NeurIPS 2025 Papers

Retrieval-augmented generation (RAG) has become a widely adopted paradigm for enabling knowledge-grounded large language models (LLMs). However, standard RAG pipelines often fail to ensure that model reasoning remains consistent with the evidence retrieved, leading to factual inconsistencies or unsupported conclusions. In this work, we reinterpret RAG as \textit{Retrieval-Augmented Reasoning} and identify a central but underexplored problem: \textit{Reasoning Misalignment}—the divergence between an LLM's internal reasoning trajectory and the evidential constraints provided by retrieval. To address this issue, we propose \textsc{AlignRAG}, a novel iterative framework grounded in \textit{Critique-Driven Alignment (CDA)}. We further introduce \textsc{AlignRAG-auto}, an autonomous variant that dynamically terminates refinement, removing the need to pre-specify the number of critique iterations. At the heart of \textsc{AlignRAG} lies a \textit{contrastive critique synthesis} mechanism that generates retrieval-sensitive critiques while mitigating self-bias. This mechanism trains a dedicated retrieval-augmented \textit{Critic Language Model (CLM)} using labeled critiques that distinguish between evidence-aligned and misaligned reasoning. Empirical evaluations show that our approach significantly improves reasoning fidelity. Our 8B-parameter CLM improves performance over the Self-Refine baseline by \textbf{12.1\%} on out-of-domain tasks and outperforms a standard 72B-parameter CLM by \textbf{2.2\%}. Furthermore, \textsc{AlignRAG-auto} achieves this state-of-the-art performance while dynamically determining the optimal number of refinement steps, enhancing efficiency and usability. \textsc{AlignRAG} remains compatible with existing RAG architectures as a \textit{plug-and-play} module and demonstrates strong robustness under both informative and noisy retrieval scenarios. Overall, \textsc{AlignRAG} offers a principled solution for aligning model reasoning with retrieved evidence, substantially improving the factual reliability and robustness of RAG systems. Our source code is provided at \href{https://github.com/upup-wei/RAG-ReasonAlignment}{link}.

Multi-modal large language models (MLLMs) are making rapid progress toward general-purpose embodied agents. However, existing MLLMs do not reliably capture fine-grained links between low-level visual features and high-level textual semantics, leading to weak grounding and inaccurate perception. To overcome this challenge, we propose ESCA, a framework that contextualizes embodied agents by grounding their perception in spatial-temporal scene graphs. At its core is SGCLIP, a novel, open-domain, promptable foundation model for generating scene graphs that is based on CLIP. SGCLIP is trained on 87K+ open-domain videos using a neurosymbolic pipeline that aligns automatically generated captions with scene graphs produced by the model itself, eliminating the need for human-labeled annotations. We demonstrate that SGCLIP excels in both prompt-based inference and task-specific fine-tuning, achieving state-of-the-art results on scene graph generation and action localization benchmarks. ESCA with SGCLIP improves perception for embodied agents based on both open-source and commercial MLLMs, achieving state of-the-art performance across two embodied environments. Notably, ESCA significantly reduces agent perception errors and enables open-source models to surpass proprietary baselines. We release the source code for SGCLIP model training at https://github.com/video-fm/LASER and for the embodied agent at https://github.com/video-fm/ESCA.

Adapter-based training has emerged as a key mechanism for extending the capabilities of powerful foundation image generators, enabling personalized and stylized text-to-image synthesis. These adapters are typically trained to capture a specific target attribute, such as subject identity, using single-image reconstruction objectives. However, because the input image inevitably contains a mixture of visual factors, adapters are prone to entangle the target attribute with incidental ones, such as pose, expression, and lighting. This spurious correlation problem limits generalization and obstructs the model's ability to adhere to the input text prompt. In this work, we uncover a simple yet effective solution: provide the very shortcuts we wish to eliminate during adapter training. In Shortcut-Rerouted Adapter Training, confounding factors are routed through auxiliary modules, such as ControlNet or LoRA, eliminating the incentive for the adapter to internalize them. The auxiliary modules are then removed during inference. When applied to tasks like facial and full-body identity injection, our approach improves generation quality, diversity, and prompt adherence. These results point to a general design principle in the era of large models: when seeking disentangled representations, the most effective path may be to establish shortcuts for what should NOT be learned.

