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Journal : Kinetik: Game Technology, Information System, Computer Network, Computing, Electronics, and Control

XGBoost and Network Analysis for Prediction of Proteins Affecting Insulin based on Protein Protein Interactions Mohammad Hamim Zajuli Al Faroby; Mohammad Isa Irawan; Ni Nyoman Tri Puspaningsih
Kinetik: Game Technology, Information System, Computer Network, Computing, Electronics, and Control Vol. 5, No. 4, November 2020
Publisher : Universitas Muhammadiyah Malang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22219/kinetik.v5i4.1076

Abstract

Protein Interaction Analysis (PPI) can be used to identify proteins that have a supporting function on the main protein, especially in the synthesis process. Insulin is synthesized by proteins that have the same molecular function covering different but mutually supportive roles. To identify this function, the translation of Gene Ontology (GO) gives certain characteristics to each protein. This study purpose to predict proteins that interact with insulin using the centrality method as a feature extractor and extreme gradient boosting as a classification algorithm. Characteristics using the centralized method produces  features as a central function of protein. Classification results are measured using measurements, precision, recall and ROC scores. Optimizing the model by finding the right parameters produces an accuracy of  and a ROC score of . The prediction model produced by XGBoost has capabilities above the average of other machine learning methods.
XGB-Hybrid Fingerprint Classification Model for Virtual Screening of Meningitis Drug Compounds Candidate Mohammad Hamim Zajuli Al Faroby; Helisyah Nur Fadhilah; Siti Amiroch; Rahmat Sigit Hidayat
Kinetik: Game Technology, Information System, Computer Network, Computing, Electronics, and Control Vol. 7, No. 2, May 2022
Publisher : Universitas Muhammadiyah Malang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22219/kinetik.v7i2.1424

Abstract

Meningitis is an infection of the lining of the brain caused by diffuse inflammation, and this condition is caused by viruses or bacteria that cause Meningitis. Prevention for this disease is still in the form of strengthening antibodies with vaccines. There is no significant compound to relieve or treat Meningitis patients. In previous studies, they got seven proteins vital to Meningitis. We continued to investigate the compounds associated with the seven proteins. We chose the in-silico process by utilizing data in an open database. We use several databases for the data collection process. After that, the compound data were extracted for bonding features and chemical elements using molecular fingerprints. We use two fingerprint methods, where both we combine with three types of combinations. The combined results produce three types of datasets with different matrix sizes. We establish the Extreme Gradient Boosting (XGB) method to form the classification model for the three datasets, select the best classification model, and compare it with other classification algorithms. The XGB model has better quality than the classification model of other algorithms. We used this model to predict and quantify compounds that strongly bind to seven vital meningitis proteins. The compound with the highest predictive score (we found more than 0.99) became a drug candidate to inhibit or neutralize Meningitis.