NeurIPS 2025 论文列表

Conference on Neural Information Processing Systems

录用类型

5,812篇论文

按官方录用论文列表统计,可能与会议公布的数字略有出入。

  • Oral
    931.6%
  • Spotlight
    73912.7%
  • Poster
    4,98085.7%

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Rationalized All-Atom Protein Design with Unified Multi-Modal Bayesian Flow

Hanlin Wu, Yuxuan Song, Zhe Zhang, Zhilong Zhang, Hao Zhou, Wei-Ying Ma, Jingjing Liu

展开摘要

Designing functional proteins is a critical yet challenging problem due to the intricate interplay between backbone structures, sequences, and side-chains. Current approaches often decompose protein design into separate tasks, which can lead to accumulated errors, while recent efforts increasingly focus on all-atom protein design. However, we observe that existing all-atom generation approaches suffering from an information shortcut issue, where models inadvertently infer sequences from side-chain information, compromising their ability to accurately learn sequence distributions. To address this, we introduce a novel rationalized information flow strategy to eliminate the information shortcut. Furthermore, motivated by the advantages of Bayesian flows over differential equation–based methods, we propose the first Bayesian flow formulation for protein backbone orientations by recasting orientation modeling as an equivalent hyperspherical generation problem with antipodal symmetry. To validate, our method delivers consistently exceptional performance in both peptide and antibody design tasks.

Poster
Exploring the Translation Mechanism of Large Language Models

Hongbin Zhang, Kehai Chen, Xuefeng Bai, Xiucheng Li, Yang Xiang, Min Zhang

展开摘要

While large language models (LLMs) demonstrate remarkable success in multilingual translation, their internal core translation mechanisms, even at the fundamental word level, remain insufficiently understood. To address this critical gap, this work introduces a systematic framework for interpreting the mechanism behind LLM translation from the perspective of computational components. This paper first proposes subspace-intervened path patching for precise, fine-grained causal analysis, enabling the detection of components crucial to translation tasks and subsequently characterizing their behavioral patterns in human-interpretable terms. Comprehensive experiments reveal that translation is predominantly driven by a sparse subset of components: specialized attention heads serve critical roles in extracting source language, translation indicators, and positional features, which are then integrated and processed by specific multi-layer perceptrons (MLPs) into intermediary English-centric latent representations before ultimately yielding the final translation. The significance of these findings is underscored by the empirical demonstration that targeted fine-tuning a minimal parameter subset (<5%) enhances translation performance while preserving general capabilities. This result further indicates that these crucial components generalize effectively to sentence-level translation and are instrumental in elucidating more intricate translation tasks.

Poster
Mechanism Design for LLM Fine-tuning with Multiple Reward Models

Haoran Sun, Yurong Chen, Siwei Wang, Xu Chu, Wei Chen, Xiaotie Deng

展开摘要

Fine-tuning large language models (LLMs) to aggregate multiple preferences has attracted considerable research attention. With aggregation algorithms advancing, a potential economic scenario arises where fine-tuning services are provided to agents with different preferences. In this context, agents may benefit from strategically misreporting their preferences, but this could harm the aggregation performance. This paper addresses such incentive issues by framing it as a mechanism design problem: an LLM provider determines the fine-tuning objective (training rule) and the pricing scheme (payment rule) for agents. We primarily focus on training rules that maximize social welfare subject to certain regularizations, referred to as SW-Max rules. First, we show that under most circumstances, truthful reporting is sub-optimal with simply a SW-Max rule, thereby highlighting the necessity of payments. Second, we extend the VCG payment to implement SW-Max rules in dominant-strategy incentive compatibility (DSIC). We characterize sufficient conditions for payment equivalence and derive the necessary conditions for a payment rule to implement a SW-Max rule in DSIC and other principles. Third, we demonstrate that our mechanism is approximately DSIC with perturbed input, showcasing its robustness against the inevitable errors in real-world applications. Experiments on real LLM training results further confirm the practical implications of our results.

Poster
ProtInvTree: Deliberate Protein Inverse Folding with Reward-guided Tree Search

Mengdi Liu, Xiaoxue Cheng, Zhangyang Gao, Hong Chang, Cheng Tan, Shiguang Shan, Xilin Chen

展开摘要

Designing protein sequences that fold into a target 3D structure—known as protein inverse folding—is a fundamental challenge in protein engineering. While recent deep learning methods have achieved impressive performance by recovering native sequences, they often overlook the one-to-many nature of the problem: multiple diverse sequences can fold into the same structure. This motivates the need for a generative model capable of designing diverse sequences while preserving structural consistency. To address this trade-off, we introduce ProtInvTree, the first reward-guided tree-search framework for protein inverse folding. ProtInvTree reformulates sequence generation as a deliberate, step-wise decision-making process, enabling the exploration of multiple design paths and exploitation of promising candidates through self-evaluation, lookahead, and backtracking. We propose a two-stage focus-and-grounding action mechanism that decouples position selection and residue generation. To efficiently evaluate intermediate states, we introduce a jumpy denoising strategy that avoids full rollouts. Built upon pretrained protein language models, ProtInvTree supports flexible test-time scaling by adjusting the search depth and breadth without retraining. Empirically, ProtInvTree outperforms state-of-the-art baselines across multiple benchmarks, generating structurally consistent yet diverse sequences, including those far from the native ground truth. The code is available at https://github.com/A4Bio/ProteinInvBench/.

