Mixture of Experts (MoE) models have emerged as the de facto architecture for scaling up language models without significantly increasing the computational cost. Recent MoE models demonstrate a clear trend towards high expert granularity (smaller expert intermediate dimension) and higher sparsity (constant number of activated experts with higher number of total experts), which improves model quality per FLOP. However, fine-grained MoEs suffer from increased activation memory footprint and reduced hardware efficiency due to higher IO costs, while sparser MoEs suffer from wasted computations due to padding in Grouped GEMM kernels. In response, we propose a memory-efficient algorithm to compute the forward and backward passes of MoEs with minimal activation caching for the backward pass. We also design GPU kernels that overlap memory IO with computation benefiting all MoE architectures. Finally, we propose a novel "token rounding" method that minimizes the wasted compute due to padding in Grouped GEMM kernels. As a result, our method SonicMoE reduces activation memory by 45% and achieves a 1.86x compute throughput improvement on Hopper GPUs compared to ScatterMoE's BF16 MoE kernel for a fine-grained 7B MoE. Concretely, SonicMoE on 64 H100s achieves a training throughput of 213 billion tokens per day comparable to ScatterMoE's 225 billion tokens per day on 96 H100s for a 7B MoE model training with FSDP-2 using the lm-engine codebase. On Blackwell GPUs, SonicMoE also achieves a 28.7% and 22.1% relative speedup on the forward and backward pass respectively compared to a highly optimized DeepGEMM baseline on OLMoE-sized 7B MoE models. Under high MoE sparsity settings, our tile-aware token rounding algorithm yields an additional 1.16x speedup on kernel execution time compared to vanilla top-K routing while maintaining similar downstream performance. We open-source all our kernels to enable faster MoE model training. An extended version of this paper can be found on arXiv.
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Applications · Chemistry and Drug Discovery
In organic reaction prediction, many recent approaches ranging from traditional task-specific models to Large Language Models (LLMs), have demonstrated notable success. However, these methods are inherently data-driven, exhibit constrained interpretability, and have hit fundamental performance bottlenecks. To overcome these limitations, we present Reaction-Thinker, a hybrid, knowledge‑and-data‑driven system that is enhanced by Retrieval‑Augmented Generation (RAG) and powered by advanced reasoning, improving both the interpretability of prediction process and the explainability of results. We develop similar-case retrieval database and train a RAG‑based LLM through supervised fine-tuning (SFT) to apply both reaction types and similar reaction cases as knowledge. We also construct a reaction reasoning chain-of-thought (CoT) dataset and train a reasoning-based LLM through SFT, then further optimize it using Group Relative Policy Optimization (GRPO). Experimental results show that our method outperforms all compared LLMs and task-specific models, achieving the highest accuracy (Exact Match) and fingerprint similarity (FTS). Ablation study indicates improvements in relative accuracy of 7.5% and 13.9% for RAG and GRPO, respectively. Further analysis of mispredictions reveals limitations in conventional evaluation metrics, which motivates our proposed benchmarking refinement.
In this work, we propose K-Flow, a novel generative learning paradigm that flows along the $K$-amplitude domain, where $K$ is a scaling parameter that organizes projected coefficients (frequency bands), and amplitude refers to the norm of such coefficients. We instantiate K-Flow with three concrete $K$-amplitude transformations: Fourier transformation, Wavelet transformation, and PCA. By incorporating the $K$-amplitude transformations, K-Flow enables flow matching across the scaling parameter as time. We discuss six properties of K-Flow, covering its theoretical foundations, energy and temporal dynamics, and practical applications. Specifically, from the perspective of practical usage, K-Flow allows for steerable generation by controlling the information at different scales. To demonstrate the effectiveness of K-Flow, we conduct experiments on both unconditional and conditional image generation tasks, showing that K-Flow achieves competitive performance. Furthermore, we perform three ablation studies to illustrate how K-Flow leverages the scaling parameter for controlled image generation. Additional results, including scientific applications, are also provided.
