495 lines
17 KiB
Python
495 lines
17 KiB
Python
import scipy.stats
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import scipy
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import warnings
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import torch
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from models import TimeAwareGPT2
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from tqdm import tqdm
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import pandas as pd
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import numpy as np
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import argparse
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from utils import load_model, get_batch, PatientEventDataset
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from pathlib import Path
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from joblib import Parallel, delayed
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def auc(x1, x2):
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n1 = len(x1)
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n2 = len(x2)
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R1 = np.concatenate([x1, x2]).argsort().argsort()[:n1].sum() + n1
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U1 = n1 * n2 + 0.5 * n1 * (n1 + 1) - R1
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if n1 == 0 or n2 == 0:
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return np.nan
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return U1 / n1 / n2
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def get_common_diseases(delphi_labels, filter_min_total=100):
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chapters_of_interest = [
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"I. Infectious Diseases",
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"II. Neoplasms",
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"III. Blood & Immune Disorders",
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"IV. Metabolic Diseases",
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"V. Mental Disorders",
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"VI. Nervous System Diseases",
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"VII. Eye Diseases",
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"VIII. Ear Diseases",
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"IX. Circulatory Diseases",
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"X. Respiratory Diseases",
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"XI. Digestive Diseases",
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"XII. Skin Diseases",
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"XIII. Musculoskeletal Diseases",
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"XIV. Genitourinary Diseases",
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"XV. Pregnancy & Childbirth",
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"XVI. Perinatal Conditions",
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"XVII. Congenital Abnormalities",
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"Death",
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]
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labels_df = delphi_labels[
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delphi_labels["ICD-10 Chapter (short)"].isin(chapters_of_interest) * (delphi_labels["count"] > filter_min_total)
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]
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return labels_df["index"].tolist()
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def optimized_bootstrapped_auc_gpu(case, control, n_bootstrap=1000):
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"""
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Computes bootstrapped AUC estimates using PyTorch on CUDA.
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Parameters:
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case: 1D tensor of scores for positive cases
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control: 1D tensor of scores for controls
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n_bootstrap: Number of bootstrap replicates
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Returns:
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Tensor of shape (n_bootstrap,) containing AUC for each bootstrap replicate
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"""
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if not torch.cuda.is_available():
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raise RuntimeError("CUDA is not available. This function requires a GPU.")
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# Convert inputs to CUDA tensors
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if not torch.is_tensor(case):
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case = torch.tensor(case, device="cuda", dtype=torch.float32)
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else:
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case = case.to("cuda", dtype=torch.float32)
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if not torch.is_tensor(control):
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control = torch.tensor(control, device="cuda", dtype=torch.float32)
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else:
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control = control.to("cuda", dtype=torch.float32)
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n_case = case.size(0)
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n_control = control.size(0)
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total = n_case + n_control
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# Generate bootstrap samples
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boot_idx_case = torch.randint(0, n_case, (n_bootstrap, n_case), device="cuda")
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boot_idx_control = torch.randint(0, n_control, (n_bootstrap, n_control), device="cuda")
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boot_case = case[boot_idx_case]
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boot_control = control[boot_idx_control]
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combined = torch.cat([boot_case, boot_control], dim=1)
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# Mask to identify case entries
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mask = torch.zeros((n_bootstrap, total), dtype=torch.bool, device="cuda")
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mask[:, :n_case] = True
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# Compute ranks and AUC
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ranks = combined.argsort(dim=1).argsort(dim=1)
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case_ranks_sum = torch.sum(ranks.float() * mask.float(), dim=1)
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min_case_rank_sum = n_case * (n_case - 1) / 2.0
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U = case_ranks_sum - min_case_rank_sum
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aucs = U / (n_case * n_control)
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return aucs.cpu().tolist()
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# AUC comparison adapted from
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# https://github.com/Netflix/vmaf/
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def compute_midrank(x):
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"""Computes midranks.
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Args:
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x - a 1D numpy array
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Returns:
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array of midranks
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"""
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J = np.argsort(x)
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Z = x[J]
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N = len(x)
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T = np.zeros(N, dtype=np.float32)
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i = 0
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while i < N:
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j = i
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while j < N and Z[j] == Z[i]:
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j += 1
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T[i:j] = 0.5 * (i + j - 1)
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i = j
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T2 = np.empty(N, dtype=np.float32)
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# Note(kazeevn) +1 is due to Python using 0-based indexing
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# instead of 1-based in the AUC formula in the paper
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T2[J] = T + 1
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return T2
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def fastDeLong(predictions_sorted_transposed, label_1_count):
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"""
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The fast version of DeLong's method for computing the covariance of
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unadjusted AUC.
