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ORCIDBioData Mining, Volume 18
Volume 18, Number 1, 2025
- Richa Gupta, Mansi Bhandari, Anhad Grover, Taher Al-Shehari
, Mohammed Kadrie, Taha Alfakih, Hussain Alsalman:
Correction: Predictive modeling of ALS progression: an XGBoost approach using clinical features. - Getnet Bogale Begashaw, Temesgen Zewotir, Haile Mekonnen Fenta:
A deep learning approach for classifying and predicting children's nutritional status in Ethiopia using LSTM-FC neural networks. - Xingyu Li, Lu Peng, Yu-Ping Wang, Weihua Zhang:
Open challenges and opportunities in federated foundation models towards biomedical healthcare. - Davide Chicco, Alessandro Fabris, Giuseppe Jurman:
The Venus score for the assessment of the quality and trustworthiness of biomedical datasets. - Lekai Xu, Tianjun Lan, Yiqian Huang, Liansheng Wang, Junqi Lin, Xinpeng Song, Hui Tang, Haotian Cao, Hua Chai:
A generative deep neural network for pan-digestive tract cancer survival analysis. - Salman Khan, Sumaiya Noor, Tahir Javed, Afshan Naseem, Fahad Aslam, Salman A. AlQahtani, Nijad Ahmad:
XGBoost-enhanced ensemble model using discriminative hybrid features for the prediction of sumoylation sites. - Patrick Schwehn, Pascal Falter-Braun:
Inferring protein from transcript abundances using convolutional neural networks. - Tayo Obafemi-Ajayi, Steven F. Jennings, Yu Zhang, Kara Li Liu, Joan Peckham, Jason H. Moore:
AI as an accelerator for defining new problems that transcends boundaries. - Subrata Das, Vatsal Patel, Shouvik Chakravarty, Arnab Ghosh, Anirban Mukhopadhyay, Nidhan K. Biswas:
An ensemble machine learning-based performance evaluation identifies top In-Silico pathogenicity prediction methods that best classify driver mutations in cancer. - Heesang Moon, Mina Rho:
MultiChem: predicting chemical properties using multi-view graph attention network. - Lane Fitzsimmons, Undiagnosed Diseases Network, Brett K. Beaulieu-Jones, Shilpa Nadimpalli Kobren:
Enriched phenotypes in rare variant carriers suggest pathogenic mechanisms in rare disease patients. - Yi-Chou Chen, Hui-Chen Su, Shih-Ming Huang, Ching-Hsiao Yu, Jen-Huei Chang, Yi-Lin Chiu:
Immune cell profiles and predictive modeling in osteoporotic vertebral fractures using XGBoost machine learning algorithms. - Hyunwook Koh, Jihun Kim, Hyojung Jang:
MiCML: a causal machine learning cloud platform for the analysis of treatment effects using microbiome profiles. - Maryam Ramezani, Mohammadreza Mobinizadeh, Ahad Bakhtiari, Hamid R. Rabiee, Maryam Ramezani, Hakimeh Mostafavi, Alireza Olyaeemanesh, Ali Akbar Fazaeli, Alireza Atashi, Saharnaz Sazgarnejad, Efat Mohamadi, Amirhossein Takian:
Agenda setting for health equity assessment through the lenses of social determinants of health using machine learning approach: a framework and preliminary pilot study. - Peter T. Nguyen, Simon G. Coetzee, Irina Silacheva, Dennis J. Hazelett:
Genome-wide association studies are enriched for interacting genes. - Lanfang Zhang, Yuan Cai, Lin Li, Jie Hu, Changsha Jia, Xu Kuang, Yi Zhou, Zhiai Lan, Chunyan Liu, Feng Jiang, Nana Sun, Ni Zeng:
Analysis of global trends and hotspots of skin microbiome in acne: a bibliometric perspective. - Christel Sirocchi, Martin Urschler, Bastian Pfeifer:
Feature graphs for interpretable unsupervised tree ensembles: centrality, interaction, and application in disease subtyping. - Arezoo Abasi, Ahmad Nazari, Azar Moezy, Seyed Ali Fatemi Aghda:
