Zichen Wang

34 papers A* 7Misc 1Journal 25Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
LC-PLM: Long-context Protein Language Modeling Using Bidirectional Mamba with Shared Projection Layers.
Trans. Mach. Learn. Res.
Yingheng Wang, Zichen Wang, Gil Sadeh, Luca Zancato, Alessandro Achille, George Karypis, Huzefa Rangwala
2025 A* conf
Protein Structure Tokenization: Benchmarking and New Recipe.
ICML
Xinyu Yuan, Zichen Wang, Marcus D. Collins, Huzefa Rangwala
2025 J jnl
Protein Structure Tokenization: Benchmarking and New Recipe.
CoRR
Xinyu Yuan, Zichen Wang, Marcus D. Collins, Huzefa Rangwala
2025 A* conf
Pushing the Limits of All-Atom Geometric Graph Neural Networks: Pre-Training, Scaling, and Zero-Shot Transfer.
ICLR
Zihan Pengmei, Zhengyuan Shen, Zichen Wang, Marcus D. Collins, Huzefa Rangwala
2024 A* conf
BioBridge: Bridging Biomedical Foundation Models via Knowledge Graphs.
ICLR
Zifeng Wang, Zichen Wang, Balasubramaniam Srinivasan, Vassilis N. Ioannidis, Huzefa Rangwala, Rishita Anubhai
2024 A* conf
DATALORE: Can a Large Language Model Find All Lost Scrolls in a Data Repository?
ICDE
Yuze Lou, Chuan Lei, Xiao Qin, Zichen Wang, Christos Faloutsos, Rishita Anubhai, Huzefa Rangwala
2024 A* conf
GraphStorm: All-in-one Graph Machine Learning Framework for Industry Applications.
KDD
Da Zheng, Xiang Song, Qi Zhu, Jian Zhang, Theodore Vasiloudis, Runjie Ma, Houyu Zhang, Zichen Wang, Soji Adeshina, Israt Nisa, Alejandro Mottini, Qingjun Cui, Huzefa Rangwala, Belinda Zeng, Christos Faloutsos, George Karypis
2024 J jnl
GraphStorm: all-in-one graph machine learning framework for industry applications.
CoRR
Da Zheng, Xiang Song, Qi Zhu, Jiani Zhang, Theodore Vasiloudis, Runjie Ma, Houyu Zhang, Zichen Wang, Soji Adeshina, Israt Nisa, Alejandro Mottini, Qingjun Cui, Huzefa Rangwala, Belinda Zeng, Christos Faloutsos, George Karypis
2024 J jnl
Long-context Protein Language Model.
CoRR
Yingheng Wang, Zichen Wang, Gil Sadeh, Luca Zancato, Alessandro Achille, George Karypis, Huzefa Rangwala
2024 J jnl
Pushing the Limits of All-Atom Geometric Graph Neural Networks: Pre-Training, Scaling and Zero-Shot Transfer.
CoRR
Zihan Pengmei, Zhengyuan Shen, Zichen Wang, Marcus D. Collins, Huzefa Rangwala
2023 A* conf
Predicting Cellular Responses with Variational Causal Inference and Refined Relational Information.
ICLR
Yulun Wu, Robert A. Barton, Zichen Wang, Vassilis N. Ioannidis, Carlo De Donno, Layne C. Price, Luis F. Voloch, George Karypis
2022 J jnl
A comprehensive digital phenotype for postpartum hemorrhage.
J. Am. Medical Informatics Assoc.
Amanda B. Zheutlin, Luciana Vieira, Ryan A. Shewcraft, Shilong Li, Zichen Wang, Emilio Schadt, Yu-Han Kao, Susan Gross, Siobhan M. Dolan, Joanne Stone, Eric E. Schadt, Li Li
2022 A* conf
Graph Neural Networks in Life Sciences: Opportunities and Solutions.
KDD
Zichen Wang, Vassilis N. Ioannidis, Huzefa Rangwala, Tatsuya Arai, Ryan Brand, Mufei Li, Yohei Nakayama
2022 J jnl
Improving postpartum hemorrhage risk prediction using longitudinal electronic medical records.
J. Am. Medical Informatics Assoc.
Amanda B. Zheutlin, Luciana Vieira, Ryan A. Shewcraft, Shilong Li, Zichen Wang, Emilio Schadt, Susan Gross, Siobhan M. Dolan, Joanne Stone, Eric E. Schadt, Li Li
2022 J jnl
Improving preeclampsia risk prediction by modeling pregnancy trajectories from routinely collected electronic medical record data.
npj Digit. Medicine
Shilong Li, Zichen Wang, Luciana Vieira, Amanda B. Zheutlin, Boshu Ru, Emilio Schadt, Pei Wang, Alan B. Copperman, Joanne Stone, Susan Gross, Yu-Han Kao, Yan Kwan Lau, Siobhan M. Dolan, Eric E. Schadt, Li Li
2022 J jnl
Predicting Cellular Responses with Variational Causal Inference and Refined Relational Information.
