NeurIPS 2025 Papers

Conference on Neural Information Processing Systems

Decision breakdown

5,812papers

Counted from the official paper list; may differ slightly from the number the conference announced.

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

Browse all papers

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

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

Expand abstract

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
Rethinking Circuit Completeness in Language Models: AND, OR, and ADDER Gates

Hang Chen, Jiaying Zhu, Xinyu Yang, Wenya Wang

Expand abstract

Circuit discovery has gradually become one of the prominent methods for mechanistic interpretability, and research on circuit completeness has also garnered increasing attention. Methods of circuit discovery that do not guarantee completeness not only result in circuits that are not fixed across different runs but also cause key mechanisms to be omitted. The nature of incompleteness arises from the presence of OR gates within the circuit, which are often only partially detected in standard circuit discovery methods. To this end, we systematically introduce three types of logic gates: AND, OR, and ADDER gates, and decompose the circuit into combinations of these logical gates. Through the concept of these gates, we derive the minimum requirements necessary to achieve faithfulness and completeness. Furthermore, we propose a framework that combines noising-based and denoising-based interventions, which can be easily integrated into existing circuit discovery methods without significantly increasing computational complexity. This framework is capable of fully identifying the logic gates and distinguishing them within the circuit. In addition to the extensive experimental validation of the framework's ability to restore the faithfulness, completeness, and sparsity of circuits, using this framework, we uncover fundamental properties of the three logic gates, such as their proportions and contributions to the output, and explore how they behave among the functionalities of language models.

Poster
Differentiable Constraint-Based Causal Discovery

Jincheng Zhou, Mengbo Wang, Anqi He, Yumeng Zhou, Hessam Olya, Murat Kocaoglu, Bruno Ribeiro

Expand abstract

Causal discovery from observational data is a fundamental task in artificial intelligence, with far-reaching implications for decision-making, predictions, and interventions. Despite significant advances, existing methods can be broadly categorized as constraint-based or score-based approaches. Constraint-based methods offer rigorous causal discovery but are often hindered by small sample sizes, while score-based methods provide flexible optimization but typically forgo explicit conditional independence testing. This work explores a third avenue: developing differentiable $d$-separation scores, obtained through a percolation theory using soft logic. This enables the implementation of a new type of causal discovery method: gradient-based optimization of conditional independence constraints. Empirical evaluations demonstrate the robust performance of our approach in low-sample regimes, surpassing traditional constraint-based and score-based baselines on a real-world dataset. Code implementing the proposed method is publicly available at [https://github.com/PurdueMINDS/DAGPA](https://github.com/PurdueMINDS/DAGPA).

Poster
An Efficient Local Search Approach for Polarized Community Discovery in Signed Networks

Linus Aronsson, Morteza Haghir Chehreghani

Expand abstract

Signed networks, where edges are labeled as positive or negative to represent friendly or antagonistic interactions, offer a natural framework for analyzing polarization, trust, and conflict in social systems. Detecting meaningful group structures in such networks is crucial for understanding online discourse, political divisions, and trust dynamics. A key challenge is to identify communities that are internally cohesive and externally antagonistic, while allowing for neutral or unaligned vertices. In this paper, we propose a method for identifying $k$ polarized communities that addresses a major limitation of prior methods: their tendency to produce highly size-imbalanced solutions. We introduce a novel optimization objective that avoids such imbalance. In addition, it is well known that approximation algorithms based on *local search* are highly effective for clustering signed networks when neutral vertices are not allowed. We build on this idea and design the first local search algorithm that extends to the setting with neutral vertices while scaling to large networks. By connecting our approach to block-coordinate Frank-Wolfe optimization, we prove a linear convergence rate, enabled by the structure of our objective. Experiments on real-world and synthetic datasets demonstrate that our method consistently outperforms state-of-the-art baselines in solution quality, while remaining competitive in computational efficiency.

Poster