Machine learning has been widely adopted in biomedical research, fueled by the increasing availability of data. However, integrating datasets across institutions is challenging due to legal restrictions and data governance complexities. Federated learning allows the direct, privacy preserving training of machine learning models using geographically distributed datasets, but faces the challenge of how to appropriately control for covariate effects. The naive implementation of conventional covariate control methods in federated learning scenarios is often impractical due to the substantial communication costs, particularly with high-dimensional data. To address this issue, we introduce dsLassoCov, a machine learning approach designed to control for covariate effects and allow an efficient training in federated learning. In biomedical analysis, this allow the biomarker selection against the confounding effects. Using simulated data, we demonstrate that dsLassoCov can efficiently and effectively manage confounding effects during model training. In our real-world data analysis, we replicated a large-scale Exposome analysis using data from six geographically distinct databases, achieving results consistent with previous studies. By resolving the challenge of covariate control, our proposed approach can accelerate the application of federated learning in large-scale biomedical studies.

Many ensemble-based models have been proposed to solve machine learning problems in the survival analysis framework, including random survival forests, the gradient boosting machine with weak survival models, ensembles of the Cox models. To extend the set of models, a new ensemble-based model called SurvBETA (the Survival Beran estimator Ensemble using Three Attention mechanisms) is proposed where the Beran estimator is used as a weak learner in the ensemble. The Beran estimator can be regarded as a kernel regression model taking into account the relationship between instances. Outputs of weak learners in the form of conditional survival functions are aggregated with attention weights taking into account the distance between the analyzed instance and prototypes of all bootstrap samples. The attention mechanism is used three times: for implementation of the Beran estimators, for determining specific prototypes of bootstrap samples and for aggregating the weak model predictions. The proposed model is presented in two forms: in a general form requiring to solve a complex optimization problem for its training; in a simplified form by considering a special representation of the attention weights by means of the imprecise Huber's contamination model which leads to solving a simple optimization problem. Numerical experiments illustrate properties of the model on synthetic data and compare the model with other survival models on real data. A code implementing the proposed model is publicly available.

Classical optimization theory requires a small step-size for gradient-based methods to converge. Nevertheless, recent findings challenge the traditional idea by empirically demonstrating Gradient Descent (GD) converges even when the step-size $\eta$ exceeds the threshold of $2/L$, where $L$ is the global smooth constant. This is usually known as the Edge of Stability (EoS) phenomenon. A widely held belief suggests that an objective function with subquadratic growth plays an important role in incurring EoS. In this paper, we provide a more comprehensive answer by considering the task of finding linear interpolator $\beta \in R^{d}$ for regression with loss function $l(\cdot)$, where $\beta$ admits parameterization as $\beta = w^2_{+} - w^2_{-}$. Contrary to the previous work that suggests a subquadratic $l$ is necessary for EoS, our novel finding reveals that EoS occurs even when $l$ is quadratic under proper conditions. This argument is made rigorous by both empirical and theoretical evidence, demonstrating the GD trajectory converges to a linear interpolator in a non-asymptotic way. Moreover, the model under quadratic $l$, also known as a depth-$2$ diagonal linear network, remains largely unexplored under the EoS regime. Our analysis then sheds some new light on the implicit bias of diagonal linear networks when a larger step-size is employed, enriching the understanding of EoS on more practical models.

Despite the widespread use of the data augmentation (DA) algorithm, the theoretical understanding of its convergence behavior remains incomplete. We prove the first non-asymptotic polynomial upper bounds on mixing times of three important DA algorithms: DA algorithm for Bayesian Probit regression (Albert and Chib, 1993, ProbitDA), Bayesian Logit regression (Polson, Scott, and Windle, 2013, LogitDA), and Bayesian Lasso regression (Park and Casella, 2008, Rajaratnam et al., 2015, LassoDA). Concretely, we demonstrate that with $\eta$-warm start, parameter dimension $d$, and sample size $n$, the ProbitDA and LogitDA require $\mathcal{O}\left(nd\log \left(\frac{\log \eta}{\epsilon}\right)\right)$ steps to obtain samples with at most $\epsilon$ TV error, whereas the LassoDA requires $\mathcal{O}\left(d^2(d\log d +n \log n)^2 \log \left(\frac{\eta}{\epsilon}\right)\right)$ steps. The results are generally applicable to settings with large $n$ and large $d$, including settings with highly imbalanced response data in the Probit and Logit regression. The proofs are based on the Markov chain conductance and isoperimetric inequalities. Assuming that data are independently generated from either a bounded, sub-Gaussian, or log-concave distribution, we improve the guarantees for ProbitDA and LogitDA to $\tilde{\mathcal{O}}(n+d)$ with high probability, and compare it with the best known guarantees of Langevin Monte Carlo and Metropolis Adjusted Langevin Algorithm. We also discuss the mixing times of the three algorithms under feasible initialization.

Dark patterns in user interfaces represent deceptive design practices intended to manipulate users' behavior, often leading to unintended consequences such as coerced purchases, involuntary data disclosures, or user frustration. Detecting and mitigating these dark patterns is crucial for promoting transparency, trust, and ethical design practices in digital environments. This paper proposes a novel approach for detecting dark patterns in user interfaces using logistic regression and bag-of-words representation. Our methodology involves collecting a diverse dataset of user interface text samples, preprocessing the data, extracting text features using the bag-of-words representation, training a logistic regression model, and evaluating its performance using various metrics such as accuracy, precision, recall, F1-score, and the area under the ROC curve (AUC). Experimental results demonstrate the effectiveness of the proposed approach in accurately identifying instances of dark patterns, with high predictive performance and robustness to variations in dataset composition and model parameters. The insights gained from this study contribute to the growing body of knowledge on dark patterns detection and classification, offering practical implications for designers, developers, and policymakers in promoting ethical design practices and protecting user rights in digital environments.