Machine learning models for reinjury risk prediction using cardiopulmonary exercise testing (CPET) data: optimizing athlete recovery. - Ya-Ting Liang, Charlotte Wang:
Motif clustering and digital biomarker extraction for free-living physical activity analysis. - Onur Erdogan, Cem Iyigun, Yesim Aydin Son:
EnSCAN: ENsemble Scoring for prioritizing CAusative variaNts across multiplatform GWASs for late-onset alzheimer's disease. - Amr Eledkawy, Taher Hamza, Sara El-Metwally:
Towards precision oncology: a multi-level cancer classification system integrating liquid biopsy and machine learning. - Belén Serrano-Antón, Manuel Insúa Villa, Santiago Pendón-Minguillón, Santiago Paramés-Estévez, Alberto Otero-Cacho, Diego López-Otero, Brais Díaz-Fernández, María Bastos-Fernández, José Ramón González-Juanatey, Alberto P. Muñuzuri:
Unsupervised clustering based coronary artery segmentation. - Patrizia Ribino, Claudia Di Napoli, Giovanni Paragliola, Davide Chicco, Francesca Gasparini:
Multivariate longitudinal clustering reveals neuropsychological factors as dementia predictors in an Alzheimer's disease progression study. - Mina Jahangiri, Anoshirvan Kazemnejad, Keith S. Goldfeld, Maryam S. Daneshpour, Mehdi Momen, Shayan Mostafaei, Davood Khalili, Mahdi Akbarzadeh:
Leveraging mixed-effects regression trees for the analysis of high-dimensional longitudinal data to identify the low and high-risk subgroups: simulation study with application to genetic study. - Wei Jiang, Weicai Ye, Xiaoming Tan, Yun-Juan Bao:
Network-based multi-omics integrative analysis methods in drug discovery: a systematic review. - Di Zhao, Wenxuan Mu, Xiangxing Jia, Shuang Liu, Yonghe Chu, Jiana Meng, Hongfei Lin:
Few-shot biomedical NER empowered by LLMs-assisted data augmentation and multi-scale feature extraction. - Hanxiang Xu, Shizhuo Mu, Jingxuan Bao, Christos Davatzikos, Haochang Shou, Li Shen:
High-dimensional mediation analysis reveals the mediating role of physical activity patterns in genetic pathways leading to AD-like brain atrophy. - Yinyao Ma, Hanlin Lv, Yanhua Ma, Xiao Wang, Longting Lv, Xuxia Liang, Lei Wang:
Advancing preeclampsia prediction: a tailored machine learning pipeline integrating resampling and ensemble models for handling imbalanced medical data. - Ibrahim Burak Özyurt, Anita E. Bandrowski:
Automatic detection and extraction of key resources from tables in biomedical papers. - Suruthy Sivanathan, Ting Hu:
Learning the therapeutic targets of acute myeloid leukemia through multiscale human interactome network and community analysis. - Zhixuan Zeng, Yang Liu, Shuo Yao, Minjie Lin, Xu Cai, Wenbin Nan, Yiyang Xie, Xun Gong:
Inter-organ correlation based multi-task deep learning model for dynamically predicting functional deterioration in multiple organ systems of ICU patients. - Sulaiman Mohammed Alnasser:
Revisiting the approaches to DNA damage detection in genetic toxicology: insights and regulatory implications. - Xi Li, Jui-Hsuan Chang, Mythreye Venkatesan, Zhiping Paul Wang, Jason H. Moore:
Enhancing clinical outcome predictions through effective sample size evaluation in graph-based digital twin modeling. - Ya-Ting Liang, Charlotte Wang:
Correction: Motif clustering and digital biomarker extraction for free-living physical activity analysis. - Tom Tubbesing, Andreas Schlüter, Alexander Sczyrba:
subMG automates data submission for metagenomics studies. - Rachit Kumar, Joseph D. Romano, Marylyn D. Ritchie:
Network-based analyses of multiomics data in biomedicine. - Suruthy Sivanathan, Ting Hu:
Correction: Learning the therapeutic targets of acute myeloid leukemia through multiscale human interactome network and community analysis. - David M. Vidmar, Jessica K. De Freitas, Will E. Thompson, John M. Pfeifer, Brandon K. Fornwalt, Noah Zimmerman, Riccardo Miotto, Ruijun Chen:
A probabilistic approach for building disease phenotypes across electronic health records. - Berit Hunsdieck, Christian Bender, Katja Ickstadt, Johanna Mielke:
Joint models in big data: simulation-based guidelines for required data quality in longitudinal electronic health records. - Mohamed Mustaf Ahmed, Olalekan John Okesanya, Majd Oweidat, Zhinya Kawa Othman, Shuaibu Saidu Musa, Don Eliseo Lucero-Prisno III:
The ethics of data mining in healthcare: challenges, frameworks, and future directions. - Xiongbin Gui, Hanlin Lv, Xiao Wang, Longting Lv, Yi Xiao, Lei Wang:
Enhancing hepatopathy clinical trial efficiency: a secure, large language model-powered pre-screening pipeline. - Jason H. Moore, Nicholas P. Tatonetti:
Vibe coding: a new paradigm for biomedical software development. - Davide Chicco, Luca Oneto, Davide Cangelosi:
DBSCAN and DBCV application to open medical records heterogeneous data for identifying clinically significant clusters of patients with neuroblastoma. - Namareq Widatalla, Sona Al Younis, Ahsan Khandoker:
Heart rate transition patterns reveal autonomic dysfunction in heart failure with renal function decline: a symbolic and Markov model approach. - Yasaman Fatapour, James P. Brody:
A compact encoding of the genome suitable for machine learning prediction of traits and genetic risk scores. - Jiafu Cui, Siqi Yang, Litai Yi, Qilemuge Xi, Dezhi Yang, Yongchun Zuo:
Recent advances in deep learning for protein-protein interaction: a review. - Tue T. Te, Alex A. T. Bui, Constance H. Fung, Mary Regina Boland:
Geospatial analysis of short sleep duration and cognitive disability in US adults: a multi-state study using machine learning techniques. - Petr Rysavý, Alikhan Anuarbekov, Michaela Dostálová Merkerová, Jirí Kléma:
circGPAcorr: an integrative tool for functional annotation of circular RNAs using expression data. - Stefan Lenz, Arsenij Ustjanzew, Marco Jeray, Meike Ressing, Torsten Panholzer:
Can open source large language models be used for tumor documentation in Germany? - An evaluation on urological doctors' notes. - Muhammad Arshad, Chengliang Wang, Wajeeh Us Sima Muhammad, Jamshed Ali Shaikh, Hanen Karamti, Raed Alharthi, Julius Selecky:
BioAug-Net: a bioimage sensor-driven attention-augmented segmentation framework with physiological coupling for early prostate cancer detection in T2-weighted MRI. - Zhiping Paul Wang, Xi Li, Nicholas Matsumoto, Mythreye Venkatesan, Jui-Hsuan Chang, Jay Moran, Hyunjun Choi, Binglan Li, Yufei Meng, Miguel E. Hernandez, Jason H. Moore:
Drug repurposing for Alzheimer's disease using a graph-of-thoughts based large language model to infer drug-disease relationships in a comprehensive knowledge graph. - Davide Chicco, Andrea Sichenze, Giuseppe Jurman:
A simple guide to the use of Student's t-test, Mann-Whitney U test, Chi-squared test, and Kruskal-Wallis test in biostatistics. - Yu Yin, Chenkai Zhao, Yibo Hua, Fei Yang, Dandan Qiu, Jiasheng Yan, Xiaodong Jin:
Exploring the common genetic basis of metabolic syndrome-related diseases and chronic kidney disease: insights from extensive genome-wide cross-trait analyses. - Seda Ceylan, Didem Demir, Cayla Harris, Semih Latif Ipek, Vasileios Vavourakis, Marco Manca, Sandrine Dubrac, Roman Bauer:
