ZH
Zhi Huang
cs.CVbioinformaticscs.LGNeoplasmsAlzheimer’s diseasecs.AIcs.CLq-bio.QMArtificial IntelligenceComputational Biology
On Valency
published · living versionsW_v2gg7nk3·v1 · currentpublished
Conformal Annotation with Randomized Expert Review: Application to Online Cell-Type Labeling
with Xuhe Zhang, Ying Jin
1 version
Preprints & journals
61 papers in the corpus · 2016–2026Topical Resiquimod Elicits Systemic Protection and Improves Anti-PD-1 Therapy in Melanoma via Priming of CD8+ T Cells.42275481 · Liu, Shujing, Rook, Alain H, Huang, Alexander C et al.2026 · 0 citationsCancer immunology research. 2026;14(9):1496-1509
CytoFormer: A Molecularly Supervised Cell Foundation Model for Histopathology Cell Classification2608.16718v1 · Jialu Yao, Songhao Li, Alina Yu et al.2026 · 0 citationsarXiv
ProBAG: Prototype-Guided Boundary-Aware Graph Diffusion for Weakly Supervised Histopathology Segmentation2608.11765v1 · Duy-Dong Nguyen, Le-Van Thai, Hoai Nhan Pham et al.2026 · 0 citationsarXiv
CoDiR: Confidence-Guided Diffusion Refinement for Semi-Supervised Histopathology Segmentation2608.11807v1 · Hoai Nhan Pham, Dang-Nguyen Bui, Le-Van Thai et al.2026 · 0 citationsarXiv
Integrative spatial profiling of 3D genome organization and gene expression in tissue.42619843 · Guo, Pengfei, Cui, Yan, He, Jincan et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
Pathology-CoT: learning visual chain-of-thought agents from expert whole-slide image diagnosis behaviour.42498734 · Wang, Sheng, Wu, Ruiming, Herndon, Charles et al.2026 · 5 citationsNature biomedical engineering. 2026
An immunocompetent model of MCPyV-driven Merkel cell carcinoma reveals tumor evolution under immune selection.42523395 · Regan, James M, Li, Xiaomei, Salvacion, Mykaela et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
From prediction to interpretation in computational pathology.42349427 · Yao, Jialu, Huang, Zhi2026 · 0 citationsCancer cell. 2026;44(8):1536-1538
Linking spatial biology and clinical histology via Haiku2605.00925v1 · Yan Cui, Jacob S. Leiby, Wenhui Lei et al.2026 · 0 citationsarXiv
SpatialFinder: a human-in-the-loop vision-language framework for prioritizing high-value regions in spatial transcriptomics.42064250 · Xu, Jonathan, Jiang, Michelle, Koga, Shunsuke et al.2026 · 2 citationsFrontiers in bioinformatics. 2026;6:1746714
AI offers way to image and assess clinical cell samples.41708815 · Xu, Yinuo, Huang, Zhi2026 · 0 citationsNature. 2026;651(8105):317-318
iSight: Towards expert-AI co-assessment for improved immunohistochemistry staining interpretation2602.04063v1 · Jacob S. Leiby, Jialu Yao, Pan Lu et al.2026 · 0 citationsarXiv
VISTA-PATH: An interactive foundation model for pathology image segmentation and quantitative analysis in computational pathology2601.16451v1 · Peixian Liang, Songhao Li, Shunsuke Koga et al.2026 · 0 citationsarXiv
Melan-Dx: a knowledge-enhanced vision-language framework improves differential diagnosis of melanocytic neoplasm pathology.41559412 · Yao, Jialu, Li, Songhao, Liang, Peixian et al.2026 · 1 citationNPJ digital medicine. 2026;9(1):171
Adaptive Multi-Scale Integration Unlocks Robust Cell Annotation in Histopathology Images2511.13586v2 · Yinuo Xu, Yan Cui, Mingyao Li et al.2025 · 0 citationsarXiv
Pathology-CoT: Learning Visual Chain-of-Thought Agent from Expert Whole Slide Image Diagnosis Behavior2510.04587v2 · Sheng Wang, Ruiming Wu, Charles Herndon et al.2025 · 0 citationsarXiv
A co-evolving agentic AI system for medical imaging analysis2509.20279v1 · Songhao Li, Jonathan Xu, Tiancheng Bao et al.2025 · 1 citationarXiv
