74 lines
2.7 KiB
YAML
74 lines
2.7 KiB
YAML
---
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title: "Provenance-backed foundation model enrichment batch 2."
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task: ""
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lineage_type: import
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upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/data/enrichment.foundation-models-v2.yml
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upstream_sha: 7a064bf0
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imported_at: 2026-08-08
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prompt_class: catalogue
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upstream_changes: accepted
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author: upstream
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validated: false
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---
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# Provenance-backed foundation model enrichment batch 2.
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resources:
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nicheformer:
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entities: [cell, gene, tissue]
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methods: [self-supervised-learning, transformer]
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modalities: [single-cell-rna-seq, spatial-transcriptomics, transcriptomics]
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tasks: [foundation-model-pretraining, representation-learning]
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year: 2024
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github: https://github.com/theislab/nicheformer
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paper: https://doi.org/10.1101/2024.04.15.589472
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last_checked: 2026-08-08
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metadata_sources:
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- https://github.com/theislab/nicheformer
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- https://doi.org/10.1101/2024.04.15.589472
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genept:
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entities: [cell, gene]
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methods: [language-model]
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modalities: [single-cell-rna-seq, transcriptomics]
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tasks: [batch-correction, classification, representation-learning]
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year: 2023
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github: https://github.com/yiqunchen/GenePT
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paper: https://www.biorxiv.org/content/10.1101/2023.10.16.562533v2
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last_checked: 2026-08-08
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metadata_sources:
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- https://github.com/yiqunchen/GenePT
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- https://www.biorxiv.org/content/10.1101/2023.10.16.562533v2
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scgpt_spatial:
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entities: [cell, gene, tissue]
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methods: [generative-model, self-supervised-learning, transformer]
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modalities: [multi-omics, single-cell-rna-seq, spatial-transcriptomics]
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tasks: [foundation-model-pretraining, imputation, representation-learning]
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year: 2025
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github: https://github.com/bowang-lab/scGPT-spatial
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paper: https://www.biorxiv.org/content/10.1101/2025.02.05.636714v1
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last_checked: 2026-08-08
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metadata_sources:
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- https://github.com/bowang-lab/scGPT-spatial
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- https://www.biorxiv.org/content/10.1101/2025.02.05.636714v1
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scprint:
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entities: [cell, gene]
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methods: [self-supervised-learning, transformer]
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modalities: [single-cell-rna-seq, transcriptomics]
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tasks:
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- batch-correction
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- cell-type-annotation
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- foundation-model-pretraining
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- gene-regulatory-network-inference
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- imputation
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- representation-learning
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year: 2025
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github: https://github.com/cantinilab/scPRINT
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documentation: https://www.jkobject.com/scPRINT/
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paper: https://www.nature.com/articles/s41467-025-58699-1
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last_checked: 2026-08-08
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metadata_sources:
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- https://github.com/cantinilab/scPRINT
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- https://www.nature.com/articles/s41467-025-58699-1
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