MLSEL: A tuned multilayer stacking ensemble learning with meta feature for flood risk prediction

Main Article Content

Rini Sovia
Yuda Irawan
Irzal Arief Wisky
Muhammad Habib Yuhandri
Randy Permana

Abstract

While stacking ensemble methods have been widely adopted for disaster risk classification, most traditional implementations are limited to shallow single-layer architectures, lacking generalization capacity and adaptive meta-feature design. This study proposes Multilayer Stacking Ensemble Learning (MLSEL), a novel approach that addresses these limitations through three key innovations: (i) a deep three-layer stacking architecture, (ii) Meta Feature Augmentation (MFA) to enrich inter-layer representations, and (iii) automated hyperparameter optimization using Optuna to enhance meta-learner performance. The model is evaluated on a multiclass flood risk dataset consisting of 50,000 structured records. Results reveal that the proposed MLSEL particularly the configuration using XGBoost + Optuna + MFA achieves superior accuracy of 98.69%, significantly outperforming both the best-performing baseline and conventional stacking models. This research demonstrates that combining deep-layered learning, meta-feature engineering, and adaptive optimization effectively overcomes overfitting, feature redundancy, and scalability issues inherent in traditional stacking. The MLSEL framework establishes a robust foundation for accurate and reliable disaster risk prediction systems.

Article Details

How to Cite
Sovia, R., Irawan, Y., Wisky, I. A., Yuhandri, M. H., & Permana, R. (2026). MLSEL: A tuned multilayer stacking ensemble learning with meta feature for flood risk prediction. Engineering and Applied Science Research, 53(2), 211–222. https://doi.org/10.64960/easr.2026.263071
Section
ORIGINAL RESEARCH

References

Zhai S, Bartkowiak N, Sibirtsev S, Jupke A. Experimental determination and model-based prediction of flooding points in a pilot-scale continuous liquid-liquid gravity separator. Sep Purif Technol. 2025;377:134177. DOI: https://doi.org/10.1016/j.seppur.2025.134177

Bian W, Fang J, Wang P, Sun Q, Fang J. Deep learning surrogate models for spatiotemporal prediction of coastal flooding inundations in Tianjin , China. J Hydrol: Reg Stud. 2025;60:102593. DOI: https://doi.org/10.1016/j.ejrh.2025.102593

Alam MG, Tripathi V, Bhatt CM, Mohanty MP. A novel framework embedding Bayesian-optimized ensemble machine learning and explainable artificial intelligence (XAI) to improve flood prediction in complex watersheds. Environ Sustain Indic. 2025;27:100760. DOI: https://doi.org/10.1016/j.indic.2025.100760

Jang SD, Yoo JH, Lee YS, Kim B. Flood prediction in urban areas based on machine learning considering the statistical characteristics of rainfall. Prog Disaster Sci. 2025;26:100415. DOI: https://doi.org/10.1016/j.pdisas.2025.100415

Antwi-Agyakwa KT, Afenyo MK, Angnuureng DB. Know to predict, forecast to warn: a review of flood risk prediction tools. Water. 2023;15(3):427. DOI: https://doi.org/10.3390/w15030427

Tian J, Yan Y, Zeng S. Intelligent identification and management of flood risk areas in high-density blocks from the perspective of flood regulation supply and demand matching. Ecol Indic. 2024;160:111799. DOI: https://doi.org/10.1016/j.ecolind.2024.111799

Wang X, Liu R, Sun C, Zhai X, Ding L, Liu X, et al. Optimizing flood resilience in China’s mountainous areas: design flood estimation using advanced machine learning techniques. J Hydrol: Reg Stud. 2025;59:102345. DOI: https://doi.org/10.1016/j.ejrh.2025.102345

Tanhapour M, Soltani J, Shakibian H, Malekmohammadi B, Hlavcova K, Kohnova S, et al. The enhanced integration of proven techniques to quantify the uncertainty of forecasting extreme flood events based on numerical weather prediction models. Weather Clim Extrem. 2025;48:100767. DOI: https://doi.org/10.1016/j.wace.2025.100767

Joubier V, Ebtehaj I, Amiri A, Gumiere SJ, Bonakdari H. Multitemporal river flow discharge prediction: a new framework for integrated environmental management and flood control. J Environ Manage. 2025;383:125372. DOI: https://doi.org/10.1016/j.jenvman.2025.125372

Islam MT, Roy SC, Jahan N, Al-Mahmud, Islam MM, Ferdaus AA, et al. Comparative evaluation of machine learning models for extreme river water level forecasting in Bangladesh: Implications for flood and drought resilience. Prog Disaster Sci. 2025;27:100449. DOI: https://doi.org/10.1016/j.pdisas.2025.100449