Video understanding, including video captioning and retrieval, is still a great challenge for video-language models (VLMs). The existing video retrieval and caption benchmarks only include short descriptions, limits their ability of detailed video understanding evaluation. To address this problem, we present CaReBench, a testing benchmark for fine-grained video Captioning and Retrieval with 1,000 high-quality pairs of videos and human-annotated detailed captions. Uniquely, it provides manually separated spatial annotations and temporal annotations for each video. Based on this design, we introduce two evaluation metrics, ReBias and CapST, specifically tailored for video retrieval and video captioning tasks, respectively. These metrics enable a comprehensive investigation into the spatial and temporal biases inherent in VLMs. In addition, to handle both video retrieval and video captioning tasks in a unified framework, we develop a simple baseline based on a Multimodal Language Model (MLLM). By implementing a two-stage Supervised Fine-Tuning (SFT), we fully unlock the potential of MLLM, enabling it not only to generate detailed video descriptions but also to extract video features. Surprisingly, experimental results demonstrate that, compared to the CLIP-based models designed for retrieval and the popular MLLMs skilled in video captioning, our baseline shows competitive performance in both fine-grained video retrieval and video detailed captioning.
Recent work has framed decision-making as a sequence modeling problem using generative models such as diffusion models. Although promising, these approaches often overlook latent factors that exhibit evolving dynamics, elements that are fundamental to environment transitions, reward structures, and high-level agent behavior. Explicitly modeling these hidden processes is essential for both precise dynamics modeling and effective decision-making. In this paper, we propose a unified framework that explicitly incorporates latent dynamic inference into generative decision-making from minimal yet sufficient observations. We theoretically show that under mild conditions, the latent process can be identified from small temporal blocks of observations. Building on this insight, we introduce Ada-Diffuser, a causal diffusion model that learns the temporal structure of observed interactions and the underlying latent dynamics simultaneously, and furthermore, leverages them for planning and control. With a modular design, Ada-Diffuser supports both planning and policy learning tasks, enabling adaptation to latent variations in dynamics, rewards, and latent actions. Experiments on locomotion and robotic manipulation benchmarks demonstrate its effectiveness in accurate latent inference, long-horizon planning, and adaptive policy learning
A common and effective human strategy to improve a poor outcome is to first identify prior experiences most relevant to the outcome and then focus on learning from those experiences. This paper investigates whether this human strategy can improve generalization of meta-reinforcement learning (MRL). MRL learns a meta-prior from a set of training tasks such that the meta-prior can adapt to new tasks in a distribution. However, the meta-prior usually has imbalanced generalization, i.e., it adapts well to some tasks but adapts poorly to others. We propose a two-stage approach to improve generalization. The first stage identifies "critical" training tasks that are most relevant to achieve good performance on the poorly adapted tasks. The second stage improves generalization by encouraging the meta-prior to pay more attention to the critical tasks. We use conditional mutual information to mathematically formalize the notion of "paying more attention". We formulate a bilevel optimization problem to maximize the conditional mutual information by augmenting the critical tasks and propose an algorithm to solve the bilevel optimization problem. We theoretically guarantee that (1) the algorithm converges at the rate of $O(1/\sqrt{K})$ and (2) the generalization improves after the task augmentation. We use two real-world experiments, two MuJoCo experiments, and a Meta-World experiment to validate the algorithm.
We study the problem of length generalization (LG) in transformers: the ability of a model trained on shorter sequences to maintain performance when evaluated on much longer, previously unseen inputs. Prior work by Huang et al. (2024) established that transformers eventually achieve length generalization once the training sequence length exceeds some finite threshold, but left open the question of how large it must be. In this work, we provide the first quantitative bounds on the required training length for length generalization to occur. Motivated by previous empirical and theoretical work, we analyze LG in several distinct problem settings: $\ell_\infty$ error control vs. average error control over an input distribution, infinite-precision softmax attention vs. finite-precision attention (which reduces to an argmax) in the transformer, as well as for one- or two-layer transformers. In all scenarios, we prove that LG occurs when the internal behavior of the transformer on longer sequences can be ``simulated'' by its behavior on shorter sequences seen during training. Our bounds give qualitative estimates for the required length of training data required for a transformer to generalize, and we verify these insights empirically. These results sharpen our theoretical understanding of the mechanisms underlying extrapolation in transformers, and formalize the intuition that richer training data is required for generalization on more complex tasks.
