Fig. 6: Clinical Transformer and TME on SKCM data. | Nature Communications

Fig. 6: Clinical Transformer and TME on SKCM data.

From: Pretrained transformers applied to clinical studies improve predictions of treatment efficacy and associated biomarkers

Fig. 6

a Survival stratification of SKCM patients from TCGA. Patients are grouped into quartiles from the Clinical Transformer survival score. The solid line represents the mean survival time across the 10 testing splits. Shaded regions represent the 95% confidence interval. b UMAP projection of patient embeddings in the TCGA SKCM dataset. c Effect of T-cell perturbations (variant and invariant populations) in TCGA SKCM dataset exclusive to patients in the Q1 and Q2 populations. The size and direction of the arrows reflect the effect and directionality, respectively, of the perturbation. d Distribution of TME signatures for the variant (n = 115) and invariant (n = 115) populations as an effect of T-cell perturbations. Bonferroni-corrected two-sided t test P value: ns, 5.00e-02 < P ≤ 1.00e + 00; *, 1.00e-02 < P ≤ 5.00e-02; **, 1.00e-03 < P ≤ 1.00e-02; ***, 1.00e-04 < P ≤ 1.00e-03; ****, P ≤ 1.00e-04). Boxplots: centerline, median; box limits, quartile 1 and 3; box whiskers, 1.5x interquartile range; diamonds, outliers; dots, data points. VAR, variant population; INV, invariant population. e CoxPH HR (error bars: 95% CI) of top gene signatures associated with response and resistance in TCGA and IO-treated populations. N for each comparison can be found in Supplementary Table 6. Source data are provided in the SourceData file.

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