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Table 2 The ARG antibiotic classes’ classification results between different methods

From: HMD-ARG: hierarchical multi-task deep learning for annotating antibiotic resistance genes

  Accuracy Precisiona Recall F1-score
HMD-ARG 0.935 0.950 0.847 0.893
CARD 0.418 0.983 0.452 0.585
DeepARG 0.887 0.914 0.757 0.814
AMRPlusPlusb 0.675 0.574 0.278 0.283
Meta-MARCc 0.909 0.750 0.782 0.745
  1. aThe precision, recall, and F1-score are the macro average over the ARG antibiotic classes
  2. bAMR++ requires the input in a paired fastq format. So, we simulated the fastq data from our test protein dataset. Details can be seen in the supplementary
  3. cThe drug class label system of AMR++ and Meta-MARC are different from ours, so we manually converted their labels into ours. Meta-MARC can work with both assembly and raw data; we tested it with the assembled sequences (our test dataset)