Vision-Language-Action (VLA) models have emerged as a powerful paradigm for robotic manipulation. Despite substantial progress enabled by large-scale pretraining and supervised fine-tuning (SFT), these models face two fundamental challenges: (i) the scarcity and high cost of large-scale robotic trajectories required for SFT scaling, and (ii) limited generalization to tasks under distribution shift. To overcome these limitations, we explore reinforcement learning (RL) as a pathway to scaling VLA training beyond limited datasets. Inspired by LLM breakthroughs where RL with outcome rewards enhances step-by-step reasoning, we ask: Can outcome-driven RL improve long-horizon step-by-step action planning of VLA? In this work, we introduce SimpleVLA-RL, an efficient RL framework tailored for VLA models. Building upon veRL, we introduce VLA-specific trajectory sampling, scalable parallelization, multi-environment rendering, and optimized loss computation. Applied to OpenVLA-OFT, SimpleVLA-RL achieves 99\% of SoTA performance on LIBERO and 80\% relative improvement on RoboTwin 1.0\&2.0, outperforming $\pi_0$ with our proposed exploration-enhancing strategies. SimpleVLA-RL reduces dependence on large-scale data, enables robust generalization, and remarkably surpasses SFT in real-world tasks. Moreover, we identify a novel phenomenon "pushcut'' during RL training, wherein the policy discovers unseen patterns beyond those seen in previous training process.
Fourier neural operator (FNO) has demonstrated substantial potential in learning mappings between function spaces, such as numerical partial differential equations (PDEs). However, FNO may suffer from inefficiencies when applied to large-scale, high-dimensional function spaces due to the computational overhead associated with high-dimensional Fourier and convolution operators. In this work, we introduce the Tucker-FNO, an efficient neural operator that decomposes the high-dimensional FNO into a series of 1-dimensional FNOs through Tucker decomposition, thereby significantly reducing computational complexity while maintaining expressiveness. Especially, by using the theoretical tools of functional decomposition in Sobolev space, we rigorously establish the universal approximation theorem of Tucker-FNO. Experiments on high-dimensional numerical PDEs such as Navier-Stokes, Plasticity, and Burger's equations show that Tucker-FNO achieves substantial improvement in execution time and performance over FNO. Moreover, by virtue of the compact Tucker decomposition, Tucker-FNO generalizes seamlessly to high-dimensional visual signals by learning mappings from the positional encoding space to the signal's implicit neural representations (INRs). Under this operator INR framework, Tucker-FNO gains consistent improvements on continuous signal restoration over traditional INR methods in terms of efficiency and accuracy.
Applications · Chemistry and Drug Discovery
Graph generation plays an important role in various domains such as molecular design, protein prediction, and drug discovery. However, generating graph-structured data poses challenges due to the complex dependencies inherent in graphs, spanning from intricate local substructures to broad global topologies. Although recent advances in graph-generative models have made notable progress, traditional node-level generative paradigms may have difficulty simultaneously capturing the multiscale dependencies in graphs. To address these challenges, we propose a unified latent diffusion model that jointly learns local and global topological information, enabling effective and efficient graph generation. Besides, our approach introduces a dual conditioning mechanism designed to promote dynamic interaction between local and global information, equipping the generative model with global and local awareness to better capture the coupled dependencies within graphs. Our method can largely promote the joint modeling of global and local information and substantially improve the quality of the generated graphs. Extensive experiments consistently demonstrate the effectiveness of our method.
