单细胞基础模型
别名: foundation model · scFM · foundation cell model
在单细胞数据上预训练的大模型，如 scGPT、Geneformer 与 scFoundation。文献库中的基准研究报告其零样本表现有限，且在扰动预测上尚不能稳定超越简单基线。 VC0008 VC0009 VC0011 VC0050
待审阅 版本 0.1.0 · 状态：初稿 · 最近专家审阅：尚未审阅
关系
出现在研究专题中
- 神经前体样（NPC 样）与少突前体样（OPC 样）胶质瘤细胞状态 (细胞状态)
- AI 虚拟细胞模型 (模型)
- 虚拟细胞的验证：基准、基线与批评 (验证)
出现在文献库条目中（26）
标题、标签或一句话摘要与该实体匹配的条目（由数据自动得出），以及用作描述证据的条目。
- VC0119 NeurIPS 2026 Workshop: Foundation Models for the Brain and Body — NeurIPS, NeurIPS 2026, Sydney, 2026
- VC0056 Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction. — Kendiukhov I., BMC genomics, 2026
- VC0112 Lessons from Ron Alfa (Noetik) on AI-native precision oncology — Pear Healthcare Playbook, Substack, 2026
- VC0047 · 预印本 Cellfm-datasets: A Unified Data Infrastructure for Single-Cell and Spatial Transcriptomics Foundation Model Pretraining — Zhang L, Pang J, Yan J, Tang W, Deng Y, He Y., bioRxiv, 2026
- VC0098 Foundation Model Based on Routine Magnetic Resonance Imaging for Brain Tumor Molecular Profiling and Progression Prediction. — Li J, Liu R, Xing Y, Gao X, Yin Q, Su Q., JCO precision oncology, 2026
- VC0035 · 预印本 CellFluxV2 : An Image Generative Foundation Model for Virtual Cell Modeling — Zhang Y, Su Y, Wefers Z, Su S, Li H, Li T, Wang C, Burgess J, Lozano A, Zhou L, Ding D, Nirschl J, Lundberg E, Yeung-Levy S., bioRxiv, 2026
- VC0034 · 预印本 scPRINT-2: Towards the next-generation of cell foundation models and benchmarks — Kalfon J, Peyré G, Cantini L., bioRxiv, 2025
- VC0025 Novae: a graph-based foundation model for spatial transcriptomics data. — Blampey Q, Benkirane H, Bercovici N, Mulder K, Gessain G, Ginhoux F, André F, Cournède PH., Nature methods, 2025
- VC0099 A foundation model for brain tumor MRI analysis: WHO grading and subtype classification. — Li J, Liu R, Xing Y, Gao X, Yin Q, Su Q., Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology, 2025
- VC0028 STPath: a generative foundation model for integrating spatial transcriptomics and whole-slide images. — Huang T, Liu T, Babadi M, Ying R, Jin W., NPJ digital medicine, 2025
- VC0024 Nicheformer: a foundation model for single-cell and spatial omics. — Tejada-Lapuerta A, Schaar AC, Gutgesell R, Palla G, Halle L, Minaeva M, Vornholz L, Dony L, Drummer F, Richter T, Bahrami M, Theis FJ., Nature methods, 2025
- VC0055 · 预印本 Multimodal Benchmarking of Foundation Model Representations for Cellular Perturbation Response Prediction — Hasanaj E, Cole E, Mohammadi S, Addagudi S, Zhang X, Song L, Xing EP., bioRxiv, 2025
- VC0045 · 预印本 X-Atlas/Orion: Genome-wide Perturb-seq Datasets via a Scalable Fix-Cryopreserve Platform for Training Dose-Dependent Biological Foundation Models — Huang AC et al., bioRxiv, 2025
- VC0114 Bioptimus: multimodal biology foundation model (NVIDIA compute) — Bioptimus, Bioptimus news, 2025
- VC0026 A visual-omics foundation model to bridge histopathology with spatial transcriptomics. — Chen W et al., Nature methods, 2025
- VC0049 Benchmarking foundation cell models for post-perturbation RNA-seq prediction. — Csendes G, Sanz G, Szalay KZ, Szalai B., BMC genomics, 2025
- VC0050 Zero-shot evaluation reveals limitations of single-cell foundation models. — Kedzierska KZ, Crawford L, Amini AP, Lu AX., Genome biology, 2025
- VC0037 · 预印本 A perturbation proteomics-based foundation model for virtual cell construction — Sun R, Qian L, Li Y, Cheng H, Xue Z, Zhang X, Tan L, Zhan Y, Hu W, Xiao Q, Liu Z, Zhang G, Weinan E, Zhou P, Wen H, Zhu Y, Guo T., bioRxiv, 2025
- VC0027 · 预印本 scGPT-spatial: Continual Pretraining of Single-Cell Foundation Model for Spatial Transcriptomics — Wang C, Cui H, Zhang A, Xie R, Goodarzi H, Wang B., bioRxiv, 2025
- VC0029 GeneCompass: deciphering universal gene regulatory mechanisms with a knowledge-informed cross-species foundation model. — Yang X et al., Cell research, 2024
- VC0051 · 预印本 PertEval-scFM: Benchmarking Single-Cell Foundation Models for Perturbation Effect Prediction — Wenteler A, Occhetta M, Branson N, Curean V, Huebner M, Dee W, Connell W, Chung SP, Hawkins-Hooker A, Ektefaie Y, Valdez Córdova CM, Gallagher-Syed A., bioRxiv, 2024
- VC0011 Large-scale foundation model on single-cell transcriptomics. — Hao M, Gong J, Zeng X, Liu C, Guo Y, Cheng X, Wang T, Ma J, Zhang X, Song L., Nature methods, 2024
- VC0039 Towards a general-purpose foundation model for computational pathology. — Chen RJ et al., Nature medicine, 2024
- VC0008 scGPT: toward building a foundation model for single-cell multi-omics using generative AI. — Cui H, Wang C, Maan H, Pang K, Luo F, Duan N, Wang B., Nature methods, 2024
- VC0012 · 预印本 Universal Cell Embeddings: A Foundation Model for Cell Biology — Rosen Y, Roohani Y, Agrawal A, Samotorcan L, Tabula Sapiens Consortium, Quake SR, Quake SR, Leskovec J., bioRxiv, 2023
- VC0009 Transfer learning enables predictions in network biology. — Theodoris CV, Xiao L, Chopra A, Chaffin MD, Al Sayed ZR, Hill MC, Mantineo H, Brydon EM, Zeng Z, Liu XS, Ellinor PT., Nature, 2023
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