NeurIPS 2026 论文列表

Conference on Neural Information Processing Systems

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6,437篇论文

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主题: 驾驶仿真 · 940 篇论文 · 重置筛选

Optimizing Computational-Statistical Runtime for Wasserstein Distance Estimation

Peter M Jacobs, Jeff M. Phillips

展开摘要

Squared Wasserstein distance is a frequently used tool to compare probability distributions. This distance is typically computed between empirical measures of size $n$ from two underlying random samples. Unfortunately, even in lower dimensional Euclidean space problems $\left( d \in \{2,3\} \right)$, Wasserstein distance algorithms with approximate or exact precision guarantees scale poorly in the runtime as a function of $n$ and the desired precision. In response, we consider the computational-statistical runtime, where the goal to estimate from samples the Wasserstein distance up to the $\varepsilon$-additive error which is achievable under a sample; we allow $O(1)$ time per sample. Towards this, we develop a Sample-Sketch-Solve paradigm where we introduce a regular cartesian grid sketch of the samples. We show that (especially under $\alpha$-H\"older smooth distributions) this can compress the data without increasing asymptotic error, and also regularizes the structure which enables faster exact algorithms. Ultimately, we approximate $W_2^2(P,Q)$ within $\varepsilon$ error in $\varepsilon^{-\max(2,\frac{d+1+o(1)}{2})}$ time for Lipschitz $P,Q$ on $(0,1)^d$; nearly an optimal $\Theta(\varepsilon^{-2})$ for $d \leq 3$.

Poster
Optimal Risk Bounds of Stochastic Gradient Descent for Shallow ReLU Networks

Yuqing Liu, Yunwen Lei

展开摘要

Recent work shows that gradient descent (GD) can achieve almost optimal risk bounds for shallow ReLU networks with a logarithmic width. However, these discussions require $O(n^2)$ gradient computations to achieve this optimality, which is not appealing for modern machine learning problems with large sample size $n$. In this paper, we significantly improve the existing gradient complexity by showing that stochastic gradient descent (SGD) can achieve similar risk bounds with $O(n)$ gradient computations for shallow ReLU networks with a logarithmic width. As compared to GD, the analysis with SGD is more challenging as there are additional fluctuations incurred by the stochastic gradient noise along the optimization process. With concentration inequalities to handle these fluctuations, we show that the entire SGD trajectory stays around its initialization point with high probability. Under an NTK separability condition with margin $\gamma$, we show SGD achieves near-optimal risk bounds $\widetilde{O}(1/(n\gamma^2))$ with a logarithmic width.

Poster
Optimal Dimension-Free Sampling for Regularized Classification

Meyam Alishahi, Alexander Munteanu, Simon Omlor, Jeff M. Phillips

展开摘要

We prove optimal sampling bounds achieving $(1\pm\varepsilon)$-relative error for a broad class of Lipschitz continuous classification loss functions under various regularization terms. This includes important functions such as logistic and sigmoid loss, hinge loss, and ReLU loss, as prominent and popular representative examples. In particular, we prove $k^2/\varepsilon^2$ upper and lower bounds for $\|\cdot\|_2/k$ regularization, and $k/\varepsilon^2$ upper and lower bounds for $\|\cdot\|_1/k$ regularization. For $\|\cdot\|_2^2/k$ regularization, the sampling complexity depends mainly on a bounded derivative property: if $|g'(x)|\leq g(x)$, and $g(0)>0$, and $g$ is monotonic or convex, then it admits linear in $k$ sampling complexity; otherwise the general bound is $k^2/\varepsilon^2$. However, if $g(0)=0$, our results indicate that no dimension-free bounds are possible, and even sublinear bounds are ruled out. All upper bounds are complemented by matching lower bounds up to polylogarithmic terms. Moreover, our work relies conceptually and algorithmically on simple uniform or (squared) norm sampling and hereby improves over recent cubic $k^3/\varepsilon^2$ sensitivity sampling bounds of (Alishahi and Phillips, ICML'24). This is achieved by refined arguments involving higher moment bounds and empirical process analyses to avoid overcounting that appears in the de-facto standard VC-dimension and sensitivity framework.