We introduce IntrinsiX, a novel method that generates high-quality intrinsic images from text description. In contrast to existing text-to-image models whose outputs contain baked-in scene lighting, our approach predicts physically-based rendering (PBR) maps. This enables the generated outputs to be used for content creation scenarios in core graphics applications that facilitate re-lighting, editing, and texture generation tasks. In order to train our generator, we exploit strong image priors, and pre-train separate models for each PBR material component (albedo, roughness, metallic, normals). We then align these models with a new cross-intrinsic attention formulation that concatenates key and value features in a consistent fashion. This allows us to exchange information between each output modality and to obtain semantically coherent PBR predictions. To ground each intrinsic component, we propose a rendering loss which provides image-space signals to constrain the model, thus facilitating sharp details also in the output BRDF properties. Our results demonstrate detailed intrinsic generation with strong generalization capabilities that outperforms existing intrinsic image decomposition methods used with generated images by a significant margin. Finally, we show a series of applications, including re-lighting, editing, and for the first time text-conditioned room-scale PBR texture generation. We will release the code and the pre-trained model weights.

Designing metal-organic frameworks (MOFs) with novel chemistries is a longstanding challenge due to their large combinatorial space and complex 3D arrangements of the building blocks. While recent deep generative models have enabled scalable MOF generation, they assume (1) a fixed set of building blocks and (2) known local 3D coordinates of building blocks. However, this limits their ability to (1) design novel MOFs and (2) generate the structure using novel building blocks. We propose a two-stage MOF generation framework that overcomes these limitations by modeling both chemical and geometric degrees of freedom. First, we train an SMILES-based autoregressive model to generate metal and organic building blocks, paired with a cheminformatics toolkit for 3D structure initialization. Second, we introduce a flow matching model that predicts translations, rotations, and torsional angles to assemble the blocks into valid 3D frameworks. Our experiments demonstrate improved reconstruction accuracy, the generation of valid, novel, and unique MOFs, and the ability to create novel building blocks. Our code is available at https://github.com/nayoung10/MOFFlow-2.

The rise of GPU-based high-performance computing (HPC) has driven the widespread adoption of parallel programming models such as CUDA. Yet, the inherent complexity of parallel programming creates a demand for the automated sequential-to-parallel approaches. However, data scarcity poses a significant challenge for machine learning-based sequential-to-parallel code translation. Although recent back-translation methods show promise, they still fail to ensure functional equivalence in the translated code. In this paper, we propose \textbf{QiMeng-MuPa}, a novel \textbf{Mu}tual-Supervised Learning framework for Sequential-to-\textbf{Pa}rallel code translation, to address the functional equivalence issue. QiMeng-MuPa consists of two models, a Translator and a Tester. Through an iterative loop consisting of Co-verify and Co-evolve steps, the Translator and the Tester mutually generate data for each other and improve collectively. The Tester generates unit tests to verify and filter functionally equivalent translated code, thereby evolving the Translator, while the Translator generates translated code as augmented input to evolve the Tester. Experimental results demonstrate that QiMeng-MuPa significantly enhances the performance of the base models: when applied to Qwen2.5-Coder, it not only improves Pass@1 by up to 28.91\% and boosts Tester performance by 68.90\%, but also outperforms the previous state-of-the-art method CodeRosetta by 1.56 and 6.92 in BLEU and CodeBLEU scores, while achieving performance comparable to DeepSeek-R1 and GPT-4.1. Our code is available at \url{https://github.com/kcxain/mupa}.

Reasoning capability is pivotal for Large Language Models (LLMs) to solve complex tasks, yet achieving reliable and scalable reasoning remains challenging. While Chain-of-Thought (CoT) prompting has become a mainstream approach, existing methods often suffer from uncontrolled generation, insufficient quality, and limited diversity in reasoning paths. Recent efforts leverage code to enhance CoT by grounding reasoning in executable steps, but such methods are typically constrained to predefined mathematical problems, hindering scalability and generalizability. In this work, we propose \texttt{Caco} (Code-Assisted Chain-of-ThOught), a novel framework that automates the synthesis of high-quality, verifiable, and diverse instruction-CoT reasoning data through code-driven augmentation. Unlike prior work, \texttt{Caco} first fine-tunes a code-based CoT generator on existing math and programming solutions in a unified code format, then scales the data generation to a large amount of diverse reasoning traces. Crucially, we introduce automated validation via code execution and rule-based filtering to ensure logical correctness and structural diversity, followed by reverse-engineering filtered outputs into natural language instructions and language CoTs to enrich task adaptability. This closed-loop process enables fully automated, scalable synthesis of reasoning data with guaranteed executability. Experiments on our created \texttt{Caco}-1.3M dataset demonstrate that \texttt{Caco}-trained models achieve strong competitive performance on mathematical reasoning benchmarks, outperforming existing strong baselines. Further analysis reveals that \texttt{Caco}’s code-anchored verification and instruction diversity contribute to superior generalization across unseen tasks. Our work establishes a paradigm for building self-sustaining, trustworthy reasoning systems without human intervention.

