Causal mediation analysis is crucial for deconstructing complex mechanisms of action. However, in current mediation analysis, complex structures derived from causal discovery lack direct interpretation of mediation pathways, while traditional mediation analysis and effect estimation are limited by the reliance on pre-specified pathways, leading to a disconnection between structure discovery and causal mechanism understanding. Therefore, a unified framework integrating structure discovery, pathway identification, and effect estimation systematically quantifies mediation pathways under structural uncertainty, enabling automated identification and inference of mediation pathways. To this end, we propose Structure-Informed Guided Mediation Analysis (SIGMA), which guides automated mediation pathway identification through probabilistic causal structure discovery and uncertainty quantification, enabling end-to-end propagation of structural uncertainty from structure learning to effect estimation. Specifically, SIGMA employs differentiable Flow-Structural Equation Models to learn structural posteriors, generating diverse Directed Acyclic Graphs (DAGs) to quantify structural uncertainty. Based on these DAGs, we introduce the Path Stability Score to evaluate the marginal probability of pathways, identifying high-confidence mediation paths. For identified mediation pathways, we integrate Efficient Influence Functions with Bayesian model averaging to fuse within-structure estimation uncertainty and between-structure effect variation, propagating uncertainty to the final effect estimates. In synthetic data experiments, SIGMA achieves state-of-the-art performance in pathway identification accuracy and effect quantification precision under structural uncertainty, concurrent multiple pathways, and nonlinear scenarios. In real-world applications using Human Phenotype Project data, SIGMA identifies mediation effects of sleep quality on cardiovascular health through inflammatory and metabolic pathways, uncovering previously unspecified multiple mediation paths.

The model was pretrained on two of the largest neuroimaging datasets to date, encompassing 64,594 T1-weighted structural MRI 3D volumes (~14 million images) and 70,933 functional MRI (fMRI) time series. BrainHarmonix is grounded in two foundational neuroscience principles: structure complements function - structural and functional modalities offer distinct yet synergistic insights into brain organization; function follows structure brain functional dynamics are shaped by cortical morphology. The modular pretraining process involves single-modality training with geometric pre-alignment followed by modality fusion through shared brain hub tokens. Notably, our dynamics encoder uniquely handles fMRI time series with heterogeneous repetition times (TRs), addressing a major limitation in existing models. BrainHarmonix is also the first to deeply compress high-dimensional neuroimaging signals into unified, continuous 1D tokens, forming a compact latent space of the human brain. BrainHarmonix achieves strong generalization across diverse downstream tasks, including neurodevelopmental and neurodegenerative disorder classification and cognition prediction - consistently outperforming previous approaches. Our models - pretrained on 8 H100 GPUs - aim to catalyze a new era of AI-driven neuroscience powered by large-scale multimodal neuroimaging.

Inductive reasoning infers general rules from observed evidence, which is one of the most critical intelligence abilities. Previous works have succeeded in formal languages but suffer from onerous and error-prone conversions between a particular formal language and the working language. As large language models (LLMs) have emerged, direct reasoning with various kinds of languages, especially natural languages, without formal language involvement has become feasible. However, existing LLM-based inductive reasoning usually relies on LLM's intrinsic generation ability, which is prone to LLM's hallucination and lacks systematic guidance according to the nature of inductive reasoning. To this end, we propose HypoBootstrap, an integrated framework for inductive reasoning that generates and confirms hypotheses both in a bootstrapping manner. Regarding hypothesis generation, we propose a novel bootstrapping generation strategy, bootstrapping object hypotheses, relational hypotheses, and functional hypotheses successively, which assists LLM in observing the evidence from trivial patterns to non-trivial patterns. Regarding hypothesis confirmation, we utilize Glymour's theory of bootstrap confirmation, a hypothesis confirmation theory from the philosophy of science that can confirm a set of hypotheses. We use its principles to confirm the object hypotheses, relational hypotheses, and functional hypotheses. Empirical studies on four inductive reasoning scenarios of different natures, involving causal induction, concept learning, grammar learning, and abstract reasoning, demonstrate that HypoBootstrap significantly outperforms existing methods.

Prediction-Powered Inference (PPI) is a recently proposed statistical inference technique for parameter estimation that leverages pseudo-labels on both labeled and unlabeled data to construct an unbiased, low-variance estimator. In this work, we extend its core idea to semi-supervised learning (SSL) for model training, introducing a novel unbiased gradient estimator. This extension addresses a key challenge in SSL: while unlabeled data can improve model performance, its benefit heavily depends on the quality of pseudo-labels. Inaccurate pseudo-labels can introduce bias, leading to suboptimal models. To balance the contributions of labeled and pseudo-labeled data, we utilize an interpolation parameter and tune it on the fly, alongside the model parameters, using a one-dimensional online learning algorithm. We verify the practical advantage of our approach through experiments on both synthetic and real datasets, demonstrating improved performance over classic SSL baselines and PPI methods that tune the interpolation parameter offline.