Poster
OpenSanctions Pairs: A Large-Scale Dataset for Pairwise Entity Matching

Chandler Smith, Magnus Sesodia, Friedrich Lindenberg, Christian Schroeder de Witt

展开摘要

We release OpenSanctions Pairs, the first large-scale public benchmark for entity matching on sanctions and OSINT data. The dataset includes 755,540 expert-labeled pairs over 1 million entities, aggregated from 293 source datasets across 45 jurisdictions. It captures real-world diversity in compliance data, spanning multiple languages and writing systems (e.g., Latin, Cyrillic, Arabic), inconsistent structure, and time-varying provenance, and is substantially more heterogeneous than prior entity matching benchmarks. As baselines, we evaluate the production rule-based matcher (nomenklatura RegressionV1) alongside open- and closed-source LLMs in both zero- and few-shot settings, each tested with and without MIPROv2 prompt optimization to control for prompt sensitivity. The rule-based baseline reaches 91.3\% F1; GPT-4o achieves the best result at 99.0\% F1, and a locally deployable open-source model (DeepSeek-R1-Distill-Qwen-14B) achieves 98.2\% F1. The rule-based baseline and LLMs fail in complementary ways: rules over-match, while LLMs struggle with cross-script transliteration. These results suggest that pairwise matching performance is approaching a practical ceiling and shift attention toward pipeline components such as blocking, clustering, and uncertainty-aware review.

Poster
Online Quantile Omniprediction for Proper Losses

Hyunsuk Kim, Isaac Gibbs, Michael Mahoney, Ryan Tibshirani

展开摘要

The task of constructing a predictor that is simultaneously accurate under multiple evaluation metrics has been popularized recently under the name omniprediction. Prior work in this area has largely focused on binary prediction tasks, and existing results for multiclass and continuous outcomes typically suffer from slow error rates. In this paper, we consider forecasts expressed as a set of quantiles over a discrete but otherwise arbitrary set of probability levels. We develop sample-efficient algorithms for constructing forecasts that are simultaneously accurate across all proper losses that satisfy mild regularity conditions, where proper losses are those minimized by predicting the true quantiles. Our algorithms are online and can operate in a dynamic environment while simultaneously taking multiple losses into account, and their forecasts offer the potential to provide diverse end-users with rich information for evaluating risk and informing a range of practical decision-making tasks. As an example, we demonstrate how our procedure can be used to ensemble quantile forecasts of COVID-19 hospitalizations made by experts during the pandemic.

Poster
One-Bit Clustering for Two Component Sub-Gaussian Mixture Models

Junren Chen, Yun Yang

展开摘要

Clustering is a fundamental problem in statistics and machine learning. We propose the first one bit clustering method for two-component sub Gaussian mixture models. The method uses only one bit per entry of each sample obtained via a dithered quantizer. Under a mild non-spikiness condition on the cluster centers, we show that a variant of Lloyd’s algorithm achieves a misclassification rate that decays exponentially with a signal to noise ratio comparable to that in the unquantized setting. This result further implies exact recovery under an explicit separation condition, which exceeds the optimal threshold for unquantized data by only a logarithmic factor. When the dimension $p$ is sufficiently large, the non-spikiness condition can be enforced by applying a random rotation using a Haar distributed matrix prior to quantization. In particular, it holds with high probability when $p \gtrsim 1$ for partial recovery and $p \gtrsim \log n \log\log n$ for exact recovery, where $n$ is the sample size. We also establish a minimax lower bound, showing that the misclassification rate and separation condition are in general optimal up to constants. Numerical results are provided to corroborate the theory and demonstrate the efficacy of the proposed method.

