Foundation-Model-Evaluation-For-Single-cell

1. [2024 Nature Methods] Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis [paper]
2. [2024 biorxiv] Metric Mirages in Cell Embeddings [paper]
3. [2023 biorxiv] A Deep Dive into Single-Cell RNA Sequencing Foundation Models [paper]
4. [2023 bioRxiv scEval] Evaluating the Utilities of Large Language Models in Single-cell Data Analysis [paper]
5. [2023 bioRxiv] Assessing the limits of zero-shot foundation models in single-cell biology [paper]
6. [2023 bioRxiv] Foundation Models Meet Imbalanced Single-Cell Data When Learning Cell Type Annotations [paper]
7. [2023 bioRxiv] Evaluation of large language models for discovery of gene set function [paper]
8. [2024 ICLR benchmark DNA FD] BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks [paper]

Foundation-Model-For-Single-cell

1. [2024 BioRxiv] A framework for gene representation on spatial transcriptomics [paper]
2. [2024 BioRxiv] Multimodal learning of transcriptomes and text enables interactive single-cell RNA-seq data exploration with natural-language chats [paper]
3. [2024 BioRxiv] CancerFoundation: A single-cell RNA sequencing foundation model to decipher drug resistance in cancer [paper]
4. [2024 BioRxiv] scChat: A Large Language Model-Powered Co-Pilot for Contextualized Single-Cell RNA Sequencing Analysis [paper]
5. [2024 BioRxiv] Cell-ontology guided transcriptome foundation model [paper]
6. [2024 BioRxiv] How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities [paper]
7. [2024 Nature Methods] Transformers in single-cell omics: a review and new perspectives [paper]
8. [2024 BioRxiv] Cell-Graph Compass: Modeling Single Cells with Graph Structure Foundation Model [paper]
9. [2024 BioRxiv] scPRINT: pre-training on 50 million cells allows robust gene network predictions [paper]
10. [2024 biorxiv] Precious3GPT: Multimodal Multi-Species Multi-Omics Multi-Tissue Transformer for Aging Research and Drug Discovery [paper]
11. [2024 biorxiv] scMulan: a multitask generative pre-trained language model for single-cell analysis [paper]
12. [2024 biorxiv] CELLama: Foundation Model for Single Cell and Spatial Transcriptomics by Cell Embedding Leveraging Language Model Abilities [paper]
13. [2024 biorxiv] LangCell: Language-Cell Pre-training for Cell Identity Understanding [paper]
14. [2024 biorxiv] Nicheformer: a foundation model for single-cell and spatial omics [paper]
15. [2024 biorxiv] Large-scale characterization of cell niches in spatial atlases using bio-inspired graph learning [paper]
16. [2024 biorxiv] scmFormer Integrates Large-Scale Single-Cell Proteomics and Transcriptomics Data by Multi-Task Transformer [paper]
17. [2024 biorxiv] Sequence modeling and design from molecular to genome scale with Evo [paper]
18. [2024] Single-cell metadata as language [paper]
19. [2023 NeurIPS] MuSe-GNN: Learning Unified Gene Representation From Multimodal Biological Graph Data [paper]
20. [2023 biorxiv] scNODE: Generative Model for Temporal Single Cell Transcriptomic Data Prediction [paper]
21. [2023 biorxiv] Universal Cell Embeddings: A Foundation Model for Cell Biology [paper]
22. [2023 NeurIPS 2023 AI for Science Workshop] scCLIP: Multi-modal Single-cell Contrastive Learning Integration Pre-training [paper]
23. [2023 NeurIPS 2023 AI for Science Workshop] Single-cell Masked Autoencoder: An Accurate and Interpretable Automated Immunophenotyper [paper]
24. [2023 biorxiv] scELMo: Embeddings from Language Models are Good Learners for Single-cell Data Analysis [paper]
25. [2023 biorxiv] Large-Scale Cell Representation Learning via Divide-and-Conquer Contrastive Learning [paper]
26. [2023 arxiv multimodal] MuSe-GNN: Learning Unified Gene Representation From Multimodal Biological Graph Data [paper]
27. [2023 Nature Machine Intelligence] Reusability report: Learning the transcriptional grammar in single-cell RNA-sequencing data using transformers [paper]
28. [2023 bioRxiv] Scalable querying of human cell atlases via a foundational model reveals commonalities across fibrosis-associated macrophages [paper]
29. [2023 bioRxiv] To Transformers and Beyond: Large Language Models for the Genome [paper]
30. [2023 bioRxiv] A pre-trained large generative model for translating single-cell transcriptome to proteome [paper]
31. [2023 bioRxiv] GENEPT: A SIMPLE BUT HARD-TO-BEAT FOUNDATION MODEL FOR GENES AND CELLS BUILT FROM CHATGPT [paper]
32. [2023 bioRxiv] CellPLM: Pre-training of Cell Language Model Beyond Single Cells [paper]
33. [2023 Nature Biotechnology multi-modal] Integration of multi-modal single-cell data [Paper]
34. [2023 bioRxiv multi-modal] Single-cell gene expression prediction from DNA sequence at large contexts [paper]
35. [2023 bioRxiv multi-modal] Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation [paper]
36. [2023 bioRxiv] CellPolaris: Decoding Cell Fate through Generalization Transfer Learning of Gene Regulatory Networks [paper]
37. [2023 bioRxiv] GeneCompass: Deciphering Universal Gene Regulatory Mechanisms with Knowledge-Informed Cross-Species Foundation Model [paper]
38. [2023 bioRxiv] scHyena: Foundation Model for Full-Length Single-Cell RNA-Seq Analysis in Brain [paper]
39. [2023 XXXX] A Deeper Dive into Single-Cell RNA Sequencing Foundation Models
40. [2023 bioRxiv] GET: a foundation model of transcription across human cell types [paper]
41. [2024 ICML] Cell2Sentence: Teaching Large Language Models the Language of Biology [paper]
42. [2023 bioRxiv][scTranslator] A pre-trained large language model for translating single-cell transcriptome to proteome [paper]
43. [2023 bioRxiv][scPoli] Population-level integration of single-cell datasets enables multi-scale analysis across samples [paper]
44. [2023 bioRxiv] Towards Universal Cell Embeddings: Integrating Single-cell RNA-seq Datasets across Species with SATURN [paper]
45. [2023 bioRxiv][scFoundation] Large Scale Foundation Model on Single-cell Transcriptomics [paper]
46. [2023 Nature][GeneFormer] Transfer learning enables predictions in network biology [paper]
47. [2023 iSchience][tGPT] Generative pretraining from large-scale transcriptomes for single-cell deciphering [paper]
48. [2023 bioRxiv][scGPT] scGPT: Towards Building a Foundation Model for Single-Cell Multi-omics Using Generative AI [paper v1], [paper v2]
49. [2023 bioRxiv][xTrimoGene] xTrimoGene: An Efficient and Scalable Representation Learner for Single-Cell RNA-Seq Data [paper]
50. [2022 arxiv][Exceiver] A single-cell gene expression language model [paper]
51. [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]
52. [2022 bioRxiv][scFormer] scFormer: a universal representation learning approach for single-cell data using transformers [paper]
53. [2022 Bioinformatics][scPretrain] scPretrain: multi-task self-supervised learning for cell-type classification [paper]

