Despite its importance to applications in protein design, predicting protein properties like binding affinity and thermostability from sparse experimental data remains a significant challenge. Accordingly, we introduce a class of sequence kernels that exploit evolutionary substitution matrices as well as local linearity and demonstrate that the resulting Gaussian processes provide data-efficient models of protein property landscapes, frequently outperforming alternatives that rely on foundation model embeddings. Furthermore--by learning what are in effect structure-aware substitution matrices--we show that our kernels can readily incorporate structural information from foundation models. We demonstrate that these structure-conditioned kernels are well suited to multi-task learning across multiple protein property landscapes and can decisively outperform local supervised learning methods.

Non-alcoholic fatty liver disease (NAFLD) affects roughly 25% of global adults, posing substantial hepatic and cardiovascular risks. Yet, population-level screening tools remain inadequate. We present Method, a machine-learning framework for NAFLD risk prediction coupling gradient-boosted decision trees with conformal prediction to yield calibrated, distribution-free coverage guarantees on individual risk estimates. It integrates a mutual-information-based stability selection procedure to identify a compact, clinically interpretable feature subset via bootstrap resampling, constructing prediction sets whose marginal coverage provably exceeds a user-specified confidence level. We evaluated Method on a multicenter cohort from Guangzhou, China (primary n=2,187; external validation n=412) using 78 candidate features across demographics, metabolic biomarkers, and lifestyle factors. Method achieves an AUROC of 0.912 internally and 0.891 externally, outperforming deep neural networks, TabNet, support vector machines, and logistic regression. Conformal prediction sets achieve 91.3% empirical coverage at the 90% nominal level. A three-tier risk stratification derived from these scores separates the population into distinct groups, with the high-risk subgroup showing a 12-month progression rate 4.7 times that of the low-risk tier. The selected features -- notably waist circumference, ALT, GGT, triglycerides, fasting glucose, and BMI -- align with established metabolic risk factors, providing biological plausibility.

Reconstruction-based methods are widely used for time series anomaly detection, where models are trained to reconstruct subsequences, and anomalies are identified through reconstruction errors. However, reported results are often hard to compare due to heterogeneous evaluation practices and underspecified inference procedures. In this paper, we revisit reconstruction-based anomaly detection in the univariate offline setting and study the role of the inference stride, which controls whether subsequences are processed as disjoint windows or with overlap. We propose a unified training, tuning, and multi-seed evaluation protocol on the curated TSB-AD benchmark, and study how overlapping inference affects anomaly detection performance for a range of reconstruction models, including PCA-based baselines, DLinear, an AutoEncoder, TimesNet, and Transformer variants. The results show that across all models, overlapping windows yield consistent improvements, with average relative gain up to +28%, and can alter method rankings. We further analyze variability across datasets, random seeds, and hyperparameter configurations. Finally, we complement the benchmark study with an evaluation on the full UCR archive using localization criteria aligned with sliding-window reconstruction. Overall, our results highlight that reconstruction-based anomaly detection performance depends not only on model architecture and training, but also on inference choices, motivating a clear and reproducible protocol. Our results show that reconstructionbased baselines achieve strong performance on both TSB-AD and UCR benchmarks, supporting them as competitive and practical approaches for univariate time series anomaly detection.

Mixture-of-Experts large language models (LLMs) scale efficiently through sparse activation, yet their deployment is fundamentally constrained by the large static parameter footprint of experts. Existing compression approaches either remove entire experts, disrupting routing topology and harming performance, or rely on unstructured weight pruning with limited practical efficiency. To address the limitations, we propose TENP, a structured Trapezoidal ExpertNeuron Pruning framework. Using a few samples, we identify and retain important experts, while applying expert neuron pruning (ENP) to less important experts, reserving model parameters in a trapezoidal pattern from shallow to deep layers. When evaluating expert importance, we jointly consider both the magnitude of the expert output and its ability to change the direction of the input vector. For ENP, we measure each neuron's projected contribution to the expert output to identify and retain important neurons. We conduct extensive experiments on the Qwen and DeepSeek models. Under a routing expert sparsity of 40% and an average of 63.76% activated expert parameters, the DeepSeek model suffers only a 1-point drop in accuracy compared to the full-parameter model. Moreover, it outperforms the full-parameter model by 10% on code generation tasks.