Poster
One World, Dual Timeline: Decoupled Spatio-Temporal Gaussian Scene Graph for 4D Cooperative Driving Reconstruction

Yulong Chen, Xiaoyun Dong, Haoyu Zhang, Zongxian Yang, Lewei Xie, Xinke Li, Yifan Zhang, Kai Wang, Jianping Wang

展开摘要

Reconstructing dynamic scenes from Vehicle-to-Infrastructure Cooperative Autonomous Driving (VICAD) data is fundamentally complicated by temporal asynchrony: vehicle and infrastructure cameras operate on independent clocks, capturing the same dynamic agent such as cars and pedestrians at different physical times. Existing Gaussian Scene Graph methods implicitly assume synchronized observations and assign a single pose per agent per frame, which is an assumption that breaks in cooperative settings, where the resulting gradient conflicts cause severe ghosting on dynamic agents. We identify this as a \textit{representation-level failure}, not an optimization artifact: we prove that any single-timeline formulation incurs an irreducible photometric loss scaling quadratically with agent velocity and cross-source time offset. To resolve this, we propose Dust (DecoUpled Spatio-Temporal) Gaussian Scene Graph for 4D Cooperative Driving Reconstruction. DUST Gaussian Scene Graph shares a canonical Gaussian set per agent for appearance consistency, while maintaining decouple pose trajectories aligned to each source's true capture timestamps. We prove that this decoupling enables the pose-gradient kernel block-diagonal, eliminating cross-source interference entirely. To make Dust practical, we further introduce a static anchor-based pose correction pipeline that corrects spatio misalignment between vehicle and infrastructure annotations, and a pose-regularized joint optimization scheme that prevents trajectory jitter and drift during early training. On 26 sequences from V2X-Seq, DUST achieves state-of-the-art performance, improving dynamic-area PSNR by 3.2 dB over the strongest baseline and reducing Fréchet Video Distance by 37.7\%, with keeping robustness under larger temporal asynchrony. Code is available at https://anonymous.4open.science/r/DUST-6A55.

Poster
One Avatar, Any Budget: Robust LoD for Dynamic Gaussian Avatars

Haoyu Zhao, Wenjuan Gong, Junang Qi, Haiyu Zhang, Wenjian Zhao, Zimu YOU

展开摘要

Cross-device deployment of a single reconstructed avatar often requires adaptation to varying Gaussian budgets with minimal degradation in visual quality. Motivated by the need for a robust budget-adaptive 3D representation, we propose RobustAvatar, a train-once Level-of-Detail (LoD) adaptation framework for dynamic Gaussian avatars based on sequential selection and compensation. RobustAvatar supports flexible compression-ratio control within a single trained avatar, without requiring fine-tuning at each compression ratio. The framework consists of two coordinated modules: Semantic Distribution-Regularized Selection (SDS) and Canonical Budget-Conditioned Compensation (CBC). SDS performs budget-aware Gaussian selection guided by semantic distribution regularization, preserving the coverage of perceptually salient facial regions relative to the full avatar under constrained budgets. CBC refines the selected primitives in a canonical, expression- and pose-neutral space by predicting ratio-conditioned attribute residuals, reducing detail loss from Gaussian removal and improving robustness to decreasing Gaussian budgets. Experiments on the NeRSemble dataset show that RobustAvatar achieves more robust budget adaptation than state-of-the-art methods, with slower quality degradation as Gaussian budgets decrease. The code will be made publicly available.

