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arXiv:2511.04534v2 Announce Type: replace Abstract: Reduced-order models (ROMs) can efficiently simulate high-dimensional physical systems but lack robust uncertainty quantification methods. Existing approaches are frequently architecture- or training-specific, which limits flexibility and generalization. We introduce a post hoc, model-agnostic framework for predictive uncertainty quantification in latent space ROMs that requires no modification to the underlying architecture or training procedure. Using conformal prediction, our approach estimates statistical prediction intervals for multiple components of the ROM pipeline: latent dynamics, reconstruction, and end-to-end predictions. We demonstrate the method on a latent space dynamical model for cloud microphysics, where it accurately predicts the evolution of droplet-size distributions and quantifies uncertainty across the ROM pipeline.

arXiv:2511.04469v2 Announce Type: replace Abstract: Market generators using deep generative models have shown promise for synthetic financial data generation, but existing approaches lack causal reasoning capabilities essential for counterfactual analysis and risk assessment. We propose a Time-series Neural Causal Model VAE (TNCM-VAE) that combines variational autoencoders with structural causal models to generate counterfactual financial time series while preserving both temporal dependencies and causal relationships. Our approach enforces causal constraints through directed acyclic graphs in the decoder architecture and employs the causal Wasserstein distance for training. We validate our method on synthetic autoregressive models inspired by the Ornstein-Uhlenbeck process, demonstrating superior performance in counterfactual probability estimation with L1 distances as low as 0.03-0.10 compared to ground truth. The model enables financial stress testing, scenario analysis, and enhanced backtesting by generating plausible counterfactual market trajectories that respect underlying causal mechanisms.

arXiv:2510.25323v3 Announce Type: replace Abstract: Normalizing flows are deep generative models that enable efficient likelihood estimation and sampling through invertible transformations. A key challenge is to design linear layers that enhance expressiveness while maintaining efficient computation of the Jacobian determinant and inverse. We introduce a novel invertible linear layer based on the product of circulant and diagonal matrices. This decomposition reduces parameter complexity from $\mathcal{O}(n^2)$ to $\mathcal{O}(mn)$ using $m$ diagonal matrices and $m-1$ circulant matrices while still approximating general linear transformations. By leveraging the Fast Fourier Transform, our approach reduces the time complexity of matrix inversion from $\mathcal{O}(n^3)$ to $\mathcal{O}(mn\log n)$ and that of computing the log-determinant from $\mathcal{O}(n^3)$ to $\mathcal{O}(mn)$, where $n$ is the input dimension. We build upon this layer to develop Circulant-Diagonal Flow (CDFlow), which achieves strong density estimation on natural image datasets and effectively models data with inherent periodic structure. Furthermore, CDFlow significantly accelerates key operations in normalizing flows, providing practical benefits for scalable generative modeling.

arXiv:2510.24039v2 Announce Type: replace Abstract: Self-Supervised Learning (SSL) for Combinatorial Optimization (CO) is an emerging paradigm for solving combinatorial problems using neural networks. In this paper, we address a central challenge of SSL for CO: solving problems with discrete constraints. We design an end-to-end differentiable framework that enables us to solve discrete constrained optimization problems with neural networks. Concretely, we leverage algorithmic techniques from the literature on convex geometry and Carath\'eodory's theorem to decompose neural network outputs into convex combinations of polytope corners that correspond to feasible sets. This decomposition-based approach enables self-supervised training but also ensures efficient quality-preserving rounding of the neural net output into feasible solutions. Extensive experiments in cardinality-constrained optimization show that our approach can consistently outperform neural baselines. We further provide worked-out examples of how our method can be applied beyond cardinality-constrained problems to a diverse set of combinatorial optimization tasks, including finding independent sets in graphs, and solving matroid-constrained problems.

