neuro-omics-kb/mkdocs.yml at main · Transconnectome/neuro-omics-kb · GitHub

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site_name: Neuro-Omics KB
site_description: Code-first knowledge base for genetics and brain foundation models and multimodal integration
repo_url: https://github.com/allison-eunse/neuro-omics-kb
edit_uri: edit/main/docs/
site_url: https://allison-eunse.github.io/neuro-omics-kb/
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copyright: |
  Maintained by Allison Eun Se You | Last updated December 2025

plugins:
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nav:
  - Home: index.md
  - Team Guide: team_guide.md
  - Guides:
      - KB overview: guide/kb_overview.md
  - Models:
      - Genetics:
          - Overview: models/genetics/index.md
          - Caduceus: models/genetics/caduceus.md
          - DNABERT-2: models/genetics/dnabert2.md
          - Evo 2: models/genetics/evo2.md
          - GENERator: models/genetics/generator.md
          - HyenaDNA: models/genetics/hyenadna.md
      - Brain:
          - Overview: models/brain/index.md
          - BrainLM: models/brain/brainlm.md
          - Brain-JEPA: models/brain/brainjepa.md
          - Brain Harmony: models/brain/brainharmony.md
          - BrainMT: models/brain/brainmt.md
          - SwiFT: models/brain/swift.md
      - Multimodal & Clinical:
          - Overview: models/multimodal/index.md
          - Flamingo: models/multimodal/flamingo.md
          - BAGEL: models/multimodal/bagel.md
          - MoT: models/multimodal/mot.md
          - M3FM: models/multimodal/m3fm.md
          - Me-LLaMA: models/multimodal/me_llama.md
          - TITAN: models/multimodal/titan.md
          - FMS-Medical Catalog: models/multimodal/fms_medical.md
  - Integration:
      - Overview: integration/index.md
      - Strategy: integration/integration_strategy.md
      - Analysis recipes:
          - CCA + permutation: integration/analysis_recipes/cca_permutation.md
          - Prediction baselines: integration/analysis_recipes/prediction_baselines.md
          - Partial correlations: integration/analysis_recipes/partial_correlations.md
      - Modality features:
          - Genomics: integration/modality_features/genomics.md
          - sMRI: integration/modality_features/smri.md
          - fMRI: integration/modality_features/fmri.md
      - Embedding policies: integration/embedding_policies.md
      - Integration cards:
          - Ensemble integration: models/integrations/ensemble_integration.md
          - Oncology multimodal review: models/integrations/oncology_multimodal_review.md
          - Multimodal FM patterns: models/integrations/multimodal_fm_patterns.md
      - Design patterns: integration/design_patterns.md
      - Multimodal architectures: integration/multimodal_architectures.md
      - Benchmarks: integration/benchmarks.md
  - Data:
      - UKB data map: data/ukb_data_map.md
      - Schemas: data/schemas.md
      - Subject keys: data/subject_keys.md
      - Governance & QC: data/governance_qc.md
  - Experiment Configs: configs/experiments.md
  - Code Walkthroughs:
      - Index: code_walkthroughs/index.md
      - Genetics:
          - Caduceus: code_walkthroughs/caduceus_walkthrough.md
          - DNABERT-2: code_walkthroughs/dnabert2_walkthrough.md
          - Evo 2: code_walkthroughs/evo2_walkthrough.md
          - GENERator: code_walkthroughs/generator_walkthrough.md
          - HyenaDNA: code_walkthroughs/hyena_walkthrough.md
      - Brain:
          - BrainLM: code_walkthroughs/brainlm_walkthrough.md
          - Brain-JEPA: code_walkthroughs/brainjepa_walkthrough.md
          - Brain Harmony: code_walkthroughs/brainharmony_walkthrough.md
          - BrainMT: code_walkthroughs/brainmt_walkthrough.md
          - SwiFT: code_walkthroughs/swift_walkthrough.md
      - Multimodal:
          - BAGEL: code_walkthroughs/bagel_walkthrough.md
          - Flamingo: code_walkthroughs/flamingo_walkthrough.md
          - MoT: code_walkthroughs/mot_walkthrough.md
          - M3FM: code_walkthroughs/m3fm_walkthrough.md
          - Me-LLaMA: code_walkthroughs/melamma_walkthrough.md
          - TITAN: code_walkthroughs/titan_walkthrough.md
          - FMS-Medical: code_walkthroughs/fms_medical_walkthrough.md
  - Research Papers:
      - Brain Models:
          - BrainLM (2024): generated/kb_curated/papers-md/brainlm_2024.md
