korea Republic of Department of Computer Science Yonsei University Yonsei-ro 50 Seodaemun-gu Seoul03722 Korea Republic of Department of Computer Science and Engineering Kangwon National University Korea Republic of

Motivation: Accurately predicting drug-target protein interactions (DTI) is a cornerstone of drug discovery, enabling the identification of potential therapeutic compounds. Sequence-based prediction models, despite their simplicity, hold great promise in extracting essential information directly from raw sequences. However, the focus in recent DTI studies has increasingly shifted toward enhancing algorithmic complexity, often at the expense of fully leveraging robust sequence representation learning methods. This shift has led to the underestimation and gradual neglect of methodologies aimed at effectively capturing discriminative features from sequences. Our work seeks to address this oversight by emphasizing the value of well-constructed sequence representation algorithms, demonstrating that even with simple interaction mapping algorithm techniques, accurate DTI models can be achieved. By prioritizing meaningful information extraction over excessive model complexity, we aim to advance the development of practical and generalizable DTI prediction frameworks. Results: We developed the KNowledge Uniting DTI model (KNU-DTI), which retrieves structural information and unites them. Protein structural properties were obtained using structural property sequence (SPS). Extended-connectivity fingerprint (ECFP) was used to estimate the structure-activity relationship in molecules. Including these two features, a total of five latent vectors were derived from protein and molecule via various neural networks and integrated by elemental-wise addition to predict binding interactions or affinity. Using four test concepts to evaluate the model, we show that the model outperforms recently published competitors. Finally, a case study indicated that our model has a competitive edge over existing docking simulations in some cases. © 2025

关键词： Prediction models

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A deep learning system for predicting time to progression of diabetic retinopathy

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NATURE MEDICINE 2024年第2期30卷 358-359页

作者： [Anonymous] Shanghai Belt and Road International Joint Laboratory for Intelligent Prevention and Treatment of Metabolic Disorders Department of Computer Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Department of Endocrinology and Metabolism Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine Shanghai Diabetes Institute Shanghai Clinical Center for Diabetes Shanghai China MOE Key Laboratory of AI School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai China Department of Ophthalmology Huadong Sanatorium Wuxi China Department of Ophthalmology Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine Shanghai China Department of Ophthalmology and Visual Sciences The Chinese University of Hong Kong Hong Kong China Singapore Eye Research Institute Singapore National Eye Centre Singapore Singapore Department of Computer Science and Engineering The Hong Kong University of Science and Technology Hong Kong China Department of Chemical and Biological Engineering The Hong Kong University of Science and Technology Hong Kong China State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center Sun Yat-sen University Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science Guangzhou China Department of Ophthalmology Peking Union Medical College Hospital Peking Union Medical College Chinese Academy of Medical Sciences Beijing China Medical Records and Statistics Office Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine Shanghai China Department of Geriatrics Tongji Hospital Tongji Medical College Huazhong University of Science and Technology Wuhan China National Engineering Research Center for Big Data Technology and System Services Computing Technology and System Lab Cluster and Grid Computing Lab School of Computer Science and Tech

We developed and validated a deep learning system (termed DeepDR Plus) in a diverse, multiethnic, multi-country dataset to predict personalized risk and time to progression of diabetic retinopathy. We show that DeepDR Plus can be integrated into the clinical workflow to promote individualized intervention strategies for the management of diabetic retinopathy.

关键词： Diabetes complications Machine learning Predictive markers

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Interactive Facial Expression Editing with Non-linear Blendshape Interpolation

Interactive Facial Expression Editing with Non-linear Blends...

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43rd Annual Conference on European Association for computer Graphics, EUROGRAPHICS 2022

作者： Roh, Ji Hyun Kim, Seong Uk Jang, Hanyoung Seol, Yeongho Kim, Jongmin Department of Computer Science and Engineering Kangwon National University Korea Republic of Interdisciplinary Graduate Program in Medical Bigdata Convergence Kangwon National University Korea Republic of Game AI Lab NC Korea Republic of NVIDIA Korea Republic of

ISBN: (纸本)9783038681694

The ability to manipulate facial animations interactively is vital for enhancing the productivity and quality of character animation. In this paper, we present a novel interactive facial animation editing system that can express the naturalness of non-linear facial movements in real-time. The proposed system is based on a fully automatic algorithm that maintains all positional constraints while deforming the facial mesh as realistic as possible. Our method is based on direct manipulation with non-linear blendshape interpolation. We formulate the facial animation editing as a two-step quadratic minimization and solve it efficiently. From our results, the proposed method produces the desired and realistic facial animation better compared to existing mesh deformation methods, which are mainly based on linear combination and optimization. © 2022 The Author(s).

