Directed acyclic graph (DAG) learning is a central task in structure discovery and causal inference. Although the field has witnessed remarkable advances over the past few years, it remains statistically and computationally challenging to learn a single (point estimate) DAG from data, let alone provide uncertainty quantification. We address the difficult task of quantifying graph uncertainty by developing a Bayesian variational inference framework based on novel, provably valid distributions that have support directly on the space of sparse DAGs. These distributions, which we use to define our prior and variational posterior, are induced by a projection operation that maps an arbitrary continuous distribution onto the space of sparse weighted acyclic adjacency matrices. While this projection is combinatorial, it can be solved efficiently using recent continuous reformulations of acyclicity constraints. We empirically demonstrate that our method, ProDAG, can outperform state-of-the-art alternatives in both accuracy and uncertainty quantification.

Decision-making in various fields, such as medicine, is heavily based on conditional average treatment effects (CATEs). Practitioners commonly make decisions by checking whether the estimated CATE is positive, even though the decision-making performance of modern CATE estimators (meta-learners) is poorly understood. In this paper, we study optimal decision-making based on two-stage meta-learners (e.g., DR-learner), which estimate CATE via a second-stage regression. We show that these meta-learners can be suboptimal when used for decision-making in common settings where the second-stage regression is over a restricted function class (e.g., when using regularization or employing fairness/interpretability constraints). Intuitively, this occurs because such estimators prioritize CATE accuracy in regions far away from the decision boundary, which is ultimately irrelevant to decision-making. As a remedy, we propose a novel two-stage learning objective that re-targets the CATE to balance CATE estimation error and decision performance. We then propose a neural method that optimizes an adaptively-smoothed approximation of our learning objective. Finally, we confirm the effectiveness of our method both empirically and theoretically.

The application of machine learning (ML) to electroencephalography (EEG) has great potential to advance both neuroscientific research and clinical applications. However, the generalisability and robustness of EEG-based ML models often hinge on the amount and diversity of training data. It is common practice to split EEG recordings into small segments, thereby increasing the number of samples substantially compared to the number of individual recordings or participants. We conceptualise this as a multi-level data generation process and investigate the scaling behaviour of model performance with respect to the overall sample size and the participant diversity through large-scale empirical studies. We then use the same framework to investigate the effectiveness of different ML strategies designed to address limited data problems: data augmentations and self-supervised learning. Our findings show that model performance scaling can be severely constrained by participant distribution shifts and provide actionable guidance for data collection and ML research. The code for our experiments is publicly available online.1

In this paper, we explore the asymptotically optimal tuning parameter choice in ridge regression for estimating nuisance functions of a statistical functional that has recently gained prominence in conditional independence testing and causal inference. Given a sample of size n, we study estimators of the Expected Conditional Covariance (ECC) between variables Y and Agiven a high-dimensional covariate X Rp. Under linear regression models for Y and A on X and the proportional asymptotic regime p/n c (0,), we evaluate three existing ECC estimators and two sample splitting strategies for estimating the required nuisance functions. Since no consistent estimator of the nuisance functions exists in the proportional asymptotic regime without imposing further structure on the problem, we first derive debiased versions of the ECC estimators that utilize the ridge regression nuisance function estimators. We show that our bias correction strategy yields n-consistent estimators of the ECC across different sample splitting strategies and estimator choices. We then derive the asymptotic variances of these debiased estimators to illustrate the nuanced interplay between the sample splitting strategy, estimator choice, and tuning parameters of the nuisance function estimators for optimally estimating the ECC. Our analysis reveals that prediction-optimal tuning parameters (i.e., those that optimally estimate the nuisance functions) may not lead to the lowest asymptotic variance of the ECC estimator - thereby demonstrating the need to be careful in selecting tuning parameters based on the final goal of inference. Finally, we verify our theoretical results through extensive numerical experiments.

Diffusion models have recently gained prominence in offline reinforcement learning due to their ability to effectively learn high-performing, generalizable policies from static datasets. Diffusion-based planners facilitate long-horizon decisionmaking by generating high-quality trajectories through iterative denoising, guided by return-maximizing objectives. However, existing guided sampling strategies such as Classifier Guidance, Classifier-Free Guidance, and Monte Carlo Sample Selection either produce suboptimal multi-modal actions, struggle with distributional drift, or incur prohibitive inference-time costs. To address these challenges, we propose Prior Guidance (PG), a novel guided sampling framework that replaces the standard Gaussian prior of a behavior-cloned diffusion model with a learnable distribution, optimized via a behavior-regularized objective. PG directly generates high-value trajectories without costly reward optimization of the diffusion model itself, and eliminates the need to sample multiple candidates at inference for sample selection. We present an efficient training strategy that applies behavior regularization in latent space, and empirically demonstrate that PG outperforms state-of-the-art diffusion policies and planners across diverse long-horizon offline RL benchmarks. Our code is available at https://github.com/ku-dmlab/PG.

