Chongle Pan - RankMe

25 papers A* 1Journal 17Unranked 6

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Benchmarking interpretability of deep learning for predictive genomics: Recall, precision, and variability of feature attribution. PLoS Comput. Biol. Justin C. Reynolds, Chongle Pan
2025	J	`jnl`	Integration of nested cross-validation, automated hyperparameter optimization, high-performance computing to reduce and quantify the variance of test performance estimation of deep learning models. Comput. Methods Programs Biomed. Paul Calle, Averi Bates, Justin C. Reynolds, Yunlong Liu, Haoyang Cui, Sinaro Ly, Chen Wang, Qinghao Zhang, Alberto J. de Armendi, Shashank S. Shettar, Kar-Ming Fu, Qinggong Tang, Chongle Pan
2025	J	`jnl`	Integration of nested cross-validation, automated hyperparameter optimization, high-performance computing to reduce and quantify the variance of test performance estimation of deep learning models. CoRR Paul Calle, Averi Bates, Justin C. Reynolds, Yunlong Liu, Haoyang Cui, Sinaro Ly, Chen Wang, Qinghao Zhang, Alberto J. de Armendi, Shashank S. Shettar, Kar-Ming Fung, Qinggong Tang, Chongle Pan
2025	—	`conf`	LLM-Empowered Patient-Provider Communication: A Data-Centric Survey From a Clinical Perspective. IJCNLP-AACL (Findings) Ruosi Shao, Md Shamim Seraj, Kangyi Zhao, Yingtao Luo, Lincan Li, Bolin Shen, Averi Bates, Yue Zhao, Chongle Pan, Lisa Hightow-Weidman, Shayok Chakraborty, Yushun Dong
2025	J	`jnl`	Octascope: A Lightweight Pre-Trained Model for Optical Coherence Tomography. IEEE Access Haoyang Cui, Chen Wang, Paul Calle, Yunlong Liu, Qinghao Zhang, Sinaro Ly, Justin C. Reynolds, Feng Yan, Ke Zhang, Ronghao Liu, Junyuan Liu, Kar-Ming Fung, Zhongxin Yu, Ajay Jain, Qinggong Tang, Chongle Pan
2025	J	`jnl`	Unified Modeling Language Code Generation from Diagram Images Using Multimodal Large Language Models. CoRR Averi Bates, Ryan Vavricka, Shane Carleton, Ruosi Shao, Chongle Pan
2024	—	`conf`	SEMQuant: Extending Sipros-Ensemble with Match-Between-Runs for Comprehensive Quantitative Metaproteomics. ISBRA (3) Bailu Zhang, Shichao Feng, Manushi Parajuli, Yi Xiong, Chongle Pan, Xuan Guo
2024	A*	`conf`	Towards AI-Driven Healthcare: Systematic Optimization, Linguistic Analysis, and Clinicians' Evaluation of Large Language Models for Smoking Cessation Interventions. CHI Paul Calle, Ruosi Shao, Yunlong Liu, Emily T. Hébert, Darla E. Kendzor, Jordan M. Neil, Michael S. Businelle, Chongle Pan
2023	J	`jnl`	Bayesian inference for survival prediction of childhood Leukemia. Comput. Biol. Medicine Yuning Cui, Yifu Li, Chongle Pan, Stephanie R. Brown, Rachel E. Gallant, Rui Zhu
2023	J	`jnl`	Deep neural network improves the estimation of polygenic risk scores for breast cancer. CoRR Adrien Badré, Li Zhang, Wellington Muchero, Justin C. Reynolds, Chongle Pan
2023	J	`jnl`	Explainable multi-task learning improves the parallel estimation of polygenic risk scores for many diseases through shared genetic basis. PLoS Comput. Biol. Adrien Badré, Chongle Pan
2022	—	`conf`	FineFDR: Fine-grained Taxonomy-specific False Discovery Rates Control in Metaproteomics. BIBM Shengze Wang, Shichao Feng, Chongle Pan, Xuan Guo
2022	—	`conf`	IDIA: An Integrative Signal Extractor for Data-Independent Acquisition Proteomics. BIBM Jiancheng Li, Chongle Pan, Xuan Guo
2022	J	`jnl`	LINA: A Linearizing Neural Network Architecture for Accurate First-Order and Second-Order Interpretations. IEEE Access Adrien Badré, Chongle Pan
2022	J	`jnl`	MetaLP: An integrative linear programming method for protein inference in metaproteomics. PLoS Comput. Biol. Shichao Feng, Hong-Long Ji, Huan Wang, Bailu Zhang, Ryan Sterzenbach, Chongle Pan, Xuan Guo
2018	—	`conf`	SORA: Scalable Overlap-graph Reduction Algorithms for Genome Assembly using Apache Spark in the Cloud. BIBM Alexander J. Paul, Dylan Lawrence, Myoungkyu Song, Seung-Hwan Lim, Chongle Pan, Tae-Hyuk Ahn
2018	J	`jnl`	Sipros Ensemble improves database searching and filtering for complex metaproteomics. Bioinform. Xuan Guo, Zhou Li, Qiuming Yao, Ryan S. Mueller, Jimmy K. Eng, David L. Tabb, IV William Judson Hervey, Chongle Pan
2015	J	`jnl`	Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance. Bioinform. Tae-Hyuk Ahn, Juanjuan Chai, Chongle Pan
2014	J	`jnl`	Omega: an Overlap-graph Bioinform. Bahlul Haider, Tae-Hyuk Ahn, Brian Bushnell, Juanjuan Chai, Alex Copeland, Chongle Pan
2013	J	`jnl`	Sipros/ProRata: a versatile informatics system for quantitative community proteomics. Bioinform. Yingfeng Wang, Tae-Hyuk Ahn, Zhou Li, Chongle Pan
2012	J	`jnl`	Exhaustive database searching for amino acid mutations in proteomes. Bioinform. Doug Hyatt, Chongle Pan
2010	J	`jnl`	A high-throughput BMC Bioinform. Chongle Pan, Byung-Hoon Park, William H. McDonald, Patricia A. Carey, Jillian F. Banfield, Nathan Verberkmoes, Robert L. Hettich, Nagiza F. Samatova
2009	—	`ch.`	Scientific Data Analysis. Scientific Data Management Chandrika Kamath, Nikil Wale, George Karypis, Gaurav Pandey, Vipin Kumar, Krishna Rajan, Nagiza F. Samatova, Paul Breimyer, Guruprasad Kora, Chongle Pan, Srikanth B. Yoginath
2005	J	`jnl`	A graph-theoretic approach for the separation of b and y ions in tandem mass spectra. Bioinform. Bo Yan, Chongle Pan, Victor Olman, Robert L. Hettich, Ying Xu
2004	—	`conf`	Separation of Ion Types in Tandem Mass Spectrometry Data Interpretation - A Graph-Theoretic Approach. CSB Bo Yan, Chongle Pan, Victor Olman, Robert L. Hettich, Ying Xu