Given the increasing complexity of omics datasets, a key challenge is not only improving classification performance but also enhancing the transparency and reliability of model decisions. Effective model performance and feature selection are fundamental for explainability and reliability. In many cases, high dimensional omics datasets suffer from limited number of samples due to clinical constraints, patient conditions, phenotypes rarity and others conditions. Current omics based classification models often suffer from narrow interpretability, making it difficult to discern meaningful insights where trust and reproducibility are critical. This study presents a machine learning based classification framework that integrates feature selection with data augmentation techniques to achieve high standard classification accuracy while ensuring better interpretability. Using the publicly available dataset (E MTAB 8026), we explore a bootstrap analysis in six binary classification scenarios to evaluate the proposed model's behaviour. We show that the proposed pipeline yields cross validated perfomance on small dataset that is conserved when the trained classifier is applied to a larger test set. Our findings emphasize the fundamental balance between accuracy and feature selection, highlighting the positive effect of introducing synthetic data for better generalization, even in scenarios with very limited samples availability.

This study proposes a novel artificial protozoa optimizer (APO) that is inspired by protozoa in nature. The APO mimics the survival mechanisms of protozoa by simulating their foraging, dormancy, and reproductive behaviors. The APO was mathematically modeled and implemented to perform the optimization processes of metaheuristic algorithms. The performance of the APO was verified via experimental simulations and compared with 32 state-of-the-art algorithms. Wilcoxon signed-rank test was performed for pairwise comparisons of the proposed APO with the state-of-the-art algorithms, and Friedman test was used for multiple comparisons. First, the APO was tested using 12 functions of the 2022 IEEE Congress on Evolutionary Computation benchmark. Considering practicality, the proposed APO was used to solve five popular engineering design problems in a continuous space with constraints. Moreover, the APO was applied to solve a multilevel image segmentation task in a discrete space with constraints. The experiments confirmed that the APO could provide highly competitive results for optimization problems. The source codes of Artificial Protozoa Optimizer are publicly available at https://seyedalimirjalili.com/projects and https://ww2.mathworks.cn/matlabcentral/fileexchange/162656-artificial-protozoa-optimizer.

Normalizing flows (NFs) provide uncorrelated samples from complex distributions, making them an appealing tool for parameter estimation. However, the practical utility of NFs remains limited by their tendency to collapse to a single mode of a multimodal distribution. In this study, we show that annealing with an adaptive schedule based on the effective sample size (ESS) can mitigate mode collapse. We demonstrate that our approach can converge the marginal likelihood for a biochemical oscillator model fit to time-series data in ten-fold less computation time than a widely used ensemble Markov chain Monte Carlo (MCMC) method. We show that the ESS can also be used to reduce variance by pruning the samples. We expect these developments to be of general use for sampling with NFs and discuss potential opportunities for further improvements.

The classical low-rank matrix recovery problem is well-known to exhibit \emph{benign nonconvexity} under the restricted isometry property (RIP): local optimization is guaranteed to converge to the global optimum, where the ground truth is recovered. We investigate whether benign nonconvexity continues to hold when the factor matrices are constrained to be elementwise nonnegative -- a common practical requirement. In the simple setting of a rank-1 nonnegative ground truth, we confirm that benign nonconvexity holds in the fully-observed case with RIP constant $δ=0$. Surprisingly, however, this property fails to extend to the partially-observed case with any arbitrarily small RIP constant $δ\to0^{+}$, irrespective of rank overparameterization. This finding exposes a critical theoretical gap: the continuity argument widely used to explain the empirical robustness of low-rank matrix recovery fundamentally breaks down once nonnegative constraints are imposed.

We propose a novel nonparametric approach for linking covariates to Continuous Time Markov Chains (CTMCs) using the mathematical framework of Reproducing Kernel Hilbert Spaces (RKHS). CTMCs provide a robust framework for modeling transitions across clinical or behavioral states, but traditional multistate models often rely on linear relationships. In contrast, we use a generalized Representer Theorem to enable tractable inference in functional space. For the Frequen-tist version, we apply normed square penalties, while for the Bayesian version, we explore sparsity inducing spike and slab priors. Due to the computational challenges posed by high-dimensional spaces, we successfully adapt the Expectation Maximization Variable Selection (EMVS) algorithm to efficiently identify the posterior mode. We demonstrate the effectiveness of our method through extensive simulation studies and an application to follicular cell lymphoma data. Our performance metrics include the normalized difference between estimated and true nonlinear transition functions, as well as the difference in the probability of getting absorbed in one the final states, capturing the ability of our approach to predict long-term behaviors.

