NeurIPS 2025 Papers

We introduce a new graph diffusion model for small drug molecule generation which simultaneously offers a 10-fold reduction in the number of diffusion steps when compared to existing methods, preservation of small molecule graph motifs via motif compression, and an average 3\% improvement in SMILES validity over the DiGress model across all real-world molecule benchmarking datasets. Furthermore, our approach outperforms the state-of-the-art DeFoG method with respect to motif-conservation by roughly 4\%, as evidenced by high ChEMBL-likeness, QED and newly introduced shingles distance scores. The key ideas behind the approach are to use a combination of deterministic and random subgraph perturbations, so that the node and edge noise schedules are codependent; to modify the loss function of the training process in order to exploit the deterministic component of the schedule; and, to ''compress'' a collection of highly relevant carbon ring and other motif structures into supernodes in a way that allows for simple subsequent integration into the molecular scaffold.

3D vector graphics play a crucial role in various applications including 3D shape retrieval, conceptual design, and virtual reality interactions due to their ability to capture essential structural information with minimal representation. While recent approaches have shown promise in generating 3D vector graphics, they often suffer from lengthy processing times and struggle to maintain view consistency. To address these limitations, we propose VC3D (**V**iew**C**raft**3D**), an efficient method that leverages 3D priors to generate 3D vector graphics. Specifically, our approach begins with 3D object analysis, employs a geometric extraction algorithm to fit 3D vector graphics to the underlying structure, and applies view-consistent refinement process to enhance visual quality. Our comprehensive experiments demonstrate that VC3D outperforms previous methods in both qualitative and quantitative evaluations, while significantly reducing computational overhead. The resulting 3D sketches maintain view consistency and effectively capture the essential characteristics of the original objects.

Differentially private (DP) synthetic data generation is a promising technique for utilizing private datasets that otherwise cannot be exposed for model training or other analytics. While much research literature has focused on generating private unstructured text and image data, in enterprise settings, structured data (e.g., tabular) is more common, often including natural language fields or components. Existing synthetic data evaluation techniques (e.g., FID) struggle to capture the structural properties and correlations of such datasets. In this work, we propose Struct-Bench, a framework and benchmark for evaluating synthetic datasets derived from structured datasets that contain natural language data. The Struct-Bench framework requires users to provide a representation of their dataset structure as a Context-Free Grammar (CFG). Our benchmark comprises 5 real-world and 2 synthetically generated datasets. We show that these datasets demonstrably present a great challenge even for state-of-the-art DP synthetic data generation methods. Struct-Bench provides reference implementations of different metrics and a leaderboard, offering a standardized platform to benchmark and investigate privacy-preserving synthetic data methods. We also present a case study showing how Struct-Bench improves the synthetic data quality of Private Evolution (PE) on structured data. The benchmark and the leaderboard have been publicly made available at https://struct-bench.github.io.

Compilers, while essential, are notoriously complex systems that demand prohibitively expensive human expertise to develop and maintain. The recent advancements in Large Language Models (LLMs) offer a compelling new paradigm: Neural Compilation, which could potentially simplify compiler development for new architectures and facilitate the discovery of innovative optimization techniques. However, several critical obstacles impede its practical adoption. Firstly, a significant lack of dedicated benchmarks and robust evaluation methodologies hinders objective assessment and tracking of progress in the field. Secondly, systematically enhancing the reliability and performance of LLM-generated assembly remains a critical challenge. Addressing these challenges, this paper introduces NeuComBack, a novel benchmark dataset specifically designed for IR-to-assembly compilation. Leveraging this dataset, we first define a foundational Neural Compilation workflow and conduct a comprehensive evaluation of the capabilities of recent frontier LLMs on Neural Compilation, establishing new performance baselines. We further propose a self-evolving prompt optimization method that enables LLMs to iteratively evolve their internal prompt strategies by extracting insights from prior self-debugging traces, thereby enhancing their neural compilation capabilities. Experiments demonstrate that our method significantly improves both the functional correctness and the performance of LLM-generated assembly code. Compared to baseline prompts, the functional correctness rates improved from 44% to 64% on x86_64 and from 36% to 58% on aarch64, respectively. More significantly, among the 16 correctly generated x86_64 programs using our method, 14 (87.5%) surpassed clang-O3 performance. These consistent improvements across diverse architectures (x86_64 and aarch64) and program distributions (NeuComBack L1 and L2) validate our method's superiority over conventional approaches and its potential for broader adoption in low-level neural compilation.

