Table 1 Summary of MILTON models’ performance when trained on various feature sets and time-models

From: Disease prediction with multi-omics and biomarkers empowers case–control genetic discoveries in the UK Biobank

Time-model (abs(time-lag))

Number of ICD10 codes

Features

Median AUC [0, 1]

Median sensitivity

Median specificity

Time-agnostic (no lag)

151

Disease-specific PRS + sex + age

0.66 ± 0.07

59.95 ± 6.50%

62.43 ± 6.60%

Time-agnostic (no lag)

151

67 traits

0.71 ± 0.12

61.93 ± 10.95%

69.44 ± 11.98%

Prognostic (≤10 years)

121

Disease-specific PRS + sex + age

0.65 ± 0.06

59.73 ± 5.99%

62.05 ± 6.21%

Prognostic (≤10 years)

121

67 traits

0.71 ± 0.12

61.56 ± 10.56%

68.18 ± 11.98%

Diagnostic (<10 years)

82

Disease-specific PRS + sex + age

0.67 ± 0.08

61.33 ± 7.47%

63.39 ± 7.07%

Diagnostic (<10 years)

82

67 traits

0.75 ± 0.14

65.65 ± 12.22%

71.49 ± 13.09%

Time-agnostic (no lag)

499

36 PRS + sex + age

0.54 ± 0.05

52.28 ± 5.07%

53.02 ± 5.17%

Time-agnostic (no lag)

499

67 traits

0.64 ± 0.09

56.46 ± 7.34%

63.79 ± 9.10%

Prognostic (≤10 years)

499

36 PRS + sex + age

0.54 ± 0.05

52.58 ± 4.32%

53.28 ± 4.42%

Prognostic (≤10 years)

499

67 traits

0.65 ± 0.10

57.87 ± 7.65%

65.20 ± 9.47%

Diagnostic (<10 years)

500

36 PRS + sex + age

0.54 ± 0.06

52.72 ± 4.63%

53.09 ± 4.74%

Diagnostic (<10 years)

500

67 traits

0.67 ± 0.10

58.71 ± 8.56%

65.76 ± 9.49%

Time-agnostic (no lag)

1,299

67 traits

0.65 ± 0.10

57.65 ± 7.82%

63.67 ± 9.26%

Time-agnostic (no lag)

1,299

3k proteins

0.67 ± 0.11

58.29 ± 8.59%

66.38 ± 10.32%

Time-agnostic (no lag)

1,299

3k proteins + 67 traits

0.68 ± 0.11

58.62 ± 8.76%

66.59 ± 10.33%

Prognostic (≤10 years)

864

67 traits

0.65 ± 0.10

58.00 ± 7.67%

63.81 ± 8.85%

Prognostic (≤10 years)

864

3k proteins

0.68 ± 0.10

58.88 ± 8.27%

67.10 ± 10.01%

Prognostic (≤10 years)

864

3k proteins + 67 traits

0.69 ± 0.11

59.20 ± 8.59%

67.36 ± 10.18%

Diagnostic (≤10 years)

435

67 traits

0.66 ± 0.11

58.79 ± 8.89%

64.07 ± 9.46%

Diagnostic (≤10 years)

435

3k proteins

0.70 ± 0.12

60.04 ± 10.22%

69.57 ± 11.38%

Diagnostic (≤10 years)

435

3k proteins + 67 traits

0.71 ± 0.12

60.00 ± 10.22%

70.05 ± 11.49%

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