关键词： Interpolation

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Protein codes promote selective subcellular compartmentalization

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science 2025年第6738期387卷 1095-1101页

作者： Kilgore, Henry R. Chinn, Itamar Mikhael, Peter G. Mitnikov, Ilan Van Dongen, Catherine Zylberberg, Guy Afeyan, Lena Banani, Salman F. Wilson-Hawken, Susana Lee, Tong Ihn Barzilay, Regina Young, Richard A. Whitehead Institute for Biomedical Research Cambridge MA United States Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology (MIT) Cambridge MA United States Abdul Latif Jameel Clinic for Machine Learning in Health MIT Cambridge MA United States Department of Biology MIT Cambridge MA United States Department of Pathology Brigham and Women's Hospital Harvard Medical School Boston MA United States Computational and Systems Biology Program MIT Cambridge MA United States

Cells have evolved mechanisms to distribute ~10 billion protein molecules to subcellular compartments where diverse proteins involved in shared functions must assemble. In this study, we demonstrate that proteins with shared functions share amino acid sequence codes that guide them to compartment destinations. We developed a protein language model, ProtGPS, that predicts with high performance the compartment localization of human proteins excluded from the training set. ProtGPS successfully guided generation of novel protein sequences that selectively assemble in the nucleolus. ProtGPS identified pathological mutations that change this code and lead to altered subcellular localization of proteins. Our results indicate that protein sequences contain not only a folding code but also a previously unrecognized code governing their distribution to diverse subcellular compartments. Copyright © 2025 the authors, some rights reserved.

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Three-dimensional C-scan-based generation adversarial network with synthetic input to improve optical coherence tomography angiography

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Journal of Biomedical Optics 2025年第5期30卷 056006页

作者： Xu, Jingjiang Feng, Zhongwu Qiu, Haixia Tang, Peijun Gao, Kai Huang, Yanping Lan, Gongpu Qin, Jia An, Lin Jia, Gangyong Wu, Qing Foshan University Guangdong-Hong Kong-Macao Intelligent Micro-Nano Optoelectronic Technology Joint Laboratory Foshan China Guangdong Weiren Meditech Co. Ltd Innovation and Entrepreneurship Teams Project of Guangdong Pearl River Talents Program Foshan China Foshan University School of Mechatronic Engineering and Automation Foshan China Chinese PLA General Hospital The First Medical Centre Department of Laser Medicine Beijing China South China Normal University College of Biophotonics Guangzhou China Sun Yat-sen University Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science State Key Laboratory of Ophthalmology Guangdong Provincial Clinical Research Center for Ocular Diseases Zhongshan Ophthalmic Center Guangzhou China Hangzhou Dianzi University School of Computer Science Hangzhou China

Significance: Optical coherence tomography angiography (OCTA) usually suffers from the inherent random fluctuations of noise and speckles in the imaging system. Previous deep learning methods have mainly focused on improving the quality of B-scan blood flow images or en face projection images. We propose a deep learning method to reconstruct high-quality 3D vasculature, which fully utilizes the volumetric OCTA data and the topological features of the vascular network. Aim: We propose a deep learning method called the three-dimensional C-scanbased generation adversarial network (3DCS-GAN) to improve vascular visualization for volumetric OCTA data. Approach: To train the network, we superimposed the single-shot en face OCTA images on avascular noisy C-scan images to synthesize the input data and used the multiple averaged en face OCTA images as the reference labels. The deep learning algorithm is based on Pix2Pix architecture and consists of a generator model and a discriminator model. A perceptual loss function was utilized by combining content loss and adversarial loss. The proposed algorithm is applied to the C-scan images depth-by-depth to suppress the background noise and enhance vascular visualization in the 3D OCTA data. Results: The proposed method has improved the contrast-to-noise ratio of crosssectional OCTA images by ∼2 times. It greatly enhances the visualization of blood vessels in the deep layer and offers much clearer blood vessel topology in the 3D volume-rendering of OCTA. 3DCS-GAN has exhibited superior image enhancement compared with alternative methods. It has been used to enhance the OCTA images of port wine stain disease for clinical investigation. Conclusions: It demonstrates that the proposed 3DCS-GAN can greatly improve vascular visualization in the deep layer, provide better image quality than the multiple averaged OCTA images, and achieve superior image enhancement for volumetric OCTA data. © 2025 SPIE. All rights reserved.