Diffusion-based generative models struggle to maintain high style consistency across generated images via text description. Although several style-aligned image generation methods have been proposed to address this issue, they exhibit suboptimal performance and are primarily built upon the U-Net architecture, limiting their compatibility with DiT diffusion models like Flux that has emerged as a predominant model in the field of image generation. To address these limitations, we propose AlignedGen, a novel training-free style-aligned image generation method for DiT models to significantly enhance style consistency across generated images. Specifically, AlignedGen incorporates two key components to achieve this: Shifted Position Embedding (ShiftPE) and Advanced Attention Sharing (AAS). ShiftPE alleviates the text controllability degradation observed in prior methods when applied to DiT models through its non-overlapping position indices design, while AAS comprises three specialized techniques to unleash the full potential of DiT for style-aligned generation. Furthermore, to broaden the applicability of our method, we present an efficient query, key, and value feature extraction algorithm, enabling our method to seamlessly incorporate external images as style references. Extensive experimental results validate that our method effectively enhances style consistency across generated images while maintaining favorable text controllability. Code: https://github.com/Jiexuanz/AlignedGen.

Scenario-based testing is essential for validating the performance of autonomous driving (AD) systems. However, such testing is limited by the scarcity of long-tailed, safety-critical scenarios in existing datasets collected in the real world. To tackle the data issue, we propose the Adv-BMT framework, which augments real-world scenarios with diverse and realistic adversarial interactions. The core component of Adv-BMT is a bidirectional motion transformer (BMT) model to perform inverse traffic motion predictions, which takes the last frame of the scenario as input and reconstruct the traffic in the inverse of chronological order, till the initial time step. The Adv-BMT framework is a two-stage pipeline: it first conducts adversarial initializations and then inverse motion predictions. Different from previous work, we do not need any collision data for pretraining and are still able to generate realistic and diverse collision interactions. Our experimental results validate the quality of generated collision scenarios by Adv-BMT: training in our augmented dataset would reduce episode collision rates by 20\% compared to previous work. The code will be made available.

Reinforcement learning (RL) agents have demonstrated strong performance in structured environments, yet they continue to struggle in real-world settings where goals are ambiguous, conditions change dynamically, and external supervision is limited. These challenges stem not primarily from the algorithmic limitations but from the characteristics of conventional training environments, which are usually static, task-specific, and externally defined. In contrast, biological agents develop autonomy and adaptivity by interacting with complex, dynamic environments, where most behaviors are ultimately driven by internal physiological needs. Inspired by these biological constraints, we introduce EVAAA (Essential Variables in Autonomous and Adaptive Agents), a 3D virtual environment for training and evaluating egocentric RL agents endowed with internal physiological state variables. In EVAAA, agents must maintain essential variables (EVs)—e.g., satiation, hydration, body temperature, and tissue integrity (the level of damage)—within viable bounds by interacting with environments that increase in difficulty at each stage. The reward system is derived from internal state dynamics, enabling agents to generate goals autonomously without manually engineered, task-specific reward functions. Built on Unity ML-Agents, EVAAA supports multimodal sensory inputs, including vision, olfaction, thermoception, collision, as well as egocentric embodiment. It features naturalistic survival environments for curricular training and a suite of unseen experimental testbeds, allowing for the evaluation of autonomous and adaptive behaviors that emerge from the interplay between internal state dynamics and environmental constraints. By integrating physiological regulation, embodiment, continual learning, and generalization, EVAAA offers a biologically inspired benchmark for studying autonomy, adaptivity, and internally driven control in RL agents. Our code is publicly available at https://github.com/cocoanlab/evaaa

