[tab] utils/nn.py (python)
import math
from typing import Tuple

from flax import linen as nn
import jax
import jax.numpy as jnp
import einops


class SpatioTemporalPositionalEncoding(nn.Module):
    """
    Applies separate sinusoidal positional encodings to the temporal and spatial dimensions.
    """
    d_model: int  # Hidden dimensionality of the input.
    max_len: int = 5000  # Maximum length for any single dimension.

    def setup(self):
        pe = jnp.zeros((self.max_len, self.d_model))
        position = jnp.arange(0, self.max_len, dtype=jnp.float32)[:, None]
        div_term = jnp.exp(
            jnp.arange(0, self.d_model, 2) * (-math.log(10000.0) / self.d_model)
        )
        pe = pe.at[:, 0::2].set(jnp.sin(position * div_term))
        pe = pe.at[:, 1::2].set(jnp.cos(position * div_term))
        self.pe = pe  # Shape: (max_len, d_model)

    def __call__(self, x: jax.Array) -> jax.Array:
        """
        Args:
            x: The input tensor of shape (Batch, Time, Space, Dimension).

        Returns:
            The input tensor with positional encodings added.
        """
        assert x.ndim == 4, f"Input must be 4-dimensional, but got shape {x.shape}"

        num_timesteps = x.shape[1]
        num_spatial_patches = x.shape[2]

        # Temporal positional encoding
        temporal_pe = self.pe[None, :num_timesteps, None, :]
        x = x + temporal_pe

        # Spatial positional encoding
        spatial_pe = self.pe[None, None, :num_spatial_patches, :]
        x = x + spatial_pe

        return x


class STBlock(nn.Module):
    dim: int
    ffn_dim: int
    num_heads: int
    dropout: float
    param_dtype: jnp.dtype
    dtype: jnp.dtype
    use_flash_attention: bool

    @nn.remat
    @nn.compact
    def __call__(self, x: jax.Array) -> jax.Array:
        # --- Spatial attention ---
        z = nn.LayerNorm(
            param_dtype=self.param_dtype,
            dtype=self.dtype,
        )(x)
        z = nn.MultiHeadAttention(
            num_heads=self.num_heads,
            qkv_features=self.dim,
            dropout_rate=self.dropout,
            param_dtype=self.param_dtype,
            dtype=self.dtype,
            attention_fn=_create_flash_attention_fn(
                self.use_flash_attention, is_causal=False
            ),
        )(z)
        x = x + z

        # --- Temporal attention ---
        x = x.swapaxes(1, 2)
        z = nn.LayerNorm(
            param_dtype=self.param_dtype,
            dtype=self.dtype,
        )(x)
        causal_mask = jnp.tri(z.shape[-2])
        z = nn.MultiHeadAttention(
            num_heads=self.num_heads,
            qkv_features=self.dim,
            dropout_rate=self.dropout,
            param_dtype=self.param_dtype,
            dtype=self.dtype,
            attention_fn=_create_flash_attention_fn(
                self.use_flash_attention, is_causal=True
            ),
            # FIXME (f.srambical): check whether we should still pass the mask if we set is_causal=True
        )(z, mask=causal_mask)
        x = x + z
        x = x.swapaxes(1, 2)

        # --- Feedforward ---
        z = nn.LayerNorm(
            param_dtype=self.param_dtype,
            dtype=self.dtype,
        )(x)
        z = nn.Dense(
            self.ffn_dim,
            param_dtype=self.param_dtype,
            dtype=self.dtype,
        )(z)
        z = nn.gelu(z)
        z = nn.Dense(
            self.dim,
            param_dtype=self.param_dtype,
            dtype=self.dtype,
        )(z)
        x = x + z

        return x


class STTransformer(nn.Module):
    model_dim: int
    ffn_dim: int
    out_dim: int
    num_blocks: int
    num_heads: int
    dropout: float
    param_dtype: jnp.dtype
    dtype: jnp.dtype
    use_flash_attention: bool
    max_len: int = 5000  # For positional encoding