Spotlight
Inference with correlated priors using sisters cells

Sina Tootoonian, Andreas T. Schaefer

展开摘要

A common view of sensory processing is as probabilistic inference of latent causes from receptor activations. Standard approaches often assume these causes are \textit{a priori} independent, yet real-world generative factors are typically correlated. Representing such structured priors in neural systems poses architectural challenges, particularly when direct interactions between units representing latent causes are biologically implausible or computationally expensive. Inspired by the architecture of the olfactory bulb, we propose a novel circuit motif that enables inference with correlated priors without requiring direct interactions among latent cause units. The key insight lies in using \textit{sister cells}: neurons receiving shared receptor input but connected differently to local interneurons. The required interactions among latent units are implemented indirectly through their connections to the sister cells, such that correlated connectivity implies anti-correlation in the prior and vice versa. We use geometric arguments to construct connectivity that implements a given prior and to bound the number of causes for which such priors can be constructed. Using simulations, we demonstrate the efficacy of such priors for inference in noisy environments and compare the inference dynamics to those experimentally observed. Finally, we show how, under certain assumptions on latent representations, the prior used can be inferred from sister cell activations. While biologically grounded in the olfactory system, our mechanism generalises to other natural and artificial sensory systems and may inform the design of architectures for efficient inference under correlated latent structure.

Poster
Gated Attention for Large Language Models: Non-linearity, Sparsity, and Attention-Sink-Free

Zihan Qiu, Zekun Wang, Bo Zheng, Zeyu Huang, Kaiyue Wen, Songlin Yang, Rui Men, Le Yu, Fei Huang, Suozhi Huang, Dayiheng Liu, Jingren Zhou, Junyang Lin

展开摘要

Gating mechanisms have been widely utilized, from early models like LSTMs and Highway Networks to recent state space models, linear attention, and also softmax attention. Yet, existing literature rarely examines the specific effects of gating. In this work, we conduct comprehensive experiments to systematically investigate gating-augmented softmax attention variants. Specifically, we perform a comprehensive comparison over 30 variants of 15B Mixture-of-Experts (MoE) models and 1.7B dense models trained on a 3.5 trillion token dataset. Our central finding is that a simple modification—applying a head-specific sigmoid gate after the Scaled Dot-Product Attention (SDPA)—consistently improves performance. This modification also enhances training stability, tolerates larger learning rates, and improves scaling properties. By comparing various gating positions and computational variants, we attribute this effectiveness to two key factors: (1) introducing non-linearity upon the low-rank mapping in the softmax attention, and (2) applying query-dependent sparse gating scores to modulate the SDPA output. Notably, we find this sparse gating mechanism mitigates `massive activation`, `attention sink` and enhances long-context extrapolation performance. We also release related codes (https://github.com/qiuzh20/gated_attention}) and models (https://huggingface.co/QwQZh/gated_attention) to facilitate future research. Furthermore, the most effective SDPA output gating is used in the Qwen3-Next models (https://huggingface.co/collections/Qwen/qwen3-next).

Oral
Limitations of Normalization in Attention

Timur Mudarisov, Mikhail Burtsev, Tatiana Petrova, Radu State

展开摘要

This paper investigates the limitations of the normalization in attention mechanisms. We begin with a theoretical framework that enables the identification of the model's selective ability and the geometric separation involved in token selection. Our analysis includes explicit bounds on distances and separation criteria for token vectors under softmax scaling. Through experiments with pre-trained GPT-2 model, we empirically validate our theoretical results and analyze key behaviors of the attention mechanism. Notably, we demonstrate that as the number of selected tokens increases, the model's ability to distinguish informative tokens declines, often converging toward a uniform selection pattern. We also show that gradient sensitivity under softmax normalization presents challenges during training, especially at low temperature settings. These findings advance current understanding of softmax-based attention mechanism and motivate the need for more robust normalization and selection strategies in future attention architectures.

Poster
Parsimonious Predictions for Strategyproof Scheduling

Richard Cole, Anupam Gupta, Pranav Jangir

展开摘要

We consider the problem of scheduling $m$ jobs on $n$ unrelated strategic machines to minimize the maximum load of any machine, but the machines are strategic and may misreport processing times to minimize their own load. The pioneering work of Nisan and Ronen gave an $n$-approximate deterministic strategyproof mechanism for this setting, and this was recently shown to be best possible by the breakthrough results of Christodoulou et al. This large approxation guarantee begs the question: how can we avoid these large worst-case results. In this work, we use the powerful framework of algorithms with (machine-learned) predictions to bypass these strong impossibility results. We show how we can predict $O(m+n)$ values to obtain a deterministic strategyproof algorithm whose makespan is within a constant factor of the optimal makespan when the predictions are correct, and $O(n)$ times the optimum no matter how poor the predictions are.

Poster