Fig. 2

The minimal set of features predictive of HAND. Model-specific feature importance was estimated using the varImp function implemented in the caret package for each of the ML algorithms except SVM. Features listed in the top 20 in two or more algorithms were selected. P values were calculated using Welch’s t test and adjusted by the FDR-based method [24]. Adjusted P values of less than 0.05 were considered significant. In this manner, seven genetic features were retained (Additional file 1: Figure 2). Stepwise feature reduction was performed, and the minimal set of features yielding the best-performing stacked classifier was obtained. a Distributions of detected features among HAND and NonHAND groups. The values of each feature were converted to Z-score for visualization purposes. b Scaled AAIndex values and relative residue frequencies in sequence sets derived from HAND and NonHAND cases. The weights of individual sequences are normalized by the respective sequencing depths of individual patients. The alignment position numbers correspond to the positions in the HXB2 HIV-1 sequence (accession: K03455)