| | --- |
| | license: cc-by-nd-4.0 |
| | language: |
| | - en |
| | --- |
| | |
| | <div align="center"> |
| | <img src="https://raw.githubusercontent.com/pulp-bio/BioFoundation/refs/heads/main/docs/model/logo/FEMBA_logo.png" alt="FEMBA Logo" width="800"/> |
| | <h1>FEMBA: Foundational Encoder Model with Bidirectional Mamba for EEG</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/2502.06438"> |
| | <img src="https://img.shields.io/badge/arXiv-2502.06438-b31b1b.svg" alt="Paper"> |
| | </a> |
| | </p> |
| | |
| | **FEMBA** is a powerful and efficient foundation model for **EEG signal analysis**, built upon a **bidirectional Mamba** state-space architecture. It supports **self-supervised pre-training** via masked reconstruction and **end-to-end supervised fine-tuning** for multiple downstream tasks (abnormal EEG, artifact detection, slowing classification). By using linear-time state-space modeling instead of quadratic attention, FEMBA scales to long EEG sequences and constrained hardware while remaining performant. |
| |
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| | --- |
| |
|
| | ## 🔒 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** FEMBA weights (including in commercial settings) **with proper attribution** to the FEMBA 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 FEMBA (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 FEMBA authors for any derivative or evaluation without our written permission. |
| | - **Use the FEMBA name** in a way that suggests your modified model is an official FEMBA 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 FEMBA 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 FEMBA paper. |
| | 4. After **maintainer review**, approved changes will be **retrained/validated** and, if accepted, **released by the maintainers** as a new **official FEMBA** checkpoint under **CC BY-ND 4.0**. |
| |
|
| | > Rationale: CC BY-ND protects users from fragmented, lower-quality “FEMBA variants,” while still enabling internal fine-tuning and a path for the community to upstream improvements through review. |
| |
|
| | --- |
| |
|
| | ## 🔎 Model Summary |
| |
|
| | - **Architecture:** Bidirectional Mamba encoder with a 2D-conv tokenizer (patching over channels × time), random masking (60%) for SSL, and either a lightweight linear head or a Mamba-enhanced head for downstream tasks. Hidden state size is fixed at 80 across variants. |
| | - **Scaling:** Linear time & memory in sequence length (state-space model), enabling efficient long-context EEG modeling and on-device scenarios. |
| | - **Pre-training data:** >21,000 hours of unlabeled clinical EEG from Temple University Hospital (TUEG). Subjects overlapping with TUAB/TUAR/TUSL are removed to prevent leakage. |
| | - **Downstream tasks:** TUAB abnormal/normal (binary), TUAR artifact detection (BC/MC/MMC/MCC), TUSL slowing (4-class). TUAB uses its predefined split; TUAR/TUSL use 80/10/10 splits. |
| | - **Optimization (typical):** Pre-training with Smooth L1 masked-patch reconstruction; fine-tuning with Adam (LR 1e-4), cosine decay, early stopping; layer-wise LR decay factor 0.75. |
| |
|
| | --- |
| |
|
| | ## 🚀 Model Variants |
| |
|
| | | Variant | Parameters | (num_blocks, embed_dim) | |
| | | :--- | :--- | :--- | |
| | | **FEMBA-tiny** | 7.8M | (2, 35) | |
| | | **FEMBA-base** | 47.7M | (12, 35) | |
| | | **FEMBA-large** | 77.8M | (4, 79) | |
| | | **FEMBA-huge** | 386M | (20, 79) | |
| |
|
| | *Hidden state size is 80 for all variants; blocks correspond to Bi-Mamba layers in the encoder.* |
| |
|
| | --- |
| |
|
| | ## 🧠 Intended Use & Limitations |
| |
|
| | **Intended use.** Research on EEG representation learning and downstream classification (e.g., abnormal EEG detection, artifact detection, slowing classification). FEMBA is particularly useful when long sequences or limited compute/memory preclude quadratic-cost attention. |
| |
|
| | **Out-of-scope / limitations.** |
| | - **Not a medical device.** Outputs are research signals and **must not** be used for clinical decision-making without appropriate validation and regulatory processes. |
| | - **Domain shift.** Performance can degrade across cohorts (e.g., neonatal vs. adult EEG) and label protocols; domain adaptation is encouraged. |
| | - **Class imbalance.** On some tasks (e.g., TUSL), AUROC may be strong while AUPR can trail attention baselines, highlighting sensitivity to class imbalance and protocol specifics. |
| |
|
| | --- |
| |
|
| | ## 🏗️ Architecture & Training Details |
| |
|
| | **Tokenizer & patches.** Raw EEG (C×T) is quartile-normalized per channel (IQR scaling) and tokenized with a 2D convolution over channel×time patches (e.g., 4×32) with learnable positional embeddings. |
| |
|
| | **Self-supervised objective.** Randomly mask **60%** of patches; reconstruct masked content with a lightweight decoder using **Smooth L1** loss (computed on masked patches only). |
| |
|
