| --- |
| license: cc-by-nd-4.0 |
| language: |
| - en |
| tags: |
| - foundation-model |
| - neuroscience |
| - eeg |
| - mamba |
| --- |
| <div align="center"> |
| <img src="https://raw.githubusercontent.com/danaebroustail/BioFoundation_Danae/refs/heads/lumamba/docs/model/logo/LuMamba_logo.png" alt="LuMamba Logo" width="800"/> |
| <h1>LuMamba: Latent Unified Mamba for Electrode |
| Topology-Invariant and Efficient EEG Modeling</h1> |
| </div> |
| <p align="center"> |
| <a href="https://github.com/pulp-bio/BioFoundation"> |
| <img src ="https://img.shields.io/github/stars/pulp-bio/BioFoundation?color=ccf" alt="Github"> |
| </a> |
| <a href="https://creativecommons.org/licenses/by-nd/4.0/"> |
| <img src="https://img.shields.io/badge/License-CC_BY--ND_4.0-lightgrey.svg" alt="License"> |
| </a> |
| <a href="https://arxiv.org/abs/2603.19100"> |
| <img src="https://img.shields.io/badge/arXiv-2510.22257-b31b1b.svg" alt="Paper"> |
| </a> |
| </p> |
| |
|
|
| **LuMamba** (Latent Unified Mamba) is an **EEG foundation model** built on efficient **Mamba state-space learning**, capable of handling **heterogeneous channel topologies**. |
| LuMamba addresses varying channel layouts with **LUNA channel unification**, projecting a given EEG channel layout to a **fixed latent topology**, and overcomes the quadratic complexity of transformers with **FEMBA**'s efficient **bidirectional Mamba encoder**. |
|
|
| --- |
|
|
| ## 🔒 License & Usage Policy (Weights) |
|
|
| **Weights license:** The released model weights are licensed under **Creative Commons Attribution–NoDerivatives 4.0 (CC BY-ND 4.0)**. This section summarizes the practical implications for users. *This is not legal advice; please read the full license text.* |
|
|
| ### ✅ You may |
| - **Use** and **redistribute** the **unmodified** LuMamba weights (including in commercial settings) **with proper attribution** to the LuMamba authors. |
| - **Fine-tune / adapt** the weights **for your internal use** (research or production) **without redistributing** the modified weights. |
| - **Publish your code, configs, logs, and papers** describing experiments with LuMamba (please cite the paper). |
|
|
| ### 🚫 You may not |
| - **Share, host, or redistribute any modified weights** (including LoRA/adapter/delta checkpoints or pruned/quantized variants). Any parameter set that encodes an adaptation is considered a derivative and cannot be shared under CC BY-ND 4.0. |
| - **Imply endorsement** by the LuMamba authors for any derivative or evaluation without our written permission. |
| - **Use the LuMamba name** in a way that suggests your modified model is an official LuMamba release. |
|
|
| ### 🤝 How to contribute improvements (PR-gated releases) |
| We welcome community improvements via a **pull-request (PR)** workflow. If you believe your improvements should become an **official LuMamba release**: |
| 1. **Open a PR** in the [BioFoundation repository](https://github.com/pulp-bio/BioFoundation) describing the change (architecture/head/training recipe, datasets, preprocessing, compute). |
| 2. Include **reproducibility artifacts**: configs, seeds, scripts, environment details, training/validation logs, and the **evaluation protocol** (e.g., TUAB/TUAR/TUSL) with exact splits. |
| 3. Provide **comprehensive results** (AUROC/AUPR/BA, FLOPs, memory) vs. the baselines reported in the LuMamba paper. |
| 4. After **maintainer review**, approved changes will be **retrained/validated** and, if accepted, **released by the maintainers** as a new **official LuMamba** checkpoint under **CC BY-ND 4.0**. |
|
|
| > Rationale: CC BY-ND protects users from fragmented, lower-quality “LuMamba variants,” while still enabling internal fine-tuning and a path for the community to upstream improvements through review. |
|
|
| --- |
|
|
| ## 🔎 Model Summary |
|
|
| - **Goal:** Efficient and topology-agnostic EEG modeling with linear complexity in sequence length. |
