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All Journal FORUM STATISTIKA DAN KOMPUTASI Media Statistika Statistika JURNAL MATEMATIKA STATISTIKA DAN KOMPUTASI IPTEK The Journal for Technology and Science CAUCHY: Jurnal Matematika Murni dan Aplikasi Sosioinforma International Journal of Advances in Intelligent Informatics Scientific Journal of Informatics JOIN (Jurnal Online Informatika) Jurnal RESTI (Rekayasa Sistem dan Teknologi Informasi) Jurnal Penelitian Pertanian Tanaman Pangan BAREKENG: Jurnal Ilmu Matematika dan Terapan JOURNAL OF APPLIED INFORMATICS AND COMPUTING SINTECH (Science and Information Technology) Journal MIND (Multimedia Artificial Intelligent Networking Database) Journal Jurnal Aplikasi Statistika & Komputasi Statistik FIBONACCI: Jurnal Pendidikan Matematika dan Matematika Inferensi International Journal of Advances in Data and Information Systems InPrime: Indonesian Journal Of Pure And Applied Mathematics Majalah Ilmiah Matematika dan Statistika (MIMS) Jurnal Lebesgue : Jurnal Ilmiah Pendidikan Matematika, Matematika dan Statistika Enthusiastic : International Journal of Applied Statistics and Data Science Prosiding Seminar Nasional Official Statistics Jurnal Natural Eduvest - Journal of Universal Studies Xplore: Journal of Statistics PROCEEDINGS OF THE INTERNATIONAL CONFERENCE ON DATA SCIENCE AND OFFICIAL STATISTICS Parameter: Jurnal Matematika, Statistika dan Terapannya Scientific Journal of Informatics Journal of Mathematics, Computation and Statistics (JMATHCOS) Advance Sustainable Science, Engineering and Technology (ASSET) Indonesian Journal of Statistics and Its Applications Journal on Mathematics Education
Kusman Sadik
Departemen Statistika, IPB University
Aerospace Engineering Agriculture, Biological Sciences & Forestry Humanities Astronomy Biochemistry, Genetics & Molecular Biology Chemistry Computer Science & IT Control & Systems Engineering Decision Sciences, Operations Research & Management Earth & Planetary Sciences Economics, Econometrics & Finance Education Electrical & Electronics Engineering Energy Engineering Health Professions Immunology & microbiology Industrial & Manufacturing Engineering Mathematics Mechanical Engineering Neuroscience Physics Social Sciences Transportation Other

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Journal : JOURNAL OF APPLIED INFORMATICS AND COMPUTING

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The Impact of the L1/L2 Ratio on Selection Stability and Solution Sparsity along the Elastic Net Regularization Path in High-Dimensional Genomic Data Fahira, Fani; Sadik, Kusman; Suhaeni, Cici; M Soleh, Agus
Journal of Applied Informatics and Computing Vol. 10 No. 1 (2026): February 2026
Publisher : Politeknik Negeri Batam

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.30871/jaic.v10i1.12059

Abstract

High-dimensional genomic datasets (p>n) pose persistent challenges for predictive modeling and biomarker-oriented feature selection due to multicollinearity and instability of selected feature sets under resampling. Although Elastic Net is widely used to address correlated predictors via combined L1/L2 regularization, the practical role of the L1/L2 mixing ratio (α) is often treated as a secondary tuning choice driven primarily by predictive accuracy. This study investigates how varying α shapes the trade-off among selection stability, solution sparsity, and predictive performance along the Elastic Net regularization path. Experiments were conducted using the publicly available METABRIC breast cancer cohort (n = 1,964) with 21,113 gene expression features and a binary overall survival status outcome. Logistic regression with Elastic Net penalty was fitted across a grid of α values, with the regularization strength (λ) selected by cross-validation. Feature selection stability was evaluated under repeated resampling using the Jaccard index, Dice coefficient, and Adjusted Rand Index (ARI), while sparsity was summarized by the average number of non-zero coefficients; predictive performance was assessed using AUC, accuracy, and F1-score. Results show a monotonic decline in stability as α increases: α = 0.2 yields the highest stability (Jaccard 0.324, Dice 0.487, ARI 0.434), whereas LASSO (α = 1.0) produces the lowest stability (Jaccard 0.278, Dice 0.431, ARI 0.400). In contrast, predictive performance varies only marginally across α (AUC 0.696–0.704; accuracy 0.666–0.671; F1-score 0.738–0.742), while sparsity changes substantially (average selected features 110–204). Coefficient path analyses further illustrate abrupt shrinkage under LASSO versus smoother, group-preserving shrinkage under Elastic Net, consistent with improved reproducibility under lower-to-moderate α. Frequency-of-selection analysis highlights genes repeatedly selected across resampling, supporting interpretability of stable configurations without claiming causal biomarker validity. Overall, the findings demonstrate that α is a substantive modeling choice that materially affects stability and sparsity even when accuracy is similar, motivating stability-aware tuning for high-dimensional genomic prediction and reproducible feature discovery.
Co-Authors . Erfiani . Indahwati A.Tuti Rumiati Aam Alamudi Abdullah, Adib Roisilmi Achmad Fauzan Agus Mohamad Soleh Ahmad Rifai Nasution Aji Hamim Wigena Akbar Rizki Akbar Rizki Akbar Rizki Akmala Firdausi Amalia, Rahmatin Nur Anadra, Rahmi Ananda Shafira Anang Kurnia Andespa, Reyuli Andi Okta Fengki ASEP SAEFUDDIN Astari, Reka Agustia Astari, Reka Agustia Aulya Permatasari Azka Ubaidillah Bagus Sartono Budi Susetyo Cici Suhaeni Cici Suhaeni Dito, Gerry Alfa Dwi Agustin Nuriani Sirodj Efriwati Efriwati Embay Rohaeti Eminita, Viarti EVITA PURNANINGRUM Fahira, Fani FARDILLA RAHMAWATI Farit Mochamad Afendi Fitrianto, Anwar Haikal, Husnul Aris Hari Wijayanto Hasnataeni, Yunia Hazan Azhari Zainuddin Hermawati, Neni I Gusti Ngurah, Sentana Putra I Made Sumertajaya I Wayan Mangku Indahwati Indahwati Indahwati Intan Arassah, Fradha Iqbal, Teuku Achmad Isnanda, Eriski Khairi A N Khairil Anwar Notodiputro Khikmah, Khusnia Nurul Khusnul Khotimah Kusni Rohani Rumahorbo Latifah, Leli Lili Puspita Rahayu Logananta Puja Kusuma M Soleh, Agus Mochamad Ridwan Mochamad Ridwan, Mochamad Mohammad Masjkur Muh Nur Fiqri Adham Muhammad Yusran Mulianto Raharjo Naima Rakhsyanda Nisrina Az-Zahra, Putri Nur Khamidah NURADILLA, SITI Nusar Hajarisman Pangestika, Dhita Elsha Parwati Sofan, Parwati Purnama Sari Rifqi Aulya Rahman Rizki, Akbar Rizqi, Tasya Anisah ROCHYATI ROCHYATI Sahamony, Nur Fitriyani Saleh, Agus Muhammad Satriyo Wibowo Siregar, Jodi jhouranda Siti Raudlah Sitti Nurhaliza Soleh, Agus M Suhaeni, Cici Supriatin, Febriyani Eka Tendi Ferdian Diputra Titin Suhartini Titin Suhartini, Titin Tri Wahyuni Uswatun Hasanah Utami Dyah Syafitri Viarti Eminita Widhiyanti Nugraheni Yenni Angraini Yenni Kurniawati Yuli Eka Putri