Protein language models (PLMs) learn probability distributions over natural protein sequences. By learning from hundreds of millions of natural protein sequences, protein understanding and design capabilities emerge. Recent works have shown that scaling these models improves structure prediction, but does not seem to improve mutation understanding and representation quality for protein function prediction. We introduce PoET-2, a multimodal, retrieval-augmented protein foundation model that incorporates in-context learning of family-specific evolutionary constraints with optional structure conditioning to learn generative distributions over protein sequences. PoET-2 uses a hierarchical transformer encoder that is equivariant to sequence context ordering and a dual decoder architecture with both causal and masked language modeling objectives, allowing PoET-2 to operate in both fully generative and bidirectional representation learning modes. PoET-2 achieves stateof-the-art performance on zero-shot variant effect prediction, excelling at scoring variants with multiple mutations and challenging indel mutations. In supervised settings, PoET-2 embeddings outperform previous methods for learning sequencefunction relationships, especially with small datasets. This work highlights the benefits of combining retrieval augmentation with multimodal, family-centric modeling for advancing protein foundation models. 1

The power of foundation models (FMs) lies in their capacity to learn highly expressive representations that can be adapted to a broad spectrum of tasks. However, these pretrained models require additional training stages to become effective for downstream applications. In the multi-task setting, prior works have shown empirically that specific meta-learning approaches for preparing a model for future adaptation through parameter-efficient fine-tuning (PEFT) can outperform standard retraining methods, but the mechanism of the benefits of meta-learning has been largely unexplored. We introduce a framework for generic PEFT-based metalearning to learn a model that can easily adapt to unseen tasks. For linear models using LoRA, we show that standard retraining is provably suboptimal for finding an adaptable set of parameters and provide strict performance guarantees for our proposed method. We verify these theoretical insights through experiments on synthetic data as well as real-data vision and language tasks. We observe significant performance benefits using a simple implementation of our proposed meta-learning scheme during retraining relative to the conventional approach.

Sampling multiple outputs from a Large Language Model (LLM) and selecting the most frequent (Self-consistency) or highest-scoring (Best-of-N) candidate is a popular approach to achieve higher accuracy in tasks with discrete final answers. Best-of-N (BoN) selects the output with the highest reward, and with perfect rewards, it often achieves near-perfect accuracy. With imperfect rewards from reward models, however, BoN fails to reliably find the correct answer and its performance degrades drastically. We consider the distribution of BoN's outputs and highlight that, although the correct answer does not usually have a probability close to one under imperfect rewards, it is often the most likely outcome. This suggests that the mode of this distribution can be more reliably correct than a sample from it. Based on this idea, we propose Majority-of-the-Bests (MoB), a novel selection mechanism that estimates the output distribution of BoN via bootstrapping and selects its mode. Experimental results across five benchmarks, three different base LLMs, and two reward models demonstrate consistent improvements over BoN in 25 out of 30 setups. We also provide theoretical results for the consistency of the bootstrapping.

A challenge in human-AI decision-making is to balance three factors: the correctness of predictions, the cost of knowledge and reasoning complexity, and the confidence about whether to abstain from automated answers or escalate to human experts. In this work, we present a cascaded LLM decision framework that adaptively delegates tasks across multiple tiers of expertise - a base model for initial candidate answers, a more capable and knowledgeable (but costlier) large model, and a human expert for when the model cascade abstains.

Tree ensembles such as random forests (RFs) and gradient boosting machines (GBMs) are among the most widely used supervised learners, yet their theoretical properties remain incompletely understood. We adopt a spectral perspective on these algorithms, with two main contributions. First, we derive minimax-optimal convergence for RF regression, showing that, under mild regularity conditions on tree growth, the eigenvalue decay of the induced kernel operator governs the statistical rate. Second, we exploit this spectral viewpoint to develop compression schemes for tree ensembles. For RFs, leading eigenfunctions of the kernel operator capture the dominant predictive directions; for GBMs, leading singular vectors of the smoother matrix play an analogous role. Learning nonlinear maps for these spectral representations yields distilled models that are orders of magnitude smaller than the originals while maintaining competitive predictive performance. Our methods compare favorably to state of the art algorithms for forest pruning and rule extraction, with applications to resource constrained computing.