arXiv:2510.23639v3 Announce Type: replace Abstract: This paper introduces an innovative Electronic Health Record (EHR) foundation model that integrates Polygenic Risk Scores (PRS) as a foundational data modality, moving beyond traditional EHR-only approaches to build more holistic health profiles. Leveraging the extensive and diverse data from the All of Us (AoU) Research Program, this multimodal framework aims to learn complex relationships between clinical data and genetic predispositions. The methodology extends advancements in generative AI to the EHR foundation model space, enhancing predictive capabilities and interpretability. Evaluation on AoU data demonstrates the model's predictive value for the onset of various conditions, particularly Type 2 Diabetes (T2D), and illustrates the interplay between PRS and EHR data. The work also explores transfer learning for custom classification tasks, showcasing the architecture's versatility and efficiency. This approach is pivotal for unlocking new insights into disease prediction, proactive health management, risk stratification, and personalized treatment strategies, laying the groundwork for more personalized, equitable, and actionable real-world evidence generation in healthcare.

arXiv:2510.22266v2 Announce Type: replace Abstract: Identifying the factors that influence student performance in basic education is a central challenge for formulating effective public policies in Brazil. This study introduces a multi-level machine learning approach to classify the proficiency of 9th-grade and high school students using microdata from the System of Assessment of Basic Education (SAEB). Our model uniquely integrates four data sources: student socioeconomic characteristics, teacher professional profiles, school indicators, and principal management profiles. A comparative analysis of four ensemble algorithms confirmed the superiority of a Random Forest model, which achieved 90.2% accuracy and an Area Under the Curve (AUC) of 96.7%. To move beyond prediction, we applied Explainable AI (XAI) using SHAP, which revealed that the school's average socioeconomic level is the most dominant predictor, demonstrating that systemic factors have a greater impact than individual characteristics in isolation. The primary conclusion is that academic performance is a systemic phenomenon deeply tied to the school's ecosystem. This study provides a data-driven, interpretable tool to inform policies aimed at promoting educational equity by addressing disparities between schools.

arXiv:2510.21788v2 Announce Type: replace Abstract: We explore the use of expert-guided bandit learning, which we refer to as online mixture-of-experts (OMoE). In this setting, given a context, a candidate committee of experts must determine how to aggregate their outputs to achieve optimal results in terms of aggregate accuracy. We propose two algorithms to address this problem. The first algorithm combines aggregate voting with UCB-driven successive elimination, efficiently pruning suboptimal exploration actions. The second algorithm employs an online weighted-majority-voting mechanism, leveraging the respective voting power of each expert proportional to their predictive power. We derive theoretical guarantees for the regret properties in the bandit setting under ideal circumstances, and empirical results are provided accordingly. As a modern study on applications, these methods are applied to the online fine-tuning of a set of expert large language models (LLMs), where after each response, the generative LLM dynamically reweighs its set of experts and/or selects the optimal committee of experts to generate the most accurate response. Our results introduce new methodologies and no-regret guarantees for combining multiple experts to improve on the performance of the an aggregate model overall.

arXiv:2510.18905v3 Announce Type: replace Abstract: AI inference scaling is often tuned through 1D heuristics (a fixed reasoning pass) or 2D bivariate trade-offs (e.g., accuracy vs. compute), which fail to consider cost and latency constraints. We introduce a 3D optimization framework that jointly calibrates accuracy, cost, and latency within a unified decision space, enabling constraints-aware inference scaling. Using Monte Carlo simulations across three representative scenarios and nine simulated large language models, we evaluate four optimization methods to address the 3D multi-objective optimization (MOO) problem. Framing inference scaling in MOO shapes a feasible space that 1D and 2D optimizations fail to capture, enabling environment-adaptive selection of the inference scaling~$k$. Results show that knee-point optimization based on Pareto frontiers achieves the best balance, while accuracy-maximization remains favorable when accuracy is prioritized. Our results further show that smaller models, when combined with optimal inference scaling, can match or exceed the performance of larger models at a fraction of the cost. The framework establishes a theoretical foundation for deployment-aware inference scaling across diverse operational conditions.