Skin in the game: a review of computational models of the skin. - Yanpeng Jian, Shijia Dong, Weijie Liu, Genfeng Li, Xiaoyu Lian, Yigong Wang:
Mapping the evolving trend of research on efferocytosis: a comprehensive data-mining-based study. - Tanja Krueger, Damla a. Durmaz, Luisa f. Jimenez-Soto:
Exo-Tox: Identifying Exotoxins from secreted bacterial proteins. - Yang Yan, Zhong Chen, Xinglei Shen, Ronald C. Chen, Hao Gao:
Short- and long-term weekly patient-reported outcomes prediction undergoing radiotherapy: single-patient time series model vs. transformer-based multi-patient time series model. - Edoardo Taccaliti, Jesús S. Aguilar-Ruiz:
Improving classification on imbalanced genomic data via KDE-based synthetic sampling. - Mohammed Abo-Zahhad, Mostafa N. Zakaria, Farida M. Sharaf, May M. Ismaiel, Habiba Hafrag, Yousef M. Amer:
Development of an AI-powered AR glasses system for real-time first aid guidance in emergency situations. - Yao Li, Siyuan Zhou, Bichen Ren, Shuai Ju, Xiaoyan Li, Wenqiang Li, Bingzhe Li, Yunmin Cai, Chunlei Chang, Lihong Huang, Zhihui Dong:
The application of artificial intelligence models in predicting the risk of diabetic foot: a multicenter study. - Sohyun Youn, Dabin Jeong, Hwijun Kwon, Eonyong Han, Sun Kim, Inuk Jung:
Identification of severity related mutation hotspots in SARS-CoV-2 using a density-based clustering approach. - Tai-Hoon Kim, Asma Aldrees, Dina Abdulaziz Alhammadi, Muhammad Umer, Taoufik Saidani, Shtwai Alsubai, Imran Ashraf:
MediNet: ensemble transfer learning approach for classification of medical drugs-related text reviews using significant combined-embeddings. - Zhong Chen, Zichen Lao, You Lu, Wensheng Zhang, Andrea Edwards, Kun Zhang:
Decoding ancestry-specific genetic risk: interpretable deep feature selection reveals prostate cancer SNP disparities in diverse populations. - Mahboube Sadat Hosseini, Seyyed Mahmoud Reza Aghamiri, Mehdi Panahi:
Cross-regional radiomics: a novel framework for relationship-based feature extraction with validation in Parkinson's disease motor subtyping. - Zarrin Basharat, Youssef Saeed Alghamdi, Mutaib M. Mashraqi, Hanan A. Ogaly, Fatimah A. M. Al-Zahrani, Calvin R. Wei, Ibrar Ahmed, Seil Kim:
Proteome mining of Yersinia Enterocolitica for drug targets and computational inhibitor identification with ADMET, anti-inflammation potential and formulation characteristics. - Fang Yang, Jia Li, Ziyi Yang, Liping Wu, Han Wang, Chao Sun:
Construction and validation of a machine learning-based model predicting early readmission in patients with decompensated cirrhosis: a prospective two-center cohort study. - Longmin Fan, Haitao Jiang, Zheyu Zhang:
Investigating causal effects of HDL-C on cognitive function through cross-sectional and Mendelian randomization analyses: concentration-response patterns and clues for Alzheimer's disease prevention. - Lele Zhang, Hao He, Xuesen Shi:
MoRFs_TransFuse: a MoRFs predictor based on multimodal feature fusion and the lightweight Transformer network. - Goodluck Okoro, Pawel Wityk, Michael B. Nelappana, Karl A. Jackiewicz, Veronica Z. Kucharczyk, Annie Tigranyan, Catherine C. Applegate, Iwona T. Dobrucki, Lawrence W. Dobrucki:
A graph-theoretic framework for quantitative analysis of angiogenic networks. - Ahed Abugabah, Prashant Kumar Shukla, Piyush Kumar Shukla, Ankur Pandey:
