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ORCIDPatterns, Volume 5
Volume 5, Number 1, January 2024
- Jingye Yang, Cong Liu, Wendy Deng, Da Wu, Chunhua Weng, Yunyun Zhou, Kai Wang
:
Enhancing phenotype recognition in clinical notes using large language models: PhenoBCBERT and PhenoGPT. 100887 - Vasileios C. Pezoulas, Fanis G. Kalatzis, Themis P. Exarchos, Andreas Goules, Athanasios G. Tzioufas, Dimitrios I. Fotiadis:
FHBF: Federated hybrid boosted forests with dropout rates for supervised learning tasks across highly imbalanced clinical datasets. 100893 - Feng Xiong, Peng Xie, Zuohan Zhao, Yiwei Li, Sujun Zhao, Linus Manubens-Gil, Lijuan Liu, Hanchuan Peng:
DSM: Deep sequential model for complete neuronal morphology representation and feature extraction. 100896
- Ahmad Nasimian, Saleena Younus, Özge Tatli, Emma U. Hammarlund, Kenneth J. Pienta, Lars Rönnstrand, Julhash U. Kazi:
AlphaML: A clear, legible, explainable, transparent, and elucidative binary classification platform for tabular data. 100897
- Weishen Pan, Zhenxing Xu, Suraj Rajendran, Fei Wang:
An adaptive federated learning framework for clinical risk prediction with electronic health records from multiple hospitals. 100898 - Jun Wen, Jue Hou, Clara-Lea Bonzel, Yihan Zhao, Victor M. Castro, Vivian S. Gainer, Dana Weisenfeld, Tianrun Cai, Yuk-Lam Ho, Vidul Ayakulangara Panickan, Lauren Costa, Chuan Hong, J. Michael Gaziano, Katherine P. Liao, Junwei Lu, Kelly Cho, Tianxi Cai:
LATTE: Label-efficient incident phenotyping from longitudinal electronic health records. 100906 - Fengda Zhang, Zitao Shuai, Kun Kuang, Fei Wu, Yueting Zhuang, Jun Xiao:
Unified fair federated learning for digital healthcare. 100907 - Arash Keshavarzi Arshadi, Milad Salem, Heather Karner, Kristle Garcia, Abolfazl Arab, Jiann-Shiun Yuan, Hani Goodarzi:
Functional microRNA-targeting drug discovery by graph-based deep learning. 100909
- Hanchuan Peng, Peng Xie, Feng Xiong:
Meet the authors: Hanchuan Peng, Peng Xie, and Feng Xiong. 100912
- Roel Roscam Abbing, Robert W. Gehl:
Shifting your research from X to Mastodon? Here's what you need to know. 100914 - Andrew L. Hufton:
Looking forward to the new year. 100916
Volume 5, Number 2, February 2024
- Li-Ju Wang, Michael Ning, Tapsya Nayak, Michael J. Kasper, Satdarshan P. Monga, Yufei Huang, Yidong Chen, Yu-Chiao Chiu:
shinyDeepDR: A user-friendly R Shiny app for predicting anti-cancer drug response using deep learning. 100894
- Jinge Wang, Runnan Cao, Puneeth N. Chakravarthula, Xin Li, Shuo Wang:
A critical period for developing face recognition. 100895 - Hyeontae Jo, Hyukpyo Hong, Hyung Ju Hwang, Won Chang, Jae Kyoung Kim:
Density physics-informed neural networks reveal sources of cell heterogeneity in signal transduction. 100899 - Michael R. Waters, Matthew Inkman, Kay Jayachandran, Roman M. Kowalchuk, Clifford Robinson, Julie K. Schwarz, S. Joshua Swamidass, Obi L. Griffith, Jeffrey J. Szymanski, Jin Zhang:
GAiN: An integrative tool utilizing generative adversarial neural networks for augmented gene expression analysis. 100910 - Yi Liu, Yuelei Zhang, Xiao Chang, Xiaoping Liu:
MDIC3: Matrix decomposition to infer cell-cell communication. 100911
- Suraj Rajendran, Weishen Pan, Mert R. Sabuncu, Yong Chen, Jiayu Zhou, Fei Wang:
Learning across diverse biomedical data modalities and cohorts: Challenges and opportunities for innovation. 100913
