Translating the internal representations and computations of models into concepts that humans can understand is a key goal of interpretability. While recent dictionary learning methods such as Sparse Autoencoders (SAEs) provide a promising route to discover human-interpretable features, they suffer from a variety of problems, including a systematic failure to capture the rich conceptual information that drives linguistic understanding. Instead, they exhibit a bias towards shallow, token-specific, or noisy features, such as "the phrase 'The' at the start of sentences". In this work, we propose that this is due to a fundamental issue with how dictionary learning methods for LLMs are trained. Language itself has a rich, well-studied structure spanning syntax, semantics, and pragmatics; however, current unsupervised methods largely ignore this linguistic knowledge, leading to poor feature discovery that favors superficial patterns over meaningful concepts. We focus on a simple but important aspect of language: semantic content has long-range dependencies and tends to be smooth over a sequence, whereas syntactic information is much more local. Building on this insight, we introduce Temporal Sparse Autoencoders (T-SAEs), which incorporate a novel contrastive loss encouraging consistent activations of high-level features over adjacent tokens. This simple yet powerful modification enables SAEs to disentangle semantic from syntactic features in a self-supervised manner. Across multiple datasets and models, T-SAEs recover smoother, more coherent semantic concepts without sacrificing reconstruction quality. Strikingly, they exhibit clear semantic structure despite being trained without explicit semantic signal, offering a new pathway for unsupervised interpretability in language models.

In recent years, Electroencephalographic analysis has gained prominence in stress research when combined with AI and Machine Learning models for validation. In this study, a lightweight dynamic brain connectivity framework based on Time Varying Directed Transfer Function is proposed, where TV DTF features were validated through ML based stress classification. TV DTF estimates the directional information flow between brain regions across distinct EEG frequency bands, thereby capturing temporal and causal influences that are often overlooked by static functional connectivity measures. EEG recordings from the 32 channel SAM 40 dataset were employed, focusing on mental arithmetic task trials. The dynamic EEG-based TV-DTF features were validated through ML classifiers such as Support Vector Machine, Random Forest, Gradient Boosting, Adaptive Boosting, and Extreme Gradient Boosting. Experimental results show that alpha-TV-DTF provided the strongest discriminative power, with SVM achieving 89.73% accuracy in 3-class classification and with XGBoost achieving 93.69% accuracy in 2 class classification. Relative to absolute power and phase locking based functional connectivity features, alpha TV DTF and beta TV DTF achieved higher performance across the ML models, highlighting the advantages of dynamic over static measures. Feature importance analysis further highlighted dominant long-range frontal parietal and frontal occipital informational influences, emphasizing the regulatory role of frontal regions under stress. These findings validate the lightweight TV-DTF as a robust framework, revealing spatiotemporal brain dynamics and directional influences across different stress levels.

We introduce an explainability method for biomedical hypothesis generation systems, built on top of the novel Hypothesis Generation Context Retriever framework. Our approach combines semantic graph-based retrieval and relevant data-restrictive training to simulate real-world discovery constraints. Integrated with large language models (LLMs) via retrieval-augmented generation, the system explains hypotheses with contextual evidence using published scientific literature. We also propose a novel feedback loop approach, which iteratively identifies and corrects flawed parts of LLM-generated explanations, refining both the evidence paths and supporting context. We demonstrate the performance of our method with multiple large language models and evaluate the explanation and context retrieval quality through both expert-curated assessment and large-scale automated analysis.

Quantitative structure-activity relationship assumes a smooth relationship between molecular structure and biological activity. However, activity cliffs defined as pairs of structurally similar compounds with large potency differences break this continuity. Recent benchmarks targeting activity cliffs have revealed that classical machine learning models with extended connectivity fingerprints outperform graph neural networks. Our analysis shows that graph embeddings fail to adequately separate structurally similar molecules in the embedding space, making it difficult to distinguish between structurally similar but functionally different molecules. Despite this limitation, molecular graph structures are inherently expressive and attractive, as they preserve molecular topology. To preserve the structural representation of molecules as graphs, we propose a new model, Graph-Cliff, which integrates short-and long-range information through a gating mechanism. Experimental results demonstrate that GraphCliff consistently improves performance on both non-cliff and cliff compounds. Furthermore, layer-wise node embedding analyses reveal reduced over-smoothing and enhanced discriminative power relative to strong baseline graph models. Quantitative Structure-Activity Relationship (QSAR) is based on the premise that molecules with similar structures have similar biological activity.

Ordinal categorical data are routinely encountered in a wide range of practical applications. When the primary goal is to construct a regression model for ordinal outcomes, cumulative link models represent one of the most popular choices to link the cumulative probabilities of the response with a set of covariates through a parsimonious linear predictor, shared across response categories. When the number of observations grows, standard sampling algorithms for Bayesian inference scale poorly, making posterior computation increasingly challenging in large datasets. In this article, we propose three scalable algorithms for approximating the posterior distribution of the regression coefficients in cumulative probit models relying on Variational Bayes and Expectation Propagation. We compare the proposed approaches with inference based on Markov Chain Monte Carlo, demonstrating superior computational performance and remarkable accuracy; finally, we illustrate the utility of the proposed algorithms on a challenging case study to investigate the structure of a criminal network.

