cortexflowx 0.1.0__tar.gz

cortexflowx-0.1.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[all]"
+          pip install pytest
+
+      - name: Run tests
+        run: pytest tests/ -v --tb=short

cortexflowx-0.1.0/.gitignore

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+__pycache__/
+*.py[cod]
+*$py.class
+*.egg-info/
+dist/
+build/
+*.egg
+.eggs/
+*.so
+.tox/
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+*.swp
+*.swo
+*~
+.DS_Store
+.env
+.venv/
+venv/

cortexflowx-0.1.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to CortexFlow will be documented in this file.
+
+## [0.1.0] - 2025-06-25
+
+### Added
+
+- **DiT backbone**: Diffusion Transformer with AdaLN-Zero conditioning, QK-Norm, SwiGLU, and cross-attention to brain tokens
+- **Rectified Flow Matching**: Linear interpolation paths, logit-normal timestep sampling (SD3-style), Euler and midpoint ODE solvers
+- **Brain Encoder**: MLP projector producing global embeddings (for AdaLN) and token sequences (for cross-attention)
+- **ROI-Aware Encoder**: Per-region sub-encoders with fusion for anatomically-informed encoding
+- **Subject Adapter**: LoRA-style per-subject low-rank adaptation
+- **Brain2Image**: Full fMRI → LatentVAE → DiT → image pipeline with classifier-free guidance
+- **Brain2Audio**: fMRI → 1D DiT → mel spectrogram → Griffin-Lim waveform
+- **Brain2Text**: fMRI → transformer decoder → autoregressive byte-level text generation
+- **LatentVAE / AudioVAE**: Lightweight convolutional VAEs for image and audio latent spaces
+- **Training utilities**: Trainer class, warmup-cosine LR scheduler, EMA, synthetic data generators
+- **Comprehensive test suite**: 100+ tests covering all modules

cortexflowx-0.1.0/CITATION.cff

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+cff-version: 1.2.0
+title: "CortexFlow: Brain Decoding with Diffusion Transformers and Flow Matching"
+message: "If you use this software, please cite it as below."
+type: software
+version: 0.1.0
+license: Apache-2.0
+repository-code: "https://github.com/stef41/cortexflow"
+authors:
+  - given-names: Zacharie
+    family-names: B

cortexflowx-0.1.0/LICENSE

@@ -0,0 +1,190 @@
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+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
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+
+   9. Accepting Warranty or Additional Liability. While redistributing
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+   END OF TERMS AND CONDITIONS
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+   Copyright 2025 Zacharie B
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+   See the License for the specific language governing permissions and
+   limitations under the License.

