YW
Yongxian Wu
Adenosine TriphosphateArtificial Cellscell-type annotationComputational Biologycomputational chemistrycs.AIcs.CLcs.LGDeep learningDeep Learning
On Valency
published · living versionsW_ku69regn·v1 · currentpublished
Auditing Tool Traces in Agentic LLMs: Source Localization and Counterfactual Dependence Testing
with Junhao Liu, Tianxiao Li, Ziheng Duan, Ren Li +2
1 version
Preprints & journals
18 papers in the corpus · 2023–2026Auditing Tool Traces in Agentic LLMs: Source Localization and Counterfactual Dependence Testing2610.25540v1 · Junhao Liu, Tianxiao Li, Yongxian Wu et al.2026 · 0 citationsarXivon Valency
pGM5P-26: A Polarizable Gaussian Multipole Water Model with Transferable Temperature-Dependent Thermodynamics.42917296 · Wu, Yongxian, Cieplak, Piotr, Duan, Yong et al.2026 · 0 citationsJournal of chemical theory and computation. 2026;22(19):10295-10308
AmberTorchPB: A Unified Framework for Poisson-Boltzmann-Based Reaction Field Energy Calculation via Tensor Computation.41906862 · Wu, Yongxian, Wang, Qiankang, Jiang, Robin et al.2026 · 0 citationsJournal of chemical theory and computation. 2026;22(7):3554-3570
Single-cell omics arena: evaluation of large language models for automatic cell-type annotations on single-cell omics data via RNA-seq bridging.41283813 · Liu, Junhao, Xu, Siwei, Wu, Yongxian et al.2025 · 1 citationBriefings in bioinformatics. 2025;26(6)
End-to-End Modeling of Reaction Field Energy Using Data-Driven Geometric Graph Neural Networks.41048018 · Wu, Yongxian, Zhu, Qiang, Luo, Ray2025 · 3 citationsJournal of chemical theory and computation. 2025;21(19):9710-9725
MULTIMODAL CELL CONTEXT INSTRUCTION TUNING FOR CONDITIONAL DNA REGULATORY SEQUENCE GENERATION WITH LARGE LANGUAGE MODELS.41426347 · Liu, Junhao, Zhang, Pengpeng, Xu, Siwei et al.2026 · 0 citationsProceedings. International Conference on Image Processing. 2025;2025:989-994
Grid-Context Convolutional Model for Efficient Molecular Surface Construction from Point Clouds.40459213 · Wu, Yongxian, Luo, Ray2025 · 3 citationsJournal of chemical theory and computation. 2025;21(15):7648-7661
Automated Refinement of Property-Specific Polarizable Gaussian Multipole Water Models Using Bayesian Black-Box Optimization.40108759 · Wu, Yongxian, Zhu, Qiang, Huang, Zhen et al.2025 · 4 citationsJournal of chemical theory and computation. 2025;21(7):3563-3575
Performance Tuning of Polarizable Gaussian Multipole Model in Molecular Dynamics Simulations.39772516 · Huang, Zhen, Wu, Yongxian, Duan, Yong et al.2025 · 6 citationsJournal of chemical theory and computation. 2025;21(2):847-858
End-to-End Reaction Field Energy Modeling via Deep Learning based Voxel-to-voxel Transform2410.03927v1 · Yongxian Wu, Qiang Zhu, Ray Luo2024 · 0 citationsarXiv
Shifting redox reaction equilibria on demand using an orthogonal redox cofactor.39138383 · Aspacio, Derek, Zhang, Yulai, Cui, Youtian et al.2024 · 43 citationsNature chemical biology. 2024;20(11):1535-1546
Targeting SHP2 Cryptic Allosteric Sites for Effective Cancer Therapy.38892388 · Rehman, Ashfaq Ur, Zhao, Cizhang, Wu, Yongxian et al.2024 · 7 citationsInternational journal of molecular sciences. 2024;25(11)
Understanding and fine tuning the propensity of ATP-driven liquid-liquid phase separation with oligolysine.38512104 · Zhu, Qiang, Wu, Yongxian, Luo, Ray2024 · 4 citationsPhysical chemistry chemical physics : PCCP. 2024;26(14):10568-10578
Clustering single-cell multi-omics data via graph regularized multi-view ensemble learning.38547401 · Chen, Fuqun, Zou, Guanhua, Wu, Yongxian et al.2024 · 26 citationsBioinformatics (Oxford, England). 2024;40(4)
Ultrasound-based deep learning radiomics nomogram for risk stratification of testicular masses: a two-center study.38240867 · Fang, Fuxiang, Sun, Yan, Huang, Hualin et al.2024 · 8 citationsJournal of cancer research and clinical oncology. 2024;150(1):18
AmberTools.37805934 · Case, David A, Aktulga, Hasan Metin, Belfon, Kellon et al.2023 · 2,140 citationsJournal of chemical information and modeling. 2023;63(20):6183-6191
Grid-Robust Efficient Neural Interface Model for Universal Molecule Surface Construction from Point Clouds.37782231 · Wu, Yongxian, Wei, Haixin, Zhu, Qiang et al.2024 · 4 citationsThe journal of physical chemistry letters. 2023;14(40):9034-9041
Streamlining and Optimizing Strategies of Electrostatic Parameterization.37676646 · Zhu, Qiang, Wu, Yongxian, Zhao, Shiji et al.2024 · 12 citationsJournal of chemical theory and computation. 2023;19(18):6353-6365
Career total: 25 works. 18 are in this corpus.
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