Table of Contents

• Determining population structure from k-mer frequenciesYana Hrytsenko, Noah M. Daniels, Rachel S. Schwartz. [doi]
• Greedy and speedy: optimal vaccination strategies in multi-region heterogeneous networksJhonatan Tavori, Hanoch Levy. [doi]
• EvoVGM: a deep variational generative model for evolutionary parameter estimationAmine M. Remita, Abdoulaye Baniré Diallo. [doi]
• Examining post-pandemic behaviors influencing human mobility trendsSatyaki Roy, Preetam Ghosh. [doi]
• Haplotype-aware variant selection for genome graphsNeda Tavakoli, Daniel Gibney, Srinivas Aluru. [doi]
• Performance portability study of epistasis detection using SYCL on NVIDIA GPUZheming Jin, Jeffrey S. Vetter. [doi]
• Deep sequence representation learning for predicting human proteins with liquid-liquid phase separation propensity and synaptic functionsAnqi Wei, Liangjiang Wang. [doi]
• Attention-based aspect reasoning for knowledge base question answering on clinical notesPing Wang, Tian Shi, Khushbu Agarwal, Sutanay Choudhury, Chandan K. Reddy. [doi]
• Neighborhood embedding and re-ranking of disease genes with ADAGIOMert Erden, Megan Gelement, Sarrah Hakimjee, Kyla Levin, Mary-Joy Sidhom, Kapil Devkota, Lenore J. Cowen. [doi]
• Transparent single-cell set classification with kernel mean embeddingsSiyuan Shan, Vishal Athreya Baskaran, Haidong Yi, Jolene Ranek, Natalie Stanley, Junier B. Oliva. [doi]
• Self-explaining neural network with concept-based explanations for ICU mortality predictionSayantan Kumar, Sean C. Yu, Thomas George Kannampallil, Zachary B. Abrams, Andrew P. Michelson, Philip R. O. Payne. [doi]
• Contextual embedding and model weighting by fusing domain knowledge on biomedical question answeringYuxuan Lu, Jingya Yan, Zhixuan Qi, Zhongzheng Ge, Yongping Du. [doi]
• TopographyNET: a deep learning model for EEG-based mind wandering detectionLillian Zhu, Feng Zhu, Jodi Price. [doi]
• SurvTRACE: transformers for survival analysis with competing eventsZifeng Wang 0008, Jimeng Sun. [doi]
• A novel three-step transcriptomic framework for cancer predictionRushank Goyal. [doi]
• Scoliosis management through appsLorella Bottino, Marzia Settino, Mario Cannataro. [doi]
• Application of machine learning for patient response prediction to cardiac resynchronization therapyBrendan E. Odigwe, Alireza Bagheri Rajeoni, Celestine I. Odigwe, Francis G. Spinale, Homayoun Valafar. [doi]
• AT[N]-net: multimodal spatiotemporal network for subtype identification in Alzheimer's diseaseJingwen Zhang, Enze Xu, Minghan Chen. [doi]
• rCom: a route-based framework inferring cell type communication and regulatory network using single cell dataHonglin Wang, Pujan Joshi, Chenyu Zhang, Peter F. Maye, David W. Rowe, Dong-Guk Shin. [doi]
• A general kernel boosting framework integrating pathways for predictive modeling based on genomic dataLi Zeng, Zhaolong Yu, Yiliang Zhang, Hongyu Zhao. [doi]
• An evolutionary approach to data valuationNatalia Khuri, Sapan Bhandari, Esteban Murillo Burford, Nathan P. Whitener, Konghao Zhao. [doi]
• Using natural language processing on free-text clinical notes to identify patients with long-term COVID effectsYuanda Zhu, Aishwarya Mahale, Kourtney Peters, Lejy Mathew, Felipe O. Giuste, Blake J. Anderson, May D. Wang. [doi]
• NBT (no-boundary thinking): needed to attend to ethical implications of data and AIJoan Peckham, Andy D. Perkins, Tayo Obafemi-Ajayi, Xiuzhen Huang. [doi]
• Optimal separation of high dimensional transcriptome for complex multigenic traitsAisharjya Sarkar, Aaditya Singh, Richard Bailey, Alin Dobra, Tamer Kahveci. [doi]
• Deep learning for assembly of haplotypes and viral quasispecies from short and long sequencing readsZiqi Ke, Haris Vikalo. [doi]
• FiT: fiber-based tensor completion for drug repurposingAysegul Bumin, Anna M. Ritz, Donna K. Slonim, Tamer Kahveci, Kejun Huang. [doi]