| - **Core idea:** **Channel-Unification Module** uses **learned queries** (Q) with **cross-attention** to map any set of channels to a fixed latent space. **bidirectional Mamba blocks** then operate on that latent sequence. |
| - **Pre-training data:** TUEG, **>21,000 hours** of raw EEG; downstream subjects removed to avoid leakage. |
| - **Downstream tasks:** **TUAB** (abnormal), **TUAR** (artifacts), **TUSL** (slowing), **SEED-V** (emotion; unseen 62-ch montage), **APAVA** (Alzheimer's disease; unseen 16-ch layout, **TDBrain** (Parkinson's disease; unseen 26-ch layout) |
|
|
| --- |
|
|
| ## 🚀 Model Variants |
|
|
| The model currently exists in a Tiny Variant, with the following parameters: |
|
|
| | Variant | Parameters | FEMBA parameters |LUNA parameters | |
| |-----------------|------------|-----------------------------|------------------------------------| |
| | LuMamba_tiny | 4.1M |(`num_blocks` = 2, `exp` = 2)|(`num_queries` = 6, `embed_dim` = 64) |
|
|
| Larger model sizes can be attained by increasing the number of bi-Mamba blocks `num_blocks` (e.g. 8 bi-Mamba blocks yields 15M parameters). |
|
|
| --- |
|
|
| ## 📊 Results (Highlights) |
|
|
| - **TUAB (abnormal vs normal):** 80.99 % Bal. Acc., 0.883 AUROC, 0.892 AUPR. |
| (LuMamba-Tiny, pre-trained with LeJEPA-reconstruction). |
| - **APAVA (Alzheimer's detection)**: 0.955 AUROC, 0.970 AUPR (LuMamba-Tiny, pre-trained with LeJEPA-reconstruction). |
| - **TDBrain (Parkinson's detection)**: 0.961 AUROC, 0.960 AUPR (LuMamba-Tiny, pre-trained with LeJEPA-reconstruction). |
|
|
| **Efficiency:** Up to **377× fewer FLOPs** relative to transformer-based baselines and supporting up to **500x longer** EEG windows, thanks to the efficient FEMBA bi-Mamba encoder. |
|
|
| --- |
|
|
| ## 🧠 Intended Use & Limitations |
|
|
| **Intended use.** Research on EEG representation learning & classification (abnormality, artifacts, slowing, emotion), especially when **montages vary** or **channel counts are high**. |
|
|
| **Limitations.** |
| - **Not a medical device.** Do **not** use for clinical decisions without proper validation & regulatory clearance. |
| - **Unseen topologies:** Zero-shot transfer to **very different/dense** layouts (e.g., SEED-V) can underperform SOTA despite positive scaling; consider augmenting pre-training montage diversity and spatial encodings. |
| - **Distribution shifts:** Performance varies across cohorts, devices, and label protocols; validate locally and consider domain adaptation. |
|
|
| --- |
|
|
| ## 🏗️ Architecture & Training |
|
|
| **LUNA Tokenizer & features.** EEG is patch-segmented; temporal features via 1D conv w/ GroupNorm+GELU; **frequency features** (FFT mag/phase → MLP) are added; 3D electrode coordinates encoded via **NeRF-style sinusoids → MLP** (positional enc). |
|
|
| **LUNA Channel-Unification Module.** **Q learned queries** cross-attend to **channel-wise patch features** to produce a **fixed Q×E latent** per patch; FFN + Transformer layers refine the query tokens. Complexity is **O(Q·C)** (linear in channels). |
|
|
| **FEMBA Bi-Mamba Temporal encoder.** **Mamba blocks** process the embeddings in separate forward and backward streams. |
|
|
| **Pre-training objectives.** **Masked-patch reconstruction** is used to reconstruct masked tokens. In parallel, the **LeJEPA loss** encourages an isotropic Gaussian embedding distribution to minimize downstream prediction risk. |
|
|
| --- |
|
|
| ## 🔧 How to Use |
|
|
| LuMamba weights are organized by pre-training configuration: |
|
|
| - **`Reconstruction-only`** → variants pre-trained with masked reconstruction exclusively |
| - **`LeJEPA-reconstruction`** → variants pre-trained with a balanced mixture of masked reconstruction and LeJEPA losses. Variants exist for two different LeJEPA hyperparameters: 128 and 300 projection slices. |
| - **`LeJEPA-only`** → variant pre-trained with LeJEPA exclusively. |