Automatic indoor layout generation has attracted increasing attention due to its potential in interior design, virtual environment construction, and embodied AI. Existing methods fall into two categories: prompt-driven approaches that leverage proprietary LLM services (e.g., GPT APIs), and learning-based methods trained on layout data upon diffusion-based models. Prompt-driven methods often suffer from spatial inconsistency and high computational costs, while learning-based methods are typically constrained by coarse relational graphs and limited datasets, restricting their generalization to diverse room categories. In this paper, we revisit LLM-based indoor layout generation and present 3D-SynthPlace, a large-scale dataset that combines synthetic layouts generated via a `GPT synthesize, Human inspect' pipeline, upgraded from the 3D-Front dataset. 3D-SynthPlace contains nearly 17,000 scenes, covering four common room types—bedroom, living room, kitchen, and bathroom—enriched with diverse objects and high-level spatial annotations. We further introduce OptiScene, a strong open-source LLM optimized for indoor layout generation, fine-tuned based on our 3D-SynthPlace dataset through our two-stage training. For the warum-up stage I, we adopt supervised fine-tuning (SFT), which is taught to first generate high-level spatial descriptions then conditionally predict concrete object placements. For the reinforcing stage II, to better align the generated layouts with human design preferences, we apply multi-turn direct preference optimization (DPO), which significantly improving layout quality and generation success rates. Extensive experiments demonstrate that OptiScene outperforms traditional prompt-driven and learning-based baselines. Moreover, OptiScene shows promising potential in interactive tasks such as scene editing and robot navigation, highlighting its applicability beyond static layout generation.

Generating high-resolution 3D shapes using volumetric representations such as Signed Distance Functions (SDFs) presents substantial computational and memory challenges. We introduce Direct3D-S2, a scalable 3D generation framework based on sparse volumes that achieves superior output quality with dramatically reduced training costs. Our key innovation is the Spatial Sparse Attention (SSA) mechanism, which greatly enhances the efficiency of Diffusion Transformer (DiT) computations on sparse volumetric data. SSA allows the model to effectively process large token sets within sparse volumes, significantly reducing computational overhead and achieving a 3.9$\times$ speedup in the forward pass and a 9.6$\times$ speedup in the backward pass. Our framework also includes a variational autoencoder (VAE) that maintains a consistent sparse volumetric format across input, latent, and output stages. Compared to previous methods with heterogeneous representations in 3D VAE, this unified design significantly improves training efficiency and stability. Our model is trained on public datasets, and experiments demonstrate that Direct3D-S2 not only surpasses state-of-the-art methods in generation quality and efficiency, but also enables training at 1024³ resolution using only 8 GPUs—a task typically requiring at least 32 GPUs for volumetric representations at $256^3$ resolution, thus making gigascale 3D generation both practical and accessible. Project page: https://www.neural4d.com/research-page/direct3d-s2.

Deciphering how visual stimuli are transformed into cortical responses is a fundamental challenge in computational neuroscience. This visual-to-neural mapping is inherently a one-to-many relationship, as identical visual inputs reliably evoke variable hemodynamic responses across trials, contexts, and subjects. However, existing deterministic methods struggle to simultaneously model this biological variability while capturing the underlying functional consistency that encodes stimulus information. To address these limitations, we propose SynBrain, a generative framework that simulates the transformation from visual semantics to neural responses in a probabilistic and biologically interpretable manner. SynBrain introduces two key components: (i) BrainVAE models neural representations as continuous probability distributions via probabilistic learning while maintaining functional consistency through visual semantic constraints; (ii) A Semantic-to-Neural Mapper acts as a semantic transmission pathway, projecting visual semantics into the neural response manifold to facilitate high-fidelity fMRI synthesis. Experimental results demonstrate that SynBrain surpasses state-of-the-art methods in subject-specific visual-to-fMRI encoding performance. Furthermore, SynBrain adapts efficiently to new subjects with few-shot data and synthesizes high-quality fMRI signals that are effective in improving data-limited fMRI-to-image decoding performance. Beyond that, SynBrain reveals functional consistency across trials and subjects, with synthesized signals capturing interpretable patterns shaped by biological neural variability. Our code is available at https://github.com/MichaelMaiii/SynBrain.

Generative modeling of discrete variables is challenging yet crucial for applications in natural language processing and biological sequence design. We introduce the Shortlisting Model (SLM), a novel simplex-based diffusion model inspired by progressive candidate pruning. SLM operates on simplex centroids, reducing generation complexity and enhancing scalability. Additionally, SLM incorporates a flexible implementation of classifier-free guidance, enhancing unconditional generation performance. Extensive experiments on DNA promoter and enhancer design, protein design, character-level and large-vocabulary language modeling demonstrate the competitive performance and strong potential of SLM. Our code can be found at https://github.com/GenSI-THUAIR/SLM.

Recent text-to-image models have revolutionized image generation, but they still struggle with maintaining concept consistency across generated images. While existing works focus on character consistency, they often overlook the crucial role of scenes in storytelling, which restricts their creativity in practice. This paper introduces scene-oriented story generation, addressing two key challenges: (i) scene planning, where current methods fail to ensure scene-level narrative coherence by relying solely on text descriptions, and (ii) scene consistency, which remains largely unexplored in terms of maintaining scene consistency across multiple stories. We propose SceneDecorator, a training-free framework that employs VLM-Guided Scene Planning to ensure narrative coherence across different scenes in a ``global-to-local'' manner, and Long-Term Scene-Sharing Attention to maintain long-term scene consistency and subject diversity across generated stories. Extensive experiments demonstrate the superior performance of SceneDecorator, highlighting its potential to unleash creativity in the fields of arts, films, and games.