arXiv:2510.16817v2 Announce Type: replace Abstract: We propose an enhanced physics-informed neural network (PINN), the Trace Regularity Physics-Informed Neural Network (TRPINN), which enforces the boundary loss in the Sobolev-Slobodeckij norm $H^{1/2}(\partial \Omega)$, the correct trace space associated with $H^1(\Omega)$. We reduce computational cost by computing only the theoretically essential portion of the semi-norm and enhance convergence stability by avoiding denominator evaluations in the discretization. By incorporating the exact $H^{1/2}(\partial \Omega)$ norm, we show that the approximation converges to the true solution in the $H^{1}(\Omega)$ sense, and, through Neural Tangent Kernel (NTK) analysis, we demonstrate that TRPINN can converge faster than standard PINNs. Numerical experiments on the Laplace equation with highly oscillatory Dirichlet boundary conditions exhibit cases where TRPINN succeeds even when standard PINNs fail, and show performance improvements of one to three decimal digits.

arXiv:2510.12934v2 Announce Type: replace Abstract: Physical systems that naturally perform energy descent offer a direct route to accelerating machine learning. Oscillator Ising Machines (OIMs) exemplify this idea: their GHz-frequency dynamics mirror both the optimization of energy-based models (EBMs) and gradient descent on loss landscapes, while intrinsic noise corresponds to Langevin dynamics - supporting sampling as well as optimization. Equilibrium Propagation (EP) unifies these processes into descent on a single total energy landscape, enabling local learning rules without global backpropagation. We show that EP on OIMs achieves competitive accuracy ($\sim 97.2 \pm 0.1 \%$ on MNIST, $\sim 88.0 \pm 0.1 \%$ on Fashion-MNIST), while maintaining robustness under realistic hardware constraints such as parameter quantization and phase noise. These results establish OIMs as a fast, energy-efficient substrate for neuromorphic learning, and suggest that EBMs - often bottlenecked by conventional processors - may find practical realization on physical hardware whose dynamics directly perform their optimization.

arXiv:2510.11677v2 Announce Type: replace Abstract: We introduce a family of chronologically consistent, instruction-tuned large language models to eliminate lookahead bias. Each model is trained only on data available before a clearly defined knowledge-cutoff date, ensuring strict temporal separation from any post-cutoff data. The resulting framework offers (i) a simple, conversational chat interface, (ii) fully open, fixed model weights that guarantee replicability, and (iii) a conservative lower bound on forecast accuracy, isolating the share of predictability that survives once training leakage is removed. Together, these features provide researchers with an easy-to-use generative AI tool useful for a wide range of prediction tasks that is free of lookahead bias.

arXiv:2510.09114v3 Announce Type: replace Abstract: While significant progress has been made in conventional fairness-aware machine learning (ML) and differentially private ML (DPML), the fairness of privacy protection across groups remains underexplored. Existing studies have proposed methods to assess group privacy risks, but these are based on the average-case privacy risks of data records. Such approaches may underestimate the group privacy risks, thereby potentially underestimating the disparity across group privacy risks. Moreover, the current method for assessing the worst-case privacy risks of data records is time-consuming, limiting their practical applicability. To address these limitations, we introduce a novel membership inference game that can efficiently audit the approximate worst-case privacy risks of data records. Experimental results demonstrate that our method provides a more stringent measurement of group privacy risks, yielding a reliable assessment of the disparity in group privacy risks. Furthermore, to promote privacy protection fairness in DPML, we enhance the standard DP-SGD algorithm with an adaptive group-specific gradient clipping strategy, inspired by the design of canaries in differential privacy auditing studies. Extensive experiments confirm that our algorithm effectively reduces the disparity in group privacy risks, thereby enhancing the fairness of privacy protection in DPML.