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Args:
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predictions_sorted_transposed: a 2D numpy.array[n_classifiers, n_examples]
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sorted such as the examples with label "1" are first
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Returns:
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(AUC value, DeLong covariance)
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Reference:
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@article{sun2014fast,
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title={Fast Implementation of DeLong's Algorithm for
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Comparing the Areas Under Correlated Receiver Operating Characteristic Curves},
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author={Xu Sun and Weichao Xu},
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journal={IEEE Signal Processing Letters},
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volume={21},
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number={11},
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pages={1389--1393},
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year={2014},
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publisher={IEEE}
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}
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"""
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# Short variables are named as they are in the paper
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m = label_1_count
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n = predictions_sorted_transposed.shape[1] - m
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positive_examples = predictions_sorted_transposed[:, :m]
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negative_examples = predictions_sorted_transposed[:, m:]
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k = predictions_sorted_transposed.shape[0]
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tx = np.empty([k, m], dtype=np.float32)
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ty = np.empty([k, n], dtype=np.float32)
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tz = np.empty([k, m + n], dtype=np.float32)
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for r in range(k):
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tx[r, :] = compute_midrank(positive_examples[r, :])
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ty[r, :] = compute_midrank(negative_examples[r, :])
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tz[r, :] = compute_midrank(predictions_sorted_transposed[r, :])
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aucs = tz[:, :m].sum(axis=1) / m / n - float(m + 1.0) / 2.0 / n
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v01 = (tz[:, :m] - tx[:, :]) / n
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v10 = 1.0 - (tz[:, m:] - ty[:, :]) / m
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sx = np.cov(v01)
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sy = np.cov(v10)
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delongcov = sx / m + sy / n
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return aucs, delongcov
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def compute_ground_truth_statistics(ground_truth):
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assert np.array_equal(np.unique(ground_truth), [0, 1])
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order = (-ground_truth).argsort()
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label_1_count = int(ground_truth.sum())
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return order, label_1_count
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def get_auc_delong_var(healthy_scores, diseased_scores):
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"""
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Computes ROC AUC value and variance using DeLong's method
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Args:
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healthy_scores: Values for class 0 (healthy/controls)
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diseased_scores: Values for class 1 (diseased/cases)
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Returns:
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AUC value and variance
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"""
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# Create ground truth labels (1 for diseased, 0 for healthy)
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ground_truth = np.array([1] * len(diseased_scores) + [0] * len(healthy_scores))
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predictions = np.concatenate([diseased_scores, healthy_scores])
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# Compute statistics needed for DeLong method
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order, label_1_count = compute_ground_truth_statistics(ground_truth)
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predictions_sorted_transposed = predictions[np.newaxis, order]
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# Calculate AUC and covariance
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aucs, delongcov = fastDeLong(predictions_sorted_transposed, label_1_count)
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assert len(aucs) == 1, "There is a bug in the code, please forward this to the developers"
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return aucs[0], delongcov
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def get_calibration_auc(j, k, d, p, offset=365.25, age_groups=range(45, 80, 5), precomputed_idx=None, n_bootstrap=1, use_delong=False):
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age_step = age_groups[1] - age_groups[0]
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# Indexes of cases with disease k
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wk = np.where(d[2] == k)
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if len(wk[0]) < 2:
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return None
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# For controls, we need to exclude cases with disease k
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wc = np.where((d[2] != k) & (~(d[2] == k).any(-1))[..., None])
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wall = (np.concatenate([wk[0], wc[0]]), np.concatenate([wk[1], wc[1]])) # All cases and controls
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# We need to take into account the offset t and use the tokens for prediction that are at least t before the event
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if precomputed_idx is None:
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pred_idx = (d[1][wall[0]] <= d[3][wall].reshape(-1, 1) - offset).sum(1) - 1
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else:
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pred_idx = precomputed_idx[wall] # It's actually much faster to precompute this
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valid_indices = pred_idx != -1
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pred_idx = pred_idx[valid_indices]
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wall = (wall[0][valid_indices], wall[1][valid_indices])
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z = d[1][(wall[0], pred_idx)] # Times of the tokens for prediction
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zk = d[3][wall] # Target times
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x = p[..., j][(wall[0], pred_idx)]
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p_idx = wall[0]
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out = []
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for i, aa in enumerate(age_groups):
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a = (z / 365.25 >= aa) & (z / 365.25 < aa + age_step)
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if not np.any(a):
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continue