Deep Learning · Everything Else
Outlier detection (OD), distinguishing inliers and outliers in completely unlabeled datasets, plays a vital role in science and engineering. Although there have been many insightful OD methods, most of them require troublesome hyperparameter tuning (a challenge in unsupervised learning) and costly model training for every task or dataset. In this work, we propose UniOD, a universal OD framework that leverages labeled datasets to train a single model capable of detecting outliers of datasets with different feature dimensions and heterogeneous feature spaces from diverse domains. Specifically, UniOD extracts uniform and comparable features across different datasets by constructing and factorizing multi-scale point-wise similarity matrices. It then employs graph neural networks to capture comprehensive within-dataset and between-dataset information simultaneously, and formulates outlier detection tasks as node classification tasks. As a result, once the training is complete, UniOD can identify outliers in datasets from diverse domains without any further model/hyperparameter selection and parameter optimization, which greatly improves convenience and accuracy in real applications. More importantly, we provide theoretical guarantees for the effectiveness of UniOD, consistent with our numerical results. We evaluate UniOD on 30 benchmark OD datasets against 17 baselines, demonstrating its effectiveness and superiority.
Social Aspects · Fairness, Equity, Justice and Safety
Fine-tuning on open-source Large Language Models (LLMs) with proprietary data is now a standard practice for downstream developers to obtain task-specific models. Surprisingly, we reveal a new and concerning risk along with the practice: the provider of the open-source LLMs can later extract the private downstream fine-tuning data through simple backdoor training, only requiring black-box access to the fine-tuned downstream model. Our comprehensive experiments, across 4 popularly used open-source models with 3B to 32B parameters and 2 downstream datasets, suggest that the extraction performance can be strikingly high: in practical settings, as much as 76.3\% downstream fine-tuning data (queries) out of a total 5,000 samples can be perfectly extracted, and the success rate can increase to 94.9\% in more ideal settings. We further investigate several defense strategies, but none achieve satisfactory effectiveness in mitigating the risk. Overall, we highlight the emergency of this newly identified data breaching risk in fine-tuning, and we hope more follow-up research can push the progress of addressing this concerning risk. Our code is available at \url{https://github.com/thu-coai/Backdoor-Data-Extraction}.
The growing use of large language models (LLMs) for sensitive applications has highlighted the need for effective watermarking techniques to ensure the provenance and accountability of AI-generated text. However, most existing watermarking methods require access to the decoding process, limiting their applicability in real-world settings. One illustrative example is the use of LLMs by dishonest reviewers in the context of academic peer review, where conference organizers have no access to the model used but still need to detect AI-generated reviews. Motivated by this gap, we introduce In-Context Watermarking (ICW), which embeds watermarks into generated text solely through prompt engineering, leveraging LLMs' in-context learning and instruction-following abilities. We investigate four ICW strategies at different levels of granularity, each paired with a tailored detection method. We further examine the Indirect Prompt Injection (IPI) setting as a specific case study, in which watermarking is covertly triggered by modifying input documents such as academic manuscripts. Our experiments validate the feasibility of ICW as a model-agnostic, practical watermarking approach. Moreover, our findings suggest that as LLMs become more capable, ICW offers a promising direction for scalable and accessible content attribution. Our code is available at \url{https://github.com/yepengliu/In-Context-Watermarks}.
Deep Learning · Everything Else
Large language model agents operate in partially observable, long-horizon settings where obtaining supervision remains a major bottleneck. We address this by utilizing a source of supervision overlooked in existing post-training methods: unintended yet successful goals embedded within agent rollouts. Specifically, we introduce Hindsight Supervised Learning (HSL), where an auxiliary LLM reviews each completed trajectory and relabels it with all of the natural-language goals the agent actually achieved. HSL then pairs the trajectory with its relabeled goals and uses these pairs for additional fine-tuning. To mitigate suboptimality in the relabeled data, we propose two learning techniques for HSL, irrelevant-action masking and sample reweighting. Our experiments show that HSL is flexible and compatible with existing post-training pipelines. It improves both SFT and DPO, with larger gains on long-horizon tasks with more diverse goal spaces. Moreover, HSL is sample-efficient: on ALFWorld, it surpasses baselines trained on the full dataset while using only one quarter of the ground-truth demonstrations.