Unsigned distance fields (UDFs) are widely used in 3D deep learning due to their ability to represent shapes with arbitrary topology. While prior work has largely focused on learning UDFs from point clouds or multi-view images, extracting meshes from UDFs remains challenging, as the learned fields rarely attain exact zero distances. A common workaround is to reconstruct signed distance fields (SDFs) locally from UDFs to enable surface extraction via Marching Cubes. However, this often introduces topological artifacts such as holes or spurious components. Moreover, local SDFs are inherently incapable of representing non-manifold geometry, leading to complete failure in such cases. To address this gap, we propose MIND ($\underline{M}aterial$ $\underline{I}nterface$ $from$ $\underline{N}on$-$manifold$ $\underline{D}istance$ $fields$), a novel algorithm for generating material interfaces directly from UDFs, enabling non-manifold mesh extraction from a global perspective. The core of our method lies in deriving a meaningful spatial partitioning from the UDF, where the target surface emerges as the interface between distinct regions. We begin by computing a two-signed local field to distinguish the two sides of manifold patches, and then extend this to a multi-labeled global field capable of separating all sides of a non-manifold structure. By combining this multi-labeled field with the input UDF, we construct material interfaces that support non-manifold mesh extraction via a multi-labeled Marching Cubes algorithm. Extensive experiments on UDFs generated from diverse data sources, including point cloud reconstruction, multi-view reconstruction, and medial axis transforms, demonstrate that our approach robustly handles complex non-manifold surfaces and significantly outperforms existing methods. The source code is available at https://github.com/jjjkkyz/MIND.

Retrieval-Augmented Generation (RAG) empowers Large Language Models (LLMs) to dynamically integrate external knowledge during inference, improving their factual accuracy and adaptability. However, adversaries can inject poisoned external knowledge to override the model’s internal memory. While existing attacks iteratively manipulate retrieval content or prompt structure of RAG, they largely ignore the model’s internal representation dynamics and neuron-level sensitivities. The underlying mechanism of RAG poisoning has not been fully studied and the effect of knowledge conflict with strong parametric knowledge in RAG is not considered. In this work, we propose NeuroGenPoisoning, a novel attack framework that generates adversarial external knowledge in RAG guided by LLM internal neuron attribution and genetic optimization. Our method first identifies a set of **Poison-Responsive Neurons** whose activation strongly correlates with contextual poisoning knowledge. We then employ a genetic algorithm to evolve adversarial passages that maximally activate these neurons. Crucially, our framework enables massive-scale generation of effective poisoned RAG knowledge by identifying and reusing promising but initially unsuccessful external knowledge variants via observed attribution signals. At the same time, Poison-Responsive Neurons guided poisoning can effectively resolves knowledge conflict. Experimental results across models and datasets demonstrate consistently achieving high Population Overwrite Success Rate (POSR) of over 90\% while preserving fluency. Empirical evidence shows that our method effectively resolves knowledge conflict.

Retrieval-Augmented Generation (RAG) significantly improves the performance of Large Language Models (LLMs) on knowledge-intensive tasks. However, varying response quality across LLMs under RAG necessitates intelligent routing mechanisms, which select the most suitable model for each query from multiple retrieval-augmented LLMs via a dedicated router model. We observe that external documents dynamically affect LLMs' ability to answer queries, while existing routing methods, which rely on static parametric knowledge representations, exhibit suboptimal performance in RAG scenarios. To address this, we formally define the new retrieval-augmented LLM routing problem, incorporating the influence of retrieved documents into the routing framework. We propose RAGRouter, a RAG-aware routing design, which leverages document embeddings and RAG capability embeddings with contrastive learning to capture knowledge representation shifts and enable informed routing decisions. Extensive experiments on diverse knowledge-intensive tasks and retrieval settings, covering open and closed-source LLMs, show that RAGRouter outperforms the best individual LLM and existing routing methods. With an extended score-threshold-based mechanism, it also achieves strong performance-efficiency trade-offs under low-latency constraints. The code and data are available at https://github.com/OwwO99/RAGRouter.

Code generation with large language models (LLMs), often termed vibe coding, is increasingly adopted in production but fails to ensure code quality, particularly in security (e.g., SQL injection vulnerabilities) and maintainability (e.g., missing type annotations). Existing methods, such as supervised fine-tuning and rule-based post-processing, rely on labor-intensive annotations or brittle heuristics, limiting their scalability and effectiveness. We propose REAL (Reinforcement rEwards from Automated anaLysis), a reinforcement learning framework that trains LLMs to generate production-quality code using program analysis–guided feedback. Specifically, REAL integrates two automated signals: (1) static analyzers detecting security and maintainability defects and (2) unit tests ensuring functional correctness. Unlike prior work, our framework is prompt-agnostic and reference-free, enabling scalable supervision without manual intervention. Experiments across multiple datasets and model scales demonstrate that REAL outperforms state-of-the-art methods in simultaneous assessments of functionality and code quality. Our work bridges the gap between rapid prototyping and production-ready code, enabling LLMs to deliver both speed and quality.