Training reasoning language models (LMs) with reinforcement learning (RL) for one-hot correctness inherently relies on the LM being able to explore and solve its task with some chance at initialization. Furthermore, a key use case of reasoning LMs is to act as teachers for distilling new students and cold-starting future RL iterations rather than being deployed themselves. From these considerations, we introduce a new framework that avoids RL's exploration challenge by training a new class of Reinforcement-Learned Teachers (RLTs) focused on yielding the most effective downstream distillation. RLTs are prompted with both the question and solution to each problem, and tasked to simply "connect-the-dots" with detailed explanations tailored for their students. We train RLTs with dense rewards obtained by feeding each explanation to the student and testing its understanding of the problem's solution. In practice, the raw outputs of a 7BRLT provide higher final performance on competition and graduate-level tasks than existing distillation and cold-starting pipelines that collect and postprocess the reasoning traces of orders of magnitude larger LMs. Furthermore, RLTs maintain their effectiveness when training larger students and when applied zero-shot to out-of-distribution tasks, unlocking new levels of efficiency and re-usability for the RL reasoning framework.

We analyse how the sampling dynamics of distributions evolve in score-based diffusion models using cross-fluctuations, a centered-moment statistic from statistical physics. Specifically, we show that starting from an unbiased isotropic normal distribution, samples undergo sharp, discrete transitions, eventually forming distinct events of a desired distribution while progressively revealing finer structure. As this process is reversible, these transitions also occur in reverse, where intermediate states progressively merge, tracing a path back to the initial distribution. We demonstrate that these transitions can be detected as discontinuities in nth-order cross-fluctuations. For variance-preserving SDEs, we derive a closed-form for these cross-fluctuations that is efficiently computable for the reverse trajectory. We find that detecting these transitions directly boosts sampling efficiency, accelerates class-conditional and rare-class generation, and improves two zero-shot tasks-image classification and style transfer-without expensive grid search or retraining. We also show that this viewpoint unifies classical coupling and mixing from finite Markov chains with continuous dynamics while extending to stochastic SDEs and non Markovian samplers.

As language models scale, their performance improves dramatically across a wide range of tasks, but so does their tendency to memorize and regurgitate parts of their training data verbatim. This tradeoff poses serious legal, ethical, and safety concerns, especially in real-world deployments. Existing mitigation techniques, such as differential privacy or model unlearning, often require retraining or access to internal weights making them impractical for most users. In this work, we introduce TOKENSWAP, a lightweight, post-hoc defense designed for realistic settings where the user can only access token-level outputs. Our key insight is that while large models are necessary for high task performance, small models (e.g., DistilGPT-2) are often sufficient to assign fluent, grammatically plausible probabilities to common function words - and crucially, they memorize far less. By selectively swapping token probabilities between models, TOKENSWAP preserves the capabilities of large models while reducing their propensity for verbatim reproduction.

Transformers have theoretical limitations in modeling certain sequence-to-sequence tasks, yet it remains largely unclear if these limitations play a role in large-scale pretrained LLMs, or whether LLMs might effectively overcome these constraints in practice due to the scale of both the models themselves and their pretraining data. We explore how these architectural constraints manifest after pretraining, by studying a family of retrieval and copying tasks inspired by Liu et al. [2024a]. We use a recently proposed framework for studying length generalization [Huang et al., 2025] to provide guarantees for each of our settings.

We introduce AutoJudge1, a method that accelerates large language model (LLM) inference with task-specific lossy speculative decoding. Instead of matching the original model output distribution token-by-token, we identify the generated tokens that affect the downstream quality of the response, relaxing the distribution match guarantee so that the "unimportant" tokens can be generated faster. Our approach relies on a semi-greedy search algorithm to test which of the mismatches between target and draft models should be corrected to preserve quality and which ones may be skipped. We then train a lightweight classifier based on existing LLM embeddings to predict, at inference time, which mismatching tokens can be safely accepted without compromising the final answer quality. We evaluate AutoJudge with multiple draft/target model pairs on mathematical reasoning and programming benchmarks, achieving significant speedups at the cost of a minor accuracy reduction. Notably, on GSM8K with the Llama 3.1 70B target model, our approach achieves up to 2 speedup over speculative decoding at the cost of a 1% drop in accuracy. When applied to the LiveCodeBench benchmark, AutoJudge automatically detects programming-specific important tokens, accepting 25 tokens per speculation cycle at a 2% drop in Pass@1. Our approach requires no human annotation and is easy to integrate with modern LLM inference frameworks.

Model-free optimization methods typically rely on cost samples gathered by perturbing the current solution estimate along a finite and fixed set of directions. However, at each iteration, only the current cost samples are used, while potentially informative, previously collected samples are discarded. In this work, we challenge this conventional approach by introducing a simple yet effective memory mechanism that maintains an auxiliary vector of iteratively updated cost samples. By leveraging this stored information, our method estimates descent directions through an averaging of all perturbing directions weighted by the auxiliary vector components.