In many areas of systems biology, including virology, pharmacokinetics, and population biology, dynamical systems are commonly used to describe biological processes. These systems can be characterized by estimating their parameters from sampled data. The key problem is how to optimally select sampling points to achieve accurate parameter estimation. Classical approaches often rely on Fisher information matrix-based criteria such as A-, D-, and E-optimality, which require an initial parameter estimate and may yield suboptimal results when the estimate is inaccurate. This study proposes two simulation-based methods for optimal sampling design that do not depend on initial parameter estimates. The first method, E-optimal-ranking (EOR), employs the E-optimal criterion, while the second utilizes a Long Short-Term Memory (LSTM) neural network. Simulation studies based on the Lotka-Volterra and three-compartment models demonstrate that the proposed methods outperform both random selection and classical E-optimal design.

In this paper we propose a sequential minimax optimization (SMO) method for solving a class of constrained bilevel optimization problems in which the lower-level part is a possibly nonsmooth convex optimization problem, while the upper-level part is a possibly nonconvex optimization problem. Specifically, SMO applies a first-order method to solve a sequence of minimax subproblems, which are obtained by employing a hybrid of modified augmented Lagrangian and penalty schemes on the bilevel optimization problems. Under suitable assumptions, we establish an operation complexity of $O(\varepsilon^{-7}\log\varepsilon^{-1})$ and $O(\varepsilon^{-6}\log\varepsilon^{-1})$, measured in terms of fundamental operations, for SMO in finding an $\varepsilon$-KKT solution of the bilevel optimization problems with merely convex and strongly convex lower-level objective functions, respectively. The latter result improves the previous best-known operation complexity by a factor of $\varepsilon^{-1}$. Preliminary numerical results demonstrate significantly superior computational performance compared to the recently developed first-order penalty method.

In differential privacy, statistics of a sensitive dataset are privatized by introducing random noise. Most privacy analyses provide privacy bounds specifying a noise level sufficient to achieve a target privacy guarantee. Sometimes, these bounds are pessimistic and suggest adding excessive noise, which overwhelms the meaningful signal. It remains unclear if such high noise levels are truly necessary or a limitation of the proof techniques. This paper explores whether we can obtain sharp privacy characterizations that identify the smallest noise level required to achieve a target privacy level for a given mechanism. We study this problem in the context of differentially private principal component analysis, where the goal is to privatize the leading principal components (PCs) of a dataset with n samples and p features. We analyze the exponential mechanism for this problem in a model-free setting and provide sharp utility and privacy characterizations in the high-dimensional limit ($p\rightarrow\infty$). Our privacy result shows that, in high dimensions, detecting the presence of a target individual in the dataset using the privatized PCs is exactly as hard as distinguishing two Gaussians with slightly different means, where the mean difference depends on certain spectral properties of the dataset. Our privacy analysis combines the hypothesis-testing formulation of privacy guarantees proposed by Dong, Roth, and Su (2022) with classical contiguity arguments due to Le Cam to obtain sharp high-dimensional privacy characterizations.

Fairness concerns are increasingly critical as machine learning models are deployed in high-stakes applications. While existing fairness-aware methods typically intervene at the model level, they often suffer from high computational costs, limited scalability, and poor generalization. To address these challenges, we propose a Bayesian data selection framework that ensures fairness by aligning group-specific posterior distributions of model parameters and sample weights with a shared central distribution. Our framework supports flexible alignment via various distributional discrepancy measures, including Wasserstein distance, maximum mean discrepancy, and $f$-divergence, allowing geometry-aware control without imposing explicit fairness constraints. This data-centric approach mitigates group-specific biases in training data and improves fairness in downstream tasks, with theoretical guarantees. Experiments on benchmark datasets show that our method consistently outperforms existing data selection and model-based fairness methods in both fairness and accuracy.

As the right to be forgotten becomes legislated worldwide, machine unlearning mechanisms have emerged to efficiently update models for data deletion and enhance user privacy protection. However, existing machine unlearning algorithms frequently neglect the fact that different data points may contribute unequally to model performance (i.e., heterogeneous data values). Treat them equally in machine unlearning procedure can potentially degrading the performance of updated models. To address this limitation, we propose Data Value-Weighted Unlearning (DVWU), a general unlearning framework that accounts for data value heterogeneity into the unlearning process. Specifically, we design a weighting strategy based on data values, which are then integrated into the unlearning procedure to enable differentiated unlearning for data points with varying utility to the model. The DVWU framework can be broadly adapted to various existing machine unlearning methods. We use the one-step Newton update as an example for implementation, developing both output and objective perturbation algorithms to achieve certified unlearning. Experiments on both synthetic and real-world datasets demonstrate that our methods achieve superior predictive performance and robustness compared to conventional unlearning approaches. We further show the extensibility of our framework on gradient ascent method by incorporating the proposed weighting strategy into the gradient terms, highlighting the adaptability of DVWU for broader gradient-based deep unlearning methods.