arXiv:2510.06190v2 Announce Type: replace Abstract: Diffusion language models have recently emerged as a competitive alternative to autoregressive language models. Beyond next-token generation, they are more efficient and flexible by enabling parallel and any-order token generation. However, despite empirical successes, their computational power and fundamental limitations remain poorly understood. In this paper, we formally study whether non-autoregressive generation in Masked Diffusion Models (MDM) enables solving problems beyond the reach of Auto-Regressive Models (ARM). Our results show that MDM with sufficiently large context length is computationally universal with decoding steps matching the optimal parallel time complexity in PRAM. However, when controlling for other factors, MDM's flexibility to generate in any-order does not expand what ARM can already solve. To address this, we propose a new form of generation called any-process generation, which extends MDM with capabilities to remask, insert and delete tokens, allowing self-correction, length-variable editing, and adaptive parallelism. Theoretically and empirically, we demonstrate these capabilities enable scalability to significantly harder reasoning problems that are otherwise intractable for ARM and vanilla MDM. Additionally, they prove essential for generation tasks where objects naturally evolve through non-sequential processes, crucial for extending current LLMs beyond natural language to domains such as coding and science.

arXiv:2510.04108v2 Announce Type: replace Abstract: Effective Uncertainty Quantification (UQ) represents a key aspect for reliable deployment of Large Language Models (LLMs) in automated decision-making and beyond. Yet, for LLM generation with multiple choice structure, the state-of-the-art in UQ is still dominated by the naive baseline given by the maximum softmax score. To address this shortcoming, we demonstrate that taking a principled approach via Bayesian statistics leads to improved performance despite leveraging the simplest possible model, namely linear regression. More precisely, we propose to train multiple Bayesian linear models, each predicting the output of a layer given the output of the previous one. Based on the obtained layer-level posterior distributions, we infer the global uncertainty level of the LLM by identifying a sparse combination of distributional features, leading to an efficient UQ scheme. Numerical experiments on various LLMs show consistent improvement over state-of-the-art baselines.

arXiv:2510.04102v2 Announce Type: replace Abstract: Motivated by the remarkable success of Foundation Models (FMs) in language modeling, there has been growing interest in developing FMs for time series prediction, given the transformative power such models hold for science and engineering. This culminated in significant success of FMs in short-range forecasting settings. However, extrapolation or long-range forecasting remains elusive for FMs, which struggle to outperform even simple baselines. This contrasts with physical laws which have strong extrapolation properties, and raises the question of the fundamental difference between the structure of neural networks and physical laws. In this work, we identify and formalize a fundamental property characterizing the ability of statistical learning models to predict more accurately outside of their training domain, hence explaining performance deterioration for deep learning models in extrapolation settings. In addition to a theoretical analysis, we present empirical results showcasing the implications of this property on current deep learning architectures. Our results not only clarify the root causes of the extrapolation gap but also suggest directions for designing next-generation forecasting models capable of mastering extrapolation.

arXiv:2509.25230v2 Announce Type: replace Abstract: A useful inductive bias for temporal data is that trajectories should stay close to the data manifold. Traditional flow matching relies on straight conditional paths, and flow matching methods which learn geodesics rely on RBF kernels or nearest neighbor graphs that suffer from the curse of dimensionality. We propose to use score matching and annealed energy distillation to learn a metric tensor that faithfully captures the underlying data geometry and informs more accurate flows. We demonstrate the efficacy of this strategy on synthetic manifolds with analytic geodesics, and interpolation of cell

arXiv:2509.25225v2 Announce Type: replace Abstract: Structure-Based Drug Design (SBDD) is a powerful strategy in computational drug discovery, utilizing three-dimensional protein structures to guide the design of molecules with improved binding affinity. However, capturing complex protein-ligand interactions across multiple scales remains challenging, as current methods often overlook the hierarchical organization and intrinsic asymmetry of these interactions. To address these limitations, we propose MSCoD, a novel Bayesian updating-based generative framework for structure-based drug design. In our MSCoD, Multi-Scale Information Bottleneck (MSIB) was developed, which enables semantic compression at multiple abstraction levels for efficient hierarchical feature extraction. Furthermore, a multi-head cooperative attention (MHCA) mechanism was developed, which employs asymmetric protein-to-ligand attention to capture diverse interaction types while addressing the dimensionality disparity between proteins and ligands. Empirical studies showed that MSCoD outperforms state-of-the-art methods on the benchmark dataset. Its real-world applicability is confirmed by case studies on difficult targets like KRAS G12D (7XKJ). Additionally, the MSIB and MHCA modules prove transferable, boosting the performance of GraphDTA on standard drug target affinity prediction benchmarks (Davis and Kiba). The code and data underlying this article are freely available at https://github.com/xulong0826/MSCoD.

