129 lines
4.6 KiB
YAML
129 lines
4.6 KiB
YAML
---
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title: "AI4Bio landscape enrichment overlay"
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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.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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# AI4Bio landscape enrichment overlay
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#
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# README.md remains the canonical source for resource membership and basic fields.
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# Add richer, independently curated metadata here, keyed by the stable resource id.
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# scripts/build_resources.py merges these fields into generated JSON/CSV artifacts.
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#
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# Enrichment values should be source-verifiable. Controlled vocabulary fields are
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# validated against data/vocabulary.yml.
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resources:
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scgpt:
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entities: [cell, gene]
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methods: [generative-model, self-supervised-learning, transformer]
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modalities: [multi-omics, single-cell-rna-seq, transcriptomics]
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tasks:
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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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- perturbation-prediction
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- representation-learning
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year: 2024
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github: https://github.com/bowang-lab/scGPT
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documentation: https://scgpt.readthedocs.io/en/latest/
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paper: https://www.nature.com/articles/s41592-024-02201-0
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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
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- https://www.nature.com/articles/s41592-024-02201-0
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geneformer:
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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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- classification
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- foundation-model-pretraining
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- perturbation-prediction
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- representation-learning
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year: 2023
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documentation: https://geneformer.readthedocs.io/
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paper: https://www.nature.com/articles/s41586-023-06139-9
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last_checked: 2026-08-08
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metadata_sources:
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- https://huggingface.co/ctheodoris/Geneformer
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- https://www.nature.com/articles/s41586-023-06139-9
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scfoundation:
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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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- cell-type-annotation
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- drug-response-prediction
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- foundation-model-pretraining
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- perturbation-prediction
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- representation-learning
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year: 2024
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github: https://github.com/biomap-research/scFoundation
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paper: https://www.nature.com/articles/s41592-024-02305-7
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last_checked: 2026-08-08
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metadata_sources:
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- https://github.com/biomap-research/scFoundation
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- https://www.nature.com/articles/s41592-024-02305-7
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genecompass:
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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: [foundation-model-pretraining, representation-learning]
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year: 2024
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github: https://github.com/xCompass-AI/GeneCompass
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paper: https://www.nature.com/articles/s41422-024-01034-y
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last_checked: 2026-08-08
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metadata_sources:
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- https://github.com/xCompass-AI/GeneCompass
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- https://www.nature.com/articles/s41422-024-01034-y
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uce:
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entities: [cell]
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methods: [self-supervised-learning]
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modalities: [single-cell-rna-seq, transcriptomics]
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tasks: [foundation-model-pretraining, representation-learning]
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year: 2026
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github: https://github.com/snap-stanford/UCE
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paper: https://www.nature.com/articles/s41586-026-10689-z
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last_checked: 2026-08-08
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metadata_sources:
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- https://github.com/snap-stanford/UCE
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- https://www.nature.com/articles/s41586-026-10689-z
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cellplm:
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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: [foundation-model-pretraining, representation-learning]
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year: 2023
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github: https://github.com/OmicsML/CellPLM
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paper: https://www.biorxiv.org/content/10.1101/2023.10.03.560734v1
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last_checked: 2026-08-08
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metadata_sources:
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- https://github.com/OmicsML/CellPLM
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- https://www.biorxiv.org/content/10.1101/2023.10.03.560734v1
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scbert:
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entities: [cell, gene]
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methods: [language-model, self-supervised-learning, transformer]
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modalities: [single-cell-rna-seq, transcriptomics]
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tasks: [cell-type-annotation, classification, foundation-model-pretraining]
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year: 2022
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github: https://github.com/TencentAILabHealthcare/scBERT
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paper: https://www.nature.com/articles/s42256-022-00534-z
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last_checked: 2026-08-08
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metadata_sources:
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- https://github.com/TencentAILabHealthcare/scBERT
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- https://www.nature.com/articles/s42256-022-00534-z
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