DeepHealth/utils.py

import torch
from typing import Tuple

DAYS_PER_YEAR = 365.25


def sample_context_in_fixed_age_bin(
    event_seq: torch.Tensor,
    time_seq: torch.Tensor,
    tau_years: float,
    age_bin: Tuple[float, float],
    seed: int,
) -> Tuple[torch.Tensor, torch.Tensor]:
    """Sample one context token per individual within a fixed age bin.

    Delphi-2M semantics for a specific (tau, age_bin):
      - Token times are interpreted as age in *days* (converted to years).
      - Follow-up end time is the last valid token time per individual.
      - A token index j is eligible iff:
            (token is valid)
        AND (age_years in [age_low, age_high))
        AND (time_seq[i, j] + tau_days <= followup_end_time[i])
      - For each individual, randomly select exactly one eligible token in this bin.

    Args:
        event_seq: (B, L) token ids, 0 is padding.
        time_seq: (B, L) token times in days.
        tau_years: horizon length in years.
        age_bin: (low, high) bounds in years, interpreted as [low, high).
        seed: RNG seed for deterministic sampling.

    Returns:
        keep: (B,) bool, True if a context was sampled for this bin.
        t_ctx: (B,) long, sampled context index (undefined when keep=False; set to 0).
    """
    low, high = float(age_bin[0]), float(age_bin[1])
    if not (high > low):
        raise ValueError(f"age_bin must satisfy high>low; got {(low, high)}")

    device = event_seq.device
    B, _ = event_seq.shape

    valid = event_seq != 0
    lengths = valid.sum(dim=1)
    last_idx = torch.clamp(lengths - 1, min=0)
    b = torch.arange(B, device=device)
    followup_end_time = time_seq[b, last_idx]  # (B,)

    tau_days = float(tau_years) * DAYS_PER_YEAR
    age_years = time_seq / DAYS_PER_YEAR

    in_bin = (age_years >= low) & (age_years < high)
    eligible = valid & in_bin & (
        (time_seq + tau_days) <= followup_end_time.unsqueeze(1))

    keep = torch.zeros((B,), dtype=torch.bool, device=device)
    t_ctx = torch.zeros((B,), dtype=torch.long, device=device)

    gen = torch.Generator(device="cpu")
    gen.manual_seed(int(seed))

    for i in range(B):
        m = eligible[i]
        if not m.any():
            continue

        idxs = m.nonzero(as_tuple=False).view(-1).cpu()
        chosen_idx_pos = int(
            torch.randint(low=0, high=int(idxs.numel()),
                          size=(1,), generator=gen).item()
        )
        chosen_t = int(idxs[chosen_idx_pos].item())

        keep[i] = True
        t_ctx[i] = chosen_t

    return keep, t_ctx


def select_context_indices(
    event_seq: torch.Tensor,
    time_seq: torch.Tensor,
    offset_years: float,
    tau_years: float = 0.0,
) -> Tuple[torch.Tensor, torch.Tensor, torch.Tensor]:
    """Select per-sample prediction context index.

    IMPORTANT SEMANTICS:
    - The last observed token time is treated as the FOLLOW-UP END time.
    - We pick the last valid token with time <= (followup_end_time - offset).
    - We do NOT interpret followup_end_time as an event time.

    Returns:
        keep_mask: (B,) bool, which samples have a valid context
        t_ctx: (B,) long, index into sequence
        t_ctx_time: (B,) float, time (days) at context
    """
    # valid tokens are event != 0 (padding is 0)
    valid = event_seq != 0
    lengths = valid.sum(dim=1)
    last_idx = torch.clamp(lengths - 1, min=0)

    b = torch.arange(event_seq.size(0), device=event_seq.device)
    followup_end_time = time_seq[b, last_idx]
    t_cut = followup_end_time - (offset_years * DAYS_PER_YEAR)

    eligible = valid & (time_seq <= t_cut.unsqueeze(1))
    eligible_counts = eligible.sum(dim=1)
    keep = eligible_counts > 0

    t_ctx = torch.clamp(eligible_counts - 1, min=0).to(torch.long)
    t_ctx_time = time_seq[b, t_ctx]

    # Horizon-aligned eligibility: require enough follow-up time after the selected context.
    # All times are in days.
    keep = keep & (followup_end_time >= (
        t_ctx_time + (tau_years * DAYS_PER_YEAR)))

    return keep, t_ctx, t_ctx_time


def multi_hot_ever_within_horizon(
    event_seq: torch.Tensor,
    time_seq: torch.Tensor,
    t_ctx: torch.Tensor,
    tau_years: float,
    n_disease: int,
) -> torch.Tensor:
    """Binary labels: disease k occurs within tau after context (any occurrence)."""
    B, L = event_seq.shape
    b = torch.arange(B, device=event_seq.device)
    t0 = time_seq[b, t_ctx]
    t1 = t0 + (tau_years * DAYS_PER_YEAR)

    idxs = torch.arange(L, device=event_seq.device).unsqueeze(0).expand(B, -1)
    # Include same-day events after context, exclude any token at/before context index.
    in_window = (
        (idxs > t_ctx.unsqueeze(1))
        & (time_seq >= t0.unsqueeze(1))
        & (time_seq <= t1.unsqueeze(1))
        & (event_seq >= 2)
        & (event_seq != 0)
    )

    if not in_window.any():
        return torch.zeros((B, n_disease), dtype=torch.bool, device=event_seq.device)

    b_idx, t_idx = in_window.nonzero(as_tuple=True)
    disease_ids = (event_seq[b_idx, t_idx] - 2).to(torch.long)

    y = torch.zeros((B, n_disease), dtype=torch.bool, device=event_seq.device)
    y[b_idx, disease_ids] = True
    return y


def multi_hot_selected_causes_within_horizon(
    event_seq: torch.Tensor,
    time_seq: torch.Tensor,
    t_ctx: torch.Tensor,
    tau_years: float,
    cause_ids: torch.Tensor,
    n_disease: int,
) -> torch.Tensor:
    """Labels for selected causes only: does cause k occur within tau after context?"""
    B, L = event_seq.shape
    device = event_seq.device
    b = torch.arange(B, device=device)
    t0 = time_seq[b, t_ctx]
    t1 = t0 + (tau_years * DAYS_PER_YEAR)

    idxs = torch.arange(L, device=device).unsqueeze(0).expand(B, -1)
    in_window = (
        (idxs > t_ctx.unsqueeze(1))
        & (time_seq >= t0.unsqueeze(1))
        & (time_seq <= t1.unsqueeze(1))
        & (event_seq >= 2)
        & (event_seq != 0)
    )

    out = torch.zeros((B, cause_ids.numel()), dtype=torch.bool, device=device)
    if not in_window.any():
        return out

    b_idx, t_idx = in_window.nonzero(as_tuple=True)
    disease_ids = (event_seq[b_idx, t_idx] - 2).to(torch.long)

    # Filter to selected causes via a boolean membership mask over the global disease space.
    selected = torch.zeros((int(n_disease),), dtype=torch.bool, device=device)
    selected[cause_ids] = True
    keep = selected[disease_ids]
    if not keep.any():
        return out

    b_idx = b_idx[keep]
    disease_ids = disease_ids[keep]

    # Map disease_id -> local index in cause_ids
    # Build a lookup table (global disease space) where lookup[disease_id] = local_index
    lookup = torch.full((int(n_disease),), -1, dtype=torch.long, device=device)
    lookup[cause_ids] = torch.arange(cause_ids.numel(), device=device)
    local = lookup[disease_ids]
    out[b_idx, local] = True
    return out