- Le Jiang, Liyan Ma, Tieyong Zeng, Shihui Ying:
UFPS: A unified framework for partially annotated federated segmentation in heterogeneous data distribution. 100917
- Upol Ehsan, Mark O. Riedl:
Social construction of XAI: Do we need one definition to rule them all? 100926
- Bingjie Yan, Danmin Cao, Xinlong Jiang, Yiqiang Chen, Weiwei Dai, Fan Dong, Wuliang Huang, Teng Zhang, Chenlong Gao, Qian Chen, Zhen Yan, Zhirui Wang:
FedEYE: A scalable and flexible end-to-end federated learning platform for ophthalmology. 100928 - David S. Goodsell, Shuchismita Dutta, Brian P. Hudson, Maria Voigt, Stephen K. Burley, Christine Zardecki:
Folding paper models of biostructures for outreach and education. 100931
Volume 5, Number 3, March 2024
- Zehua Jing, Qianhua Zhu, Linxuan Li, Yue Xie, Xinchao Wu, Qi Fang, Bolin Yang, Baojun Dai, Xun Xu, Hailin Pan, Yinqi Bai:
Spaco: A comprehensive tool for coloring spatial data at single-cell resolution. 100915 - Matthew J. Sniatynski, John A. Shepherd, Lynne R. Wilkens, D. Frank Hsu, Bruce S. Kristal:
The DIRAC framework: Geometric structure underlies roles of diversity and accuracy in combining classifiers. 100924 - Yang Li, Yizhong Wang, Cankun Wang, Anjun Ma, Qin Ma, Bingqiang Liu:
A weighted two-stage sequence alignment framework to identify motifs from ChIP-exo data. 100927
- Bo Qian, Hao Chen, Xiangning Wang, Zhouyu Guan, Tingyao Li, Yixiao Jin, Yilan Wu, Yang Wen, Haoxuan Che, Gitaek Kwon, Jaeyoung Kim, Sungjin Choi, Seoyoung Shin, Felix Krause, Markus Unterdechler, Junlin Hou, Rui Feng, Yihao Li, Mostafa El Habib Daho, Dawei Yang, Bin Sheng:
DRAC 2022: A public benchmark for diabetic retinopathy analysis on ultra-wide optical coherence tomography angiography images. 100929
- Georgios Rizos, Jenna Lawson, Simon Mitchell, Pranay Shah, Xin Wen, Cristina Banks-Leite, Robert M. Ewers, Björn W. Schuller:
Propagating variational model uncertainty for bioacoustic call label smoothing. 100932
- Jenna Kefeli, Nicholas P. Tatonetti:
TCGA-Reports: A machine-readable pathology report resource for benchmarking text-based AI models. 100933
- Leticia Márquez-Magaña:
Anti-deficit is anti-racist and transformative. 100934
- Valentin Liévin, Christoffer Egeberg Hother, Andreas Geert Motzfeldt, Ole Winther:
Can large language models reason about medical questions? 100943 - Brandon Theodorou, Lucas Glass, Cao Xiao, Jimeng Sun:
FRAMM: Fair ranking with missing modalities for clinical trial site selection. 100944 - Benjamin P. Danek, Mary B. Makarious, Anant Dadu, Dan Vitale, Paul Suhwan Lee, Andrew B. Singleton, Mike A. Nalls, Jimeng Sun, Faraz Faghri:
Federated learning for multi-omics: A performance evaluation in Parkinson's disease. 100945
- Yosra Magdi Mekki:
Physicians should build their own machine-learning models. 100948
- Georgios Rizos, Jenna L. Lawson, Björn W. Schuller:
Meet the authors: Georgios Rizos, Jenna L. Lawson, and Björn W. Schuller. 100952 - Alejandra Alvarado, Andrew L. Hufton:
From scraped to published. 100953
Volume 5, Number 4, 2024
- Gongshu Wang, Ning Jiang, Yunxiao Ma, Dingjie Suo, Tiantian Liu, Shintaro Funahashi, Tianyi Yan:
Using a deep generation network reveals neuroanatomical specificity in hemispheres. 100930 - Lamin Juwara, Alaa El-Hussuna, Khaled El Emam:
An evaluation of synthetic data augmentation for mitigating covariate bias in health data. 100946 - Debsindhu Bhowmik, Pei Zhang, Zachary R. Fox, Stephan Irle, John Gounley:
