[2023 Nature Machine Intelligence] Reusability report: Learning the transcriptional grammar in single-cell RNA-sequencing data using transformers[paper]
[2023 bioRxiv] Scalable querying of human cell atlases via a foundational model reveals commonalities across fibrosis-associated macrophages[paper]
[2023 bioRxiv] To Transformers and Beyond: Large Language Models for the Genome[paper]
[2023 bioRxiv] A pre-trained large generative model for translating single-cell transcriptome to proteome[paper]
[2023 bioRxiv] GENEPT: A SIMPLE BUT HARD-TO-BEAT FOUNDATION MODEL FOR GENES AND CELLS BUILT FROM CHATGPT[paper]
[2023 bioRxiv] CellPLM: Pre-training of Cell Language Model Beyond Single Cells[paper]
[2023 Nature Biotechnology multi-modal] Integration of multi-modal single-cell data[Paper]
[2023 bioRxiv multi-modal] Single-cell gene expression prediction from DNA sequence at large contexts[paper]
[2023 bioRxiv multi-modal] Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation[paper]
[2023 bioRxiv] CellPolaris: Decoding Cell Fate through Generalization Transfer Learning of Gene Regulatory Networks[paper]
[2023 bioRxiv] GeneCompass: Deciphering Universal Gene Regulatory Mechanisms with Knowledge-Informed Cross-Species Foundation Model[paper]
[2023 bioRxiv] scHyena: Foundation Model for Full-Length Single-Cell RNA-Seq Analysis in Brain[paper]
[2023 XXXX] A Deeper Dive into Single-Cell RNA Sequencing Foundation Models
[2023 bioRxiv] GET: a foundation model of transcription across human cell types[paper]
[2023 bioRxiv] Cell2Sentence: Teaching Large Language Models the Language of Biology[paper]
[2023 bioRxiv][scTranslator] A pre-trained large language model for translating single-cell transcriptome to proteome[paper]
[2023 bioRxiv][scPoli] Population-level integration of single-cell datasets enables multi-scale analysis across samples[paper]
[2023 bioRxiv] Towards Universal Cell Embeddings: Integrating Single-cell RNA-seq Datasets across Species with SATURN[paper]
[2023 bioRxiv][scFoundation] Large Scale Foundation Model on Single-cell Transcriptomics[paper]
[2023 Nature][GeneFormer] Transfer learning enables predictions in network biology[paper]
[2023 iSchience][tGPT] Generative pretraining from large-scale transcriptomes for single-cell deciphering[paper]
[2023 bioRxiv][scGPT] scGPT: Towards Building a Foundation Model for Single-Cell Multi-omics Using Generative AI[paper v1], [paper v2]
[2023 bioRxiv][xTrimoGene] xTrimoGene: An Efficient and Scalable Representation Learner for Single-Cell RNA-Seq Data[paper]
[2022 arxiv][Exceiver] A single-cell gene expression language model[paper]
[2022 Nature Machine Intelligence][scBERT] scBERT as a large-scale pretrained deep language model for cell type annotation of single-cell RNA-seq data[paper]
[2022 bioRxiv][scFormer] scFormer: a universal representation learning approach for single-cell data using transformers[paper]
[2022 Bioinformatics][scPretrain] scPretrain: multi-task self-supervised learning for cell-type classification[paper]
Foundation-Model-For-Pathology
[2024 bioRxiv] BiomedParse: a biomedical foundation model for image parsing of everything everywhere all at once[paper]
[2024 Nature] A whole-slide foundation model for digital pathology from real-world data[paper]
[2024 Nature Medicine FM4Pathology] Towards a general-purpose foundation model for computational pathology[paper]
[2024 Nature Medicine FM4Pathology] A visual-language foundation model for computational pathology[paper]
[2023 Nature Medicine] A visual–language foundation model for pathology image analysis using medical Twitter[paper]
awesome-foundation-model-single-cell-papers's People