关键词： Image enhancement

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High Spatial Resolution Terahertz Time-Domain Imaging of Murine Pancreatic Ductal Adenocarcinoma Tissues

High Spatial Resolution Terahertz Time-Domain Imaging of Mur...

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2023 Conference on Lasers and Electro-Optics, CLEO 2023

作者： Chakraborty, Debamitra Mills, Bradley N. Cheng, Jing Komissarov, Ivan Gerber, Scott Sobolewski, Roman Materials Science Graduate Program University of Rochester RochesterNY14627-1299 United States Laboratory for Laser Energetics University of Rochester RochesterNY14623 United States Department of Surgery University of Rochester Medical Center RochesterNY14642 United States Department of Electrical and Computer Engineering University of Rochester RochesterNY14627-0231 United States

We developed a terahertz time-domain spectroscopy system to generate high-resolution 2-dimensional images of paraffin-embedded murine pancreatic ductal adenocarcinoma tissues using the refractive index and absorption ... 详细信息

ISBN: (纸本)9781957171258

关键词： Tissue

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Predicting Metabolic Syndrome With Machine Learning Models of Hybrid Analysis

Predicting Metabolic Syndrome With Machine Learning Models o...

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2023 International Conference on Consumer Electronics - Taiwan, ICCE-Taiwan 2023

作者： Wu, Yi-Syuan Wang, Wei-Yun Wu, Hao-Yi Chen, Chao-Wen Chu, Chi-Ming Wu, Cheng-Wei Division of Trauma and Surgical Critical Care Department of Surgery Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan Master Program of E-Learning for Multimedia and Network Communications National I-Lan University Yilan Taiwan National Defense Medical Center Tri-Service General Hospital Songshan Branch School of Nursing Department of Nursing Taipei Taiwan National Defense Medical Center Department of Nursing Tri-Service General Hospital Taipei Taiwan Kaohsiung Medical University Hospital Kaohsiung Medical University Trauma and Critical Care Service Department of Surgery Kaohsiung Taiwan National Defense Medical Center School of Public Health Taipei Taiwan National I-Lan University Department of Computer Science and Information Engineering Yilan Taiwan

ISBN: (纸本)9798350324174

The study uses machine learning to determine the accuracy of different algorithms for predicting MetS. Early prediction of MetS through routine health screening is an important goal for preventive medicine. The subjects in this study were employees aged 20 to 65 years old who signed a consent form for in-hospital health screening data were collected from 2015 to 2020. Total of 3538 individuals who underwent health screening were included in this study. Baseline characteristics of the 315 participants diagnosed with metabolic syndrome and 3222 participants without metabolic syndrome. This is a machine learning approach to identify metabolic syndrome using biochemical values and lifestyle habits. We found that the F1 score for detection of metabolic syndrome by neural network is the most accurate and higher compared to other models. Our study also identified some new indicators, including heart rhythm, RBC, WBC, Hb, and uric acid, as candidates for better detection of metabolic syndrome. © 2023 IEEE.

关键词： Forecasting

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A data-driven approach to discover and quantify systemic lupus erythematosus etiological heterogeneity from electronic health records

arXiv

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arXiv 2025年

作者： Mota, Marco Barbero Still, John M. Gamboa, Jorge L. Strobl, Eric V. Stein, Charles M. Kawai, Vivian K. Lasko, Thomas A. Vanderbilt University Medical Center Department of Biomedical Informatics United States Vanderbilt University Medical Center Department of Medicine United States Vanderbilt University Medical Center Department of Psychiatry and Behavioral Sciences United States Vanderbilt University Medical Center Department of Computer Science United States Vanderbilt DBMI PhD program 2525 West End Ave NashvilleTN United States

Systemic lupus erythematosus (SLE) is a complex heterogeneous disease with many manifestational facets. We propose a data-driven approach to discover probabilistic independent sources from multimodal imperfect EHR data. These sources represent exogenous variables in the data generation process causal graph that estimate latent root causes of the presence of SLE in the health record. We objectively evaluated the sources against the original variables from which they were discovered by training supervised models to discriminate SLE from negative health records using a reduced set of labelled instances. We found 19 predictive sources with high clinical validity and whose EHR signatures define independent factors of SLE heterogeneity. Using the sources as input patient data representation enables models to provide with rich explanations that better capture the clinical reasons why a particular record is (not) an SLE case. Providers may be willing to trade patient-level interpretability for discrimination especially in challenging cases. © 2025, CC BY-NC-ND.