• Incorporating antigen processing into CD4+ T cell epitope prediction with integer linear programmingAvik Bhattacharya, Molly C. Lyons, Samuel J. Landry, Ramgopal R. Mettu. [doi]
• DeepVS: a deep learning approach for RF-based vital signs sensingZongxing Xie, HanRui Wang, Song Han, Elinor Schoenfeld, Fan Ye 0003. [doi]
• Deep graph learning to estimate protein model quality using structural constraints from multiple sequence alignmentsMahdi Rahbar, Rahul Kumar Chauhan, Pankil Nimeshbhai Shah, Renzhi Cao, Dong-Si, Jie Hou. [doi]
• Trajectory-based and sound-based medical data clusteringMaria Mannone, Veronica Distefano. [doi]
• An Italian lexicon-based sentiment analysis approach for medical applicationsMaria Chiara Martinis, Chiara Zucco, Mario Cannataro. [doi]
• Development of a generalizable multi-site and multi-modality clinical data cloud infrastructure for pediatric patient careAndrew Hornback, Wenqi Shi, Felipe O. Giuste, Yuanda Zhu, Ashley M. Carpenter, Coleman Hilton, Vinieth N. Bijanki, Hiram Stahl, Gary S. Gottesman, Chad Purnell, Henry J. Iwinski, J. Michael Wattenbarger, May D. Wang. [doi]
• A multi-omics graph database for data integration and knowledge extractionSuyeon Kim, Ishwor Thapa, Hesham Ali 0001. [doi]
• Team building without boundariesAndy Perkins, Joan Peckham, Tayo Obafemi-Ajayi, Xiuzhen Huang. [doi]
• Analysis of impact of diabetes mellitus in Arkansas and U.SVinay Raj. [doi]
• B-cell epitope prediction for antipeptide paratopes with the HAPTIC2/HEPTAD user toolkit (HUT)Salvador Eugenio C. Caoili. [doi]
• Implementing algorithms for sorting by strip swapsAsai Asaithambi, Chandrika Rao, Swapnoneel Roy. [doi]
• Computational framework for generating synthetic signal peptidesTom Johnsten, Aishwarya Prakash, Grant T. Daly, Ryan G. Benton, Tristan Clark. [doi]
• LINgroups as a principled approach to compare and integrate multiple bacterial taxonomiesReza Mazloom, Leighton Pritchard, C. Titus Brown, Boris A. Vinatzer, Lenwood S. Heath. [doi]
• Applying graph convolution neural network in digital breast tomosynthesis for cancer classificationJun Bai, Annie Jin, Andre Jin, Tianyu Wang, Clifford Yang, Sheida Nabavi. [doi]
• PRRSView: an analytical platform for the assessment of PRRSV ORF5 genetic sequencesMichael A. Zeller, Anugrah Saxena, Giovani Trevisan, Aditi Sharma, Daniel Linhares, Karen M. Krueger, Jianqiang Zhang, Phillip C. Gauger. [doi]
• Timestamp analysis of mental health tweets of Twitter users along with COVID-19 confirmed casesSudha Tushara Sadasivuni, Yanqing Zhang. [doi]
• Robust self-training strategy for various molecular biology prediction tasksHehuan Ma, Feng Jiang, Yu Rong, Yuzhi Guo, JunZhou Huang. [doi]
• Identification of co-existing embeddings of a motif in multilayer networksYuanfang Ren, Aisharjya Sarkar, Aysegul Bumin, Kejun Huang, Pierangelo Veltri, Alin Dobra, Tamer Kahveci. [doi]
• Data adequacy bias impact in a data-blinded semi-supervised GAN for privacy-aware COVID-19 chest X-ray classificationJavier Pastorino, Ashis Kumer Biswas. [doi]
• Predicting acute events using the movement patterns of older adults: an unsupervised clustering methodRamin Ramazi, Mary Elizabeth Bowen, Rahmatollah Beheshti. [doi]
• Semi-supervised classification of disease prognosis using CR images with clinical data structured graphJun Bai, Bingjun Li, Sheida Nabavi. [doi]
• Mitigating health disparities in EHR via deconfounderZheng Liu, Xiaohan Li, Philip S. Yu. [doi]
• Modeling long-term dependencies and short-term correlations in patient journey data with temporal attention networks for health predictionYuxi Liu, Zhenhao Zhang, Antonio Jimeno-Yepes, Flora D. Salim. [doi]
• Offspring GAN augments biased human genomic dataSupratim Das, Xinghua Shi. [doi]
• CytoEMD: detecting and visualizing between-sample variation in relation to phenotype with earth mover's distanceHaidong Yi, Natalie Stanley. [doi]
