LeNEPA Encoder trained on Aionoscope balanced dataset

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README.md

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+---
+license: cc-by-nc-4.0
+library_name: pytorch
+tags:
+  - time-series
+  - ecg
+  - representation-learning
+---
+
+# LeNEPA encoder (balanced, encoder-only)
+
+This repository contains an **encoder-only** LeNEPA checkpoint exported to `safetensors` for minimal inference.
+
+What is included:
+
+- `lenepa_encoder.safetensors` — **encoder weights only** (no projector, no training/probe state)
+- `inference.py` — minimal end-to-end inference (no Hydra, no W&B)
+- `lenepa_encoder_config.json` — fixed IO + architecture contract
+- `provenance.json` — original `.pt` checkpoint path + W&B URL
+
+## IO contract
+
+Inputs:
+
+- `x_waveform`: `torch.float32` with shape `[B, 1, 5000]`
+- sampling frequency: `500` Hz
+- channels: `["I"]` (so `C=1`)
+
+Outputs:
+
+- `patch_tokens`: `[B, 200, 192]` (post-final-norm tokens)
+- `embedding`: `[B, 192]` (mean pooled over tokens)
+
+## Usage
+
+Smoke test (loads `lenepa_encoder.safetensors` from the current directory and prints output shapes):
+
+```bash
+python inference.py
+```
+
+Programmatic usage:
+
+```python
+from pathlib import Path
+
+import torch
+
+from inference import encode_lenepa, load_lenepa_encoder
+
+device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
+model = load_lenepa_encoder(weights_path=Path("lenepa_encoder.safetensors"), device=device)
+x = torch.randn(2, 1, 5000, device=device, dtype=torch.float32)  # [B, C, L]
+out = encode_lenepa(model=model, x_waveform=x)
+print(out.embedding.shape)
+```
+