AI Scientists for Building Virtual-Cell Models2508.02276v3 · Xiangru Tang, Jiapeng Chen, Daniel Shao et al.2025 · 4 citationsarXiv
Quantifying large language model usage in scientific papers.40760036 · Liang, Weixin, Zhang, Yaohui, Wu, Zhengxuan et al.2025 · 79 citationsNature human behaviour. 2025;9(12):2599-2609
DANCE 2.0: Transforming single-cell analysis from black box to transparent workflow10.1101/2025.07.17.665427v1 · Ding, J., Xing, Z., Wang, Y. et al.2025 · 1 citationbioRxiv
Accelerating biomedical discoveries in brain health through transformative neuropathology of aging and neurodegeneration.40683248 · Murray, Melissa E, Smith, Colin, Menon, Vilas et al.2025 · 14 citationsNeuron. 2025;113(22):3703-3721
Optimizing generative AI by backpropagating language model feedback.40108317 · Yuksekgonul, Mert, Bianchi, Federico, Boen, Joseph et al.2025 · 85 citationsNature. 2025;639(8055):609-616
Explainable machine-learning model to classify culprit calcified carotid plaque in embolic stroke of undetermined source.39574846 · Sakai, Yu, Kim, Jiehyun, Phi, Huy Q et al.2026 · 4 citationsmedRxiv : the preprint server for health sciences. 2024
A pathologist-AI collaboration framework for enhancing diagnostic accuracies and efficiencies.38898173 · Huang, Zhi, Yang, Eric, Shen, Jeanne et al.2025 · 59 citationsNature biomedical engineering. 2025;9(4):455-470
TextGrad: Automatic "Differentiation" via Text2406.07496v1 · Mert Yuksekgonul, Federico Bianchi, Joseph Boen et al.2024 · 12 citationsarXiv
Mapping the Increasing Use of LLMs in Scientific Papers2404.01268v1 · Weixin Liang, Yaohui Zhang, Zhengxuan Wu et al.2024 · 54 citationsarXiv
Monitoring AI-Modified Content at Scale: A Case Study on the Impact of ChatGPT on AI Conference Peer Reviews2403.07183v4 · Weixin Liang, Zachary Izzo, Yaohui Zhang et al.2024 · 73 citationsarXiv
Systematic analysis of off-label and off-guideline cancer therapy usage in a real-world cohort of 165,912 US patients.38428426 · Liu, Ruishan, Wang, Lisa, Rizzo, Shemra et al.2024 · 21 citationsCell reports. Medicine. 2024;5(3):101444
Understanding the molecular basis of resilience to Alzheimer's disease.38192507 · Montine, Kathleen S, Berson, Eloïse, Phongpreecha, Thanaphong et al.2026 · 12 citationsFrontiers in neuroscience. 2023;17:1311157
Unveiling Resilience to Alzheimer's Disease: Insights From Brain Regional Proteomic Markers.37810186 · Huang, Zhi, Merrihew, Gennifer E, Larson, Eric B et al.2026 · 3 citationsNeuroscience insights. 2023;18:26331055231201600
A visual-language foundation model for pathology image analysis using medical Twitter.37592105 · Huang, Zhi, Bianchi, Federico, Yuksekgonul, Mert et al.2023 · 688 citationsNature medicine. 2023;29(9):2307-2316
Brain proteomic analysis implicates actin filament processes and injury response in resilience to Alzheimer's disease.37173305 · Huang, Zhi, Merrihew, Gennifer E, Larson, Eric B et al.2023 · 37 citationsNature communications. 2023;14(1):2747
Leveraging medical Twitter to build a visual-language foundation model for pathology AI10.1101/2023.03.29.534834v1 · Huang, Z., Bianchi, F., Yuksekgonul, M. et al.2023 · 27 citationsbioRxiv
Artificial intelligence reveals features associated with breast cancer neoadjuvant chemotherapy responses from multi-stain histopathologic images.36707660 · Huang, Zhi, Shao, Wei, Han, Zhi et al.2023 · 89 citationsNPJ precision oncology. 2023;7(1):14
Systematic analysis of off-label and off-guideline cancer therapy usage in a real-world cohort of 153,122 U.S. patients10.1101/2023.01.17.23284689v1 · Liu, R., Wang, L., Rizzo, S. et al.2023 · 0 citationsmedRxiv