cortexflowx-0.1.0/PKG-INFO

@@ -0,0 +1,218 @@
+Metadata-Version: 2.4
+Name: cortexflowx
+Version: 0.1.0
+Summary: Brain-to-image/audio/text reconstruction using Diffusion Transformers and Flow Matching. Decode what someone saw, heard, or thought from fMRI.
+Project-URL: Homepage, https://github.com/stef41/cortexflow
+Project-URL: Repository, https://github.com/stef41/cortexflow
+Project-URL: Issues, https://github.com/stef41/cortexflow/issues
+Author: Zacharie B
+License: Apache-2.0
+License-File: LICENSE
+Keywords: bci,brain-computer-interface,brain-decoding,diffusion-transformer,dit,flow-matching,fmri,image-reconstruction,neural-decoding,neuroscience
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Typing :: Typed
+Requires-Python: >=3.9
+Requires-Dist: numpy>=1.21
+Requires-Dist: torch>=2.0
+Provides-Extra: all
+Requires-Dist: click>=8.0; extra == 'all'
+Requires-Dist: rich>=13.0; extra == 'all'
+Requires-Dist: torchaudio>=2.0; extra == 'all'
+Provides-Extra: audio
+Requires-Dist: torchaudio>=2.0; extra == 'audio'
+Provides-Extra: cli
+Requires-Dist: click>=8.0; extra == 'cli'
+Requires-Dist: rich>=13.0; extra == 'cli'
+Description-Content-Type: text/markdown
+
+# CortexFlow
+
+**Brain-to-image/audio/text reconstruction using Diffusion Transformers and Flow Matching.**
+
+Decode what someone *saw*, *heard*, or *thought* from fMRI brain activity using a modern generative backbone — the same DiT + Rectified Flow architecture behind FLUX, Stable Diffusion 3, and Wan2.1.
+
+## Architecture
+
+```
+fMRI voxels
+    → BrainEncoder (MLP projector → global embedding + token sequence)
+    → DiffusionTransformer (AdaLN-Zero conditioning + cross-attention)
+    → Rectified Flow Matching (linear ODE: noise → data)
+    → Modality Decoder (VAE / Griffin-Lim / autoregressive)
+    → Image / Audio / Text
+```
+
+### Key Components
+
+| Module | Description |
+|--------|-------------|
+| `DiffusionTransformer` | DiT backbone with AdaLN-Zero, QK-Norm, SwiGLU, cross-attention |
+| `RectifiedFlowMatcher` | Linear interpolation paths, logit-normal sampling, Euler/midpoint ODE |
+| `BrainEncoder` | fMRI → global embedding (AdaLN) + token sequence (cross-attention) |
+| `LatentVAE` / `AudioVAE` | Lightweight VAE for image/audio latent compression |
+| `Brain2Image` | Full brain → image pipeline with classifier-free guidance |
+| `Brain2Audio` | Brain → mel spectrogram → waveform (Griffin-Lim) |
+| `Brain2Text` | Brain → transformer decoder → autoregressive text (byte-level) |
+
+## Installation
+
+```bash
+pip install cortexflow
+```
+
+With audio support:
+```bash
+pip install cortexflow[audio]
+```
+
+## Quick Start
+
+### Brain → Image
+
+```python
+import torch
+from cortexflow import build_brain2img, BrainData
+
+model = build_brain2img(n_voxels=15000, img_size=256, hidden_dim=768, depth=12)
+
+fmri = torch.randn(1, 15000)  # your fMRI data
+brain = BrainData(voxels=fmri, subject_id="sub-01")
+
+# Reconstruct
+model.eval()
+result = model.reconstruct(brain, num_steps=50, cfg_scale=4.0)
+image = result.output  # (1, 3, 256, 256)
+```
+
+### Brain → Audio
+
+```python
+from cortexflow import build_brain2audio, BrainData
+
+model = build_brain2audio(n_voxels=15000, n_mels=80, audio_len=256)
+
+result = model.reconstruct(BrainData(voxels=fmri), num_steps=50)
+mel = result.output  # (1, 80, 256) mel spectrogram
+
+# Convert to waveform
+from cortexflow import Brain2Audio