| | **Encoder.** Stacked **Bidirectional Mamba** blocks (forward + backward over a reversed copy), merged and residually connected; hidden size fixed to 80. |
| |
|
| | **Fine-tuning heads.** |
| | - *Linear classifier:* small MLP (≈0.5M params). |
| | - *Mamba-enhanced classifier:* adds one Mamba block before the linear layer (up to ≈0.7M params). |
| |
|
| | **Optimization notes.** Layer-wise LR decay (0.75); fine-tuning with Adam (initial LR 1e-4), cosine decay, early stopping; end-to-end updates (encoder + head). |
| |
|
| | --- |
| |
|
| | ## 📚 Training Data |
| |
|
| | - **Pre-training:** Temple University Hospital EEG (TUEG), ~21k hours, ~15k subjects; broad clinical coverage. Overlaps with TUAB/TUAR/TUSL removed to avoid leakage. |
| | - **Downstream:** |
| | - **TUAB** (abnormal vs normal; predefined split). |
| | - **TUAR** (artifact detection, BC/MC/MMC/MCC protocols; randomized 80/10/10). |
| | - **TUSL** (4-class slowing/seizure/complex/normal; randomized 80/10/10). |
| |
|
| | *See paper for dataset licenses and curation details; users are responsible for complying with source dataset terms.* |
| |
|
| | --- |
| |
|
| | ## 🔧 How to Use |
| |
|
| | FEMBA weights are organized by downstream task: |
| |
|
| | - **`TUAB/`** → base/large variants pre-trained on TUEG (excluding TUAB), for TUAB abnormal EEG. |
| | - **`TUAR/`** → tiny/base/large variants pre-trained on TUEG (excluding TUAR), for TUAR artifact detection. |
| | - **`TUSL/`** → variants pre-trained on TUEG (excluding TUSL), for TUSL slowing classification. |
| |
|
| | **Example:** fine-tune TUAR with the base checkpoint: |
| |
|
| | ``` |
| | TUAR/base.safetensors |
| | ``` |
| |
|
| | Open `run_train.py` from the [BioFoundation GitHub repository](https://github.com/pulp-bio/BioFoundation.git) and configure: |
| |
|
| | ```python |
| | # Set paths (example) |
| | os.environ['DATA_PATH'] = "/path/to/dataset" |
| | os.environ['CHECKPOINT_DIR'] = "/my_directory/TUAR/base.safetensors" |
| | ``` |
| |
|
| | Then launch fine-tuning (Hydra): |
| |
|
| | ```bash |
| | python -u run_train.py +experiment=FEMBA_finetune |
| | ``` |
| |
|
| | **Environment variables** |
| | - `DATA_PATH`: directory of the fine-tuning dataset. |
| | - `CHECKPOINT_DIR`: path to the chosen task-specific checkpoint. |
| |
|
| | --- |
| |
|
| | ## 📊 Results (Key Highlights) |
| |
|
| | **TUAB (Abnormal EEG Detection)** |
| | - **FEMBA-Huge:** **81.82%** balanced accuracy, **0.892** AUROC. |
| |
|
| | **TUAR (Artifact Detection)** |
| | - **Binary (BC):** **FEMBA-Base** AUROC **0.949**, AUPR **0.932**. |
| |
|
| | **TUSL (Slowing Classification, 4-class)** |
| | - **FEMBA-Base:** AUROC **0.731**. |
| |
|
| | > Full metrics, protocols, and comparisons—including MC/MMC on TUAR and multiple FEMBA sizes—are reported in the paper. |
| |
|
| | --- |
| |
|
| | ## ⚡ Efficiency |
| |
|
| | FEMBA provides strong accuracy with reduced compute/memory relative to Transformer baselines: |
| |
|
| | - **FEMBA-Huge (386M):** ~**58.7B FLOPs**, ~**30% less** memory than comparable Transformer baselines, with competitive TUAB accuracy. |
| | - **FEMBA-Tiny (7.8M):** ~**1.31B FLOPs**—substantially fewer than large Transformer baselines—while achieving strong TUAR MCC performance. |
| | - **FEMBA-Base (47.7M):** ~**7.52B FLOPs**, markedly lower than many attention-based baselines. |
| |
|
| | See the paper for details on measurement setup and baseline references. |
| |
|
| | --- |
| |
|
| | ## ✅ Responsible AI, Risks & Biases |
| |
|
| | - **Clinical safety:** This model is **not** a certified medical device and should **not** be used for diagnosis. Human oversight is required. |
| | - **Bias & drift:** Clinical EEG cohorts vary by device, montage, age, and pathology. Expect distribution shift and validate locally; consider domain adaptation (e.g., neonatal vs adult). |
| | - **Artifacts:** While artifact detection is strong, rare/complex artifacts may still be misclassified; use robust pre-processing and QC procedures. |
| |
|
| | --- |
| |
|
| | ## 🔗 Sources |
| |
|
| | - **Code:** https://github.com/pulp-bio/BioFoundation |
| | - **Paper:** FEMBA: Efficient and Scalable EEG Analysis with a Bidirectional Mamba Foundation Model (arXiv:2502.06438). |
| |
|
| | --- |
| |
|
| | ## 📜 Citation |
| |
|
| | If you use FEMBA in your research, please cite: |
| |
|
| | ```bibtex |
| | @misc{tegon2025fembaefficientscalableeeg, |
| | title={FEMBA: Efficient and Scalable EEG Analysis with a Bidirectional Mamba Foundation Model}, |
| | author={Anna Tegon and Thorir Mar Ingolfsson and Xiaying Wang and Luca Benini and Yawei Li}, |
| | year={2025}, |
| | eprint={2502.06438}, |
| | archivePrefix={arXiv}, |
| | primaryClass={cs.LG}, |
| | url={https://arxiv.org/abs/2502.06438} |
| | } |
| | ``` |
| |
|
| | --- |
| |
|
| | ## 🛠️ Maintenance & Contact |
| |
|
| | - **Issues & support:** please open a GitHub issue in the BioFoundation repository. |
| |
|
| | --- |
| |
|
| | ## 🗒️ Changelog |
| |
|
| | - **v1.0:** Initial release of FEMBA model card with task-specific checkpoints and instructions. |
| |
|