关键词： Electronic health record

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Comparisons of Student Outcomes and Evaluations in Hybrid Versus Face-to-Face Anatomy and Physiology I Courses

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Journal of College science Teaching 2021年第1期51卷 58-66页

作者： Jafar, Sanjeeda Sitther, Viji Medical Laboratory Science Program School of Computer Mathematical and Natural Sciences (SCMNS) Morgan State University Baltimore MD United States Department of Biology in SCMNS Morgan State University Baltimore MD United States

In this study, two sections of undergraduate Introductory Anatomy and Physiology taught in the traditional face-to-face format (n = 58) was compared to two hybrid classes (n = 38) using the flipped-classroom model taught by the same instructor. Formative and summative examination scores were compared to determine the effect of the different learning methods. Our results revealed no significant difference between the mean scores of summative examinations and between the traditional and hybrid classes (p > 0.05). Of five quizzes administered, students taught in the traditional format scored significantly higher in only one of five quizzes. In addition, comparison of in-class laboratory examination scores showed no difference (P > 0.05) in three out of four. However, student evaluations of the hybrid classes were more positive as determined by end-of-course evaluations (4.54 versus 2.9 on a 1–5 Likert scale). This is the first study that compares a hybrid versus a traditional science course at a historically black college or university. We conclude that comparison of student outcomes in traditional versus hybrid Anatomy and Physiology I classes were similar. At a time when all institutions of higher learning have adopted online learning and distance learning due to the COVID-19 pandemic, this is a timely comparison. © 2021 National science Teaching Association.

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Design and Development of Low-cost Wearable Electroencephalograms (EEG) Headset

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Intelligent Automation & Soft Computing 2023年第3期35卷 2821-2835页

作者： Riaz Muhammad Ahmed Ali M.Abid Anwar Toufique Ahmed Soomro Omar AlShorman Adel Alshahrani Mahmoud Masadeh Ghulam Md Ashraf Naif H.Ali Muhammad Irfan Athanasios Alexiou Department of Electrical Engineering Sukkur IBA University65200SukkurPakistan Department of Electronic Engineering Quaid-e-Awam University of EngineeringScience and TechnologyLarkana77150Pakistan Faculty of Engineering and AlShrouk Trading Company Najran UniversityNajran61441Saudi Arabia Department of Medical Rehabilitation Sciences-Physiotherapy Program College of Applied Medical SciencesNajran UniversityNajran61441Saudi Arabia Computer Engineering Department Yarmouk UniversityIrbid21163Jordan Pre-Clinical Research Unit King Fahd Medical Research CenterKing Abdulaziz UniversityJeddah21589Saudi Arabia Department of Medical Laboratory Technology Faculty of Applied Medical SciencesKing Abdulaziz UniversityJeddah21589Saudi Arabia Department of Internal Medicine Medical CollegeNajran UniversityNajran61441Saudi Arabia Electrical Engineering Department College of EngineeringNajran University Saudi ArabiaNajran61441Saudi Arabia Novel Global Community Educational Foundation HebershamNSW 2770AustraliaAFNP Med AustriaWien2770Austria

Electroencephalogram(EEG)is a method of capturing the electrophy-siological signal of the *** EEG headset is a wearable device that records electrophysiological data from the *** paper presents the design and fab-rication of a customized low-cost Electroencephalogram(EEG)headset based on the open-source OpenBCI Ultracortex Mark IV *** electrode placement locations are modiﬁed under a 10–20 standard *** fabricated headset is then compared to commercially available headsets based on the following para-meters:affordability,accessibility,noise,signal quality,and ***,the data is recorded from 20 subjects who used the EEG Headset,and signals were ***,the participants marked the accuracy,set up time,participant comfort,and participant perceived ease of set-up on a scale of 1 to 7(7 being excellent).Thirdly,the self-designed EEG headband is used by 5 participants for slide *** raw EEG signal is decomposed into a series of band sig-nals using discrete wavelet transform(DWT).Lastly,theseﬁndings have been compared to previously reported *** concluded that when used for slide-changing control,our self-designed EEG headband had an accuracy of 82.0 *** also concluded from the results that our headset performed well on the cost-effectiveness scale,had a reduced setup time of 2±0.5 min(the short-est among all being compared),and demonstrated greater ease of use.

关键词： Brain-computer interface EEG consumer-grade accessibility headset

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