Deep Learning · Graph Neural Networks
Counterfactual explanations offer an intuitive way to interpret graph neural networks (GNNs) by identifying minimal changes that alter a model’s prediction, thereby answering “what must differ for a different outcome?”. In this work, we propose a novel framework, ATEX-CF that unifies adversarial attack techniques with counterfactual explanation generation—a connection made feasible by theirshared goal of flipping a node’s prediction, yet differing in perturbation strategy:adversarial attacks often rely on edge additions, while counterfactual methods typically use deletions. Unlike traditional approaches that treat explanation and attack separately, our method efficiently integrates both edge additions and deletions, grounded in theory, leveraging adversarial insights to explore impactful counterfactuals. In addition, by jointly optimizing fidelity, sparsity, and plausibility under a constrained perturbation budget, our method produces instance-level explanations that are both informative and realistic. Experiments on synthetic and real-world node classification benchmarks demonstrate that ATEX-CF generates faithful, concise, and plausible explanations, highlighting the effectiveness of integrating adversarial insights into counterfactual reasoning for GNNs.
Deep Learning · Graph Neural Networks
Graph Neural Networks (GNNs) achieve strong empirical performance across domains, yet their fundamental statistical behavior remains poorly understood. This paper develops a minimax analysis of ReLU message-passing GNNs with explicit architectural assumptions, in both inductive (graph-level) and transductive (node-level) settings. For arbitrary graphs without structural constraints, we show that the worst-case generalization error scales as $\sqrt{\log d / n}$ with sample size $n$ and input dimension $d$, matching the $1/\sqrt{n}$ behavior of feed-forward networks. Under a spectral--homophily condition combining strong label homophily and bounded spectral expansion, we prove a stronger minimax lower bound of $d/\log n$ for transductive node prediction. We complement these results with a systematic empirical study on three large-scale benchmarks (ogbn\_arxiv, ogbn\_products\_50k, Reddit\_50k) and two controlled synthetic datasets representing the worst-case and structured regimes of our theory. All benchmark graphs we study fall in the slow-mixing, bottlenecked regime captured by our spectral-homophily condition, and ratio-based scaling tests show error decay consistent with the $d/\log n$ rate in real and structured settings, while the worst-case synthetic dataset follows the $\sqrt{\log d / n}$ curve. Together, these results indicate that practical GNN tasks often operate in the spectral-homophily regime, where our lower bound $d/\log n$ is tight and effective sample complexity is driven by graph topology rather than universal $1/\sqrt{n}$ behavior.
Deep Learning · Graph Neural Networks
Retrieval-Augmented Generation (RAG) enhances the reasoning ability of Large Language Models (LLMs) by dynamically integrating external knowledge, thereby mitigating hallucinations and strengthening contextual grounding for structured data such as graphs. Nevertheless, most existing RAG variants for textual graphs concentrate on low-dimensional structures—treating nodes as entities (0-dimensional) and edges or paths as pairwise or sequential relations (1-dimensional), but overlook cycles, which are crucial for reasoning over relational loops. Such cycles often arise in questions requiring closed-loop inference about similar objects or relative positions. This limitation often results in incomplete contextual grounding and restricted reasoning capability. In this work, we propose Topology-enhanced Retrieval-Augmented Generation (TopoRAG), a novel framework for textual graph question answering that effectively captures higher dimensional topological and relational dependencies. Specifically, TopoRAG first lifts textual graphs into cellular complexes to model multi-dimensional topological structures. Leveraging these lifted representations, a topology-aware subcomplex retrieval mechanism is proposed to extract cellular complexes relevant to the input query, providing compact and informative topological context. Finally, a multi-dimensional topological reasoning mechanism operates over these complexes to propagate relational information and guide LLMs in performing structured, logic-aware inference. Empirical evaluations demonstrate that our method consistently surpasses existing baselines across diverse textual graph tasks.
