Sequence-Based Therapeutic Peptide Classification with Augmented Negative Sampling

Therapeutic peptides offer high target specificity, low toxicity, and the ability to modulate protein-protein interactions, yet experimental functional characterization remains costly and slow. Computational prediction of therapeutic function directly from sequence could accelerate peptide screening and enable generative design pipelines, but requires reliable discrimination between therapeutic and non-therapeutic peptides. Existing multi-label predictors cover few functions, rely on limited datasets, and exhibit high False Positive Rates (FPRs), limiting their practical utility.

We present a lightweight CNN classifier trained on the most comprehensive therapeutic peptide database to date (54,655 peptides, 48 functional categories). A key contribution is a statistically motivated negative sampling strategy using Markov models to generate diverse synthetic decoys at multiple difficulty levels. When evaluated on this controlled decoy benchmark, the FPR is reduced from over 60% for previous models to 2.1% for our approach. On positive therapeutic samples, our fine-tuned five-model ensemble achieves 79.9% Micro F1 and 54.6% Macro F1 while requiring only amino acid sequences as inputs.

Analysis using a sparse L1-constrained variant of our model shows that convolutional filters capture conserved functional motifs and statistically improbable non-therapeutic patterns, with downstream layers combining these signals, providing mechanistic evidence that the network learns biologically meaningful structure. On an external generalization benchmark derived from TPpred-LE, our model achieves 55.3% Micro F1 and 38.6% Macro F1 on the 12 shared labels, close to the benchmark-specific baseline (57.9%/38.1%), while retaining substantially broader therapeutic label coverage. Code and models will be made available at https://github.com/terra-quantum-public/tq-therapep-ai .