Understanding the evolving dependence between two sets of multivariate signals is fundamental in neuroscience and other domains where sub-networks in a system interact dynamically over time. Despite the growing interest in multivariate time series analysis, existing methods for between-clusters dependence typically rely on the assumption of stationarity and lack the temporal resolution to capture transient, frequency-specific interactions. To overcome this limitation, we propose scale-specific wavelet canonical coherence (WaveCanCoh), a novel framework that extends canonical coherence analysis to the nonstationary setting by leveraging the multivariate locally stationary wavelet model. The proposed WaveCanCoh enables the estimation of time-varying canonical coherence between clusters, providing interpretable insight into scale-specific time-varying interactions between clusters. Through extensive simulation studies, we demonstrate that WaveCanCoh accurately recovers true coherence structures under both locally stationary and general nonstationary conditions. Application to local field potential (LFP) activity data recorded from the hippocampus reveals distinct dynamic coherence patterns between correct and incorrect memory-guided decisions, illustrating the capacity of the method to detect behaviorally relevant neural coordination.

LLM-based web agents have recently made significant progress, but much of it has occurred in closed-source systems, widening the gap with open-source alternatives. Progress has been held back by two key challenges, first, a narrow focus on singlestep tasks that overlooks the complexity of multi-step web interactions, and second, the high compute costs required to post-train LLM-based web agents. To address this, we present the first statistically grounded study on compute allocation for LLM web-agent post-training. Our approach uses a two-stage pipeline, training a Llama 3.1 8B student to imitate a Llama 3.3 70B teacher via SFT, followed by on-policy reinforcement learning. We find this process highly sensitive to hyperparameter choices in setting where exhaustive sweeps are impractical. To spare others from expensive trial-and-error, we sample 1,370 configurations and use bootstrapping to estimate effective hyperparameters. Our results show that combining SFT with on-policy RL consistently outperforms either approach alone on both WorkArena and MiniWob++. Further, this strategy only requires 55% of the compute to match the peak of pure SFT on MiniWob++, pushing the compute-performance Pareto frontier and is the only strategy that can close the gap with closed-source models.

Sparse neural networks promise efficiency, yet training them effectively remains a fundamental challenge. Despite advances in pruning methods that create sparse architectures, understanding why some sparse structures are better trainable than others with the same level of sparsity remains poorly understood. Aiming to develop a systematic approach to this fundamental problem, we propose a novel theoretical framework based on the theory of graph limits, particularly graphons, that characterizes sparse neural networks in the infinite-width regime. Our key insight is that connectivity patterns of sparse neural networks induced by pruning methods converge to specific graphons as networks' width tends to infinity, which encodes implicit structural biases of different pruning methods. We postulate the Graphon Limit Hypothesis and provide empirical evidence to support it. Leveraging this graphon representation, we derive a Graphon Neural Tangent Kernel (Graphon NTK) to study the training dynamics of sparse networks in the infinite width limit. Graphon NTK provides a general framework for the theoretical analysis of sparse networks. We empirically show that the spectral analysis of Graphon NTK correlates with observed training dynamics of sparse networks, explaining the varying convergence behaviours of different pruning methods. Our framework provides theoretical insights into the impact of connectivity patterns on the trainability of various sparse network architectures.

Equivariant neural networks have proven to be effective for tasks with known underlying symmetries. However, optimizing equivariant networks can be tricky and best training practices are less established than for standard networks. In particular, recent works have found small training benefits from relaxing equivariance constraints. This raises the question: do equivariance constraints introduce fundamental obstacles to optimization? Or do they simply require different hyperparameter tuning?

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

Autoregressive (AR) models have demonstrated strong potential in visual generation, offering superior performance with simple architectures and optimization objectives. However, existing methods are typically limited to single-modality conditions, e.g., text, restricting their applicability in real-world scenarios that demand image synthesis from diverse controls.

