DeepHealthExpo/models.py

from dataclasses import dataclass

import torch
import torch.nn as nn
import torch.nn.functional as F

from backbones import (
    AgeSinusoidalEncoding,
    GPTBlock,
)
from targets import PAD_IDX


@dataclass
class DeepHealthOutput:
    hidden: torch.Tensor
    time_seq: torch.Tensor
    padding_mask: torch.Tensor
    event_len: int


class DeepHealth(nn.Module):
    def __init__(
        self,
        vocab_size: int,
        n_embd: int,
        n_head: int,
        n_hist_layer: int,
        target_mode: str = "next_token",  # "next_token" or "all_future"
        dist_mode: str = "exponential",  # "exponential", "weibull" or "mixed"
        dropout: float = 0.0,
        use_exposure_embeddings: bool = False,
    ):
        super().__init__()
        if target_mode not in ["next_token", "all_future"]:
            raise ValueError(
                "target_mode must be either 'next_token' or 'all_future'")
        if dist_mode not in ["exponential", "weibull", "mixed"]:
            raise ValueError(
                "dist_mode must be either 'exponential', 'weibull' or 'mixed'")
        self.token_embedding = nn.Embedding(vocab_size, n_embd, padding_idx=0)
        self.gender_embedding = nn.Embedding(
            2, n_embd)  # Assuming binary gender
        self.target_mode = target_mode
        self.dist_mode = dist_mode
        self.use_exposure_embeddings = bool(use_exposure_embeddings)
        self.n_embd = n_embd
        self.vocab_size = vocab_size
        nn.init.normal_(self.token_embedding.weight, mean=0.0, std=0.02)
        nn.init.zeros_(self.token_embedding.weight[0])
        nn.init.normal_(self.gender_embedding.weight, mean=0.0, std=0.02)
        if dist_mode == "weibull":
            self.rho_head = nn.Linear(n_embd, vocab_size)
            nn.init.zeros_(self.rho_head.weight)
            nn.init.constant_(self.rho_head.bias, 0.5413)

        if dist_mode == "mixed":
            self.death_idx = vocab_size - 1
            self.rho_death_head = nn.Linear(n_embd, 1)
            nn.init.zeros_(self.rho_death_head.weight)
            nn.init.constant_(self.rho_death_head.bias, 0.5413)

        self.age_encoding = AgeSinusoidalEncoding(n_embd)
        self.blocks = nn.ModuleList([
            GPTBlock(
                n_embd=n_embd,
                n_head=n_head,
                mlp_dropout=dropout,
            ) for _ in range(n_hist_layer)
        ])

        self.final_ln = nn.LayerNorm(n_embd)
        self.risk_head = nn.Linear(n_embd, vocab_size, bias=False)
        if target_mode == "next_token":
            self.risk_head.weight = self.token_embedding.weight
        if target_mode == "all_future":
            self.query_token = nn.Parameter(torch.zeros(n_embd))
            nn.init.normal_(self.query_token, mean=0.0, std=0.02)
        else:
            self.register_parameter("query_token", None)

    def _make_history_attn_mask(
        self,
        padding_mask: torch.Tensor,
        time_seq: torch.Tensor,
        dtype: torch.dtype,
    ) -> torch.Tensor:
        valid_key = padding_mask[:, None, :]  # (B, 1, L)
        visible_by_time = time_seq[:, None, :] <= time_seq[:, :, None]
        valid = valid_key & visible_by_time
        return torch.zeros(
            valid.shape,
            device=valid.device,
            dtype=dtype,
        ).masked_fill(~valid, -1e4)[:, None, :, :]

    def _forward_shared(
        self,
        event_seq: torch.LongTensor,
        time_seq: torch.FloatTensor,
        sex: torch.LongTensor,
        mode: str,
        padding_mask: torch.Tensor | None = None,
        t_query: torch.FloatTensor | None = None,
        exposure_embedding: torch.Tensor | None = None,
        return_output: bool = False,
        **unused_kwargs,
    ) -> torch.Tensor | DeepHealthOutput:
        if unused_kwargs:
            unknown = ", ".join(sorted(unused_kwargs))
            raise TypeError(f"Unexpected DeepHealth forward arguments: {unknown}")
        if mode not in {"next_token", "all_future"}:
            raise ValueError("mode must be either 'next_token' or 'all_future'")
        if mode == "all_future" and t_query is None:
            raise ValueError("t_query is required when mode='all_future'")

