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Patterns, 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
FHBF: Federated hybrid boosted forests with dropout rates for supervised learning tasks across highly imbalanced clinical datasets. 100893 - Feng Xiong
DSM: Deep sequential model for complete neuronal morphology representation and feature extraction. 100896
- Ahmad Nasimian, Saleena Younus, Özge Tatli
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
LATTE: Label-efficient incident phenotyping from longitudinal electronic health records. 100906 - Fengda Zhang
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
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
Density physics-informed neural networks reveal sources of cell heterogeneity in signal transduction. 100899 - Michael R. Waters, Matthew Inkman
GAiN: An integrative tool utilizing generative adversarial neural networks for augmented gene expression analysis. 100910 - Yi Liu
MDIC3: Matrix decomposition to infer cell-cell communication. 100911
- Suraj Rajendran
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
Social construction of XAI: Do we need one definition to rule them all? 100926
- Bingjie Yan
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
Spaco: A comprehensive tool for coloring spatial data at single-cell resolution. 100915 - Matthew J. Sniatynski
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
A weighted two-stage sequence alignment framework to identify motifs from ChIP-exo data. 100927
- Bo Qian, Hao Chen, Xiangning Wang, Zhouyu Guan
DRAC 2022: A public benchmark for diabetic retinopathy analysis on ultra-wide optical coherence tomography angiography images. 100929
- Georgios Rizos
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
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
Meet the authors: Georgios Rizos, Jenna L. Lawson, and Björn W. Schuller. 100952 - Alejandra Alvarado
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
An evaluation of synthetic data augmentation for mitigating covariate bias in health data. 100946 - Debsindhu Bhowmik
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
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
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
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
Early warning of atrial fibrillation using deep learning. 100970 - Upol Ehsan
Explainability pitfalls: Beyond dark patterns in explainable AI. 100971 - Fabio Crameri
Navigating color integrity in data visualization. 100972 - Ruoqi Liu
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
Active sensing with predictive coding and uncertainty minimization. 100983 - Seyednami Niyakan
MUSTANG: Multi-sample spatial transcriptomics data analysis with cross-sample transcriptional similarity guidance. 100986 - Peter S. Park
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
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
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
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
Advancing LGBTQ+ inclusion in STEM education and AI research. 101010
Volume 5, Number 7, 2024
- Sarthak Pati
Privacy preservation for federated learning in health care. 100974 - Guangyu Wang, Kai Wang, Yuanxu Gao
A generalized AI system for human embryo selection covering the entire IVF cycle via multi-modal contrastive learning. 100985 - Kelly Rootes-Murdy
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
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
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
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
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
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
Reliable imputation of spatial transcriptomes with uncertainty estimation and spatial regularization. 101021 - Shumin Li
CellContrast: Reconstructing spatial relationships in single-cell RNA sequencing data via deep contrastive learning. 101022 - Torec T. Luik
BIOMERO: A scalable and extensible image analysis framework. 101024 - Kang Zhang, Hong-Yu Zhou, Daniel T. Baptista-Hon, Yuanxu Gao, Xiaohong Liu, Eric K. 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
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
Volume 5, Number 9, 2024
- Ali Burak Ünal, Nico Pfeifer, Mete Akgün:
A privacy-preserving approach for cloud-based protein fold recognition. 101023 - Parham Pourdavood, Michael Jacob
EEG spectral attractors identify a geometric core of brain dynamics. 101025 - Mel Andrews, Andrew Smart
The reanimation of pseudoscience in machine learning and its ethical repercussions. 101027 - Da Wu, Jingye Yang, Kai Wang
Exploring the reversal curse and other deductive logical reasoning in BERT and GPT-based large language models. 101030 - Xun Lin
Exposing image splicing traces in scientific publications via uncertainty-guided refinement. 101038 - Malachy Guzman, Brian Geuther, Gautam S. Sabnis, Vivek Kumar
Highly accurate and precise determination of mouse mass using computer vision. 101039 - Mol Mir, Stephanie H. Nowotarski:
The stacking cell puzzle. 101040 - Marike L. Reimer, Sierra D. Kauer, Curtis A. Benson, Jared F. King, Siraj Patwa, Sarah Feng, Maile A. Estacion, Lakshmi Bangalore, Stephen G. Waxman, Andrew M. Tan:
A FAIR, open-source virtual reality platform for dendritic spine analysis. 101041
Volume 5, Number 10, 2024
- A. N. M. Nafiz Abeer
Multi-objective latent space optimization of generative molecular design models. 101042 - Gale M. Lucas, Burcin Becerik-Gerber, Shawn C. Roll:
Calibrating workers' trust in intelligent automated systems. 101045 - Michael A. Lones
Avoiding common machine learning pitfalls. 101046 - Julius Vetter
Generating realistic neurophysiological time series with denoising diffusion probabilistic models. 101047 - Roberto De Filippo, Dietmar Schmitz
Transcriptomic mapping of the 5-HT receptor landscape. 101048 - Erik-Jan van Kesteren:
To democratize research with sensitive data, we should make synthetic data more accessible. 101049 - J. Scott Christianson:
End the AI detection arms race. 101058 - Mingxuan Liu, Yilin Ning, Yuhe Ke, Yuqing Shang, Bibhas Chakraborty, Marcus Eng Hock Ong, Roger Vaughan, Nan Liu:
FAIM: Fairness-aware interpretable modeling for trustworthy machine learning in healthcare. 101059 - Claudia Chu
AnnoMate: Exploring and annotating integrated molecular data through custom interactive visualizations. 101060 - Andrew L. Hufton
Balancing innovation and integrity in peer review. 101061 - Brent A. Anders
Student skills need to evolve to match our new AI society. 101062 - Euijeong Song
VONet: A deep learning network for 3D reconstruction of organoid structures with a minimal number of confocal images. 101063 - Giacomo B. Marino, Daniel J. B. Clarke, Alexander Lachmann, Eden Z. Deng, Avi Ma'ayan:
RummaGEO: Automatic mining of human and mouse gene sets from GEO. 101072 - Yinqi Bai, Clayton W. Kosonocky, James Z. Wang:
How our authors are using AI tools in manuscript writing. 101075 - Andrew L. Hufton, Alejandra Alvarado:
Type less, think more. 101076
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