{"id":"foundation-model","type":"method","name_en":"Single-cell foundation model","name_zh":"单细胞基础模型","aliases":["foundation model","scFM","foundation cell model"],"description":{"en":"Large pretrained models on single-cell data such as scGPT, Geneformer and scFoundation. Benchmarks in the library report limited zero-shot performance and no reliable gain over simple baselines for perturbation prediction.","zh":"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。"},"externalIds":{},"graphNames":["foundation model"],"mentions":{"items":["VC0008","VC0011","VC0012","VC0024","VC0025","VC0026","VC0027","VC0028","VC0029","VC0034","VC0035","VC0037","VC0039","VC0045","VC0047","VC0049","VC0050","VC0051","VC0055","VC0056","VC0098","VC0099","VC0112","VC0114","VC0119"],"topics":["cell-state-npc-opc-like","model-virtual-cell","validation-benchmarks"]},"evidenceRefs":["VC0008","VC0009","VC0011","VC0050"],"reviewStatus":"draft","version":"0.1.0","page_url":"https://gliostate.com/entities/foundation-model/","page_url_zh":"https://gliostate.com/zh/entities/foundation-model/","api_url":"https://gliostate.com/api/entities/foundation-model.json","external_links":[],"source_file":"https://gliostate.com/data/entities/foundation-model.json","evidence_items":[{"id":"VC0008","title":"scGPT: toward building a foundation model for single-cell multi-omics using generative AI.","year":"2024","page_url":"https://gliostate.com/library/VC0008/","api_url":"https://gliostate.com/api/items/VC0008.json"},{"id":"VC0009","title":"Transfer learning enables predictions in network biology.","year":"2023","page_url":"https://gliostate.com/library/VC0009/","api_url":"https://gliostate.com/api/items/VC0009.json"},{"id":"VC0011","title":"Large-scale foundation model on single-cell transcriptomics.","year":"2024","page_url":"https://gliostate.com/library/VC0011/","api_url":"https://gliostate.com/api/items/VC0011.json"},{"id":"VC0050","title":"Zero-shot evaluation reveals limitations of single-cell foundation models.","year":"2025","page_url":"https://gliostate.com/library/VC0050/","api_url":"https://gliostate.com/api/items/VC0050.json"}],"mentioned_in_items":[{"id":"VC0008","title":"scGPT: toward building a foundation model for single-cell multi-omics using generative AI.","year":"2024","page_url":"https://gliostate.com/library/VC0008/","api_url":"https://gliostate.com/api/items/VC0008.json"},{"id":"VC0011","title":"Large-scale foundation model on single-cell transcriptomics.","year":"2024","page_url":"https://gliostate.com/library/VC0011/","api_url":"https://gliostate.com/api/items/VC0011.json"},{"id":"VC0012","title":"Universal Cell Embeddings: A Foundation Model for Cell Biology","year":"2023","page_url":"https://gliostate.com/library/VC0012/","api_url":"https://gliostate.com/api/items/VC0012.json"},{"id":"VC0024","title":"Nicheformer: a foundation model for single-cell and spatial omics.","year":"2025","page_url":"https://gliostate.com/library/VC0024/","api_url":"https://gliostate.com/api/items/VC0024.json"},{"id":"VC0025","title":"Novae: a graph-based foundation model for spatial transcriptomics data.","year":"2025","page_url":"https://gliostate.com/library/VC0025/","api_url":"https://gliostate.com/api/items/VC0025.json"},{"id":"VC0026","title":"A visual-omics foundation model to bridge histopathology with spatial transcriptomics.","year":"2025","page_url":"https://gliostate.com/library/VC0026/","api_url":"https://gliostate.com/api/items/VC0026.json"},{"id":"VC0027","title":"scGPT-spatial: Continual Pretraining of Single-Cell Foundation Model for Spatial Transcriptomics","year":"2025","page_url":"https://gliostate.com/library/VC0027/","api_url":"https://gliostate.com/api/items/VC0027.json"},{"id":"VC0028","title":"STPath: a generative foundation model for integrating spatial transcriptomics and whole-slide images.","year":"2025","page_url":"https://gliostate.com/library/VC0028/","api_url":"https://gliostate.com/api/items/VC0028.json"},{"id":"VC0029","title":"GeneCompass: deciphering universal gene regulatory mechanisms with a knowledge-informed cross-species foundation model.","year":"2024","page_url":"https://gliostate.com/library/VC0029/","api_url":"https://gliostate.com/api/items/VC0029.json"},{"id":"VC0034","title":"scPRINT-2: Towards the next-generation of cell foundation models and benchmarks","year":"2025","page_url":"https://gliostate.com/library/VC0034/","api_url":"https://gliostate.com/api/items/VC0034.json"},{"id":"VC0035","title":"CellFluxV2 : An Image Generative Foundation Model for Virtual Cell Modeling","year":"2026","page_url":"https://gliostate.com/library/VC0035/","api_url":"https://gliostate.com/api/items/VC0035.json"},{"id":"VC0037","title":"A perturbation proteomics-based foundation model for virtual cell construction","year":"2025","page_url":"https://gliostate.com/library/VC0037/","api_url":"https://gliostate.com/api/items/VC0037.json"},{"id":"VC0039","title":"Towards a general-purpose foundation model for computational pathology.","year":"2024","page_url":"https://gliostate.com/library/VC0039/","api_url":"https://gliostate.com/api/items/VC0039.json"},{"id":"VC0045","title":"X-Atlas/Orion: Genome-wide Perturb-seq Datasets via a Scalable Fix-Cryopreserve Platform for Training Dose-Dependent Biological Foundation Models","year":"2025","page_url":"https://gliostate.com/library/VC0045/","api_url":"https://gliostate.com/api/items/VC0045.json"},{"id":"VC0047","title":"Cellfm-datasets: A Unified Data Infrastructure for Single-Cell and Spatial Transcriptomics Foundation Model Pretraining","year":"2026","page_url":"https://gliostate.com/library/VC0047/","api_url":"https://gliostate.com/api/items/VC0047.json"},{"id":"VC0049","title":"Benchmarking foundation cell models for post-perturbation RNA-seq prediction.","year":"2025","page_url":"https://gliostate.com/library/VC0049/","api_url":"https://gliostate.com/api/items/VC0049.json"},{"id":"VC0050","title":"Zero-shot evaluation reveals limitations of single-cell foundation models.","year":"2025","page_url":"https://gliostate.com/library/VC0050/","api_url":"https://gliostate.com/api/items/VC0050.json"},{"id":"VC0051","title":"PertEval-scFM: Benchmarking Single-Cell Foundation Models for Perturbation Effect Prediction","year":"2024","page_url":"https://gliostate.com/library/VC0051/","api_url":"https://gliostate.com/api/items/VC0051.json"},{"id":"VC0055","title":"Multimodal Benchmarking of Foundation Model Representations for Cellular Perturbation Response Prediction","year":"2025","page_url":"https://gliostate.com/library/VC0055/","api_url":"https://gliostate.com/api/items/VC0055.json"},{"id":"VC0056","title":"Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction.","year":"2026","page_url":"https://gliostate.com/library/VC0056/","api_url":"https://gliostate.com/api/items/VC0056.json"},{"id":"VC0098","title":"Foundation Model Based on Routine Magnetic Resonance Imaging for Brain Tumor Molecular Profiling and Progression Prediction.","year":"2026","page_url":"https://gliostate.com/library/VC0098/","api_url":"https://gliostate.com/api/items/VC0098.json"},{"id":"VC0099","title":"A foundation model for brain tumor MRI analysis: WHO grading and subtype classification.","year":"2025","page_url":"https://gliostate.com/library/VC0099/","api_url":"https://gliostate.com/api/items/VC0099.json"},{"id":"VC0112","title":"Lessons from Ron Alfa (Noetik) on AI-native precision oncology","year":"2026","page_url":"https://gliostate.com/library/VC0112/","api_url":"https://gliostate.com/api/items/VC0112.json"},{"id":"VC0114","title":"Bioptimus: multimodal biology foundation model (NVIDIA compute)","year":"2025","page_url":"https://gliostate.com/library/VC0114/","api_url":"https://gliostate.com/api/items/VC0114.json"},{"id":"VC0119","title":"NeurIPS 2026 Workshop: Foundation Models for the Brain and Body","year":"2026","page_url":"https://gliostate.com/library/VC0119/","api_url":"https://gliostate.com/api/items/VC0119.json"}],"mentioned_in_topics":[{"id":"cell-state-npc-opc-like","title_en":"Neural-progenitor-like (NPC-like) and OPC-like glioma cell states","title_zh":"神经前体样（NPC 样）与少突前体样（OPC 样）胶质瘤细胞状态","url":"https://gliostate.com/cell-states/neural-progenitor-like-opc-like/","api_url":"https://gliostate.com/api/topics/cell-state-npc-opc-like.json"},{"id":"model-virtual-cell","title_en":"AI virtual cell models","title_zh":"AI 虚拟细胞模型","url":"https://gliostate.com/models/virtual-cell/","api_url":"https://gliostate.com/api/topics/model-virtual-cell.json"},{"id":"validation-benchmarks","title_en":"Validating virtual cells: benchmarks, baselines and critiques","title_zh":"虚拟细胞的验证：基准、基线与批评","url":"https://gliostate.com/validation/benchmarks-and-baselines/","api_url":"https://gliostate.com/api/topics/validation-benchmarks.json"}],"relations":[{"subject":"geneformer","subject_name_en":"Geneformer","subject_name_zh":"Geneformer","predicate":"associated_with","object":"foundation-model","object_name_en":"Single-cell