Enhancing molecular design efficiency: Uniting language models and generative networks with genetic algorithms. 100947 - Yu-Ching Hsu, Yu-Chiao Chiu, Tzu-Pin Lu, Tzu-Hung Hsiao, Yidong Chen:
Predicting drug response through tumor deconvolution by cancer cell lines. 100949 - Xinmei Yuan, Jiangbiao He, Yutong Li, Yu Liu, Yifan Ma, Bo Bao, Leqi Gu, Lili Li, Hui Zhang, Yucheng Jin, Long Sun:
Data-driven evaluation of electric vehicle energy consumption for generalizing standard testing to real-world driving. 100950 - Junyi Gao, Yinghao Zhu, Wenqing Wang, Zixiang Wang, Guiying Dong, Wen Tang, Hao Wang, Yasha Wang, Ewen M. Harrison, Liantao Ma:
A comprehensive benchmark for COVID-19 predictive modeling using electronic health records in intensive care. 100951 - Khoi Minh Huynh, Wei-Tang Chang, Ye Wu, Pew-Thian Yap:
Optimal shrinkage denoising breaks the noise floor in high-resolution diffusion MRI. 100954
Volume 5, Number 5, 2024
- Tong Xie, Yuwei Wan, Yufei Zhou, Wei Huang, Yixuan Liu, Qingyuan Linghu, Shaozhou Wang, Chunyu Kit, Clara Grazian, Wenjie Zhang, Bram Hoex:
Creation of a structured solar cell material dataset and performance prediction using large language models. 100955 - Lizhen Zhu, James Z. Wang, Wonseuk Lee, Brad Wyble:
Incorporating simulated spatial context information improves the effectiveness of contrastive learning models. 100964 - Yanzhi Wang, Jianxiao Wang, Feng Gao, Jie Song:
Unveiling value patterns via deep reinforcement learning in heterogeneous data analytics. 100965 - Meera A. Desai, Irene V. Pasquetto, Abigail Z. Jacobs, Dallas Card:
An archival perspective on pretraining data. 100966 - Sarah M. Burbach, Bryan Briney:
Improving antibody language models with native pairing. 100967
Volume 5, Number 6, 2024
- Rita González-Márquez, Luca Schmidt, Benjamin M. Schmidt, Philipp Berens, Dmitry Kobak:
The landscape of biomedical research. 100968 - Jiawei Huang, Yuxuan Du, Andres Stucky, Kevin R. Kelly, Jiang F. Zhong, Fengzhu Sun:
DeepDecon accurately estimates cancer cell fractions in bulk RNA-seq data. 100969 - Marino E. Gavidia, Hongling Zhu, Arthur N. Montanari, Jesús Fuentes, Cheng Cheng, Sergio Dubner, Martin Chames, Pierre Maison-Blanche, Md. Moklesur Rahman, Roberto Sassi, Fabio Badilini, Yinuo Jiang, Shengjun Zhang, Hai-Tao Zhang, Hao Du, Basi Teng, Ye Yuan, Guohua Wan, Zhouping Tang, Xin He, Xiaoyun Yang, Jorge Gonçalves:
Early warning of atrial fibrillation using deep learning. 100970 - Upol Ehsan, Mark O. Riedl:
Explainability pitfalls: Beyond dark patterns in explainable AI. 100971 - Fabio Crameri, Sari Hason:
Navigating color integrity in data visualization. 100972 - Ruoqi Liu, Pin-Yu Chen, Ping Zhang:
CURE: A deep learning framework pre-trained on large-scale patient data for treatment effect estimation. 100973 - Taykhoom Dalal, Chirag J. Patel:
PYPE: A pipeline for phenome-wide association and Mendelian randomization in investigator-driven biobank scale analysis. 100982 - Abdelrahman Sharafeldin, Nabil Imam, Hannah Choi:
Active sensing with predictive coding and uncertainty minimization. 100983 - Seyednami Niyakan, Jianting Sheng, Yuliang Cao, Xiang Zhang, Zhan Xu, Ling Wu, Stephen T. C. Wong, Xiaoning Qian:
MUSTANG: Multi-sample spatial transcriptomics data analysis with cross-sample transcriptional similarity guidance. 100986 - Peter S. Park, Simon Goldstein, Aidan O'Gara, Michael Chen, Dan Hendrycks:
