Zichen Wang

Orcid: 0000-0002-1415-1286

Affiliations:
  • Amazon AWS AI, New York, NY, USA


According to our database1, Zichen Wang authored at least 31 papers between 2013 and 2025.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

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Online presence:

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Bibliography

2025
Protein Structure Tokenization: Benchmarking and New Recipe.
CoRR, March, 2025

LC-PLM: Long-context Protein Language Modeling Using Bidirectional Mamba with Shared Projection Layers.
Trans. Mach. Learn. Res., 2025

Pushing the Limits of All-Atom Geometric Graph Neural Networks: Pre-Training, Scaling, and Zero-Shot Transfer.
Proceedings of the Thirteenth International Conference on Learning Representations, 2025

2024
Long-context Protein Language Model.
CoRR, 2024

GraphStorm: all-in-one graph machine learning framework for industry applications.
CoRR, 2024

GraphStorm: All-in-one Graph Machine Learning Framework for Industry Applications.
Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 2024

BioBridge: Bridging Biomedical Foundation Models via Knowledge Graphs.
Proceedings of the Twelfth International Conference on Learning Representations, 2024

DATALORE: Can a Large Language Model Find All Lost Scrolls in a Data Repository?
Proceedings of the 40th IEEE International Conference on Data Engineering, 2024

2023
Predicting Cellular Responses with Variational Causal Inference and Refined Relational Information.
Proceedings of the Eleventh International Conference on Learning Representations, 2023

2022
Improving preeclampsia risk prediction by modeling pregnancy trajectories from routinely collected electronic medical record data.
npj Digit. Medicine, 2022

A comprehensive digital phenotype for postpartum hemorrhage.
J. Am. Medical Informatics Assoc., 2022

Improving postpartum hemorrhage risk prediction using longitudinal electronic medical records.
J. Am. Medical Informatics Assoc., 2022

Training self-supervised peptide sequence models on artificially chopped proteins.
CoRR, 2022

Variational Causal Inference.
CoRR, 2022

Graph Neural Networks in Life Sciences: Opportunities and Solutions.
Proceedings of the KDD '22: The 28th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, Washington, DC, USA, August 14, 2022

2019
ChEA3: transcription factor enrichment analysis by orthogonal omics integration.
Nucleic Acids Res., 2019

Drug Gene Budger (DGB): an application for ranking drugs to modulate a specific gene based on transcriptomic signatures.
Bioinform., 2019

Predicting opioid dependence from electronic health records with machine learning.
BioData Min., 2019

2018
eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks.
Nucleic Acids Res., 2018

L1000FWD: fireworks visualization of drug-induced transcriptomic signatures.
Bioinform., 2018

Cell-specific prediction and application of drug-induced gene expression .
Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018

2017
Predicting age by mining electronic medical records with deep learning characterizes differences between chronological and physiological age.
J. Biomed. Informatics, 2017

2016
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update.
Nucleic Acids Res., 2016

An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.
F1000Research, 2016

Drug-induced adverse events prediction with the LINCS L1000 data.
Bioinform., 2016

The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins.
Database J. Biol. Databases Curation, 2016

2015
Reprint of "Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction".
Comput. Biol. Chem., 2015

Dynamics of the discovery process of protein-protein interactions from low content studies.
BMC Syst. Biol., 2015

Principle Angle Enrichment Analysis (PAEA): Dimensionally reduced multivariate gene set enrichment analysis tool.
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

2014
Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets.
Bioinform., 2014

2013
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool.
BMC Bioinform., 2013


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