inference.py

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+"""Minimal inference for the published LeNEPA *encoder* checkpoint (no projector).
+
+Published IO contract:
+  - x_waveform: torch.float32 [B, 1, 5000] at 500 Hz, channel order: ["I"]
+  - outputs:
+      patch_tokens: [B, 200, 192]
+      embedding:    [B, 192]
+
+This code intentionally does NOT:
+  - resample / crop / pad / normalize inputs
+  - support other checkpoints or architectures
+"""
+
+from __future__ import annotations
+
+from dataclasses import dataclass
+from pathlib import Path
+
+import torch
+from safetensors.torch import load_file as safetensors_load
+from torch import nn
+from torch.nn import functional as F
+
+# -----------------------------
+# Published constants (no knobs)
+# -----------------------------
+
+SAMPLING_FREQUENCY_HZ = 500
+CHANNELS = ("I",)
+
+NUM_CHANNELS = 1
+CHANNEL_SIZE = 5000
+PATCH_SIZE = 25
+NUM_PATCHES = 200  # 5000 / 25
+
+DIM = 192
+DEPTH = 8
+NUM_HEADS = 4
+MLP_RATIO = 4.0
+
+QKV_BIAS = True
+NORM_EPS = 1e-6
+
+ROPE_BASE = 10_000
+QK_NORM_EPS = 1e-6
+
+
+@dataclass(frozen=True)
+class LeNEPAEncoderOutput:
+    """Outputs of the published LeNEPA encoder."""
+
+    patch_tokens: torch.Tensor  # [B, T=200, D=192]
+    embedding: torch.Tensor  # [B, D=192]
+
+
+class RotaryEmbedding(nn.Module):
+    """Rotary positional embeddings (RoPE) applied to Q/K."""
+
+    def __init__(self, *, dim: int, base: int) -> None:
+        super().__init__()
+        if dim % 2 != 0:
+            raise ValueError(f"RoPE requires even head_dim, got {dim}")
+        inv_freq = 1.0 / (base ** (torch.arange(0, dim, 2, dtype=torch.float32) / dim))  # [Dh/2]
+        self.register_buffer("inv_freq", inv_freq, persistent=False)
+        self._seq_len_cached: int | None = None
+        self._cos_cached: torch.Tensor | None = None
+        self._sin_cached: torch.Tensor | None = None
+        self._device_cached: torch.device | None = None
+        self._dtype_cached: torch.dtype | None = None
+
+    def _build_cache(self, *, seq_len: int, device: torch.device, dtype: torch.dtype) -> None:
+        positions = torch.arange(seq_len, device=device, dtype=self.inv_freq.dtype)  # [T]
+        freqs = torch.einsum("i,j->ij", positions, self.inv_freq)  # [T, Dh/2]
+        self._cos_cached = freqs.cos().to(dtype)  # [T, Dh/2]
+        self._sin_cached = freqs.sin().to(dtype)  # [T, Dh/2]
+        self._seq_len_cached = seq_len
+        self._device_cached = device
+        self._dtype_cached = dtype
+
+    def _get_cos_sin(
+        self, *, seq_len: int, device: torch.device, dtype: torch.dtype
+    ) -> tuple[torch.Tensor, torch.Tensor]:
+        if (
+            self._cos_cached is None
+            or self._sin_cached is None
+            or self._seq_len_cached != seq_len
+            or self._device_cached != device
+            or self._dtype_cached != dtype
+        ):
+            self._build_cache(seq_len=seq_len, device=device, dtype=dtype)
+        if self._cos_cached is None or self._sin_cached is None:
+            raise RuntimeError("RoPE cache was not built; this is a bug")
+        return self._cos_cached, self._sin_cached
+
+    def _apply_rotary(self, x: torch.Tensor, *, cos: torch.Tensor, sin: torch.Tensor) -> torch.Tensor:
+        # x: [B, H, T, Dh]
+        B, H, T, Dh = x.shape
+        x_2 = x.view(B, H, T, Dh // 2, 2)  # [B, H, T, Dh/2, 2]
+        x1 = x_2[..., 0]  # [B, H, T, Dh/2]
+        x2 = x_2[..., 1]  # [B, H, T, Dh/2]
+        cos = cos.unsqueeze(0).unsqueeze(0)  # [1, 1, T, Dh/2]
+        sin = sin.unsqueeze(0).unsqueeze(0)  # [1, 1, T, Dh/2]
+        out1 = x1 * cos - x2 * sin
+        out2 = x1 * sin + x2 * cos
+        return torch.stack((out1, out2), dim=-1).flatten(-2)  # [B, H, T, Dh]
+
+    def apply(self, q: torch.Tensor, k: torch.Tensor) -> tuple[torch.Tensor, torch.Tensor]:
+        """Apply RoPE to Q/K."""
+        cos, sin = self._get_cos_sin(seq_len=q.size(-2), device=q.device, dtype=q.dtype)  # [T, Dh/2]
+        return self._apply_rotary(q, cos=cos, sin=sin), self._apply_rotary(k, cos=cos, sin=sin)
+
+
+class Attention(nn.Module):
+    """Causal self-attention with RoPE + QK-Norm (no dropout)."""
+
+    def __init__(self) -> None:
+        super().__init__()
+        if DIM % NUM_HEADS != 0:
+            raise ValueError(f"DIM must be divisible by NUM_HEADS, got DIM={DIM} NUM_HEADS={NUM_HEADS}")
+        head_dim = DIM // NUM_HEADS
+        self.num_heads = NUM_HEADS
+        self.rope = RotaryEmbedding(dim=head_dim, base=ROPE_BASE)
+        self.qk_norm = nn.LayerNorm(head_dim, eps=QK_NORM_EPS, elementwise_affine=False)
+        self.qkv = nn.Linear(DIM, DIM * 3, bias=QKV_BIAS)
+        self.proj = nn.Linear(DIM, DIM, bias=True)
+
+    def forward(self, x: torch.Tensor) -> torch.Tensor:
+        # x: [B, T, D]
+        B, T, D = x.shape
+        qkv = (
+            self.qkv(x)  # [B, T, 3*D]
+            .reshape(B, T, 3, self.num_heads, D // self.num_heads)  # [B, T, 3, H, Dh]
+            .permute(2, 0, 3, 1, 4)  # [3, B, H, T, Dh]
+        )
+        q, k, v = qkv[0], qkv[1], qkv[2]  # each [B, H, T, Dh]
+        q, k = self.rope.apply(q, k)  # [B, H, T, Dh] each
+        q = self.qk_norm(q)  # [B, H, T, Dh]
