N4-methylcytosine as one kind of modification of DNA has a critical role which alters genetic performance such as protein interactions, conformation, stability in DNA as well as the regulation of gene expression same cell developmental and genomic imprinting. Some different 4mC site identifiers have been proposed for various species. Herein, we proposed a computational model, DNC4mC-Deep, including six encoding techniques plus a deep learning model to predict 4mC sites in the genome of F. vesca, R. chinensis, and Cross-species dataset. It was demonstrated by the 10-fold cross-validation test to get superior performance. The DNC4mC-Deep obtained 0.829 and 0.929 of MCC on F. vesca and R. chinensis training dataset, respectively, and 0.814 on cross-species. This means the proposed method outperforms the state-of-the-art predictors at least 0.284 and 0.265 on F. vesca and R. chinensis training dataset in turn. Furthermore, the DNC4mC-Deep achieved 0.635 and 0.565 of MCC on F. vesca and R. chinensis independent dataset, respectively, and 0.562 on cross-species which shows it can achieve the best performance to predict 4mC sites as compared to the state-of-the-art predictor.

One of the most common and well studied post-transcription modifications in RNAs is N6-methyladenosine (m6A) which has been involved with a wide range of biological processes. Over the past decades, N6-methyladenosine produced some positive consequences through the high-throughput laboratory techniques but still, these lab processes are time consuming and costly. Diverse computational methods have been proposed to identify m6A sites accurately. In this paper, we proposed a computational model named iMethyl-deep to identify m6A Saccharomyces Cerevisiae on two benchmark datasets M6A2614 and M6A6540 by using single nucleotide resolution to convert RNA sequence into a high quality feature representation. The iMethyl-deep obtained 89.19% and 87.44% of accuracy on M6A2614 and M6A6540 respectively which show that our proposed method outperforms the state-of-the-art predictors, at least 8.44%, 8.96%, 8.69% and 0.173 on M6A2614 and 15.47%, 28.52%, 25.54 and 0.5 on M6A6540 higher in terms of four metrics Sp, Sn, ACC and MCC respectively. Meanwhile, M6A6540 dataset never used to train a model.

The energies of the Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) are important determinants of molecular reactivity and stability. Traditional quantum chemical (QC) methods for calculating the HOMO and LUMO energies face drawbacks, including their costliness and long computational time. Therefore, machine learning is well-positioned to act as a catalyst for QC predictions. In this study, we report a stacking ensemble model named HLP-Stack (HOMO–LUMO predictor via stacking) to predict the energy values using molecular descriptors and the QM9 dataset. The stacking achieved robust predictive performance superior to any single model by combining 2D/3D descriptors of the QM9 dataset. It achieved high predictive performance on the test set (R² ≈ 9.999 × 10⁻¹, RMSE ≈ 3.219 × 10⁻⁴ Hartree (E_h) for HOMO; R² ≈ 9.999 × 10⁻¹, RMSE ≈ 1.903 × 10⁻⁴ E_h for LUMO), outperforming individual baseline models. Feature selection using the SelectKBest algorithm with mutual information regression identified the most influential descriptors. To ensure these descriptors did not trivially encode HOMO or LUMO energies, we performed correlation analysis between each descriptor and the target properties. SHAP Tree Explainer analysis further revealed the feature contribution of each feature to model predictions. In addition, analysis of molecular topology and functional groups highlighted trends in aromaticity and ring structures, and their impact on electronic behavior. Finally, HOMO–LUMO gap analysis demonstrated how molecular structure and functionalization affect electronic properties.