Foundation-Model-Genetic-Perturbation

1. [2024 biorxiv] Benchmarking a foundational cell model for post-perturbation RNAseq prediction [paper]
2. [2024 biorxiv] Benchmarking Transcriptomics Foundation Models for Perturbation Analysis: one PCA still rules them all [paper]
3. [2024 biorxiv] PertEval-scFM: Benchmarking Single-Cell Foundation Models for Perturbation Effect Prediction [paper]
4. [2024 BioRxiv] scGenePT: Is language all you need for modeling single-cell perturbations? [paper]
5. [2024 Cell, FM4perturbation data: a review] Toward a foundation model of causal cell and tissue biology with a Perturbation Cell and Tissue Atlas [paper]
6. [2023 NM] Causal identification of single-cell experimental perturbation effects with CINEMA-OT [paper]

Foundation-Model-For-Pathology

1. [2024 bioRxiv] BiomedParse: a biomedical foundation model for image parsing of everything everywhere all at once [paper]
2. [2024 Nature] A whole-slide foundation model for digital pathology from real-world data [paper]
3. [2024 Nature Medicine FM4Pathology] Towards a general-purpose foundation model for computational pathology [paper]
4. [2024 Nature Medicine FM4Pathology] A visual-language foundation model for computational pathology [paper]
5. [2023 Nature Medicine] A visual–language foundation model for pathology image analysis using medical Twitter [paper]

Foundation-Model-For-DNA

1. [2024 bioRxiv] CpGPT: a Foundation Model for DNA Methylation [paper]
2. [2024 bioRxiv] Evaluating the representational power of pre-trained DNA language models for regulatory genomics [paper]