foundation model","object_name_zh":"单细胞基础模型","confidence":"high","evidence":[{"id":"VC0009","role":"supports","title":"Transfer learning enables predictions in network biology.","page_url":"https://gliostate.com/library/VC0009/","api_url":"https://gliostate.com/api/items/VC0009.json"}],"note":null,"sources":[{"kind":"topic","id":"model-virtual-cell","url":"https://gliostate.com/models/virtual-cell/","api_url":"https://gliostate.com/api/topics/model-virtual-cell.json"}]},{"subject":"scgpt","subject_name_en":"scGPT","subject_name_zh":"scGPT","predicate":"associated_with","object":"foundation-model","object_name_en":"Single-cell foundation model","object_name_zh":"单细胞基础模型","confidence":"high","evidence":[{"id":"VC0008","role":"supports","title":"scGPT: toward building a foundation model for single-cell multi-omics using generative AI.","page_url":"https://gliostate.com/library/VC0008/","api_url":"https://gliostate.com/api/items/VC0008.json"}],"note":null,"sources":[{"kind":"topic","id":"model-virtual-cell","url":"https://gliostate.com/models/virtual-cell/","api_url":"https://gliostate.com/api/topics/model-virtual-cell.json"}]},{"subject":"scfoundation","subject_name_en":"scFoundation","subject_name_zh":"scFoundation","predicate":"associated_with","object":"foundation-model","object_name_en":"Single-cell foundation model","object_name_zh":"单细胞基础模型","confidence":"high","evidence":[{"id":"VC0011","role":"supports","title":"Large-scale foundation model on single-cell transcriptomics.","page_url":"https://gliostate.com/library/VC0011/","api_url":"https://gliostate.com/api/items/VC0011.json"}],"note":null,"sources":[{"kind":"topic","id":"model-virtual-cell","url":"https://gliostate.com/models/virtual-cell/","api_url":"https://gliostate.com/api/topics/model-virtual-cell.json"}]}],"related_entities":[{"id":"geneformer","type":"model","name_en":"Geneformer","name_zh":"Geneformer","page_url":"https://gliostate.com/entities/geneformer/","page_url_zh":"https://gliostate.com/zh/entities/geneformer/","api_url":"https://gliostate.com/api/entities/geneformer.json","via":"relation"},{"id":"scgpt","type":"model","name_en":"scGPT","name_zh":"scGPT","page_url":"https://gliostate.com/entities/scgpt/","page_url_zh":"https://gliostate.com/zh/entities/scgpt/","api_url":"https://gliostate.com/api/entities/scgpt.json","via":"relation"},{"id":"scfoundation","type":"model","name_en":"scFoundation","name_zh":"scFoundation","page_url":"https://gliostate.com/entities/scfoundation/","page_url_zh":"https://gliostate.com/zh/entities/scfoundation/","api_url":"https://gliostate.com/api/entities/scfoundation.json","via":"relation"},{"id":"perturbation-prediction","type":"method","name_en":"Perturbation response prediction","name_zh":"扰动反应预测","page_url":"https://gliostate.com/entities/perturbation-prediction/","page_url_zh":"https://gliostate.com/zh/entities/perturbation-prediction/","api_url":"https://gliostate.com/api/entities/perturbation-prediction.json","via":"co-mention"},{"id":"zero-shot-evaluation","type":"method","name_en":"Zero-shot evaluation","name_zh":"零样本评估","page_url":"https://gliostate.com/entities/zero-shot-evaluation/","page_url_zh":"https://gliostate.com/zh/entities/zero-shot-evaluation/","api_url":"https://gliostate.com/api/entities/zero-shot-evaluation.json","via":"co-mention"},{"id":"diffuse-midline-glioma","type":"disease","name_en":"Diffuse midline glioma, H3 K27-altered (DMG)","name_zh":"弥漫性中线胶质瘤，H3 K27 改变型（DMG）","page_url":"https://gliostate.com/entities/diffuse-midline-glioma/","page_url_zh":"https://gliostate.com/zh/entities/diffuse-midline-glioma/","api_url":"https://gliostate.com/api/entities/diffuse-midline-glioma.json","via":"co-mention"},{"id":"glioblastoma","type":"disease","name_en":"Glioblastoma (GBM)","name_zh":"胶质母细胞瘤（GBM）","page_url":"https://gliostate.com/entities/glioblastoma/","page_url_zh":"https://gliostate.com/zh/entities/glioblastoma/","api_url":"https://gliostate.com/api/entities/glioblastoma.json","via":"co-mention"},{"id":"linear-baseline","type":"method","name_en":"Simple linear baseline","name_zh":"简单线性基线","page_url":"https://gliostate.com/entities/linear-baseline/","page_url_zh":"https://gliostate.com/zh/entities/linear-baseline/","api_url":"https://gliostate.com/api/entities/linear-baseline.json","via":"co-mention"}]}