+        k = self.qk_norm(k)  # [B, H, T, Dh]
+        attn = F.scaled_dot_product_attention(q, k, v, dropout_p=0.0, is_causal=True)  # [B, H, T, Dh]
+        out = attn.transpose(1, 2).reshape(B, T, D)  # [B, T, D]
+        return self.proj(out)  # [B, T, D]
+
+
+class GatedMLP(nn.Module):
+    """SwiGLU MLP used in this checkpoint."""
+
+    def __init__(self) -> None:
+        super().__init__()
+        hidden_dim = int((2 / 3) * MLP_RATIO * DIM)
+        if hidden_dim <= 0:
+            raise ValueError(f"hidden_dim must be > 0, got {hidden_dim}")
+        self.fc1 = nn.Linear(DIM, hidden_dim * 2, bias=True)
+        self.fc2 = nn.Linear(hidden_dim, DIM, bias=True)
+        self.act = nn.SiLU()
+
+    def forward(self, x: torch.Tensor) -> torch.Tensor:
+        # x: [B, T, D]
+        gate_and_value = self.fc1(x)  # [B, T, 2H]
+        gate, value = gate_and_value.chunk(2, dim=-1)  # each [B, T, H]
+        return self.fc2(self.act(gate) * value)  # [B, T, D]
+
+
+class Block(nn.Module):
+    """Transformer block: LN -> Attn -> residual -> LN -> MLP -> residual."""
+
+    def __init__(self) -> None:
+        super().__init__()
+        self.norm1 = nn.LayerNorm(DIM, eps=NORM_EPS)
+        self.attn = Attention()
+        self.norm2 = nn.LayerNorm(DIM, eps=NORM_EPS)
+        self.mlp = GatedMLP()
+
+    def forward(self, x: torch.Tensor) -> torch.Tensor:
+        # x: [B, T, D]
+        x = x + self.attn(self.norm1(x))  # [B, T, D]
+        x = x + self.mlp(self.norm2(x))  # [B, T, D]
+        return x
+
+
+class PatchEmbedding(nn.Module):
+    """Conv patch embedding: Conv1d(C->D, kernel=stride=patch_size)."""
+
+    def __init__(self) -> None:
+        super().__init__()
+        self.proj = nn.Conv1d(
+            in_channels=NUM_CHANNELS,
+            out_channels=DIM,
+            kernel_size=PATCH_SIZE,
+            stride=PATCH_SIZE,
+            bias=True,
+        )
+
+    def forward(self, x: torch.Tensor) -> torch.Tensor:
+        # x: [B, C, L]
+        z_t = self.proj(x)  # [B, D, T]
+        return z_t.transpose(1, 2)  # [B, T, D]
+
+
+class LeNEPAEncoder(nn.Module):
+    """LeNEPA encoder trunk for this exact checkpoint (static conv patch embed, causal)."""
+
+    def __init__(self) -> None:
+        super().__init__()
+        if CHANNEL_SIZE % PATCH_SIZE != 0:
+            raise ValueError("CHANNEL_SIZE must be divisible by PATCH_SIZE")
+        self.patch_embed = PatchEmbedding()
+        self.blocks = nn.ModuleList([Block() for _ in range(DEPTH)])
+        self.norm = nn.LayerNorm(DIM, eps=NORM_EPS)
+
+    def forward(self, x: torch.Tensor) -> torch.Tensor:
+        """Return final-layer patch tokens (post-final-norm)."""
+        z = self.patch_embed(x)  # [B, T, D]
+        for block in self.blocks:
+            z = block(z)  # [B, T, D]
+        return self.norm(z)  # [B, T, D]
+
+
+@torch.inference_mode()
+def encode_lenepa(*, model: LeNEPAEncoder, x_waveform: torch.Tensor) -> LeNEPAEncoderOutput:
+    """Encode a batch of waveforms.
+
+    Args:
+      model: LeNEPA encoder (on the same device as x_waveform).
+      x_waveform: [B, 1, 5000] float32.
+    """
+    if x_waveform.dtype is not torch.float32:
+        raise ValueError(f"x_waveform must be float32, got {x_waveform.dtype}")
+    if x_waveform.dim() != 3:
+        raise ValueError(f"x_waveform must be [B, C, L], got {tuple(x_waveform.shape)}")
+    B, C, L = x_waveform.shape
+    if C != NUM_CHANNELS or L != CHANNEL_SIZE:
+        raise ValueError(
+            "Input must match the published contract: "
+            f"expected [B, {NUM_CHANNELS}, {CHANNEL_SIZE}], got {tuple(x_waveform.shape)}"
+        )
+    model_device = next(model.parameters()).device
+    if x_waveform.device != model_device:
+        raise ValueError(
+            "x_waveform must be on the same device as the model. "
+            f"x_waveform.device={x_waveform.device} model.device={model_device}"
+        )
+
+    patch_tokens = model(x_waveform)  # [B, T, D]
+    embedding = patch_tokens.mean(dim=1)  # [B, D]
+    return LeNEPAEncoderOutput(patch_tokens=patch_tokens, embedding=embedding)
+
+
+def load_lenepa_encoder(*, weights_path: Path, device: torch.device) -> LeNEPAEncoder:
+    """Load the published encoder weights from a safetensors file."""
+    if not weights_path.is_file():
+        raise ValueError(f"weights_path does not exist: {str(weights_path)!r}")
+    state = safetensors_load(str(weights_path))
+    model = LeNEPAEncoder()
+    model.load_state_dict(state, strict=True)
+    model.eval()
+    model.requires_grad_(False)
+    return model.to(device)
+
+
+def _smoke_test() -> None:
+    """Small end-to-end smoke test (random input, prints output shapes)."""
+    device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
+    here = Path(__file__).resolve().parent
+    model = load_lenepa_encoder(weights_path=here / "lenepa_encoder.safetensors", device=device)
+    x = torch.randn(2, 1, 5000, device=device, dtype=torch.float32)  # [B=2, C=1, L=5000]
+    out = encode_lenepa(model=model, x_waveform=x)
+    print("patch_tokens", tuple(out.patch_tokens.shape))
+    print("embedding", tuple(out.embedding.shape))
+
+
+if __name__ == "__main__":
+    _smoke_test()

