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 capacity of the method to detect behaviorally relevant neural coordination.

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 and provide empirical evidence to support it. Leveraging this graphon representation, we derive a 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 state-of-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 sequence-function relationships, especially with small datasets. This work highlights the benefits of combining retrieval augmentation with multimodal, family-centric modeling for advancing protein foundation models.

We expand this analysis to 25 models and find that only 5 (Claude 3 Opus, Claude 3.5 Sonnet, Llama 3 405B, Grok 3, Gemini 2.0 Flash) comply with harmful queries more when they infer they are in training than when they infer they are in deployment. First, we study the motivations of these 5 models. Results from perturbing details of the scenario suggest that only Claude 3 Opus's compliance gap is primarily and consistently motivated by trying to keep its goals. Second, we investigate why many chat models don't fake alignment. Our results suggest this is not entirely due to a lack of capabilities: many base models fake alignment some of the time, and post-training eliminates alignment-faking for some models and amplifies it for others. We investigate 5 hypotheses for how post-training may suppress alignment faking and find that variations in refusal behavior may account for a significant portion of differences in alignment faking.

Autoregressive (AR) models have demonstrated strong potential in visual generation, offering competitive performance with simple architectures and optimization objectives. However, existing methods are typically limited to single-modality conditions, \eg, text or category labels, restricting their applicability in real-world scenarios that demand image synthesis from diverse forms of 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.

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 multi-turn 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.

Options markets represent one of the most sophisticated segments of the financial ecosystem, with prices that directly reflect market uncertainty. In this paper, we introduce the first reinforcement learning (RL) framework specifically designed for volatility trading through options, focusing on profit from the difference between implied volatility and realized volatility. Our multi-agent architecture consists of an Option Position Agent (OP-Agent) responsible for volatility timing by controlling long/short volatility positions, and a Hedger Routing Agent (HR-Agent) that manages risk and maximizes path-dependent profits by selecting optimal hedging strategies with different risk preferences. Evaluating our approach using cryptocurrency options data from 2021-2024, we demonstrate superior performance on BTC and ETH, significantly outperforming traditional strategies and machine learning baselines across all profit and risk-adjusted metrics while exhibiting sophisticated trading behavior.