    @nn.compact
    def __call__(self, x: jax.Array) -> jax.Array:
        x = nn.Sequential(
            [
                nn.LayerNorm(
                    param_dtype=self.param_dtype,
                    dtype=self.dtype,
                ),
                nn.Dense(
                    self.model_dim,
                    param_dtype=self.param_dtype,
                    dtype=self.dtype,
                ),
                nn.LayerNorm(
                    param_dtype=self.param_dtype,
                    dtype=self.dtype,
                ),
            ]
        )(x)
        # x is expected to be (B, T, S, D)
        x = SpatioTemporalPositionalEncoding(
            d_model=self.model_dim, max_len=self.max_len
        )(x)
        for _ in range(self.num_blocks):
            x = STBlock(
                dim=self.model_dim,
                ffn_dim=self.ffn_dim,
                num_heads=self.num_heads,
                dropout=self.dropout,
                param_dtype=self.param_dtype,
                dtype=self.dtype,
                use_flash_attention=self.use_flash_attention,
            )(x)
        x = nn.Dense(
            self.out_dim,
            param_dtype=self.param_dtype,
            dtype=self.dtype,
        )(x)
        return x  # (B, T, E)


def normalize(x):
    return x / (jnp.linalg.norm(x, ord=2, axis=-1, keepdims=True) + 1e-8)


class VectorQuantizer(nn.Module):
    latent_dim: int
    num_latents: int
    dropout: float

    def setup(self):
        self.codebook = normalize(
            self.param(
                "codebook",
                nn.initializers.lecun_uniform(),
                (self.num_latents, self.latent_dim),
            )
        )
        self.drop = nn.Dropout(self.dropout, deterministic=False)

    def __call__(
        self, x: jax.Array, training: bool
    ) -> Tuple[jax.Array, jax.Array, jax.Array, jax.Array]:
        # --- Compute distances ---
        x = normalize(x)
        codebook = normalize(self.codebook)
        distance = -jnp.matmul(x, codebook.T)
        if training:
            dropout_key = self.make_rng("dropout")
            distance = self.drop(distance, rng=dropout_key)

        # --- Get indices and embeddings ---
        indices = jnp.argmin(distance, axis=-1)
        z = self.codebook[indices]

        # --- Straight through estimator ---
        z_q = x + jax.lax.stop_gradient(z - x)
        return z_q, z, x, indices

    def get_codes(self, indices: jax.Array):
        return self.codebook[indices]


def _create_flash_attention_fn(use_flash_attention: bool, is_causal: bool):
    """
    Create an attention function that uses flash attention if enabled.

    Flax MultiHeadAttention provides tensors with shape (batch..., length, num_heads, head_dim)
    jax.nn.dot_product_attention expects (batch, length, num_heads, head_dim).

    We need to reshape to ensure compatibility. cuDNN's flash attention additionally
    requires a sequence length that is a multiple of 4. We pad the sequence length to the nearest
    multiple of 4 and mask accordingly.
    """

    def attention_fn(query, key, value, bias=None, mask=None, **kwargs):
        implementation = "cudnn" if use_flash_attention else None

        def _rearrange(x):
            return einops.rearrange(x, "... l h d -> (...) l h d")

        def _pad(x):
            return jnp.pad(x, ((0, 0), (0, pad_size), (0, 0), (0, 0)))

        def _fuse_masks(mask: jax.Array, attention_mask: jax.Array) -> jax.Array:
            mask_bool = mask.astype(jnp.bool_)
            expanded_mask = jnp.pad(
                mask_bool, ((0, pad_size), (0, pad_size)), constant_values=False
            )
            return jnp.logical_and(attention_mask, expanded_mask)

        original_shape = query.shape
        original_seq_len = query.shape[-3]

        # Pad to nearest multiple of 4
        target_seq_len = ((original_seq_len + 3) // 4) * 4
        pad_size = target_seq_len - original_seq_len

        query_4d = _pad(_rearrange(query))
        key_4d = _pad(_rearrange(key))
        value_4d = _pad(_rearrange(value))

        attention_mask = jnp.ones((target_seq_len, target_seq_len), dtype=jnp.bool_)
        attention_mask = attention_mask.at[original_seq_len:, :].set(False)
        attention_mask = attention_mask.at[:, original_seq_len:].set(False)

        mask_4d = (
            _fuse_masks(mask, attention_mask) if mask is not None else attention_mask
        )
        mask_4d = mask_4d[jnp.newaxis, jnp.newaxis, :, :]  # (1, 1, seq_len, seq_len)

        bias_4d = _pad(_rearrange(bias)) if bias is not None else None

        output_4d = jax.nn.dot_product_attention(
            query=query_4d,
            key=key_4d,
            value=value_4d,
            bias=bias_4d,
            mask=mask_4d,
            implementation=implementation,
            is_causal=is_causal,
            **kwargs
        )
        return output_4d[..., :original_seq_len, :, :].reshape(original_shape)

    return attention_fn