Deep Learning · Graph Neural Networks
Graph Neural Networks (GNNs) excel at learning from pairwise interactions but often overlook multi-way and hierarchical relationships. Topological Deep Learning (TDL) addresses this limitation by leveraging combinatorial topological spaces, such as simplicial or cell complexes. However, existing TDL models are restricted to undirected settings and fail to capture the higher-order directed patterns prevalent in many complex systems, e.g., brain networks, where such interactions are both abundant and functionally significant. To fill this gap, we introduce Semi-Simplicial Neural Networks (SSNs), a principled class of TDL models that operate on semi-simplicial sets---combinatorial structures that encode directed higher-order motifs and their directional relationships. To enhance scalability, we propose Routing-SSNs, which dynamically select the most informative relations in a learnable manner. We theoretically characterize SSNs by proving they are strictly more expressive than standard graph and TDL models, and they are able to recover several topological descriptors. Building on previous evidence that such descriptors are critical for characterizing brain activity, we then introduce a new principled framework for brain dynamics representation learning centered on SSNs. Empirically, we test SSNs on 4 distinct tasks across 13 datasets, spanning from brain dynamics to node classification, showing competitive performance. Notably, SSNs consistently achieve state-of-the-art performance on brain dynamics classification tasks, outperforming the second-best model by up to 27\%, and message passing GNNs by up to 50\% in accuracy. Our results highlight the potential of topological models for learning from structured brain data, establishing a unique real-world case study for TDL. Code and data are uploaded as supplementary material.
Deep Learning · Everything Else
Transformers have achieved remarkable success across a wide range of applications, a feat often attributed to their scalability. Yet training them without residual (skip) connections remains notoriously difficult. While skips stabilize optimization, they also disrupt the hierarchical structure of representations, raising the long-standing question of whether transformers can be trained efficiently without them. In this work, we address this problem by analyzing the Jacobian of a skipless transformer block, showing why residuals improve conditioning and revealing that their stabilization benefits can be recovered through a principled initialization strategy. Building on this insight, we introduce the first method that enables stable and efficient training of skipless transformers without altering the standard architecture. We validate our approach on Vision Transformers (ViTs) in both supervised and self-supervised settings, demonstrating that skipless ViTs trained with our initialization overcome the usual optimization barriers, learn richer hierarchical representations, and outperform strong residual baselines on dense prediction benchmarks. These results show that skip connections are not a fundamental requirement for training ViTs and open new avenues for hierarchical representation learning in vision models.
Deep Learning · Graph Neural Networks
As a topological invariant for discrete structures, discrete curvature has been widely adopted in the study of complex networks and graph neural networks. A prevailing viewpoint posits that edges with highly negative curvature will induce graph bottlenecks and the over-squashing phenomenon. In this paper, we critically re-examine this view and put forward our central claim: **high negative curvature is a sufficient but not a necessary condition for over-squashing**. We first construct a family of counterexamples demonstrating the failure of discrete curvature, where some edges are severely squashed, but the curvature still appears positive. Furthermore, extensive experiments demonstrate that the most commonly used discrete curvature measure --- Ollivier–Ricci curvature --- fails to detect as many as 30%~40% of over-squashed edges. To alleviate this limitation, we propose Weighted Augmented Forman-3 Curvature ($\mathsf{WAF3}$), which significantly improves the detection of over-squashed edges. Additionally, we develop a highly efficient approximation algorithm for $\mathsf{WAF3}$, enabling curvature computation on graphs with five million edges in only 23.6 seconds, which is 133.7 times faster than the existing algorithm with the lowest complexity for curvatures.