Poster
On the Nonlinearity of Learning Rate Scaling for LLM Training

Zaiwen Yang, Huaqing Zhang, Jing Xu, Jingzhao Zhang

展开摘要

Learning-rate transfer is critical for reducing the cost of training large language models: instead of sweeping learning rates at target scale, practitioners extrapolate from smaller runs. Existing approaches often assume that the optimal learning rate follows a log-linear scaling law in data scale and model size. We carefully examine and evaluate this scaling law. In our empirical study of GPT-2--style models from 22M to 407M parameters trained on 5B to 100B tokens, the optimal learning rate develops upward curvature at larger scales, leading to inaccurate extrapolation. We find that this curvature largely disappears when learning rates are replaced by effective learning rate (the step size in normalized weight space), and when data $D$ extrapolation is used instead of model size $N$ extrapolation. Next, we explain nonlinearity in scaling: weight-norm converges to equilibrium slower when optimal learning is small, requiring a larger step size to reduce the transient phase. Experiments with AdamH, which directly controls the effective learning rate, further support this explanation.

Spotlight
On the Memorization of Consistency Distillation for Diffusion Models

Bingqing Jiang, Difan Zou

展开摘要

Diffusion models are central to modern generative modeling, and understanding how they balance memorization and generalization is critical for reliable deployment. Recent work has shown that memorization in diffusion models is shaped by training dynamics, with generalization and memorization emerging at different stages of training. However, deployed diffusion models are often further distilled, introducing an additional training phase whose impact on memorization remains unclear. In this work, we analyze how distillation reshapes memorization behavior in diffusion models, taking consistency distillation as a representative framework. Empirically, we show that when applied to a teacher model that has memorized data, consistency distillation significantly reduces transferred memorization in the student while preserving, and sometimes improving, sample quality. To explain this behavior, we provide a theoretical analysis using a random feature neural network model [Bonnaire et al., 2025], showing that consistency distillation suppresses unstable feature directions associated with memorization while preserving stable, generalizable modes. Our findings suggest that distillation can serve not only as an acceleration tool, but also as a mechanism for improving the memorization-generalization trade-off.

Poster
On Data Engineering for Scaling LLM Terminal Capabilities

Renjie Pi, Grace Lam, Mohammad Shoeybi, Pooya Jannaty, Bryan Catanzaro, Wei Ping

展开摘要

Despite rapid recent progress in the terminal capabilities of large language models, the training data strategies behind state-of-the-art terminal agents remain largely undisclosed. We address this gap through a systematic study of data engineering practices for terminal agents, making two key contributions: (1) Terminal-Task-Gen, a lightweight synthetic task generation pipeline that supports seed-based and skill-based task construction, and (2) a comprehensive analysis of data and training strategies, including filtering, curriculum learning, long context training, and scaling behavior. Our pipeline yields Terminal-Corpus, a large-scale open-source dataset for terminal tasks. Using this dataset, we train Nemotron-Terminal, a family of models initialized from Qwen3 (8B, 14B, 32B) that achieve substantial gains on Terminal-Bench 2.0: Nemotron-Terminal-8B improves from 2.5% to 13.0%, Nemotron-Terminal-14B improves from 4.0% to 20.2%, and Nemotron-Terminal-32B improves from 3.4% to 27.4%, matching the performance of significantly larger models. We release Nemotron-Terminal checkpoints and Terminal-Corpus through the Nemotron-Terminal Hugging Face collection.

Poster
On Concentration Inequalities for Sampling without Replacement

Shaojie Li, Bowei Zhu, Yong Liu

展开摘要

This paper studies concentration inequalities for sampling without replacement. We introduce a general inequality that provides simple guidelines for proving concentration inequalities, offers a degree of unification of existing results, and is strong enough to yield sharper bounds. As applications, we revisit several standard statistics and either recover classical inequalities through streamlined proofs or strengthen them to tighter bounds, with rates optimal up to constants.