Building generative models for relational databases (RDBs) is important for many applications, such as privacy-preserving data release and augmenting real datasets. However, most prior works either focus on single-table generation or adapt single-table models to the multi-table setting by relying on autoregressive factorizations and sequential generation. These approaches limit parallelism, restrict flexibility in downstream applications, and compound errors due to commonly made conditional independence assumptions. In this paper, we propose a fundamentally different approach: jointly modeling all tables in an RDB without imposing any table order. By using a natural graph representation of RDBs, we propose the Graph-Conditional Relational Diffusion Model (GRDM), which leverages a graph neural network to jointly denoise row attributes and capture complex inter-table dependencies. Extensive experiments on six real-world RDBs demonstrate that our approach substantially outperforms autoregressive baselines in modeling multi-hop inter-table correlations and achieves state-of-the-art performance on single-table fidelity metrics. Our code is available at https://github.com/ketatam/rdb-diffusion.

We introduce transductive program synthesis, a new formulation of the program synthesis task that explicitly leverages test inputs during synthesis. While prior approaches to program synthesis--whether based on natural language descriptions or input-output examples--typically aim to generalize from training examples, they often struggle with robustness, especially in real-world settings where training examples are limited and test inputs involve various edge cases. To address this, we propose a novel framework that improves robustness by treating synthesis as an active learning over a finite hypothesis class defined by programs' outputs. We use an LLM to predict outputs for selected test inputs and eliminate inconsistent hypotheses, where the inputs are chosen via a greedy maximin algorithm to minimize the number of LLM queries required. We evaluate our approach on four benchmarks: Playgol, MBPP+, 1D-ARC, and programmatic world modeling on MiniGrid. We demonstrate that our method significantly improves program synthesis in both accuracy and efficiency. We release our code at https://github.com/klee972/SYNTRA.

Training large language models (LLMs) models directly in low-precision offers a way to address computational costs by improving both throughput and energy efficiency. For those purposes, NVIDIA's recent Blackwell architecture facilitates very low-precision operations using FP4 variants. Yet, current algorithms for training LLMs in FP4 precision face significant accuracy degradation and often rely on mixed-precision fallbacks. In this paper, we investigate hardware-supported FP4 training and introduce a new approach for accurate, end-to-end FP4 training with all the major computations (i.e., linear layers) in low precision. Through extensive evaluations on Llama-type models, we reveal a new low-precision scaling law that quantifies performance trade-offs across bit-widths and training setups. Guided by this investigation, we design an "optimal" technique in terms of accuracy-vs-computation, called Quartet. We implement Quartet using optimized CUDA kernels tailored for Blackwell, demonstrating that fully FP4-based training is a competitive alternative to FP16 half-precision and to FP8 training. Our code is available at https://github.com/IST-DASLab/Quartet .

Optimizing Register Transfer Level (RTL) code is crucial for improving the efficiency and performance of digital circuits in the early stages of synthesis. Manual rewriting, guided by synthesis feedback, can yield high-quality results but is time-consuming and error-prone. Most existing compiler-based approaches have difficulty handling complex design constraints. Large Language Model (LLM)-based methods have emerged as a promising alternative to address these challenges. However, LLM-based approaches often face difficulties in ensuring alignment between the generated code and the provided prompts. This paper introduces SymRTLO, a neuron-symbolic framework that integrates LLMs with symbolic reasoning for the efficient and effective optimization of RTL code. Our method incorporates a retrieval-augmented system of optimization rules and Abstract Syntax Tree (AST)-based templates, enabling LLM-based rewriting that maintains syntactic correctness while minimizing undesired circuit behaviors. A symbolic module is proposed for analyzing and optimizing finite state machine (FSM) logic, allowing fine-grained state merging and partial specification handling beyond the scope of pattern-based compilers. Furthermore, a fast verification pipeline, combining formal equivalence checks with test-driven validation, further reduces the complexity of verification. Experiments on the RTL-Rewriter benchmark with Synopsys Design Compiler and Yosys show that SymRTLO improves power, performance, and area (PPA) by up to 43.9%, 62.5%, and 51.1%, respectively, compared to the state-of-the-art methods. We will release the code as open source upon the paper's acceptance.