CoRR
Yulun Wu, Robert A. Barton, Zichen Wang, Vassilis N. Ioannidis, Carlo De Donno, Layne C. Price, Luis F. Voloch, George Karypis
2022 J jnl
Training self-supervised peptide sequence models on artificially chopped proteins.
CoRR
Gil Sadeh, Zichen Wang, Jasleen Grewal, Huzefa Rangwala, Layne Price
2022 J jnl
Variational Causal Inference.
CoRR
Yulun Wu, Layne C. Price, Zichen Wang, Vassilis N. Ioannidis, George Karypis
2019 J jnl
ChEA3: transcription factor enrichment analysis by orthogonal omics integration.
Nucleic Acids Res.
Alexandra B. Keenan, Denis Torre, Alexander Lachmann, Ariel K. Leong, Megan L. Wojciechowicz, Vivian Utti, Kathleen M. Jagodnik, Eryk Kropiwnicki, Zichen Wang, Avi Ma'ayan
2019 J jnl
Drug Gene Budger (DGB): an application for ranking drugs to modulate a specific gene based on transcriptomic signatures.
Bioinform.
Zichen Wang, Edward He, Kevin Sani, Kathleen M. Jagodnik, Moshe C. Silverstein, Avi Ma'ayan
2019 J jnl
Predicting opioid dependence from electronic health records with machine learning.
BioData Min.
Randall J. Ellis, Zichen Wang, Nicholas Genes, Avi Ma'ayan
2018 Misc conf
Cell-specific prediction and application of drug-induced gene expression .
PSB
Rachel Hodos, Ping Zhang, Hao-Chih Lee, Qiaonan Duan, Zichen Wang, Neil R. Clark, Avi Ma'ayan, Fei Wang, Brian A. Kidd, Jianying Hu, David A. Sontag, Joel Dudley
2018 J jnl
L1000FWD: fireworks visualization of drug-induced transcriptomic signatures.
Bioinform.
Zichen Wang, Alexander Lachmann, Alexandra B. Keenan, Avi Ma'ayan
2018 J jnl
eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks.
Nucleic Acids Res.
Daniel J. B. Clarke, Maxim V. Kuleshov, Brian M. Schilder, Denis Torre, Mary E. Duffy, Alexandra B. Keenan, Alexander Lachmann, Axel S. Feldmann, Gregory W. Gundersen, Moshe C. Silverstein, Zichen Wang, Avi Ma'ayan
2017 J jnl
Predicting age by mining electronic medical records with deep learning characterizes differences between chronological and physiological age.
J. Biomed. Informatics
Zichen Wang, Li Li, Benjamin S. Glicksberg, Ariel Israel, Joel T. Dudley, Avi Ma'ayan
2016 J jnl
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.
F1000Research
Zichen Wang, Avi Ma'ayan
2016 J jnl
Drug-induced adverse events prediction with the LINCS L1000 data.
Bioinform.
Zichen Wang, Neil R. Clark, Avi Ma'ayan
2016 J jnl
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update.
Nucleic Acids Res.
Maxim V. Kuleshov, Matthew R. Jones, Andrew D. Rouillard, Nicolas F. Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L. Jenkins, Kathleen M. Jagodnik, Alexander Lachmann, Michael G. McDermott, Caroline D. Monteiro, Gregory W. Gundersen, Avi Ma'ayan
2016 J jnl
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins.
Database J. Biol. Databases Curation
Andrew D. Rouillard, Gregory W. Gundersen, Nicolas F. Fernandez, Zichen Wang, Caroline D. Monteiro, Michael G. McDermott, Avi Ma'ayan
2015 J jnl
Dynamics of the discovery process of protein-protein interactions from low content studies.
BMC Syst. Biol.
Zichen Wang, Neil R. Clark, Avi Ma'ayan
2015 — conf
Principle Angle Enrichment Analysis (PAEA): Dimensionally reduced multivariate gene set enrichment analysis tool.
BIBM
Neil R. Clark, Maciej Szymkiewicz, Zichen Wang, Caroline D. Monteiro, Matthew R. Jones, Avi Ma'ayan
2015 J jnl
Reprint of "Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction".
Comput. Biol. Chem.
Andrew D. Rouillard, Zichen Wang, Avi Ma'ayan
2014 J jnl
Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets.
Bioinform.
Qiaonan Duan, Zichen Wang, Nicolas F. Fernandez, Andrew D. Rouillard, Christopher M. Tan, Cyril H. Benes, Avi Ma'ayan
2013 J jnl
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool.
BMC Bioinform.
Edward Y. Chen, Christopher M. Tan, Yan Kou, Qiaonan Duan, Zichen Wang, Gabriela Vaz Meirelles, Neil R. Clark, Avi Ma'ayan