arXiv:2509.24122v2 Announce Type: replace Abstract: At the heart of time-series forecasting (TSF) lies a fundamental challenge: how can models efficiently and effectively capture long-range temporal dependencies across ever-growing sequences? While deep learning has brought notable progress, conventional architectures often face a trade-off between computational complexity and their ability to retain accumulative information over extended horizons. Echo State Networks (ESNs), a class of reservoir computing models, have recently regained attention for their exceptional efficiency, offering constant memory usage and per-step training complexity regardless of input length. This makes them particularly attractive for modeling extremely long-term event history in TSF. However, traditional ESNs fall short of state-of-the-art performance due to their limited nonlinear capacity, which constrains both their expressiveness and stability. We introduce Echo Flow Networks (EFNs), a framework composed of a group of extended Echo State Networks (X-ESNs) with MLP readouts, enhanced by our novel Matrix-Gated Composite Random Activation (MCRA), which enables complex, neuron-specific temporal dynamics, significantly expanding the network's representational capacity without compromising computational efficiency. In addition, we propose a dual-stream architecture in which recent input history dynamically selects signature reservoir features from an infinite-horizon memory, leading to improved prediction accuracy and long-term stability. Extensive evaluations on five benchmarks demonstrate that EFNs achieve up to 4x faster training and 3x smaller model size compared to leading methods like PatchTST, reducing forecasting error from 43% to 35%, a 20% relative improvement. One instantiation of our framework, EchoFormer, consistently achieves new state-of-the-art performance across five benchmark datasets: ETTh, ETTm, DMV, Weather, and Air Quality.

arXiv:2509.22272v2 Announce Type: replace Abstract: As Large Language Models (LLMs) are increasingly integrated in diverse applications, obtaining reliable measures of their predictive uncertainty has become critically important. A precise distinction between aleatoric uncertainty, arising from inherent ambiguities within input data, and epistemic uncertainty, originating exclusively from model limitations, is essential to effectively address each uncertainty source. In this paper, we introduce Spectral Uncertainty, a novel approach to quantifying and decomposing uncertainties in LLMs. Leveraging the Von Neumann entropy from quantum information theory, Spectral Uncertainty provides a rigorous theoretical foundation for separating total uncertainty into distinct aleatoric and epistemic components. Unlike existing baseline methods, our approach incorporates a fine-grained representation of semantic similarity, enabling nuanced differentiation among various semantic interpretations in model responses. Empirical evaluations demonstrate that Spectral Uncertainty outperforms state-of-the-art methods in estimating both aleatoric and total uncertainty across diverse models and benchmark datasets.

arXiv:2509.21746v2 Announce Type: replace Abstract: The goal of coreset selection methods is to identify representative subsets of datasets for efficient model training. Yet, existing methods often ignore the possibility of annotation errors and require fixed pruning ratios, making them impractical in real-world settings. We present HyperCore, a robust and adaptive coreset selection framework designed explicitly for noisy environments. HyperCore leverages lightweight hypersphere models learned per class, embedding in-class samples close to a hypersphere center while naturally segregating out-of-class samples based on their distance. By using Youden's J statistic, HyperCore can adaptively select pruning thresholds, enabling automatic, noise-aware data pruning without hyperparameter tuning. Our experiments reveal that HyperCore consistently surpasses state-of-the-art coreset selection methods, especially under noisy and low-data regimes. HyperCore effectively discards mislabeled and ambiguous points, yielding compact yet highly informative subsets suitable for scalable and noise-free learning.