|
|
| All variants are pre-trained on TUEG. |
|
|
| LuMamba experiments are categorized by two Hydra configurations, in `BioFoundation/config/experiments`: |
| - **`LuMamba_finetune.yaml`** → configuration for fine-tuning experiments. |
| - **`LuMamba_pretrain.yaml`** → configuration for pre-training experiments. |
|
|
| --- |
|
|
| ## 🔧 Fine-tuning — General Checklist |
|
|
| 0. **Install & read data prep**: clone the [BioFoundation repo](https://github.com/pulp-bio/BioFoundation), set up the environment as described there, then open `make_datasets/README.md` for dataset-specific notes (naming, expected folder layout, and common pitfalls). |
| 1. **Point to weights**: set `pretrained_safetensors_path: /path/to/LuMamba_*.safetensors` in the experiment YAML. |
| 2. **Preprocess data**: acquire fine-tuning dataset and follow preprocessing protocol (see guide in `/make_datasets/README.md`) to generate `train/test/val.h5` files. |
| 3. **Update data module of `LuMamba_finetune.yaml` config**: |
| - **TUH datasets (TUAB/TUSL/TUAR)** → change `_target_` in `/data_module:` to `datasets.tuh_dataset.TUH_Dataset`. |
| - **Other** → change `/data_module:_target_` to corresponding dataset.py file in `BioFoundation/datasets` (e.g., for TDBrain dataset use `_target_:datasets.tdbrain_dataset.TDBrain_Dataset`) |
| - **HDF5 file location** → change `/data_module:hdf5_file` for `train`, `test`, and `val` with the path to the corresponding HDF5 data split file. |
| 4. **Task settings**: |
| - **Task type**: override with `/task:finetune_task_LUNA` for classification and `/task:finetune_regression_task_LuMamba` for regression tasks |
| - **Classification type**: set `classification_type` (`bc`, `mcc`) and `model.num_classes` to match your downstream task. In a regression scenario,`mcc` is used and `model.num_classes` describes the number of features in the output. |
| - **Classifier choice**: set `/model:classifier_option` (`mamba` for FEMBA classifier, `linear` for single-layer linear classifier,`null` for default LUNA classifier) |
| - Configuration file includes further `#CHANGEME` tags and instructions for a working example. |
| 5. **Env vars**: export `DATA_PATH` (dataset root) and `CHECKPOINT_DIR` (artifacts). |
| 6. **Trainer/optimizer**: adjust `gpus/devices`, `batch_size`, `max_epochs`, LR/scheduler if needed. |
| 7. **I/O**: set `io.base_output_path` and confirm `io.checkpoint_dirpath` exists. |
|
|
|
|
| To launch fine-tuning (Hydra): |
|
|
| ```bash |
| python -u run_train.py +experiment=LuMamba_finetune |
| ``` |
|
|
| --- |
|
|
| ## ⚖️ Responsible AI, Risks & Biases |
|
|
| - **Clinical safety:** research-only; human oversight required. |
| - **Bias & drift:** montage/device/population differences can induce shifts; validate and monitor. |
| - **Artifacts & rare events:** robustness varies; use QC and task-appropriate preprocessing. |
|
|
| --- |
|
|
| ## 🔗 Sources |
|
|
| - **Code:** https://github.com/pulp-bio/BioFoundation |
| - **Paper:** LuMamba: Latent Unified Mamba for Electrode Topology-Invariant and Efficient EEG Modeling (arxiv:2603.19100) |
|
|
| --- |
|
|
| ## 📜 Citation |
|
|
| If you use LuMamba, please cite: |
|
|
| ```bibtex |
| @misc{broustail2026lumambalatentunifiedmamba, |
| title={LuMamba: Latent Unified Mamba for Electrode Topology-Invariant and Efficient EEG Modeling}, |
| author={Danaé Broustail and Anna Tegon and Thorir Mar Ingolfsson and Yawei Li and Luca Benini}, |
| year={2026}, |
| eprint={2603.19100}, |
| archivePrefix={arXiv}, |
| primaryClass={cs.AI}, |
| url={https://arxiv.org/abs/2603.19100}, |
| } |
| ``` |
|
|
| --- |
|
|
| ## 🛠️ Maintenance & Contact |
|
|
| - **Issues & support:** please open a GitHub issue in the BioFoundation repository. |
|
|
| --- |
|
|
| ## 🗒️ Changelog |
|
|
| - **v1.0:** Initial release of LuMamba model card with task-specific checkpoints and instructions. |
|
|