AI deception: A survey of examples, risks, and potential solutions. 100988 - Zhehuan Fan, Jie Yu, Xiang Zhang, Yijie Chen, Shihui Sun, Yuanyuan Zhang, Mingan Chen, Fu Xiao, Wenyong Wu, Xutong Li, Mingyue Zheng, Xiaomin Luo, Dingyan Wang:
Reducing overconfident errors in molecular property classification using Posterior Network. 100991 - Rita González-Márquez, Philipp Berens, Dmitry Kobak:
Meet the authors: Rita González-Márquez, Philipp Berens, and Dmitry Kobak. 100993 - Eve Richardson, Raphael Trevizani, Jason A. Greenbaum, Hannah Carter, Morten Nielsen, Bjoern Peters:
The receiver operating characteristic curve accurately assesses imbalanced datasets. 100994 - Sheng Li:
Large pre-trained models for treatment effect estimation: Are we there yet? 101005 - Fan Zhang, Daniel Kreuter, Yichen Chen, Sören Dittmer, Samuel Tull, Tolou Shadbahr, Martijn Schut, Folkert W. Asselbergs, Sujoy Kar, Suthesh Sivapalaratnam, Sophie Williams, Mickey Koh, Yvonne Henskens, Bart de Wit, Umberto D'alessandro, Bubacarr Bah, Ousman Secka, Parashkev Nachev, Rajeev Gupta, Sara Trompeter, Nancy Boeckx, Christine van Laer, Gordon A. Awandare, Kwabena Sarpong, Lucas Amenga-Etego, Mathie Leers, Mirelle Huijskens, Samuel McDermott, Willem H. Ouwehand, Jacobus Preller, James H. F. Rudd, John A. D. Aston, Carola-Bibiane Schönlieb, Nicholas S. Gleadall, Michael Roberts:
Recent methodological advances in federated learning for healthcare. 101006 - Zhuokun Feng, Yuanyuan Fu, Youping Deng:
Enhancing visibility and inclusivity of queer scientists to advance equality in academia. 101008 - Sam Freesun Friedman, Shaan Khurshid:
Consider this a WARNing. 101009 - Emily Wong, Ryan J. Urbanowicz, Tiffani J. Bright, Nicholas P. Tatonetti, Yi-Wen Hsiao, Xiuzhen Huang, Jason H. Moore, Pei-Chen Peng:
Advancing LGBTQ+ inclusion in STEM education and AI research. 101010
Volume 5, Number 7, 2024
- Sarthak Pati, Sourav Kumar, Amokh Varma, Brandon Edwards, Charles Lu, Liangqiong Qu, Justin J. Wang, Anantharaman Lakshminarayanan, Shih-han Wang, Micah J. Sheller, Ken Chang, Praveer Singh, Daniel L. Rubin, Jayashree Kalpathy-Cramer, Spyridon Bakas:
Privacy preservation for federated learning in health care. 100974 - Guangyu Wang, Kai Wang, Yuanxu Gao, Longbin Chen, Tianrun Gao, Yuanlin Ma, Zeyu Jiang, Guoxing Yang, Fajin Feng, Shuoping Zhang, Yifan Gu, Guangdong Liu, Lei Chen, Li-Shuang Ma, Ye Sang, Yanwen Xu, Ge Lin, Xiaohong Liu:
A generalized AI system for human embryo selection covering the entire IVF cycle via multi-modal contrastive learning. 100985 - Kelly Rootes-Murdy, Sandeep R. Panta, Ross Kelly, Javier Tomas Romero, Yann Quidé, Murray J. Cairns, C. M. Loughland, Vaughan J. Carr, Stanley V. Catts, Assen Jablensky, Melissa J. Green, Frans Henskens, Dylan Kiltschewskij, Patricia T. Michie, Bryan J. Mowry, Christos Pantelis, Paul E. Rasser, William R. Reay, Ulrich Schall, Rodney J. Scott, Oliver J. Watkeys, Gloria M. P. Roberts, Philip B. Mitchell, Janice M. Fullerton, Bronwyn J. Overs, Masataka Kikuchi, Ryota Hashimoto, Junya Matsumoto, Masaki Fukunaga, Perminder S. Sachdev, Henry Brodaty, Wei Wen, Jiyang Jiang, Negar Fani, Timothy D. Ely, Adriana Lorio, Jennifer S. Stevens, Kerry J. Ressler, Tanja Jovanovic, Sanne J. H. van Rooij, Lydia M. Federmann, Christiane Jockwitz, Alexander Teumer, Andreas J. Forstner, Svenja Caspers, Sven Cichon, Sergey M. Plis, Anand D. Sarwate, Vince D. Calhoun:
Cortical similarities in psychiatric and mood disorders identified in federated VBM analysis via COINSTAC. 100987 - Eivind Heggernes Ask, Astrid Tschan-Plessl, Hanna Julie Hoel, Arne Kolstad, Harald Holte, Karl-Johan Malmberg:
MetaGate: Interactive analysis of high-dimensional cytometry data with metadata integration. 100989 - Samar Samir Khalil, Noha S. Tawfik, Marco Spruit:
Federated learning for privacy-preserving depression detection with multilingual language models in social media posts. 100990 - Dimitrios I. Zaridis, Eugenia Mylona, Nikos Tsiknakis, Nikolaos S. Tachos, George K. Matsopoulos, Kostas Marias, Manolis Tsiknakis, Dimitrios I. Fotiadis:
ProLesA-Net: A multi-channel 3D architecture for prostate MRI lesion segmentation with multi-scale channel and spatial attentions. 100992 - Hannah Sawall, Seraphim Alvanides:
Embroidering the city map. 101004 - Guanqiao Shan, Yu Sun:
The potential of self-supervised learning in embryo selection for IVF success. 101012 - Fernanda D. A. O. Matos, Gildo Girotto Junior, Ana de Medeiros Arnt, Adriana Lippi:
A proposal in Brazil to use generative AI in education threatens quality and equity. 101020 - Guang Yang, Brandon Edwards, Spyridon Bakas, Qi Dou, Daguang Xu, Xiaoxiao Li, Wanying Wang:
Federated learning as a catalyst for digital healthcare innovations. 101026
Volume 5, Number 8, 2024
- John J. Stephen, Padraig Carolan, Amy E. Krefman, Sanaz Sedaghat, Maxwell Mansolf, Norrina B. Allen, Denise M. Scholtens:
psHarmonize: Facilitating reproducible large-scale pre-statistical data harmonization and documentation in R. 101003 - Wu Chen, Mingwei Liao, Shengda Bao, Sile An, Wenwei Li, Xin Liu, Ganghua Huang, Hui Gong, Qingming Luo, Chi Xiao, Anan Li:
A hierarchically annotated dataset drives tangled filament recognition in digital neuron reconstruction. 101007 - Kenneth S. Kosik:
Why brain organoids are not conscious yet. 101011 - Chen Qiao, Yuanhua Huang:
Reliable imputation of spatial transcriptomes with uncertainty estimation and spatial regularization. 101021 - Shumin Li, Jiajun Ma, Tianyi Zhao, Yuran Jia, Bo Liu, Ruibang Luo, Yuanhua Huang:
CellContrast: Reconstructing spatial relationships in single-cell RNA sequencing data via deep contrastive learning. 101022 - Torec T. Luik, Rodrigo Rosas-Bertolini, Eric A. J. Reits, Ron A. Hoebe, Przemek M. Krawczyk:
BIOMERO: A scalable and extensible image analysis framework. 101024 - Kang Zhang, Hong-Yu Zhou, Daniel T. Baptista-Hon, Yuanxu Gao, Xiaohong Liu, Eric Oermann, Sheng Xu, Shengwei Jin, Jian Zhang, Zhuo Sun, Yun Yin, Ronald M. Razmi, Alexandre Loupy, Stephan Beck, Jia Qu, Joseph Wu:
Concepts and applications of digital twins in healthcare and medicine. 101028 - Zixin Jiang, Bing Dong:
Modularized neural network incorporating physical priors for future building energy modeling. 101029 - Dimitris Stripelis, Umang Gupta, Hamza Saleem, Nikhil J. Dhinagar, Tanmay Ghai, Chrysovalantis Anastasiou, Rafael Sanchez, Greg Ver Steeg, Srivatsan Ravi, Muhammad Naveed, Paul M. Thompson, José Luis Ambite:
A federated learning architecture for secure and private neuroimaging analysis. 101031 - Xiaozhi Fu:
How deep can we decipher protein evolution with deep learning models. 101043 - Zixin Jiang, Bing Dong:
Meet the authors: Zixin Jiang and Bing Dong. 101044
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