Understanding how animals learn is a central challenge in neuroscience, with growing relevance to the development of animal-or human-aligned artificial intelligence. However, existing approaches tend to assume fixed parametric forms for the learning rule (e.g., Q-learning, policy gradient), which may not accurately describe the complex forms of learning employed by animals in realistic settings. Here we address this gap by developing a framework to infer learning rules directly from behavioral data collected during task learning. We assume that animals follow a decision policy parameterized by a generalized linear model (GLM), and we model their learning rule--the mapping from task covariates to per-trial weight updates--using a deep neural network (DNN). This formulation allows flexible, data-driven inference of learning rules while maintaining an interpretable form of the decision policy itself.

Modern deep generative models can now produce high-quality synthetic samples that are often indistinguishable from real training data. A growing body of research aims to understand why recent methods, such as diffusion and flow matching techniques, generalize so effectively. Among the proposed explanations are the inductive biases of deep learning architectures and the stochastic nature of the conditional flow matching loss. In this work, we rule out the noisy nature of the loss as a key factor driving generalization in flow matching. First, we empirically show that in high-dimensional settings, the stochastic and closed-form versions of the flow matching loss yield nearly equivalent losses. Then, using state-of-the-art flow matching models on standard image datasets, we demonstrate that both variants achieve comparable statistical performance, with the surprising observation that using the closed-form can even improve performance.

Graph Foundation Models (GFMs) have demonstrated remarkable potential across graph learning tasks but face significant challenges in knowledge updating and reasoning faithfulness. To address these issues, we introduce the Retrieval-Augmented Generation (RAG) paradigm for GFMs, which leverages graph knowledge retrieval. We propose RAG4GFM, an end-to-end framework that seamlessly integrates multi-level graph indexing, task-aware retrieval, and graph fusion enhancement. RAG4GFM implements a hierarchical graph indexing architecture, enabling multi-granular graph indexing while achieving efficient logarithmic-time retrieval. The task-aware retriever implements adaptive retrieval strategies for node, edge, and graph-level tasks to surface structurally and semantically relevant evidence. The graph fusion enhancement module fuses retrieved graph features with query features and augments the topology with sparse adjacency links that preserve structural and semantic proximity, yielding a fused graph for GFM inference.

Explaining complex machine learning models is a fundamental challenge when developing safe and trustworthy deep learning applications. To date, a broad selection of explainable AI (XAI) algorithms exist. One popular choice is SmoothGrad, which has been conceived to alleviate the well-known shattered gradient problem by smoothing gradients through convolution. SmoothGrad proposes to solve this high-dimensional convolution integral by sampling -- typically approximating the convolution with limited precision. Higher numbers of samples would amount to higher precision in approximating the convolution but also to higher computing demand, therefore in practice only few samples are used in SmoothGrad. In this work we propose a well founded novel method to resolve this tradeoff yielding a . Specifically, leverages automatic differentiation to decompose the expected values of Jacobians across a network architecture, directly targeting only the non-linearities responsible for shattered gradients and making it easy to implement. We demonstrate SmoothDiff's excellent speed and performance in a number of experiments and benchmarks. Thus, SmoothDiff greatly enhances the usability (quality and speed) of SmoothGrad -- a popular workhorse of XAI.

While RLHF has demonstrated promising results, many algorithms are highly sensitive to misspecifications in the underlying preference model (e.g., the Bradley-Terry model), the reference policy, or the reward function, resulting in undesirable fine-tuning. To address model misspecification, we propose a doubly robust preference optimization algorithm that remains consistent when either the preference model or the reference policy is correctly specified (without requiring both). Our proposal demonstrates superior and more robust performance than state-of-the-art algorithms, both in theory and in practice.

The remarkable performance of Large Language Models (LLMs) can be enhanced with test-time computation, which relies on external tools and even other deep learning models. However, existing approaches for integrating non-text modality representations into LLMs typically require additional costly supervised training, restricting on-the-fly adaptation to new domains and modalities. In this work, we explore the feasibility of integrating representations from non-text foundational models (FMs) into text-based LLMs in a training-free manner. We propose In-Context Representation Learning (ICRL) as a proof-of-concept to allow LLMs to adaptively utilize non-text modality representations with few-shot learning. Unlike traditional in-context learning, which incorporates text-label pairs, ICRL replaces text inputs with FM representations, enabling the LLM to perform multi-modal inference without fine-tuning. We evaluate ICRL on a suite of tasks in the molecular domain, investigating three core research questions: (i) how to map FM representations into LLMs in a training-free manner, (ii) what factors influence ICRL performance, and (iii) what mechanisms underlie the effectiveness of ICRL. To the best of our knowledge, ICRL is the first training-free framework for integrating non-text modality representations into text-based LLMs, presenting a promising direction for adaptable, multi-modal generalization.

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.