Nazli S, Liu J, Song T, Soomro S, Wang H. A hybrid machine learning approach to unravel monsoon variability and meteorological dynamics of Pakistan’s 2010 and 2022 historic floods. J Hydrol: Reg Stud. 2025;60:102505. DOI: https://doi.org/10.1016/j.ejrh.2025.102505

Asfaw W, Rientjes T, Bekele TW, Haile AT. Estimating elements susceptible to urban flooding using multisource data and machine learning. Int J Disaster Risk Reduct. 2025;116:105169. DOI: https://doi.org/10.1016/j.ijdrr.2024.105169

Lubis A, Irawan Y, Junadhi J, Defit S. Leveraging K-Nearest neighbors with SMOTE and Boosting techniques for data imbalance and accuracy improvement. J Appl Data Sci. 2024;5(4):1625-38. DOI: https://doi.org/10.47738/jads.v5i4.343

Yang PB, Chan YJ, Yazdi SK, Lim JW. Optimisation and economic analysis of industrial-scale anaerobic co-digestion (ACoD) of palm oil mill effluent (POME) and decanter cake (DC) using machine learning models: a comparative study of Gradient Boosting Machines (GBM), K-nearest neighbours (KNN). J Water Process Eng. 2024;58:104752. DOI: https://doi.org/10.1016/j.jwpe.2023.104752

Yousefi M, Oskoei V, Esmaeli HR, Baziar M. An innovative combination of extra trees within adaboost for accurate prediction of agricultural water quality indices. Results Eng. 2024;24:103534. DOI: https://doi.org/10.1016/j.rineng.2024.103534

Wei X, Xu Y, Li X, Fan G, Cheng X, Yu T, et al. Study on prediction model of nitrogen oxide concentration in reprocessing plant based on random forest. Int J Adv Nucl React Des Technol. 2025;7:63-9. DOI: https://doi.org/10.1016/j.jandt.2025.04.011

Farooq O, Shahid M, Arshad S, Altaf A, Iqbal F, Vera YAM, et al. An enhanced approach for predicting air pollution using quantum support vector machine. Sci Rep. 2024;14:19521 DOI: https://doi.org/10.1038/s41598-024-69663-2

Zheng H, Sherazi SWA, Lee JY. A stacking ensemble prediction model for the occurrences of major adverse cardiovascular events in patients with acute coronary syndrome on imbalanced data. IEEE Access. 2021;9:113692-704. DOI: https://doi.org/10.1109/ACCESS.2021.3099795

Lin S, Nong X, Luo J, Wang C. A novel multi-model stacking ensemble learning method for metro traction energy prediction. IEEE Access. 2022;10:129231-44. DOI: https://doi.org/10.1109/ACCESS.2022.3228441

Song D, Yi T, Xiang Q, Chen H. Leveraging ISMOTE-KPCA-STACKING Algorithm for enhanced vascular vertigo / dizziness diagnosis and clinical decision support. IEEE Access. 2023;11:99734-51. DOI: https://doi.org/10.1109/ACCESS.2023.3313506

Garouani M, Barhrhouj A, Teste O. XStacking : an effective and inherently explainable framework for stacked ensemble learning. Inf Fusion. 2025;124:103358. DOI: https://doi.org/10.1016/j.inffus.2025.103358

Mostofi S, Yilmaz Z, Başağa HB, Okur FY, Altunişik AC, Taciroglu E. A hybrid stacked ensemble model for rapid seismic damage assessment with imbalanced training data: a case study on the 2023 Kahramanmaraş earthquakes. Eng Struct. 2025;340:120754. DOI: https://doi.org/10.1016/j.engstruct.2025.120754

Chen X, Liu J, Wu C. Multi-class financial distress prediction based on hybrid feature selection and improved stacking ensemble model. Expert Syst Appl. 2025;282:127832. DOI: https://doi.org/10.1016/j.eswa.2025.127832

Shafieian S, Zulkernine M. Multi-layer stacking ensemble learners for low footprint network intrusion detection. Complex Intell Syst. 2023;9:3787-99. DOI: https://doi.org/10.1007/s40747-022-00809-3

Li M, Chen L. An interpretable and stacking ensemble model for predicting heat and mass transfer of desiccant wheel. Results Eng. 2025;25:104181. DOI: https://doi.org/10.1016/j.rineng.2025.104181

Naveen Venkatesh S, Sripada D, Sugumarna V, Aghaei M. Detection of visual faults in photovoltaic modules using a stacking ensemble approach. Heliyon. 2024;10(6):e27894. DOI: https://doi.org/10.1016/j.heliyon.2024.e27894

Shishodia V, Singh V, Thampi SG. Implementation of stack-based ensemble technique for classification of glaciers in the western Himalayan catchments. Phys Chem Earth, Parts A/B/C. 2024;136:103723. DOI: https://doi.org/10.1016/j.pce.2024.103723