Multi-Task Learning (MTL) seeks to boost statistical power and learning efficiency by discovering structure shared across related tasks. State-of-the-art MTL representation methods, however, usually treat the latent representation matrix as a point in ordinary Euclidean space, ignoring its often non-Euclidean geometry, thus sacrificing robustness when tasks are heterogeneous or even adversarial. We propose GeoERM, a geometry-aware MTL framework that embeds the shared representation on its natural Riemannian manifold and optimizes it via explicit manifold operations. Each training cycle performs (i) a Riemannian gradient step that respects the intrinsic curvature of the search space, followed by (ii) an efficient polar retraction to remain on the manifold, guaranteeing geometric fidelity at every iteration. The procedure applies to a broad class of matrix-factorized MTL models and retains the same per-iteration cost as Euclidean baselines. Across a set of synthetic experiments with task heterogeneity and on a wearable-sensor activity-recognition benchmark, GeoERM consistently improves estimation accuracy, reduces negative transfer, and remains stable under adversarial label noise, outperforming leading MTL and single-task alternatives.

Bioprocess mechanistic modeling is essential for advancing intelligent digital twin representation of biomanufacturing, yet challenges persist due to complex intracellular regulation, stochastic system behavior, and limited experimental data. This paper introduces a symbolic and statistical learning framework to identify key regulatory mechanisms and quantify model uncertainty. Bioprocess dynamics is formulated with stochastic differential equations characterizing intrinsic process variability, with a predefined set of candidate regulatory mechanisms constructed from biological knowledge. A Bayesian learning approach is developed, which is based on a joint learning of kinetic parameters and regulatory structure through a formulation of the mixture model. To enhance computational efficiency, a Metropolis-adjusted Langevin algorithm with adjoint sensitivity analysis is developed for posterior exploration. Compared to state-of-the-art Bayesian inference approaches, the proposed framework achieves improved sample efficiency and robust model selection. An empirical study demonstrates its ability to recover missing regulatory mechanisms and improve model fidelity under data-limited conditions.

Partial label learning (PLL) is a significant weakly supervised learning framework, where each training example corresponds to a set of candidate labels and only one label is the ground-truth label. For the first time, this paper investigates the partial label clustering problem, which takes advantage of the limited available partial labels to improve the clustering performance. Specifically, we first construct a weight matrix of examples based on their relationships in the feature space and disambiguate the candidate labels to estimate the ground-truth label based on the weight matrix. Then, we construct a set of must-link and cannot-link constraints based on the disambiguation results. Moreover, we propagate the initial must-link and cannot-link constraints based on an adversarial prior promoted dual-graph learning approach. Finally, we integrate weight matrix construction, label disambiguation, and pairwise constraints propagation into a joint model to achieve mutual enhancement. We also theoretically prove that a better disambiguated label matrix can help improve clustering performance. Comprehensive experiments demonstrate our method realizes superior performance when comparing with state-of-the-art constrained clustering methods, and outperforms PLL and semi-supervised PLL methods when only limited samples are annotated. The code is publicly available at https://github.com/xyt-ml/PLC.

Handling missing values at test time is challenging for machine learning models, especially when aiming for both high accuracy and interpretability. Established approaches often add bias through imputation or excessive model complexity via missingness indicators. Moreover, either method can obscure interpretability, making it harder to understand how the model utilizes the observed variables in predictions. We propose missingness-avoiding (MA) machine learning, a general framework for training models to rarely require the values of missing (or imputed) features at test time. We create tailored MA learning algorithms for decision trees, tree ensembles, and sparse linear models by incorporating classifier-specific regularization terms in their learning objectives. The tree-based models leverage contextual missingness by reducing reliance on missing values based on the observed context. Experiments on real-world datasets demonstrate that MA-DT, MA-LASSO, MA-RF, and MA-GBT effectively reduce the reliance on features with missing values while maintaining predictive performance competitive with their unregularized counterparts. This shows that our framework gives practitioners a powerful tool to maintain interpretability in predictions with test-time missing values.

Uncertainty Quantification (UQ) is pivotal in enhancing the robustness, reliability, and interpretability of Machine Learning (ML) systems for healthcare, optimizing resources and improving patient care. Despite the emergence of ML-based clinical decision support tools, the lack of principled quantification of uncertainty in ML models remains a major challenge. Current reviews have a narrow focus on analyzing the state-of-the-art UQ in specific healthcare domains without systematically evaluating method efficacy across different stages of model development, and despite a growing body of research, its implementation in healthcare applications remains limited. Therefore, in this survey, we provide a comprehensive analysis of current UQ in healthcare, offering an informed framework that highlights how different methods can be integrated into each stage of the ML pipeline including data processing, training and evaluation. We also highlight the most popular methods used in healthcare and novel approaches from other domains that hold potential for future adoption in the medical context. We expect this study will provide a clear overview of the challenges and opportunities of implementing UQ in the ML pipeline for healthcare, guiding researchers and practitioners in selecting suitable techniques to enhance the reliability, safety and trust from patients and clinicians on ML-driven healthcare solutions.