Poster
OmniSimulator: Aligning Small Language Models for Authentic Heterogeneous Behavior Modeling

Jiawei Chen, Ruoxi Xu, Boxi Cao, Zhuoqun Li, Ruotong Pan, Zhang yunfei, Zhirui Yang, Jingyan Chen, Tingting Gao, Han Li, Yaojie Lu, Xianpei Han, Le Sun, Xiangyu Wu, Hongyu Lin

展开摘要

Large language models (LLMs) have shown great potential as general-purpose user simulators for interactive systems. Prior studies have demonstrated that training on high-quality data can substantially improve model reasoning and downstream task performance. However, the upper bound of user simulation is still constrained by the model's reasoning paradigm: standard chain-of-thought often degenerates into shallow pattern matching and fails to capture the latent mental process underlying real user behavior. In this paper, we propose OmniSimulator, a novel training framework designed to improve the predictive ability of small LLMs for realistic user simulation on short-video platform environments. Specifically, OmniSimulator models human internal deliberation through a structured reasoning schema with five dimensions, carefully selects data from real user-behavior scenarios, and introduces a teacher model to generate high-quality reasoning traces under the proposed schema, boosting small models to learn the latent logic of human decision-making during the CoT process, rather than relying on superficial behavioral correlations. Based on this process, we construct 9,881 high-quality training instances from three months of historical interaction trajectories of 200 real users, averaging about 50 distilled examples per user. Experimental results show that OmniSimulator improves performance over the baseline by 38.93\%, surpasses strong frontier models such as Claude-Sonnet-4.5, and significantly reduces inference cost. These results suggest that learning structured human-like internal reasoning is a key step toward scalable and high-fidelity LLM-based user simulation.

Poster
OgBench: A Framework for Evaluating Graph Neural Networks on Omics Data

Louisa Cornelis, Johan Mathe, Louis Van Langendonck, Guillermo Bernardez, Nina Miolane

展开摘要

Graph Neural Networks (GNNs) have become the dominant framework for inductive graph-level learning. Yet most benchmarks focus on the regime $n \gg p$, where the number of graphs $n$ greatly exceeds the number of nodes per graph $p$. This overlooks biological domains such as omics, which operate in the opposite $n \ll p$ regime, characterized by large graphs of genes, transcripts, or proteins across few patient samples. This raises the question: \textit{how do GNNs perform in this low-sample, high-node omics setting?} We introduce \texttt{OgBench} (Omics-Graph Bench), the first benchmarking platform for graph-level prediction in the $n \ll p$ regime characteristic of omics data. We provide a standardized, end-to-end modular infrastructure from raw omics data to families of featured graphs with varied structural properties. We benchmark classical GNNs, as well as GNNs designed for large graphs and omics applications, alongside MLPs and machine learning baselines to establish reference performances. Our results show that widely used GNNs often do not outperform simple MLPs and classical baselines. These findings challenge the prevailing assumption that graph structure inherently adds value in this domain, fostering a critical reassessment of current learning paradigms. Ultimately, by exposing these limitations, OgBench provides the open-source ecosystem necessary for the community to develop and validate novel architectures explicitly tailored for biological graphs. The code is available at \url{https://anonymous.4open.science/r/ogbench-C1A9/README.md}.

Poster
OdysSim: Building Foundation Models for Human Behavior Simulation

Xuhui Zhou, Weiwei Sun, Weihua Du, Jiarui Liu, Haojia Sun, Qianou Ma, Sherry Wu, Yiming Yang, Maarten Sap

展开摘要

Large language models are increasingly used as human simulators for interactive evaluation and social simulation, yet current post-training often produces homogeneous, overly helpful systems unlike real people, creating a behavioral Sim2Real gap that prompting alone cannot close. We present Odyssim, a large-scale open study of behavioral foundation models organized around SOUL, whose five capability Axes (CONV, SS, COG, ROLE, EVAL) jointly guide data curation and evaluation. We release three artifacts: (1) SOULIndex, a 23-task evaluation suite for human-behavior simulation; (2) OdysSim, a corpus of 21.4M interactions, approximately 10B tokens, from 63 public sources, unified into a conversational format and retrofitted with back-generated social contexts; and (3) an end-to-end recipe combining midtraining, task-specific RL with VFRL, and expert distillation into a single deployable model. On SOULIndex, OdysSim-8B achieves an average score of 62.4, comparable to frontier models such as GPT-5.5 (62.6), ranks first on 8 of 23 tasks, and outperforms prior open behavioral-simulation baselines by 14.2 points on average. We also identify and mitigate reward-hacking failures in judge-based behavioral RL, including judge manipulation and short-response collapse. We release the corpus, benchmark, recipes, and checkpoints.