• Image processing segmentation algorithms evaluation through implementation choicesPatrizia Vizza, Mattia Cannistrà, Raffaele Giancotti, Pierangelo Veltri. [doi]
• MoDNA: motif-oriented pre-training for DNA language modelWeizhi An, Yuzhi Guo, Yatao Bian, Hehuan Ma, Jinyu Yang, Chunyuan Li, JunZhou Huang. [doi]
• Semi-supervised 3D neural networks to track iPS cell division in label-free phase contrast time series imagesAdele P. Peskin, Joe Chalfoun, Michael Halter, Anne L. Plant. [doi]
• DeepViFi: detecting oncoviral infections in cancer genomes using transformersUtkrisht Rajkumar, Sara Javadzadeh, Mihir Bafna, Dongxia Wu, Rose Yu, Jingbo Shang, Vineet Bafna. [doi]
• Comparison of cohort-based identical-by-descent (IBD) segment finding methods for endogamous populationsHuyen Trang Dang, Shi Jie Samuel Tan, Sara Mathieson. [doi]
• Neisseria gonorrhoeaeRushank Goyal, Rashmi Chowdhary. [doi]
• Scalable deep learning for healthcare: methods and applicationsLuca Barillaro, Giuseppe Agapito, Mario Cannataro. [doi]
• ArcheGEO: towards improving relevance of gene expression omnibus search resultsHuey-Eng Chua, Lisa Tucker-Kellogg, Sourav S. Bhowmick. [doi]
• A comparison of dimensionality reduction methods for large biological dataAshley Babjac, Taylor M. Royalty, Andrew D. Steen, Scott J. Emrich. [doi]
• Low-dimensional genotype embeddings for predictive modelsSyed Fahad Sultan, Xingzhi Guo, Steven Skiena. [doi]
• Computing attractors of large-scale asynchronous boolean networks using minimal trap spacesVan-Giang Trinh, Kunihiko Hiraishi, Belaid Benhamou. [doi]
• Geographic ensembles of observations using randomised ensembles of autoregression chains: ensemble methods for spatio-temporal time series forecasting of influenza-like illnessNooriyan Poonawala-Lohani, Patricia Riddle, Mehnaz Adnan, Jörg Wicker. [doi]
• Identification of covid-19 severity and associated genetic biomarkers based on scrna-SEQ dataAekansh Goel, Zachary Mudge, Sarah Bi, Charles Brenner, Nicholas Huffman, Felipe O. Giuste, Benoit Marteau, Wenqi Shi, May D. Wang. [doi]
• Connectome transformer with anatomically inspired attention for Parkinson's diagnosisDiego Machado Reyes, Mansu Kim, Hanqing Chao, Li Shen 0001, Pingkun Yan. [doi]
• The impact of gene sequence alignment and gene tree estimation error on summary-based species network estimationMeijun Gao, Wei Wang, Kevin J. Liu. [doi]
• Predicting the need for blood transfusion in intensive care units with reinforcement learningYuqing Wang, Yun Zhao 0001, Linda R. Petzold. [doi]
• Statistical methodology for ribosomal frameshift detectionAlisa Yurovsky, Justin Gardin, Bruce Futcher, Steven Skiena. [doi]
• rG4detector: convolutional neural network to predict RNA G-quadruplex propensity based on rG4-seq dataMaor Turner, Mira Barshai, Yaron Orenstein. [doi]
• Combining spectral clustering and large cut algorithms to find compensatory functional modules from yeast physical and genetic interaction data with GLASSBlessing Kolawole, Lenore J. Cowen. [doi]
• Detecting synchronization in brain activityGangadhar Katuri, Epaminondas Rosa Jr., Rosangela Follmann. [doi]
• Multi-target integration and annotation of single-cell RNA-sequencing dataSapan Bhandari, Nathan P. Whitener, Konghao Zhao, Natalia Khuri. [doi]
• Supervised pretraining through contrastive categorical positive samplings to improve COVID-19 mortality predictionTingyi Wanyan, Mingquan Lin, Eyal Klang, Kartikeya M. Menon, Faris F. Gulamali, Ariful Azad, Yiye Zhang, Ying Ding 0001, Zhangyang Wang, Fei Wang 0001, Benjamin S. Glicksberg, Yifan Peng. [doi]
• Distribution-based sketching of single-cell samplesVishal Athreya Baskaran, Jolene Ranek, Siyuan Shan, Natalie Stanley, Junier B. Oliva. [doi]
• Predicting diabetes in imbalanced datasets using neural networksHannah Guan, Chonghao Zhang. [doi]
• Identifying patient-specific root causes of diseaseEric V. Strobl, Thomas A. Lasko. [doi]