Author

Yiming Xue

Shanghai Jiao Tong University

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 2

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Approach:contrastive learning· 1 Approach:deep learning· 1 Research Focus:drug response / drug discovery· 1 Research Focus:gene regulatory network inference· 1 Approach:large language model· 1 Research Focus:protein design· 1

Frequent Co-Authors

Xiaoyong PaniD· 2 shared Badong CheniD· 1 shared Hong-Bin SheniD· 1 shared Jiabei ChengiD· 1 shared Kaiyuan YangiD· 1 shared Qingran Yan· 1 shared Shengfan WangiD· 1 shared Weimin ZhuiD· 1 shared

Activity by Year

2024-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 25 mutual co-author links

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2 shared papersBioinformatics

Xiaoyong PanORCID

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2 papers

Recent·Most cited

Auditing Protein-Protein Interaction Signals with Sparse Autoencoder Fingerprints

Weimin Zhu, Shengfan Wang, Xiaojian Liu, Yiming Xue, Hong-Bin Shen, Badong Chen, Xiaoyong Pan

AuditPPI evaluates PPI predictors by transforming language model features into auditable fingerprints, revealing that predictive success does not necessarily reflect biological signal capture.

bioRxiv · Oct 2, 2026 · PreprintBioinformatics

GexMolGen: Cross-modal Generation of Hit-like Molecules via Large Language Model Encoding of Gene Expression Signatures

Jiabei Cheng, Xiaoyong Pan, Yi Fang, Kaiyuan Yang, Yiming Xue, Qingran Yan, Ye Yuan

GexMolGen generates hit-like molecules using gene expression signatures through a cross-modal approach, producing valid molecules from both in- and out-of-domain transcriptome data.

Briefings in Bioinformatics · Sep 23, 2024Peer-reviewedBioinformatics