          - Brain-JEPA (2024): generated/kb_curated/papers-md/brainjepa_2024.md
          - Brain Harmony (2025): generated/kb_curated/papers-md/brainharmony_2025.md
          - BrainMT (2025): generated/kb_curated/papers-md/brainmt_2025.md
          - SwiFT (2023): generated/kb_curated/papers-md/swift_2023.md
      - Genetics Models:
          - Caduceus (2024): generated/kb_curated/papers-md/caduceus_2024.md
          - DNABERT-2 (2024): generated/kb_curated/papers-md/dnabert2_2024.md
          - Evo 2 (2024): generated/kb_curated/papers-md/evo2_2024.md
          - GENERator (2024): generated/kb_curated/papers-md/generator_2024.md
          - HyenaDNA (2023): generated/kb_curated/papers-md/hyenadna_2023.md
      - Multimodal Models:
          - BAGEL (2025): generated/kb_curated/papers-md/bagel_2025.md
          - MoT (2025): generated/kb_curated/papers-md/mot_2025.md
          - M3FM (2025): generated/kb_curated/papers-md/m3fm_2025.md
          - Me-LLaMA (2024): generated/kb_curated/papers-md/me_llama_2024.md
          - TITAN (2025): generated/kb_curated/papers-md/titan_2025.md
          - Flamingo (2022): generated/kb_curated/papers-md/flamingo_2022.md
      - Integration & Methods:
          - Ensemble integration (Li 2022): generated/kb_curated/papers-md/ensemble_integration_li2022.md
          - Multimodal FMs (2025): generated/kb_curated/papers-md/mmfm_2025.md
          - MM-LLM imaging (2025): generated/kb_curated/papers-md/mm_llm_imaging_2025.md
          - Oncology multimodal (Waqas 2024): generated/kb_curated/papers-md/oncology_multimodal_waqas2024.md
          - Yoon BioKDD (2025): generated/kb_curated/papers-md/yoon_biokdd2025.md
          - RC-equivariant networks (2021): generated/kb_curated/papers-md/reverse-complement-equivariant_2021.md
          - RC consistency for DNA LMs (2025): generated/kb_curated/papers-md/reverse-complement-consistency_2025.md
          - Systems & algorithms for multi-hybrid LMs (2025): generated/kb_curated/papers-md/systems-algorithms-multihybrid_2025.md
          - Brain MRI bias unlearning (2021): generated/kb_curated/papers-md/brain-mri-bias-unlearning_2021.md
          - Brain multisite harmonization (MURD 2024): generated/kb_curated/papers-md/murd_2024.md
          - Site unlearning (Dinsdale 2021): generated/kb_curated/papers-md/dinsdale_site_unlearning_2021.md
      - Genomics & Population:
          - GWAS diverse populations: generated/kb_curated/papers-md/gwas_diverse_populations.md
          - PRS guide: generated/kb_curated/papers-md/prs_guide.md
      - Tabular Baselines:
          - TabPFN (2023): generated/kb_curated/papers-md/tabpfn_2024.md
      - General:
          - Representation learning (2012): generated/kb_curated/papers-md/representation-learning_2012.md
          - Foundation models overview (2024): generated/kb_curated/papers-md/fm_general_2024.md
  - Decisions:
      - Integration plan (Nov 2025): decisions/2025-11-integration-plan.md
      - Dev validation plan: decisions/dev_validation_plan.md
  - KB Templates (Reference):
      - Generated Templates:
          - Analysis recipe (CCA): generated/templates/analysis_recipe_cca.md
          - Analysis recipe (prediction): generated/templates/analysis_recipe_prediction.md
          - Dataset card: generated/templates/dataset_card.md
          - Integration strategy: generated/templates/integration_strategy.md
          - Modality features (fMRI): generated/templates/modality_features_fmri.md
          - Modality features (genomics): generated/templates/modality_features_genomics.md
          - Modality features (sMRI): generated/templates/modality_features_smri.md
          - Model card: generated/templates/model_card_template.md
      - KB Templates:
          - Cross-domain eval card: kb/templates/cross_domain_eval_card.md
          - Dataset card: kb/templates/dataset_card.md
          - Experiment config stub: kb/templates/experiment_config_stub.md
          - External model pattern: kb/templates/external_model_pattern_card.md
          - Integration principles: kb/templates/integration_principles_card.md
          - Method family card: kb/templates/method_family_card.md
          - Model card: kb/templates/model_card_template.md
      - Paper & Integration Card Templates:
          - Integration card template: models/integrations/template.md
          - Paper summary template: generated/kb_curated/papers-md/template.md