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selected_groups = p_idx[a]
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_, unique_indices = np.unique(selected_groups, return_index=True)
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a_filtered = a[a]
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a_filtered[:] = False
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a_filtered[unique_indices] = True
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a[a] = a_filtered
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is_case = np.zeros_like(x, dtype=bool)
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is_case[:len(wk[0])] = True
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control = x[~is_case & a]
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case = x[is_case & a]
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if len(control) == 0 or len(case) == 0:
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continue
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if use_delong:
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auc_value_delong, auc_variance_delong = get_auc_delong_var(control, case)
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auc_delong_dict = {"auc_delong": auc_value_delong, "auc_variance_delong": auc_variance_delong}
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else:
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auc_delong_dict = {}
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if n_bootstrap > 1:
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aucs_bootstrapped = optimized_bootstrapped_auc_gpu(case, control, n_bootstrap)
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for bootstrap_idx in range(n_bootstrap):
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y = auc_value_delong if n_bootstrap == 1 else aucs_bootstrapped[bootstrap_idx]
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out_item = {
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"token": k,
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"auc": y,
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"age": aa,
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"n_healthy": len(control),
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"n_diseased": len(case),
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}
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out.append(out_item | auc_delong_dict)
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if n_bootstrap > 1:
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out_item["bootstrap_idx"] = bootstrap_idx
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return out
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def process_chunk(disease_chunk_idx, diseases_chunk, d100k, p100k, pred_idx_precompute, age_groups, offset, n_bootstrap):
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all_aucs = []
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for sex, sex_idx in [("female", 2), ("male", 3)]:
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sex_mask = ((d100k[0] == sex_idx).sum(1) > 0).cpu().detach().numpy()
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p_sex = p100k[sex_mask]
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d100k_sex = [d_.cpu().detach().numpy()[sex_mask] for d_ in d100k]
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precomputed_idx_subset = pred_idx_precompute[sex_mask].cpu().detach().numpy()
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for j, k in tqdm(
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list(enumerate(diseases_chunk)), desc=f"Processing diseases in chunk {disease_chunk_idx}, {sex}"
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):
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out = get_calibration_auc(
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j,
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k,
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d100k_sex,
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p_sex,
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age_groups=age_groups,
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offset=offset,
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precomputed_idx=precomputed_idx_subset,
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n_bootstrap=n_bootstrap,
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use_delong=True,
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)
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if out is None:
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continue
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for out_item in out:
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out_item["sex"] = sex
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all_aucs.append(out_item)
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return all_aucs
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# New internal function that performs the AUC evaluation pipeline.
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def evaluate_auc_pipeline(
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model,
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d100k,
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output_path,
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delphi_labels,
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diseases_of_interest=None,
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filter_min_total=100,
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disease_chunk_size=200,
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age_groups=np.arange(40, 80, 5),
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offset=0.1,
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batch_size=256,
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device="cpu",
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seed=1337,
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n_bootstrap=1,
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meta_info={},
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n_jobs=-1,
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):
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"""
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Runs the AUC evaluation pipeline.
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Args:
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model (torch.nn.Module): The loaded model set to eval().
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d100k (tuple): Data batch from get_batch.
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delphi_labels (pd.DataFrame): DataFrame with label info (token names, etc. "delphi_labels_chapters_colours_icd.csv").
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output_path (str | None): Directory where CSV files will be written. If None, files will not be saved.
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diseases_of_interest (np.ndarray or list, optional): If provided, these disease indices are used.
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filter_min_total (int): Minimum total token count to include a token.
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disease_chunk_size (int): Maximum chunk size for processing diseases.
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age_groups (np.ndarray): Age groups to use in calibration.
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offset (float): Offset used in get_calibration_auc.
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batch_size (int): Batch size for model forwarding.
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device (str): Device identifier.
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seed (int): Random seed for reproducibility.
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n_bootstrap (int): Number of bootstrap samples. (1 for no bootstrap)
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n_jobs (int): Number of parallel jobs to run.
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Returns:
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tuple: (df_auc_unpooled, df_auc, df_both) DataFrames.