We study the generalization of ridge-regularized nonlinear least-squares models via on-average algorithmic stability, deriving error bounds for local minimizers in terms of a data-dependent effective dimension that reflects the geometry of the gradient model at the trained parameters, through the empirical Jacobian Gram matrix and a residual-curvature term. In the linear case, where the curvature term vanishes, this recovers the classical effective dimension of the Jacobian kernel covariance, but evaluated at the trained model rather than at initialization as is typical in neural tangent kernel analyses. We further bound this effective dimension via covering complexity of the gradient features, leading to guarantees that depend on learned geometry rather than parameter count. In particular, for manifold-supported data and piecewise Lipschitz Jacobians, the bounds scale with intrinsic dimension, while for one-hidden-layer ReLU networks, the mechanism can be made explicit through counts of activation-stable regions. Experiments on synthetic manifolds, clustered distributions, and benchmark datasets illustrate trained-Jacobian compression, the tightness of the residual-curvature linearization, and agreement between the stability bound and observed generalization gaps. A key feature of our bounds is the simplicity of their derivation, which follows from first principles using the Brascamp-Lieb inequality under strongly log-concave noise.

We introduce a new tool, Express, for converting a non-causal attention approximation into a causal approximation with matching approximation guarantees. When combined with the state-of-the-art Thinformer approximation, Express improves upon the best known causal attention guarantees, delivering $\log^{3/2}(n)/s$ approximation error with only $O(s)$ memory and $O(s^2 \log^2(n))$ compression overhead for a sequence of length $n$. We pair these developments with an efficient I/O-aware Triton implementation, demonstrate substantial speedups over FlashAttention 2, and use Express to overcome four resource bottlenecks in the language modeling pipeline: long-context prefill, KV cache compression, long-form memory-constrained decoding, and long-form compute-constrained decoding.

The analogy between deep neural network forward passes and renormalization group (RG) flows has been repeatedly noted in the literature, but existing treatments remain qualitative: depth is described as a coarse-graining scale, attention is likened to a partition function, and representations are said to flow toward fixed points. No existing work has defined a measurable RG order parameter, tested it under controlled variation of the input distribution, or made quantitative predictions that are empirically verified. We study the simplest architecture for which the analogy is tractable: a pure MLP residual stack trained on masked token prediction over synthetic Markov chain sequences with known spectral properties. We report three findings. (i) The effective rank of the residual stream decreases monotonically with depth after training, consistent with progressive integration of irrelevant degrees of freedom. (ii) This rank collapse is selective: it occurs for chains with short correlation length approximately 1 but is absent for chains with long correlation length approximately 7, measured at the position level to control for mean-pooling artifacts. The network preserves exactly the degrees of freedom relevant to the prediction task, the content of the RG relevance criterion. (iii) Inter-layer kernel drift is concentrated at one or two specific transitions, with the remainder of the network near a fixed point, consistent with a discrete fixed-point plateau. Together these findings constitute the first quantitative, position-level evidence that MLP residual networks implement a selective coarse-graining procedure governed by the spectral structure of the input distribution.

Embodied agents equipped with large language models (LLMs) and online constructed navigation maps can perform ObjNav in a zero-shot manner. However, existing agents heavily rely on giant LLMs on the cloud, e.g., GPT-4, while directly switching to small LLMs, e.g., LLaMA3.2-11b,

Recent advances in Scientific Machine Learning have shown that second-order methods can enhance the training of Physics-Informed Neural Networks (PINNs), making them a suitable alternative to traditional numerical methods for Partial Differential Equations (PDEs). However, second-order methods induce large memory requirements, making them scale poorly with the model size. In this paper, we define a local Mixture of Experts (MoE) combining the parameter-efficiency of ensemble models and sparse coding to enable the use of second-order training. Our model -- PINN Balls -- also features a fully learnable domain decomposition structure, achieved through the use of Adversarial Adaptive Sampling (AAS), which adapts the DD to the PDE and its domain. PINN Balls achieves better accuracy than the state-of-the-art in scientific machine learning, while maintaining invaluable scalability properties and drawing from a sound theoretical background.

Large Language Models (LLMs), such as OpenAI's o1 and DeepSeek's R1, excel at advanced reasoning tasks like math and coding via Reinforcement Learning with Verifiable Rewards (RLVR), but still struggle with puzzles solvable by humans without domain knowledge. We introduce ENIGMATA, the first comprehensive suite tailored for improving LLMs with puzzle reasoning skills. It includes 36 tasks across 7 categories, each with: 1) a generator that produces unlimited examples with controllable difficulty, and 2) a rule-based verifier for automatic evaluation. This generator-verifier design supports scalable, multi-task RL training, fine-grained analysis, and seamless RLVR integration. We further propose ENIGMATA-Eval, a rigorous benchmark, and develop optimized multi-task RLVR strategies.