A kind of pancreatic cancer called Pancreatic Ductal Adenocarcinoma (PDAC) is anticipated to be one of the main causes of mortality during past years. Evidence from several researches supported the concept that the oncogenic KRAS (Ki-ras2 Kirsten rat sarcoma viral oncogene) mutation is the major cause of pancreatic cancer. KRAS acts as an on-off switch that promotes cell growth. But when the KRAS gene is mutated, it will be in one position, allowing the cell growth uncontrollably. This uncontrollable multiplication of cells causes cancer growth. Therefore, KRAS was selected as the target protein in the study. Fifty plant-derived compounds are selected for the study. To determine whether the examined drugs could bind to the KRAS complex's binding pocket, molecular docking was performed. Computational analyses were used to assess the possible ability of tested substances to pass the Blood Brain Barrier (BBB). To predict the bioactivity of ligands a machine learning model was created. Five machine learning models were created and have chosen the best one among them for analyzing the bioactivity of each ligand. From the fifty plant-derived compounds the compounds with the least binding energies are selected. Then bioactivity of these six compounds is analyzed using Random Forest Regression model. Adsorption, Distribution, Metabolism, Excretion (ADME) properties of compounds are analyzed. The results showed that borneol has powerful effects and acts as a promising agent for the treatment of pancreatic cancer. This suggests that borneol found in plants like mint, ginger, rosemary, etc., is a successful compound for the treatment of pancreatic cancer.

The efficiency of active learning (AL) approaches to identify materials with desired properties relies on the knowledge of a few parameters describing the property. However, these parameters are unknown if the property is governed by a high intricacy of many atomistic processes. Here, we develop an AL workflow based on the sure-independence screening and sparsifying operator (SISSO) symbolic-regression approach. SISSO identifies the few, key parameters correlated with a given materials property via analytical expressions, out of many offered primary features. Crucially, we train ensembles of SISSO models in order to quantify mean predictions and their uncertainty, enabling the use of SISSO in AL. By combining bootstrap sampling to obtain training datasets with Monte-Carlo feature dropout, the high prediction errors observed by a single SISSO model are improved. Besides, the feature dropout procedure alleviates the overconfidence issues observed in the widely used bagging approach. We demonstrate the SISSO-guided AL workflow by identifying acid-stable oxides for water splitting using high-quality DFT-HSE06 calculations. From a pool of 1470 materials, 12 acid-stable materials are identified in only 30 AL iterations. The materials property maps provided by SISSO along with the uncertainty estimates reduce the risk of missing promising portions of the materials space that were overlooked in the initial, possibly biased dataset.

Understanding the effect of uncertainty and noise in data on machine learning models (MLM) is crucial in developing trust and measuring performance. In this paper, a new model is proposed to quantify uncertainties and noise in data on MLMs. Using the concept of signal-to-noise ratio (SNR), a new metric called deterministic-non-deterministic ratio (DDR) is proposed to formulate performance of a model. Using synthetic data in experiments, we show how accuracy can change with DDR and how we can use DDR-accuracy curves to determine performance of a model.

Explainable Artificial Intelligence (XAI) addresses the growing need for transparency and interpretability in AI systems, enabling trust and accountability in decision-making processes. This book offers a comprehensive guide to XAI, bridging foundational concepts with advanced methodologies. It explores interpretability in traditional models such as Decision Trees, Linear Regression, and Support Vector Machines, alongside the challenges of explaining deep learning architectures like CNNs, RNNs, and Large Language Models (LLMs), including BERT, GPT, and T5. The book presents practical techniques such as SHAP, LIME, Grad-CAM, counterfactual explanations, and causal inference, supported by Python code examples for real-world applications. Case studies illustrate XAI's role in healthcare, finance, and policymaking, demonstrating its impact on fairness and decision support. The book also covers evaluation metrics for explanation quality, an overview of cutting-edge XAI tools and frameworks, and emerging research directions, such as interpretability in federated learning and ethical AI considerations. Designed for a broad audience, this resource equips readers with the theoretical insights and practical skills needed to master XAI. Hands-on examples and additional resources are available at the companion GitHub repository: https://github.com/Echoslayer/XAI_From_Classical_Models_to_LLMs.

In this paper we study the asymptotics of linear regression in settings with non-Gaussian covariates where the covariates exhibit a linear dependency structure, departing from the standard assumption of independence. We model the covariates using stochastic processes with spatio-temporal covariance and analyze the performance of ridge regression in the high-dimensional proportional regime, where the number of samples and feature dimensions grow proportionally. A Gaussian universality theorem is proven, demonstrating that the asymptotics are invariant under replacing the non-Gaussian covariates with Gaussian vectors preserving mean and covariance, for which tools from random matrix theory can be used to derive precise characterizations of the estimation error. The estimation error is characterized by a fixed-point equation involving the spectral properties of the spatio-temporal covariance matrices, enabling efficient computation. We then study optimal regularization, overparameterization, and the double descent phenomenon in the context of dependent data. Simulations validate our theoretical predictions, shedding light on how dependencies influence estimation error and the choice of regularization parameters.