Research and Reviews : Journal of Computational Biology
Volume 15, Issue 2 (2026)
Table of contents
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Genomic Selection for Grain Yield in Wheat Using Machine Learning on DArT Molecular Markers: A Comparative Evaluation Across Multi-Environment Trials
Abstract: Genomic selection (GS) predicts complex quantitative traits directly from genome-wide molecular markers, bypassing the need for extensive phenotypic trials and accelerating plant breeding cycles. We conducted a comparative evaluation of seven regression approaches — ridge regression (the machine-learning equivalent of RR-BLUP), Lasso, Elastic Net, Partial Least Squares, linear Support Vector Regression, Random Forest, and Gradient Boosting — for predicting grain yield from 1,279 Diversity Array Technology (DArT) molecular markers genotyped …
Published in Research and Reviews : Journal of Computational Biology · Vol. 15, Issue 2, 2026 Read article
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A Factorial Investigation of Hyperparameter Tuning Strategies for Lasso- Based Genomic Prediction
Abstract: In an earlier comparative study of machine-learning methods for genomic prediction of wheat grain yield, we reported a counter-intuitive result: automated nested-cross-validation tuning of the Lasso regularization penalty reduced mean predictive ability relative to a fixed, arbitrarily chosen penalty (mean Pearson r falling from 0.408 to 0.349 across four environments), the opposite of the expected effect of hyperparameter tuning. We hypothesized two possible explanations at the time — high-variance penalty …
Published in Research and Reviews : Journal of Computational Biology · Vol. 15, Issue 2, 2026 Read article
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A Smart Framework that Combines Data Mining and Optimization for Different Applications
Abstract: Blending predictive data mining with metaheuristic optimization has become essential for tackling tough, real-world problems across all kinds of fields. Most existing methods stick to fixed algorithms, each focused on a tiny slice of the puzzle, barely budging when new variables or unpredictability show up—especially with messy, human-generated data. So, here’s the idea: a Unified Metaheuristic and Predictive Data Mining (UMPDM) framework that finally connects adaptive search methods with powerful …
Published in Research and Reviews : Journal of Computational Biology · Vol. 15, Issue 2, 2026 Read article
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Neuro-Symbolic Agentic AI for Autonomous Scientific Discovery: Integrating Deep Reinforcement Learning, Quantum Simulation, and XAI-Audited LLM Hypothesis Generation in Drug Target Identification
Abstract: The exponential growth of multi-omics data and the increasing complexity of disease-associated protein interactomes have rendered conventional drug target identification pipelines computationally and epistemologically inadequate. This paper presents the Neuro-Symbolic Agentic AI for Scientific Discovery (NS-AASD) framework, a unified architecture that cohesively integrates deep reinforcement learning (DRL) exploration strategies, variational quantum simulation (VQS) of protein conformational dynamics, and XAI-audited large language model (LLM) hypothesis generation within an autonomous scientific discovery …
Published in Research and Reviews : Journal of Computational Biology · Vol. 15, Issue 2, 2026 Read article