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"""
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assert n_bootstrap > 0, "n_bootstrap must be greater than 0"
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# Set random seeds
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torch.manual_seed(seed)
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torch.cuda.manual_seed(seed)
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# Get common diseases
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if diseases_of_interest is None:
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diseases_of_interest = get_common_diseases(delphi_labels, filter_min_total)
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# Split diseases into chunks for processing
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num_chunks = (len(diseases_of_interest) + disease_chunk_size - 1) // disease_chunk_size
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diseases_chunks = np.array_split(diseases_of_interest, num_chunks)
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# Precompute prediction indices for calibration
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pred_idx_precompute = (d100k[1][:, :, np.newaxis] < d100k[3][:, np.newaxis, :] - offset).sum(1) - 1
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p100k = []
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model.to(device)
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with torch.no_grad():
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for dd in tqdm(
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zip(*[torch.split(x, batch_size) for x in d100k]),
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desc=f"Model inference",
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total=d100k[0].shape[0] // batch_size + 1,
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):
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dd = [x.to(device) for x in dd]
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outputs = model(dd[0], dd[1]).cpu().detach().numpy()
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p100k.append(outputs.astype("float16"))
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p100k = np.vstack(p100k)
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results = Parallel(n_jobs=n_jobs)(
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delayed(process_chunk)(
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disease_chunk_idx, diseases_chunk, d100k, p100k[:, :, diseases_chunk], pred_idx_precompute, age_groups, offset, n_bootstrap
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)
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for disease_chunk_idx, diseases_chunk in enumerate(diseases_chunks)
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)
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all_aucs = [item for sublist in results for item in sublist]
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df_auc_unpooled = pd.DataFrame(all_aucs)
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for key, value in meta_info.items():
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df_auc_unpooled[key] = value
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delphi_labels_subset = delphi_labels[['index', 'ICD-10 Chapter (short)', 'name', 'color', 'count']]
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df_auc_unpooled_merged = df_auc_unpooled.merge(delphi_labels_subset, left_on="token", right_on="index", how="inner")
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def aggregate_age_brackets_delong(group):
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# For normal distributions, when averaging n of them:
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# The variance of the sum is the sum of variances
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# The variance of the average is the sum of variances divided by n^2
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n = len(group)
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mean = group['auc_delong'].mean()
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# Since we're taking the average, divide combined variance by n^2
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var = group['auc_variance_delong'].sum() / (n**2)
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return pd.Series({
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'auc': mean,
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'auc_variance_delong': var,
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'n_samples': n,
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'n_diseased': group['n_diseased'].sum(),
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'n_healthy': group['n_healthy'].sum(),
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})
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print('Using DeLong method to calculate AUC confidence intervals..')
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df_auc = df_auc_unpooled.groupby(["token"]).apply(aggregate_age_brackets_delong).reset_index()
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df_auc_merged = df_auc.merge(delphi_labels, left_on="token", right_on="index", how="inner")
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if output_path is not None:
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Path(output_path).mkdir(exist_ok=True, parents=True)
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df_auc_merged.to_parquet(f"{output_path}/df_both.parquet", index=False)
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df_auc_unpooled_merged.to_parquet(f"{output_path}/df_auc_unpooled.parquet", index=False)
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return df_auc_unpooled_merged, df_auc_merged
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def main():
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parser = argparse.ArgumentParser(description="Evaluate AUC")
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parser.add_argument("--dataset_subset_size", type=int, default=-1, help="Dataset subset size for evaluation")
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parser.add_argument("--n_bootstrap", type=int, default=1, help="Number of bootstrap samples")
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# Optional filtering/chunking parameters:
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parser.add_argument("--filter_min_total", type=int, default=100, help="Minimum total count to filter tokens")
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parser.add_argument("--disease_chunk_size", type=int, default=200, help="Chunk size for processing diseases")
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parser.add_argument("--n_jobs", type=int, default=-1, help="Number of parallel jobs to run")
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args = parser.parse_args()
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output_path = './'
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dataset_subset_size = args.dataset_subset_size
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# Create output folder if it doesn't exist.
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Path(output_path).mkdir(exist_ok=True, parents=True)
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device = "cuda"
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seed = 1337
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# Load model checkpoint and initialize model.
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model = load_model('config_n_embd_256_n_layer_16_n_head_16.json',
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'best_model_n_embd_256_n_layer_16_n_head_16.pt',
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1270)
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model.eval()
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model = model.to(device)
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# Load training and validation data.
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val_data_path = 'ukb_real_val.bin'
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|
val_data_arr = np.memmap(val_data_path, dtype=np.uint32, mode='r').reshape(-1, 3)
|
|
block_length = 128
|
|
val_dataset = PatientEventDataset(val_data_arr, block_length)
|
|
|
|
if dataset_subset_size == -1:
|
|
dataset_subset_size = len(val_dataset)
|
|
|
|
# Get a subset batch for evaluation.
|
|
d100k = get_batch(val_dataset, slice(dataset_subset_size))
|
|
|
|
# Load labels (external) to be passed in.
|
|
delphi_labels = pd.read_csv("delphi_labels_chapters_colours_icd.csv")
|
|
|
|
# Call the internal evaluation function.
|
|
df_auc_unpooled, df_auc_merged = evaluate_auc_pipeline(
|
|
model,
|
|
d100k,
|
|
output_path,
|
|
delphi_labels,
|
|
diseases_of_interest=None,
|
|
filter_min_total=args.filter_min_total,
|
|
disease_chunk_size=args.disease_chunk_size,
|
|
device=device,
|
|
seed=seed,
|
|
n_bootstrap=args.n_bootstrap,
|
|
n_jobs=args.n_jobs,
|
|
)
|
|
|
|
|
|
if __name__ == "__main__":
|
|
main()
|