An intelligent healthcare system for rare disease diagnosis utilizing electronic health records based on a knowledge-guided multimodal transformer framework. - Patrizia Ribino, Maria Mannone, Claudia Di Napoli, Giovanni Paragliola, Davide Chicco, Francesca Gasparini:
Temporal phenotyping and prognostic stratification of patients with sepsis through longitudinal clustering. - Nora Mahdavi, Arman Daliri, Mahdieh Zabihimayvan, Yalda Yaghooti, Mohammad Mahdi Mir, Parastoo Ghazanfari, Avin Zarrabi, Pedram Khalaj, Reza Sadeghi:
WHFDL: an explainable method based on World Hyper-heuristic and Fuzzy Deep Learning approaches for gastric cancer detection using metabolomics data. - Rehman Abbas, Naijie Gu, Stephen Ojo, Thomas I. Nathaniel, Nagwan Abdelsamee, Muhammad Umer, Mona M. Jamjoom:
FISM: harnessing deep learning and reinforcement learning for precision detection of microaneurysms and retinal exudates for early diabetic retinopathy diagnosis. - Abrar Yaqoob, Mushtaq Ahmad Mir, R. Vijaya Lakshmi, Tejaswini Pradhan, G. V. V. Jagannadha Rao, Ghanshyam G. Tejani, Mohd Asif Shah:
Optimizing accuracy and dimensionality: a swarm intelligence strategy for robust cancer genomics classification. - Yanhong Xiong, Xiaoyan Zhou, Qi Wang:
Computational prediction of cellular elastic modulus from mechanosensitive gene expression at multiple biological levels. - Kenneth D. Doig, Rashindrie Perera, Yamuna Kankanige, Andrew Fellowes, Jason Li, Richard Lupat, Ella R. Thompson, Piers Blombery, Stephen B. Fox:
Using artificial intelligence (AI) to model clinical variant reporting for next generation sequencing (NGS) oncology assays. - Hui-min Mao, Jia Geng, Bin Zhu, Shun-gen Huang, Wan-liang Guo:
An explainable machine learning model for predicting postoperative cholangitis in pediatric surgical patients with pancreaticobiliary maljunction. - Tongfei Shen, Yifei Sheng, Wan Nie, Shuo Yang, Kaiqi Li, Ziwei Ma, Zhao Ling, Bowen Tan, Xikang Feng, Miaozhe Huo:
Deep learning-driven TCR$$\beta$$ repertoire analysis enhances diagnosis and enables mining of immunological biomarkers in systemic lupus erythematosus. - Jason H. Moore, Nicholas P. Tatonetti:
From prompt engineering to agent engineering: expanding the AI toolbox with autonomous agentic AI collaborators for biomedical discovery. - Dat Thanh Pham, Khai Quang Tran, Viet Anh Nguyen:
CAUSALRLSTACK: adaptive balancing of deep representation and causal effect estimation with application to HIV-related health data. - Ana Niño-López, Álvaro Martínez-Rubio, Rocío Picón-González, Ana Castillo Robleda, Manuel Ramirez-Orellana, Salvador Chulián, María Rosa:
Automatic computational classification of bone marrow cells for B cell pediatric leukemia using UMAP. - Ana María Nevado-Bulnes, Dixan Agustin Benitez, Guadalupe Cumplido-Laso, Jose María Carvajal-González, Sonia Mulero-Navarro, Angel-Carlos Román:
FARFOOD: a database of potential interactions between food compounds and drugs. - Zarrin Basharat, Hanan A. Ogaly, Fatimah A. M. Al-Zahrani, Calvin R. Wei, Syed Shah Hassan, Muhammad Salman, Madiha Islam, Ibrar Ahmed, Yasir Waheed, Seil Kim:
Bioinformatics analysis of Rickettsia typhi autoimmune associations and screening of Streptomyces-derived inhibitors. - Roberta Coletti, J. Orestes Cerdeira, Marcos Raydan, Marta B. Lopes:
An unsupervised tool for biomarker discovery and cancer subtyping applied to glioblastoma. - Proshenjit Sarker, Kwonhue Choi, Abdullah Al Nahid, Md Abdus Samad:
CatBoost with physics-based metaheuristics for thyroid cancer recurrence prediction.
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