Poster
Observations Drift, Structures Remain: Structural Pretraining with Time Alignment for Electromagnetic Signals

Wenjin Gui, Junyu Shen, Haibo Xu, Yuchuang Sun, Luqing Luo, Wupeng Xie, Qian Huang, Fengxiang Wang, Yangang Sun, Maosong Sun

展开摘要

Electromagnetic signal modeling is increasingly moving toward self-supervised pretraining on heterogeneous I/Q observations. However, an observed waveform is jointly shaped by signal generation, propagation environments, and acquisition processes, which mix reusable structural regularities with observation-specific variations. Existing methods usually pursue unified pretraining with reconstruction objectives on mixed observations. This heterogeneity creates two key mismatches for reconstruction pretraining: (1) appearance mismatch, induced by propagation-dependent waveform variations; and (2) temporal mismatch, induced by acquisition-dependent sampling coordinates. These mismatches make observation-specific appearances and sampling coordinates easier to reconstruct than stable signal structures, inducing observational shortcuts. We identify this failure mode as observation-biased pretraining. To address this, we propose Structural Pretraining with Time Alignment for heterogeneous EM signals. It mitigates temporal mismatch with RoPE-fs, which maps token positions to sampling-rate-normalized physical-time positions, and reduces reliance on appearance shortcuts by replacing waveform reconstruction with masked prediction of discrete structural units. These units are organized into atomic structural units and emergent units that capture variable-length compositional patterns beyond fixed patch boundaries. Across diverse EM benchmarks, our method improves both full-supervision and few-shot adaptation over existing EM pretraining baselines, showing that the learned representations better preserve structural consistency when observations drift in waveform appearance and temporal scale.

Poster
Objective-Aligned Amortized Inference for Offline Bayes-Adaptive MDP Model Learning

Toru Hishinuma, Kei Senda

展开摘要

Learning latent environment representations from offline datasets is an important challenge for Bayes-adaptive Markov decision process model learning. A key difficulty is that offline datasets collected under heterogeneous protocols can differ in state--action visitation even when the underlying dynamics are identical. Visitation-decoupled objectives address this by evaluating transition predictive fit under a protocol-independent reference distribution via a change of measure. We show, however, that the resulting objective-induced invariances need not be inherited by amortized inference. An unconstrained encoder can depend on protocol-induced visitation variations that are invisible to the objective, a structural failure mode we term \emph{amortization mismatch}. To address this issue, we formalize an \emph{objective-aligned} design principle as an objective--inference compatibility condition: the encoder should factor through the objective-induced dataset signature. We instantiate this principle in multiple set-encoder families and, through targeted experiments, provide evidence that objective-aligned encoders improve posterior consistency and can mitigate downstream planning discrepancy across protocols.

Poster
OT-Robust3DVLA: A Wasserstein Barycenter is the Right Inductive Bias for Robust Multi-View 3D Vision-Language-Action Policies

