KEMP-PIP: A Feature-Fusion Based Approach for Pro-inflammatory Peptide Prediction

TL;DR

KEMP-PIP is a hybrid machine learning framework that combines deep protein embeddings with handcrafted features to accurately predict pro-inflammatory peptides, outperforming existing methods on benchmark datasets.

Contribution

This paper introduces KEMP-PIP, a novel feature-fusion approach that integrates deep embeddings and handcrafted descriptors for improved pro-inflammatory peptide prediction.

Findings

Achieved MCC of 0.505, accuracy of 0.752, and AUC of 0.762 on benchmark dataset.

Outperformed existing methods like ProIn-fuse, MultiFeatVotPIP, and StackPIP.

Feature integration consistently improved predictive performance.

Abstract

Pro-inflammatory peptides (PIPs) play critical roles in immune signaling and inflammation but are difficult to identify experimentally due to costly and time-consuming assays. To address this challenge, we present KEMP-PIP, a hybrid machine learning framework that integrates deep protein embeddings with handcrafted descriptors for robust PIP prediction. Our approach combines contextual embeddings from pretrained ESM protein language models with multi-scale k-mer frequencies, physicochemical descriptors, and modlAMP sequence features. Feature pruning and class-weighted logistic regression manage high dimensionality and class imbalance, while ensemble averaging with an optimized decision threshold enhances the sensitivity--specificity balance. Through systematic ablation studies, we demonstrate that integrating complementary feature sets consistently improves predictive performance. On the standard benchmark dataset, KEMP-PIP achieves an MCC of 0.505, accuracy of 0.752, and AUC of 0.762, outperforming ProIn-fuse, MultiFeatVotPIP, and StackPIP. Relative to StackPIP, these results represent improvements of 9.5% in MCC and 4.8% in both accuracy and AUC. The KEMP-PIP web server is freely available at https://nilsparrow1920-kemp-pip.hf.space/ and the full implementation at https://github.com/S18-Niloy/KEMP-PIP.