Proteomics of resilience to Alzheimer's disease identifies brain regional soluble Aβ levels, actin filament processes, and response to injury10.1101/2022.10.09.511430v1 · Huang, Z., Merrihew, G. E., Larson, E. B. et al.2022 · 1 citationbioRxiv
Systematic pan-cancer analysis of mutation-treatment interactions using large real-world clinicogenomics data.35773542 · Liu, Ruishan, Rizzo, Shemra, Waliany, Sarah et al.2022 · 53 citationsNature medicine. 2022;28(8):1656-1661
Diagnostic Evidence GAuge of Single cells (DEGAS): a flexible deep transfer learning framework for prioritizing cells in relation to disease.35105355 · Johnson, Travis S, Yu, Christina Y, Huang, Zhi et al.2022 · 48 citationsGenome medicine. 2022;14(1):11
Weakly Supervised Deep Ordinal Cox Model for Survival Prediction From Whole-Slide Pathological Images.34264823 · Shao, Wei, Wang, Tongxin, Huang, Zhi et al.2021 · 87 citationsIEEE transactions on medical imaging. 2021;40(12):3739-3747
A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data.34301623 · Alghamdi, Norah, Chang, Wennan, Dang, Pengtao et al.2022 · 252 citationsGenome research. 2021;31(10):1867-1884
MOGONET integrates multi-omics data using graph convolutional networks allowing patient classification and biomarker identification.34103512 · Wang, Tongxin, Shao, Wei, Huang, Zhi et al.2021 · 667 citationsNature communications. 2021;12(1):3445
TSUNAMI: Translational Bioinformatics Tool Suite for Network Analysis and Mining.33705981 · Huang, Zhi, Han, Zhi, Wang, Tongxin et al.2022 · 19 citationsGenomics, proteomics & bioinformatics. 2021;19(6):1023-1031
Combinatorial analyses reveal cellular composition changes have different impacts on transcriptomic changes of cell type specific genes in Alzheimer's Disease.33432017 · Johnson, Travis S, Xiang, Shunian, Dong, Tianhan et al.2021 · 33 citationsScientific reports. 2021;11(1):353
Aberrant Chloride Intracellular Channel 4 Expression Is Associated With Adverse Outcome in Cytogenetically Normal Acute Myeloid Leukemia.33014825 · Huang, Sai, Huang, Zhi, Chen, Ping et al.2024 · 12 citationsFrontiers in oncology. 2020;10:1648
Low-Rank Reorganization via Proportional Hazards Non-negative Matrix Factorization Unveils Survival Associated Gene Clusters2008.03776v2 · Zhi Huang, Paul Salama, Wei Shao et al.2020 · 0 citationsarXiv
Multi-task multi-modal learning for joint diagnosis and prognosis of human cancers.32745975 · Shao, Wei, Wang, Tongxin, Sun, Liang et al.2021 · 96 citationsMedical image analysis. 2020;65:101795
Volumetric GWAS of medial temporal lobe structures identifies an ERC1 locus using ADNI high-resolution T2-weighted MRI data.32768867 · Cong, Shan, Yao, Xiaohui, Huang, Zhi et al.2021 · 9 citationsNeurobiology of aging. 2020;95:81-93
Deep learning-based cancer survival prognosis from RNA-seq data: approaches and evaluations.32241264 · Huang, Zhi, Johnson, Travis S, Han, Zhi et al.2021 · 99 citationsBMC medical genomics. 2020;13(Suppl 5):41
Acidic leucine-rich nuclear phosphoprotein-32A expression contributes to adverse outcome in acute myeloid leukemia.32355789 · Huang, Sai, Huang, Zhi, Ma, Chao et al.2022 · 14 citationsAnnals of translational medicine. 2020;8(6):345
Brain-wide structural connectivity alterations under the control of Alzheimer risk genes.32095160 · Yan, Jingwen, Raja V, Vinesh, Huang, Zhi et al.2022 · 16 citationsInternational journal of computational biology and drug design. 2020;13(1):58-70
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