Li Y, Li K, Wang K, Li G, Wang Z. An improved stacking model for forest fire susceptibility prediction in Chongqing City, China. 2023 IEEE Smart World Congress (SWC); 2023 Aug 28-31; Portsmouth, United Kingdom. USA: IEEE; 2023. p. 1-6. DOI: https://doi.org/10.1109/SWC57546.2023.10449165

Hoc HT, Silhavy R, Prokopova Z, Silhavy P. Comparing stacking ensemble and deep learning for software project effort estimation. IEEE Access. 2023;11:60590-604. DOI: https://doi.org/10.1109/ACCESS.2023.3286372

Mota LFM, Giannuzzi D, Bisutti V, Pegolo S, Trevisi E, Schiavon S, et al. Real-time milk analysis integrated with stacking ensemble learning as a tool for the daily prediction of cheese-making traits in Holstein cattle. J Dairy Sci. 2022;105(5):4237-55. DOI: https://doi.org/10.3168/jds.2021-21426

Herianto, Kurniawan B, Hartomi ZH, Irawan Y, Anam MK. Machine learning algorithm optimization using stacking technique for graduation prediction. J Appl Data Sci. 2024;5(3):1272-85. DOI: https://doi.org/10.47738/jads.v5i3.316

Cawood P, van Zyl TL. Feature-weighted stacking for nonseasonal time series forecasts: a case study of the COVID-19 epidemic curves. 2021 8th International Conference on Soft Computing & Machine Intelligence (ISCMI); 2021 Nov 26-27; Cario, Egypt. USA: IEEE; 2021. p. 53-9. DOI: https://doi.org/10.1109/ISCMI53840.2021.9654809

Devis Y, Muhamadiah, Yulanda, Irawan Y, Wahyuni R. Optimization of machine learning models for risk prediction of DHF spread to support management strategies in urban areas. J Appl Data Sci. 2025;6(4):2407-20. DOI: https://doi.org/10.47738/jads.v6i4.898

Muhaimin A, Edriyansyah, Wahyat, Irawan Y, Wahyuni R. Optimized IoT-based multimodal fusion for early forest fire detection and prediction. ECTI Trans Comput Inf Technol. 2025;19(4):569-82. DOI: https://doi.org/10.37936/ecti-cit.2025194.262839

Fonda H, Irawan Y, Melyanti R, Wahyuni R, Muhaimin A. A comprehensive stacking ensemble approach for stress level classification in higher education. J Appl Data Sci. 2024;5(4):1701-14. DOI: https://doi.org/10.47738/jads.v5i4.388

Alalwany E, Alsharif B, Alotaibi Y, Alfahaid A, Mahgoub I, Ilyas M. Stacking ensemble deep learning for real-time intrusion detection in IoMT environments. Sensors. 2025;25(3):624. DOI: https://doi.org/10.3390/s25030624

Gu J, Liu S, Zhou Z, Chalov SR, Zhuang Q. A stacking ensemble learning model for monthly rainfall prediction in the Taihu Basin, China. Water. 2022;14(3):492. DOI: https://doi.org/10.3390/w14030492

Hassanali M, Soltanaghaei M, Javdani Gandomani T, Zamani Boroujeni F. Exploring stacking methods for software effort estimation with hyperparameter tuning. Cluster Comput. 2025;28:241. DOI: https://doi.org/10.1007/s10586-024-04876-8

Alqahtani AF, Ilyas M. An ensemble-based multi-classification machine learning classifiers approach to detect multiple classes of cyberbullying. Mach Learn Knowl Extr. 2024;6(1):156-70. DOI: https://doi.org/10.3390/make6010009

Megouo TGP, Pierre S. A stacking ensemble machine learning model for emergency call forecasting. IEEE Access. 2024;12:115820-37. DOI: https://doi.org/10.1109/ACCESS.2024.3445591

Öz E, Bulut O, Cellat ZF, Yürekli H. Stacking: an ensemble learning approach to predict student performance in PISA 2022. Educ Inf Technol. 2025;30:7753-79. DOI: https://doi.org/10.1007/s10639-024-13110-2

Kalabarige LR, Rao RS, Pais AR, Gabralla LA. A boosting-based hybrid feature selection and multi-layer stacked ensemble learning model to detect phishing websites. IEEE Access. 2023;11:71180-93. DOI: https://doi.org/10.1109/ACCESS.2023.3293649

Abbas S, Sampedro GA, Abisado M, Almadhor AS, Kim TH, Zaidi MM. A novel drug-drug indicator dataset and ensemble stacking model for detection and classification of drug-drug interaction indicators. IEEE Access. 2023;11:101525-36. DOI: https://doi.org/10.1109/ACCESS.2023.3315241

Khosravi Y, Ouarda TBMJ, Homayouni S. Developing an ensemble machine learning framework for enhanced climate projections using CMIP6 data in the Middle East. Npj Clim Atmos Sci. 2025;8:174. DOI: https://doi.org/10.1038/s41612-025-01033-9