Imbalanced regression refers to prediction tasks where the target variable is skewed. This skewness hinders machine learning models, especially neural networks, which concentrate on dense regions and therefore perform poorly on underrepresented (minority) samples. Despite the importance of this problem, only a few methods have been proposed for imbalanced regression. Many of the available solutions for imbalanced regression adapt techniques from the class imbalance domain, such as linear interpolation and the addition of Gaussian noise, to create synthetic data in sparse regions. However, in many cases, the underlying distribution of the data is complex and non-linear. Consequently, these approaches generate synthetic samples that do not accurately represent the true feature-target relationship. To overcome these limitations, we propose SMOGAN, a two-step oversampling framework for imbalanced regression. In Stage 1, an existing oversampler generates initial synthetic samples in sparse target regions. In Stage 2, we introduce DistGAN, a distribution-aware GAN that serves as SMOGAN’s filtering layer and refines these samples via adversarial loss augmented with a Maximum Mean Discrepancy objective, aligning them with the true joint feature-target distribution. Extensive experiments on 23 imbalanced datasets show that SMOGAN consistently outperforms the default oversampling method without the DistGAN filtering layer.

Imbalanced regression arises when the target distribution is skewed, causing models, especially neural networks, to focus on dense regions and struggle with underrepresented (minority) samples. Despite its relevance across many applications, few methods have been designed specifically for this challenge. Existing approaches often rely on fixed, ad hoc thresholds to label samples as rare or common, overlooking the continuous complexity of the joint feature-target space and fail to represent the true underlying rare regions. To address these limitations, we propose a fully data-driven GAN-based augmentation framework that uses Mahalanobis-Gaussian Mixture Modeling (GMM) to automatically identify minority samples and employs deterministic nearest-neighbour matching to enrich sparse regions. Rather than preset thresholds, our method lets the data determine which observations are truly rare. Evaluation on 32 benchmark imbalanced regression datasets demonstrates that our approach consistently outperforms state-of-the-art data augmentation methods.

Designing de novo 3D molecules with desirable properties remains a fundamental challenge in drug discovery and molecular engineering. While diffusion models have demonstrated remarkable capabilities in generating high-quality 3D molecular structures, they often struggle to effectively control complex multi-objective constraints critical for real-world applications. In this study, we propose an uncertainty-aware Reinforcement Learning (RL) framework to guide the optimization of 3D molecular diffusion models toward multiple property objectives while enhancing the overall quality of the generated molecules. Our method leverages surrogate models with predictive uncertainty estimation to dynamically shape reward functions, facilitating balance across multiple optimization objectives. We comprehensively evaluate our framework across three benchmark datasets and multiple diffusion model architectures, consistently outperforming baselines for molecular quality and property optimization. Additionally, Molecular Dynamics (MD) simulations and ADMET profiling of top generated candidates indicate promising drug-like behavior and binding stability, comparable to known Epidermal Growth Factor Receptor (EGFR) inhibitors. Our results demonstrate the strong potential of RL-guided generative diffusion models for advancing automated molecular design.

This study addresses the heterogeneity of Breast Cancer (BC) by employing a Conditional Probabilistic Diffusion Model (CPDM) to synthesize Magnetic Resonance Images (MRIs) based on multi-omic data, including gene expression, copy number variation, and DNA methylation. The lack of paired medical images and genomics data in previous studies presented a challenge, which the CPDM aims to overcome. The well-trained CPDM successfully generated synthetic MRIs for 726 TCGA-BRCA patients, who lacked actual MRIs, using their multi-omic profiles. Evaluation metrics such as Frechet's Inception Distance (FID), Mean Square Error (MSE), and Structural Similarity Index Measure (SSIM) demonstrated the CPDM's effectiveness, with an FID of 2.02, an MSE of 0.02, and an SSIM of 0.59 based on the 15-fold cross-validation. The synthetic MRIs were used to predict clinical attributes, achieving an Area Under the Receiver-Operating-Characteristic curve (AUROC) of 0.82 and an Area Under the Precision-Recall Curve (AUPRC) of 0.84 for predicting ER+/HER2+ subtypes. Additionally, the MRIs served to accurately predicted BC patient survival with a Concordance-index (C-index) score of 0.88, outperforming other baseline models. This research demonstrates the potential of CPDMs in generating MRIs based on BC patients' genomic profiles, offering valuable insights for radiogenomic research and advancements in precision medicine. The study provides a novel approach to understanding BC heterogeneity for early detection and personalized treatment.

To meet the world's growing food and nutrition demands, agricultural breeders need to grow crops with improved phenotypes and create varieties that allow increased production. Genomic selection enables the breeders to select individuals with improved phenotypes even before growing them. Existing genomic selection is made mostly through statistical methods that do not accurately predict complex non-linear traits. Deep learning and other machine learning methods have been applied, but most of the deep learning methods are not specifically designed for genomic selection. Also, there has been relatively little comparison between different machine learning methods. We propose three ensemble learning methods: i) ensemble support vector regression; ii) ensemble deep convolutional neural networks and iii) random forests; to predict phenotype with high accuracy. We also propose a feature selection strategy that identifies important markers and contributes to improved phenotype prediction. The proposed marker selection strategy is independent of machine learning methods; thus, the markers that are selected remain the same when the machine learning model is changed. We employed our methods to Iranian wheat landraces. The result shows that ensemble learning methods are better than the single machine learning methods with the lowest PCC 0.339 for plant height and the highest PCC 0.747 for grain length. Our models are also robust as they rank both top twenty and bottom twenty individuals well with nDCG@20 ranges from 0.188 to 0.712.

BACKGROUND: Metabolic networks are represented by the set of metabolic pathways. Metabolic pathways are a series of biochemical reactions, in which the product (output) from one reaction serves as the substrate (input) to another reaction. Many pathways remain incompletely characterized. One of the major challenges of computational biology is to obtain better models of metabolic pathways. Existing models are dependent on the annotation of the genes. This propagates error accumulation when the pathways are predicted by incorrectly annotated genes. Pairwise classification methods are supervised learning methods used to classify new pair of entities. Some of these classification methods, e.g., Pairwise Support Vector Machines (SVMs), use pairwise kernels. Pairwise kernels describe similarity measures between two pairs of entities. Using pairwise kernels to handle sequence data requires long processing times and large storage. Rational kernels are kernels based on weighted finite-state transducers that represent similarity measures between sequences or automata. They have been effectively used in problems that handle large amount of sequence information such as protein essentiality, natural language processing and machine translations. RESULTS: We create a new family of pairwise kernels using weighted finite-state transducers (called Pairwise Rational Kernel (PRK)) to predict metabolic pathways from a variety of biological data. PRKs take advantage of the simpler representations and faster algorithms of transducers. Because raw sequence data can be used, the predictor model avoids the errors introduced by incorrect gene annotations. We then developed several experiments with PRKs and Pairwise SVM to validate our methods using the metabolic network of Saccharomyces cerevisiae. As a result, when PRKs are used, our method executes faster in comparison with other pairwise kernels. Also, when we use PRKs combined with other simple kernels that include evolutionary information, the accuracy values have been improved, while maintaining lower construction and execution times. CONCLUSIONS: The power of using kernels is that almost any sort of data can be represented using kernels. Therefore, completely disparate types of data can be combined to add power to kernel-based machine learning methods. When we compared our proposal using PRKs with other similar kernel, the execution times were decreased, with no compromise of accuracy. We also proved that by combining PRKs with other kernels that include evolutionary information, the accuracy can also also be improved. As our proposal can use any type of sequence data, genes do not need to be properly annotated, avoiding accumulation errors because of incorrect previous annotations.