Pawan Kumar

展开摘要

Multi-view 3D vision-language-action (VLA) policies are brittle to small sensor perturbations: depth jitter, partial occlusion, calibration drift and per-view dropout can move the predicted action chunk by far more than the perturbation itself. We trace the brittleness to the *fusion stage*: concatenating per-view tokens lets a small geometric shift flip arbitrary token indices, turning a continuous-mass-transport problem into a discrete indexing problem. We propose **a single substitution**: replace concat-then-attention fusion with a *differentiable Wasserstein barycentric tokenizer* that fuses $K$ view measures into $M$ barycentric tokens by transport. We prove a chain of Lipschitz-style stability bounds that hold conditional on a declared OT perturbation set, calibrated Lipschitz constants, and bounded Sinkhorn-solver residuals. Empirically, the barycenter is the single dominant mechanism behind the gain: (i) the proposed model has the lowest mean clean $\ell_2$ on synthetic, LIBERO, RLBench and CALVIN ABC→D (3-of-4 with non-overlapping 95% CIs); (ii) a controlled ablation on synthetic regresses by $46\times$ on the corruption-stability metric when the barycenter is removed and by $<1.5\times$ when any other component is; (iii) the same mechanism transfers to LIBERO with a $+37\%$ clean $\ell_2$ regression and $+62\%$ action-OT regression on real data; (iv) in synthetic closed-loop the concat-fusion baseline collapses from 85% clean to 0% under per-view dropout while the barycenter keeps a 92% worst-case across all five conditions (3 seeds, narrowest CI of all four methods).

Poster
OCTOPUS: Optimized KV Cache for Transformers via Octahedral Parametrization Under optimal Squared error quantization

Mark Boss, Vikram Voleti, Simon Donne, Shimon Vainer

展开摘要

The key-value (KV) cache dominates memory bandwidth and footprint in long-context autoregressive inference. Recent rotation-preconditioned codecs (TurboQuant, PolarQuant) show that a structured random rotation followed by a per-coordinate scalar quantizer matched to an analytically tractable marginal is a near-optimal recipe for KV compression. OCTOPUS advances this paradigm through joint quantization of rotated coordinate triplets. Each triplet's direction is mapped to a square via an octahedral parameterization, and the two resulting coordinates and the triplet norm are Lloyd-Max quantized against implementation-matched marginals. Optimizing the per-triplet squared error gives a strictly non-uniform bit allocation depending only on the total dimensionality of the keys. We find the finite-dimensional quality optimum with sweeps to be constant on every real decoder we test. The codec is data-oblivious, online, and deterministic given a seed. Across text, video, and audio, OCTOPUS matches or beats every prior rotation codec at every reported bit width and metric, with a lead that grows as bits drop for extreme compression. Furthermore, a fused Triton implementation reconstructs keys on the fly without materializing the uncompressed key, so the codec adds no decode-time bandwidth or latency over the existing dequantization.

Poster
Nüwa.RNA: An RNA Foundation Model for Unified Representation with Deep Structure Infusion

Kun Huang, Jiyang Li, Xin Guo, Limei Han, Yuan Cheng

展开摘要

RNA function arises from a hierarchical folding process in which primary sequences form secondary structures that govern biological activity. While foundation models have proven effective for learning transferable RNA representations, most existing approaches rely on primary sequence alone or incorporate structural information only superficially during pre-training. Three problems limit current approaches: experimentally determined secondary structures are scarce, computational pseudo-labels are noisy, and no existing model integrates structure at multiple levels across masking, architecture, and supervision. Here, we present \textbf{N\"uwa.RNA}, a pre-trained foundation model built on a \emph{structure-driven multi-level pre-training framework} that integrates secondary structure at all three stages of pre-training simultaneously. N\"uwa.RNA introduces dual-granularity masking that combines single-token masking with structure motif masking, treating entire structural elements as indivisible units; a noisy structural attention bias that injects curriculum-corrupted contact maps into every Transformer layer to model pseudo-label uncertainty; and a structure denoising objective that recovers clean base-pairing states from corrupted input, completing a closed denoising loop. Pre-trained on a large-scale non-coding RNA corpus, N\"uwa.RNA achieves state-of-the-art performance on 10 of 13 BEACON benchmark tasks, with up to $+$7.83 F1 improvement on structure prediction, and attains the highest zero-shot secondary structure prediction accuracy among single-sequence RNA foundation models.

Poster