AetherCell: A generative engine for virtual cell perturbation and in vivo drug discovery
Li et al. · bioRxiv · 2026-03-16
AetherCell unifies clinical RNA-seq and perturbation assays for generative response prediction and in vivo repurposing.
Tag: Foundation model
17 items, newest first.
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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 · 2026-02-20
MRI foundation model for brain tumor molecular profiling and progression.
scPRINT-2: Towards the next-generation of cell foundation models and benchmarks
Kalfon J, Peyré G, Cantini L. · bioRxiv · 2025-12-15
scPRINT-2: next-gen cell foundation models and benchmarks.
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 · 2025-12-10
Novae: graph-based foundation model for spatial transcriptomics.
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 · 2025-11-19
Foundation model for brain tumor MRI: WHO grading & subtyping.
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 · 2025-10-30
Nicheformer (Theis lab): single-cell + spatial foundation model, Nat Methods 2025.
A visual-omics foundation model to bridge histopathology with spatial transcriptomics.
Chen W et al. · Nature methods · 2025-05-29
OmiCLIP/Loki: visual-omics foundation model bridging H&E and spatial transcriptomics.
A Cross-Species Generative Cell Atlas Across 1.5 Billion Years of Evolution: The TranscriptFormer Single-cell Model
Pearce JD, Simmonds SE, Mahmoudabadi G, Krishnan L, Palla G, Istrate A, Tarashansky A, Nelson B, Valenzuela O, Li D, Quake SR, Karaletsos T. · bioRxiv · 2025-04-29
TranscriptFormer (CZI): generative cross-species cell atlas, 112M cells, 12 species.
Scaling Dense Representations for Single Cell with Transcriptome-Scale Context
Ho N, Ellington CN, Hou J, Addagudi S, Mo S, Tao T, Li D, Zhuang Y, Wang H, Cheng X, Song L, Xing EP. · bioRxiv · 2024-12-03
AIDO.Cell (GenBio AI): dense transcriptome-scale context single-cell models.
GeneCompass: deciphering universal gene regulatory mechanisms with a knowledge-informed cross-species foundation model.
Yang X et al. · Cell research · 2024-10-08
GeneCompass: knowledge-informed cross-species foundation model (CAS).
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 · 2024-06-06
scFoundation: 100M-parameter model on ~50M human cells (Tsinghua/BioMap).
Towards a general-purpose foundation model for computational pathology.
Chen RJ et al. · Nature medicine · 2024-03-19
UNI: general-purpose computational pathology foundation model (incl. brain tumor tasks).
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 · 2024-02-26
scGPT: generative pretrained transformer on 33M cells (Bo Wang lab).
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 · 2023-11-29
Universal Cell Embeddings (UCE), cross-species zero-shot cell embedding (Leskovec/Quake).
CellPLM: Pre-training of Cell Language Model Beyond Single Cells
Wen H, Tang W, Dai X, Ding J, Jin W, Xie Y, Tang J. · bioRxiv · 2023-10-05
CellPLM: cell language model beyond single cells (spatial context).
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 · 2023-05-31
Geneformer: context-aware transformer enabling in silico deletion/network predictions.
scBERT as a Large-scale Pretrained Deep Language Model for Cell Type Annotation of Single-cell RNA-seq Data
Yang F, Wang W, Wang F, Fang Y, Tang D, Huang J, Lu H, Yao J. · bioRxiv · 2021-12-07
scBERT: early pretrained language model for cell type annotation.