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Multimodal Gene-Brain Integration Project

A unified dashboard for tracking research progress across multiple repositories in the Gene-Brain project.

Overview

This repository serves as the central tracking hub for the Multimodal Gene-Brain Integration Project. Individual team members maintain their own repositories for source code, while this hub aggregates:

  • Commit feeds (on every push from team repos)
  • Daily logs (end-of-day summaries, manually published after review)

The GitHub Pages site provides a single view of all team activity.

Live Dashboard

πŸ”— View the Gene-Brain Hub

  • Home β€” Project overview & team roster
  • Commits β€” Latest commits from all team repositories
  • Daily Logs β€” End-of-day summaries

Project Goal

We aim to construct a unified representation connecting:

  • DNA (upstream biological blueprint)
  • Proteomic profiles (intermediate molecular processes)
  • Brain imaging/phenotypic measurements (downstream outcomes)

within a shared latent space that is predictive, generative, and interpretable.

Team & Research Components

Research Component Member(s) GitHub Key Responsibility
Gene-Brain CCA & Prediction μœ μ€μ„œ allison-eunse CCA between Gene FM embeddings and brain data; pilot regression for cognitive decline
LLM-based Evaluation 이은지, κ³½μˆ˜μ§€, μ†ν˜œλ Ή leee4321, sujigwak, hayleyson Pipeline for interpreting CCA results via fine-tuned LLM
Genomic-Conditional Diffusion μ΅œμŠΉμ—°, λ―Όμ •μœ€ syunchoi Pilot diffusion model conditioned on genomic embeddings for brain image generation
Genomic FM 김채연 cykim-saihst Gene region parsing for cognitive decline; regression with genomic embeddings
Gene-Text μ‘°μ€μˆ˜ ssikssikhan-cho Training pipeline aligning DNA FM embeddings with LLM embeddings (NCBI/UniProt)
Proteomics Adapter κΉ€μˆ˜ν˜„ Shunamo Multi-View Adapter with Gating Network for plasma proteomics

Repository Structure

gene-brain/
β”œβ”€β”€ site/                      # GitHub Pages source
β”‚   β”œβ”€β”€ index.html             # Home (project intro + team table)
β”‚   β”œβ”€β”€ commits.html           # Commits dashboard
β”‚   β”œβ”€β”€ daily.html             # Daily logs viewer
β”‚   β”œβ”€β”€ log.html               # Single markdown viewer
β”‚   β”œβ”€β”€ styles.css             # Theme (pastel + purple/blue/green)
β”‚   β”œβ”€β”€ js/                    # Loaders, renderers, refresh logic
β”‚   β”œβ”€β”€ config/
β”‚   β”‚   └── projects.json      # Member/repo roster
β”‚   β”œβ”€β”€ assets/
β”‚   β”‚   └── project_overview.png
β”‚   └── data/                  # Commit JSONs pushed by team repos
β”‚       └── <owner>__<repo>/commits.json
β”œβ”€β”€ team-tracking/             # Daily logs (markdown)
β”‚   └── <owner>/<repo>/daily/YYYY-MM-DD.md
β”œβ”€β”€ scripts/
β”‚   └── build_pages_artifact.py
β”œβ”€β”€ templates/
β”‚   └── individual-project/
β”‚       β”œβ”€β”€ sync_commits_to_central.yml
β”‚       └── publish_today.sh
└── .github/workflows/
    └── pages.yml

For Team Members (Individual Project Repo Setup)

1. Add the commit-sync workflow

Copy templates/individual-project/sync_commits_to_central.yml to your repo's .github/workflows/.

2. Set the required secret

Create a secret named BIG_REPO_TOKEN with a PAT that has write access to this central repo.

3. (Optional) Publish daily logs

Use templates/individual-project/publish_today.sh to push your reviewed TODAY.md to the central repo.

Auto-Discovery

You don't need to tell the central repo your exact repository name. The dashboard will automatically discover any project that syncs commits. Projects will appear with their GitHub username and repo name.

To add custom display names (e.g., "Gene-Text" instead of "gene-text"), update site/config/projects.json.

See PLAN.md for implementation details and conventions.