Model Prediksi Interaksi Senyawa dan Protein untuk Drug Repositioning menggunakan Deep Semi-Supervised Learning

Penulis

Larasati Larasati, Wisnu Ananta Kusuma, Annisa Annisa

Abstrak

Drug repositioning adalah penggunaan senyawa obat yang sudah lolos uji sebelumnya untuk mengatasi penyakit baru selain penyakit awal obat tersebut ditujukan. Drug repositioning dapat dilakukan dengan memprediksi interaksi senyawa obat dengan protein penyakit yang bereaksi positif. Salah satu tantangan dalam prediksi interaksi senyawa dan protein adalah masalah ketidakseimbangan data. Deep semi-supervised learning dapat menjadi alternatif untuk menangani model prediksi dengan data yang tidak seimbang. Proses pre-training berbasis unsupervised learning pada deep semi-supervised learning dapat merepresentasikan input dari unlabeled data (data mayoritas) dengan baik dan mengoptimasi inisialisasi bobot pada classifier. Penelitian ini mengimplementasikan Deep Belief Network (DBN) sebagai pre-training dan Deep Neural Network (DNN) sebagai classifier. Data yang digunakan pada penelitian ini adalah dataset ion channel, GPCR, dan nuclear receptor yang bersumber dari pangkalan data KEGG BRITE, BRENDA, SuperTarget, dan DrugBank. Hasil penelitian ini menunjukkan pada dataset tersebut, pre-training berupa ekstraksi fitur memberikan efek optimasi dilihat dari peningkatan performa model DNN pada akurasi (3-4.5%), AUC (4.5%), precision (5.9-6%), dan F-measure (3.8%).

 

Abstract

Drug repositioning is the reuse of an existing drug to treat a new disease other than its original medical indication. Drug repositioning can be done by predicting the interaction of drug compounds with disease proteins that react positively. One of the challenges in predicting the interaction of compounds and proteins is imbalanced data. Deep semi-supervised learning can be an alternative to handle prediction models with imbalanced data. The unsupervised learning based pre-training process in deep semi-supervised learning can represent input from unlabeled data (majority data) properly and optimize initialization of weights on the classifier. This study implements the Deep Belief Network (DBN) as a pre-training with Deep Neural Network (DNN) as a classifier. The data used in this study are ion channel, GPCR, and nuclear receptor dataset sourced from KEGG BRITE, BRENDA, SuperTarget, and DrugBank databases. The results of this study indicate that pre-training as feature extraction had an optimization effect. This can be seen from DNN performance improvement in accuracy (3-4.5%), AUC (4.5%), precision (5.9-6%), and F-measure (3.8%).


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Referensi


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DOI: http://dx.doi.org/10.25126/jtiik.2020742236