Survival

SURVIVE!

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hazards_to_survival_torch

def hazards_to_survival_torch(
    preds
):

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hazards_to_survival

def hazards_to_survival(
    preds
):

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make_cuts_days

def make_cuts_days(
    min_year:float, max_year:float, bin_years:float
):

Build right-edges of bins (in DAYS) for the discrete-time hazard model.

Returns: cuts_days (np.ndarray): shape [J], right edges in days.

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discretize_time

def discretize_time(
    time_days, bin_years:float=0.25, min_year:float=0.0, max_year:float=10.0
):

Discretize a tensor of observed times (in days) into bin indices for discrete-time survival.

Args: time_days (Tensor): observed times in days (event or censoring). bin_years (float): width of bins in years (e.g., 0.25 = quarter-year). min_year (float): lower bound of the window in years. max_year (float): upper bound of the window in years.

Returns: bin_idx (Tensor): indices in [0, n_bins-1] for each input time

Cox w Momentum

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PatchTFTSurvivalDemo

def PatchTFTSurvivalDemo(
    learning_rate, train_size, batch_size, n_gpus, linear_probing_head, preloaded_model,
    evaluate_risk_years:list=[1, 5, 10], discretize_time:bool=True, discrete_time_bins:float=0.25,
    time_range_years:tuple=(0, 15), fine_tune:bool=False, epochs:int=100, scheduler_type:str='OneCycle',
    optimizer_type:str='AdamW', weight_decay:float=0.001, final_weight_decay:float=1e-06,
    use_weight_decay_scheduler:bool=False,
    demographic_embeddings:dict={'age_bin_idx': 9, 'bmi_bin_idx': 7, 'gender': 2}, age_mlp_hidden_size:int=32,
    demographics_only:bool=False, scheduler_kwargs:dict={}, transforms:NoneType=None
):

Hooks to be used in LightningModule.

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SurvivalDemo

def SurvivalDemo(
    learning_rate, train_size, batch_size, n_gpus, evaluate_risk_years:list=[1, 5, 10], discretize_time:bool=True,
    discrete_time_bins:float=0.25, time_range_years:tuple=(0, 15), fine_tune:bool=False, epochs:int=100,
    scheduler_type:str='OneCycle', optimizer_type:str='AdamW', weight_decay:float=0.001,
    final_weight_decay:float=1e-06, use_weight_decay_scheduler:bool=False,
    demographic_embeddings:dict={'age_bin_idx': 9, 'bmi_bin_idx': 7, 'gender': 2}, age_mlp_hidden_size:int=32,
    scheduler_kwargs:dict={}, transforms:NoneType=None
):

Hooks to be used in LightningModule.