Low-Rank Adaptation (LoRA) has emerged as a highly efficient framework for finetuning the weights of large foundation models, and has become the go-to method for data-driven customization of LLMs. Despite the promise of highly customized behaviors and capabilities, switching between relevant LoRAs in a multiturn setting is inefficient, as the key-value (KV) cache of the entire turn history must be recomputed with the LoRA weights before generation can begin. To address this problem, we propose Activated LoRA (aLoRA), an adapter architecture which modifies the LoRA framework to only adapt weights for the tokens in the sequence after the aLoRA is invoked. This change crucially allows aLoRA to accept the base model's KV cache of the input string, meaning that aLoRA can be instantly activated whenever needed in a chain without recomputing the prior keys and values. This enables building what we call intrinsics, i.e. specialized models invoked to perform well-defined operations on portions of an input chain or conversation that otherwise uses the base model by default. We train a set of aLoRA-based intrinsics models, demonstrating competitive accuracy with standard LoRA while significantly improving inference efficiency. We contributed our Activated LoRA implementation to the Huggingface PEFT library.1

Human-centered images often suffer from severe generic degradation during transmission and are prone to human motion blur (HMB), making restoration challenging. Existing research lacks sufficient focus on these issues, as both problems often coexist in practice. To address this, we design a degradation pipeline that simulates the coexistence of HMB and generic noise, generating synthetic degraded data to train our proposed HAODiff, a human-aware one-step diffusion. Specifically, we propose a triple-branch dual-prompt guidance (DPG), which leverages high-quality images, residual noise (LQ minus HQ), and HMB segmentation masks as training targets. It produces a positive-negative prompt pair for classifier-free guidance (CFG) in a single diffusion step. The resulting adaptive dual prompts let HAODiff exploit CFG more effectively, boosting robustness against diverse degradations. For fair evaluation, we introduce MPII-Test, a benchmark rich in combined noise and HMB cases. Extensive experiments show that our HAODiff surpasses existing state-of-the-art (SOTA) methods in terms of both quantitative metrics and visual quality on synthetic and real-world datasets, including our introduced MPII-Test. Code is available at: https://github.com/gobunu/HAODiff.

Large Language Models (LLMs) are increasingly used to simulate human users in interactive settings such as therapy, education, and social role-play. While these simulations enable scalable training and evaluation of AI agents, off-the-shelf LLMs often drift from their assigned personas, contradict earlier statements, or abandon role-appropriate behavior. We introduce a unified framework for evaluating and improving persona consistency in LLM-generated dialogue. We define three automatic metrics--prompt-to-line consistency, line-to-line consistency, and Q&A consistency--that capture different types of persona drift and validate each against human annotations. Using these metrics as reward signals, we apply multiturn reinforcement learning to fine-tune LLMs for three user roles: a patient, a student, and a social chat partner. Our method reduces inconsistency by over 55%, resulting in more coherent, faithful, and trustworthy simulated users.

Predicting protein complex structures is essential for protein function analysis, protein design, and drug discovery. While AI methods like AlphaFold can predict accurate structural models for many protein complexes, reliably estimating the quality of these predicted models (estimation of model accuracy, or EMA) for model ranking and selection remains a major challenge. A key barrier to developing effective machine learning-based EMA methods is the lack of large, diverse, and well-annotated datasets for training and evaluation. To address this gap, we introduce PSBench, a benchmark suite comprising five large-scale, labeled datasets, four of which were generated during the 15th and 16th community-wide Critical Assessment of Protein Structure Prediction (CASP15 and CASP16), and one curated for new Protein Data Bank (PDB) entries deposited between July 2024 and August 2025. PSBench includes over 1.4 million structural models covering a wide range of protein sequence lengths, complex stoichiometries, functional classes, and modeling difficulties. Each model is annotated with multiple complementary quality scores at the global, local, and interface levels. PSBench also provides multiple evaluation metrics and baseline EMA methods to facilitate rigorous comparisons. To demonstrate PSBench's utility, we trained and evaluated GATE, a graph transformer-based EMA method, on the CASP15 data. GATE was blindly tested in CASP16 (2024), where it ranked among the top-performing EMA methods.