+waveform = Brain2Audio.mel_to_waveform(mel)
+```
+
+### Brain → Text
+
+```python
+from cortexflow import build_brain2text, BrainData
+
+model = build_brain2text(n_voxels=15000, max_len=128, hidden_dim=512, depth=8)
+
+result = model.reconstruct(BrainData(voxels=fmri), temperature=0.8, top_k=50)
+print(result.metadata["texts"])  # ["The cat sat on the mat"]
+```
+
+### Training
+
+```python
+from cortexflow import build_brain2img, BrainData, Trainer, TrainingConfig
+
+model = build_brain2img(n_voxels=15000, img_size=256)
+trainer = Trainer(model, TrainingConfig(learning_rate=1e-4, batch_size=16))
+
+# Your training loop
+for images, fmri in dataloader:
+    brain = BrainData(voxels=fmri)
+    loss = trainer.train_step(
+        {"stimulus": images, "fmri": fmri},
+        loss_fn=lambda m, b: m.training_loss(b["stimulus"], BrainData(voxels=b["fmri"]))
+    )
+```
+
+## Advanced Features
+
+### ROI-Aware Brain Encoding
+
+```python
+from cortexflow import ROIBrainEncoder
+
+encoder = ROIBrainEncoder(
+    roi_sizes={"V1": 2000, "V2": 1500, "FFA": 800, "PPA": 600, "A1": 1000},
+    cond_dim=768,
+)
+brain_global, brain_tokens = encoder({"V1": v1_voxels, "V2": v2_voxels, ...})
+```
+
+### Per-Subject Adaptation
+
+```python
+from cortexflow import SubjectAdapter
+
+adapter = SubjectAdapter(cond_dim=768, rank=16, n_subjects=8)
+adapted = adapter(brain_global, subject_idx=torch.tensor([0]))
+```
+
+### EMA for Stable Sampling
+
+```python
+from cortexflow import EMAModel
+
+ema = EMAModel(model, decay=0.9999)
+# During training:
+ema.update(model)
+# For sampling:
+originals = ema.apply_to(model)
+result = model.reconstruct(brain_data)
+ema.restore(model, originals)
+```
+
+## Technical Details
+
+### Why DiT + Flow Matching?
+
+The Diffusion Transformer with rectified flow matching is the current state-of-the-art generative backbone:
+
+- **FLUX** (Black Forest Labs): DiT + flow matching
+- **Stable Diffusion 3** (Stability AI): MMDiT + rectified flow
+- **Wan2.1** (Alibaba): DiT + flow matching, 14B params
+- **Movie Gen** (Meta): DiT + flow matching, 30B params
+
+We bring this architecture to brain decoding, replacing the dated UNet backbones used in prior work (MindEye, Brain-Diffuser).
+
+### Flow Matching Objective
+
+Rectified flow uses linear interpolation paths:
+
+$$x_t = (1 - t) \cdot x_0 + t \cdot x_1$$
+
+The model learns the velocity field $v_\theta(x_t, t, c)$ that transports noise to data:
+
+$$\mathcal{L} = \mathbb{E}_{t, x_0, x_1} \left[ \| v_\theta(x_t, t, c) - (x_1 - x_0) \|^2 \right]$$
+
+At inference, we solve the ODE from $t=0$ (noise) to $t=1$ (data) using Euler or midpoint methods.
+
+### AdaLN-Zero Conditioning
+
+Brain embeddings modulate the transformer via Adaptive Layer Normalization:
+
+$$h = \gamma(c) \odot \text{LayerNorm}(x) + \beta(c)$$
+
+with zero-initialized gating for stable training (Peebles & Xie 2022).
+
+## References
+
+- Peebles & Xie (2022). "Scalable Diffusion Models with Transformers." arXiv:2212.09748
+- Esser et al. (2024). "Scaling Rectified Flow Transformers for High-Resolution Image Synthesis." arXiv:2403.03206
+- Lipman et al. (2024). "Flow Matching Guide and Code." arXiv:2412.06264
+- Scotti et al. (2023). "Reconstructing the Mind's Eye: fMRI-to-Image with Contrastive Learning and Diffusion Priors."
+- Ozcelik & VanRullen (2023). "Brain-Diffuser: Natural Scene Reconstruction from fMRI Using a Latent Diffusion Model."
+
+## License
+
+Apache-2.0