        if padding_mask is None:
            padding_mask = event_seq > PAD_IDX
        else:
            padding_mask = padding_mask.to(device=event_seq.device, dtype=torch.bool)

        event_len = event_seq.size(1)
        h_disease = self.token_embedding(event_seq)
        if self.use_exposure_embeddings:
            if exposure_embedding is None:
                raise ValueError(
                    "exposure_embedding is required when "
                    "use_exposure_embeddings=True"
                )
            if exposure_embedding.shape != h_disease.shape:
                raise ValueError(
                    "exposure_embedding must have shape "
                    f"{tuple(h_disease.shape)}, got {tuple(exposure_embedding.shape)}"
                )
            h_disease = h_disease + exposure_embedding.to(
                device=h_disease.device, dtype=h_disease.dtype
            )
        elif exposure_embedding is not None:
            raise ValueError(
                "exposure_embedding provided but use_exposure_embeddings=False"
            )
        t_disease = time_seq
        h_disease = h_disease * padding_mask.unsqueeze(-1).to(h_disease.dtype)

        if mode == "all_future":
            if self.query_token is None:
                raise RuntimeError(
                    "all_future forward requires a model initialized with "
                    "target_mode='all_future'"
                )
            batch_size = event_seq.size(0)
            query = self.query_token.view(1, 1, -1).expand(batch_size, 1, -1)
            h_disease = torch.cat([h_disease, query], dim=1)
            t_disease = torch.cat([t_disease, t_query[:, None]], dim=1)
            query_mask = torch.ones(
                batch_size,
                1,
                dtype=torch.bool,
                device=event_seq.device,
            )
            padding_mask = torch.cat([padding_mask, query_mask], dim=1)

        sex_emb = self.gender_embedding(sex)[:, None, :]
        h_disease = h_disease + sex_emb
        h_disease = h_disease * padding_mask.unsqueeze(-1).to(h_disease.dtype)

        h_disease = h_disease + self.age_encoding(t_disease)
        h_disease = h_disease * padding_mask.unsqueeze(-1).to(h_disease.dtype)

        attn_mask = self._make_history_attn_mask(
            padding_mask=padding_mask,
            time_seq=t_disease,
            dtype=h_disease.dtype,
        )
        for block in self.blocks:
            h_disease = block(
                h_disease,
                attn_mask=attn_mask,
            )
            h_disease = h_disease * padding_mask.unsqueeze(-1).to(h_disease.dtype)

        h_disease = self.final_ln(h_disease)
        h_disease = h_disease * padding_mask.unsqueeze(-1).to(h_disease.dtype)

        if mode == "all_future":
            hidden = h_disease[:, -1, :]
            if return_output:
                return DeepHealthOutput(
                    hidden=hidden,
                    time_seq=t_query[:, None],
                    padding_mask=torch.ones(
                        hidden.size(0),
                        1,
                        dtype=torch.bool,
                        device=hidden.device,
                    ),
                    event_len=event_len,
                )
            return hidden
        if return_output:
            h_event = h_disease[:, :event_len, :]
            t_event = t_disease[:, :event_len]
            event_mask = padding_mask[:, :event_len]
            return DeepHealthOutput(
                hidden=h_event,
                time_seq=t_event,
                padding_mask=event_mask,
                event_len=event_len,
            )
        return h_disease[:, :event_len, :]

    def forward_next_token(self, **kwargs) -> torch.Tensor:
        return self._forward_shared(mode="next_token", **kwargs)

    def forward_all_future(self, **kwargs) -> torch.Tensor:
        return self._forward_shared(mode="all_future", **kwargs)

    def forward(self, target_mode: str | None = None, **kwargs) -> torch.Tensor:
        mode = self.target_mode if target_mode is None else target_mode
        return self._forward_shared(mode=mode, **kwargs)

    def calc_risk(self, x: torch.Tensor) -> torch.Tensor:
        return self.risk_head(x)

    def calc_weibull_rho(self, x: torch.Tensor) -> torch.Tensor:
        if self.dist_mode != "weibull":
            raise RuntimeError(
                f"calc_weibull_rho called with dist_mode={self.dist_mode!r}"
            )
        return F.softplus(self.rho_head(x)) + 1e-6

    def calc_death_rho(self, x: torch.Tensor) -> torch.Tensor:
        if self.dist_mode != "mixed":
            raise RuntimeError(
                f"calc_death_rho called with dist_mode={self.dist_mode!r}"
            )
        return F.softplus(self.rho_death_head(x)).squeeze(-1) + 1e-6