lenepa_encoder.safetensors

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:99d6bd0388e2376e01929e3d1524b0fb94c40a4c00f65f082b20fc7a43f6a9dd
+size 14274312

lenepa_encoder_config.json

@@ -0,0 +1,24 @@
+{
+  "bias": true,
+  "channel_size": 5000,
+  "channels": [
+    "I"
+  ],
+  "depth": 8,
+  "dim": 192,
+  "format": "lenepa_encoder",
+  "format_version": 1,
+  "is_causal": true,
+  "mlp_ratio": 4.0,
+  "norm_eps": 1e-06,
+  "num_heads": 4,
+  "num_patches": 200,
+  "patch_size": 25,
+  "qk_norm_eps": 1e-06,
+  "qkv_bias": true,
+  "rope_base": 10000,
+  "sampling_frequency": 500,
+  "use_qk_norm": true,
+  "use_rope": true,
+  "use_swiglu": true
+}

provenance.json

@@ -0,0 +1,14 @@
+{
+  "checkpoint_step": 20000,
+  "exported_at_utc": "2026-03-04T16:00:59.982056+00:00",
+  "git_commit": "7f1960a2581535b2356f757f378c98dce349b189",
+  "notes": "encoder-only export (proj.* and sigreg.* removed)",
+  "pretrain_wandb": {
+    "entity": "langotime",
+    "project": "ECG-LeJEPA",
+    "run_id": "vjtzford",
+    "run_name": "AIONO_LENEPA_SIGREGT20_L0-8_PD0_PROJ_BAL_s0",
+    "url": "https://wandb.ai/langotime/ECG-LeJEPA/runs/vjtzford"
+  },
+  "source_checkpoint_path": "pretrain/AIONO_LENEPA_SIGREGT20_L0-8_PD0_PROJ_BAL_s0/chkpt_20000.pt"
+}

requirements.txt

@@ -0,0 +1,3 @@
+torch
+safetensors
+