cortexflowx-0.1.0/README.md

@@ -0,0 +1,183 @@
+# CortexFlow
+
+**Brain-to-image/audio/text reconstruction using Diffusion Transformers and Flow Matching.**
+
+Decode what someone *saw*, *heard*, or *thought* from fMRI brain activity using a modern generative backbone — the same DiT + Rectified Flow architecture behind FLUX, Stable Diffusion 3, and Wan2.1.
+
+## Architecture
+
+```
+fMRI voxels
+    → BrainEncoder (MLP projector → global embedding + token sequence)
+    → DiffusionTransformer (AdaLN-Zero conditioning + cross-attention)
+    → Rectified Flow Matching (linear ODE: noise → data)
+    → Modality Decoder (VAE / Griffin-Lim / autoregressive)
+    → Image / Audio / Text
+```
+
+### Key Components
+
+| Module | Description |
+|--------|-------------|
+| `DiffusionTransformer` | DiT backbone with AdaLN-Zero, QK-Norm, SwiGLU, cross-attention |
+| `RectifiedFlowMatcher` | Linear interpolation paths, logit-normal sampling, Euler/midpoint ODE |
+| `BrainEncoder` | fMRI → global embedding (AdaLN) + token sequence (cross-attention) |
+| `LatentVAE` / `AudioVAE` | Lightweight VAE for image/audio latent compression |
+| `Brain2Image` | Full brain → image pipeline with classifier-free guidance |
+| `Brain2Audio` | Brain → mel spectrogram → waveform (Griffin-Lim) |
+| `Brain2Text` | Brain → transformer decoder → autoregressive text (byte-level) |
+
+## Installation
+
+```bash
+pip install cortexflow
+```
+
+With audio support:
+```bash
+pip install cortexflow[audio]
+```
+
+## Quick Start
+
+### Brain → Image
+
+```python
+import torch
+from cortexflow import build_brain2img, BrainData
+
+model = build_brain2img(n_voxels=15000, img_size=256, hidden_dim=768, depth=12)
+
+fmri = torch.randn(1, 15000)  # your fMRI data
+brain = BrainData(voxels=fmri, subject_id="sub-01")
+
+# Reconstruct
+model.eval()
+result = model.reconstruct(brain, num_steps=50, cfg_scale=4.0)
+image = result.output  # (1, 3, 256, 256)
+```
+
+### Brain → Audio
+
+```python
+from cortexflow import build_brain2audio, BrainData
+
+model = build_brain2audio(n_voxels=15000, n_mels=80, audio_len=256)
+
+result = model.reconstruct(BrainData(voxels=fmri), num_steps=50)
+mel = result.output  # (1, 80, 256) mel spectrogram
+
+# Convert to waveform
+from cortexflow import Brain2Audio
+waveform = Brain2Audio.mel_to_waveform(mel)
+```
+
+### Brain → Text
+
+```python
+from cortexflow import build_brain2text, BrainData
+
+model = build_brain2text(n_voxels=15000, max_len=128, hidden_dim=512, depth=8)
+
+result = model.reconstruct(BrainData(voxels=fmri), temperature=0.8, top_k=50)
+print(result.metadata["texts"])  # ["The cat sat on the mat"]
+```
+
+### Training
+
+```python
+from cortexflow import build_brain2img, BrainData, Trainer, TrainingConfig
+
+model = build_brain2img(n_voxels=15000, img_size=256)
+trainer = Trainer(model, TrainingConfig(learning_rate=1e-4, batch_size=16))
+
+# Your training loop
+for images, fmri in dataloader:
+    brain = BrainData(voxels=fmri)
+    loss = trainer.train_step(
+        {"stimulus": images, "fmri": fmri},
+        loss_fn=lambda m, b: m.training_loss(b["stimulus"], BrainData(voxels=b["fmri"]))
+    )
+```
+
+## Advanced Features
+
+### ROI-Aware Brain Encoding
+
+```python
+from cortexflow import ROIBrainEncoder
+
+encoder = ROIBrainEncoder(
+    roi_sizes={"V1": 2000, "V2": 1500, "FFA": 800, "PPA": 600, "A1": 1000},
+    cond_dim=768,
+)
+brain_global, brain_tokens = encoder({"V1": v1_voxels, "V2": v2_voxels, ...})
+```
+
+### Per-Subject Adaptation
+
+```python
+from cortexflow import SubjectAdapter
+
+adapter = SubjectAdapter(cond_dim=768, rank=16, n_subjects=8)
+adapted = adapter(brain_global, subject_idx=torch.tensor([0]))
+```
+
+### EMA for Stable Sampling
+
+```python
+from cortexflow import EMAModel
+
+ema = EMAModel(model, decay=0.9999)
+# During training:
+ema.update(model)
+# For sampling:
+originals = ema.apply_to(model)
+result = model.reconstruct(brain_data)
+ema.restore(model, originals)
+```
+
+## Technical Details
+
+### Why DiT + Flow Matching?
+
+The Diffusion Transformer with rectified flow matching is the current state-of-the-art generative backbone:
+
+- **FLUX** (Black Forest Labs): DiT + flow matching
+- **Stable Diffusion 3** (Stability AI): MMDiT + rectified flow
+- **Wan2.1** (Alibaba): DiT + flow matching, 14B params
+- **Movie Gen** (Meta): DiT + flow matching, 30B params
+
+We bring this architecture to brain decoding, replacing the dated UNet backbones used in prior work (MindEye, Brain-Diffuser).
+
+### Flow Matching Objective
+
+Rectified flow uses linear interpolation paths:
+
+$$x_t = (1 - t) \cdot x_0 + t \cdot x_1$$
+
+The model learns the velocity field $v_\theta(x_t, t, c)$ that transports noise to data:
+
+$$\mathcal{L} = \mathbb{E}_{t, x_0, x_1} \left[ \| v_\theta(x_t, t, c) - (x_1 - x_0) \|^2 \right]$$
+
+At inference, we solve the ODE from $t=0$ (noise) to $t=1$ (data) using Euler or midpoint methods.
+
+### AdaLN-Zero Conditioning
+
+Brain embeddings modulate the transformer via Adaptive Layer Normalization:
+
+$$h = \gamma(c) \odot \text{LayerNorm}(x) + \beta(c)$$
+
+with zero-initialized gating for stable training (Peebles & Xie 2022).
+
+## References
+
+- Peebles & Xie (2022). "Scalable Diffusion Models with Transformers." arXiv:2212.09748
+- Esser et al. (2024). "Scaling Rectified Flow Transformers for High-Resolution Image Synthesis." arXiv:2403.03206
+- Lipman et al. (2024). "Flow Matching Guide and Code." arXiv:2412.06264
+- Scotti et al. (2023). "Reconstructing the Mind's Eye: fMRI-to-Image with Contrastive Learning and Diffusion Priors."
+- Ozcelik & VanRullen (2023). "Brain-Diffuser: Natural Scene Reconstruction from fMRI Using a Latent Diffusion Model."
+
+## License
+
+Apache-2.0