Large language models (LLMs) have shown promise in transforming machine learning research, yet their capability to faithfully implement genuinely novel ideas from recent research papers—ideas unseen during pretraining—remains unclear. We introduce ResearchCodeBench, a benchmark that evaluates LLMs’ ability to translate cutting-edge ML contributions from top 2024-2025 research papers into executable code. We assessed 30+ proprietary and open-source LLMs, finding that even the best models correctly implement less than 40% of the code. We present empirical findings on performance comparison, contamination, and error patterns. By providing a rigorous evaluation platform, ResearchCodeBench enables continuous understanding and advancement of LLM-driven innovation in research code generation.

In this paper, we propose Tortoise and Hare Guidance (THG), a training-free strategy that accelerates diffusion sampling while maintaining high-fidelity generation. We demonstrate that the noise estimate and the additional guidance term exhibit markedly different sensitivity to numerical error by reformulating the classifier-free guidance (CFG) ODE as a multirate system of ODEs. Our error-bound analysis shows that the additional guidance branch is more robust to approximation, revealing substantial redundancy that conventional solvers fail to exploit. Building on this insight, THG significantly reduces the computation of the additional guidance: the noise estimate is integrated with the tortoise equation on the original, fine-grained timestep grid, while the additional guidance is integrated with the hare equation only on a coarse grid. We also introduce (i) an error-bound-aware timestep sampler that adaptively selects step sizes and (ii) a guidance-scale scheduler that stabilizes large extrapolation spans. THG reduces the number of function evaluations (NFE) by up to 30% with virtually no loss in generation fidelity (∆ImageReward ≤ 0.032) and outperforms state-of-the-art CFG-based training-free accelerators under identical computation budgets. Our findings highlight the potential of multirate formulations for diffusion solvers, paving the way for real-time high-quality image synthesis without any model retraining. The source code is available at https://github.com/yhlee-add/THG.

This paper introduces VeriThoughts, a novel dataset designed for reasoning-based Verilog code generation. We establish a new benchmark framework grounded in formal verification methods to evaluate the quality and correctness of generated hardware descriptions. Additionally, we present a suite of specialized small-scale models optimized specifically for Verilog generation. Our work addresses the growing need for automated hardware design tools that can produce verifiably correct implementations from high-level specifications, potentially accelerating the hardware development process while maintaining rigorous correctness guarantees.

Large language models (LLMs), despite their impressive performance across a wide range of tasks, often struggle to balance two competing objectives in open-ended text generation: fostering diversity and creativity while preserving logical coherence. Existing truncated sampling techniques, including temperature scaling, top-*p* (nucleus) sampling, and min-*p* sampling, aim to manage this trade-off. However, they exhibit limitations, particularly in the effective incorporation of the confidence of the model into the corresponding sampling strategy. For example, min-*p* sampling relies on a single top token as a heuristic for confidence, eventually underutilizing the information of the probability distribution. To effectively incorporate the model confidence, this paper presents **_top-H_ decoding**. We first establish the theoretical foundation of the interplay between creativity and coherence in truncated sampling by formulating an **entropy-constrained minimum divergence** problem. We then prove this minimization problem to be equivalent to an **entropy-constrained mass maximization (ECMM)** problem, which is NP-hard. Finally, we present top-H decoding, a computationally efficient greedy algorithm to solve the ECMM problem. Extensive empirical evaluations demonstrate that top-H outperforms the state-of-the-art (SoTA) alternative of min-*p* sampling by up to **25.63%** on creative writing benchmarks, while maintaining robustness on question-answering datasets such as GPQA, GSM8K, and MT-Bench. Additionally, an *LLM-as-judge* evaluation confirms that top-H indeed produces coherent outputs even at higher temperatures, where creativity is especially critical. In summary, top-H advances SoTA in open-ended text generation and can be *easily integrated* into creative writing applications. The code is available at [https://github.com/ErfanBaghaei/Top-H-Decoding](https://github.com/ErfanBaghaei/Top-H-Decoding).

We introduce HBLLM, a wavelet-enhanced high-fidelity $1$-bit post-training quantization method for Large Language Models (LLMs). By leveraging Haar wavelet transforms to enhance expressive capacity through frequency decomposition, HBLLM significantly improves quantization fidelity while maintaining minimal overhead. This approach features two innovative structure-aware grouping strategies: (1) frequency-aware multi-parameter intra-row grouping and (2) $\ell_2$-norm-based saliency-driven column selection. For non-salient weights, a shared mean is employed across quantization groups within each frequency band to optimize storage efficiency. Experiments conducted on the OPT and LLaMA models demonstrate that HBLLM achieves state-of-the-art performance in $1$-bit quantization, attaining a perplexity of $6.71$ on LLaMA$2$-$13$B with an average weight storage of only $1.08$ bits. Code available at: https://github.com/Yeyke/HBLLM.

Autoregressive models have transformed protein engineering by enabling the generation of novel protein sequences beyond those found in nature. However, their sequential inference introduces significant latency, limiting their utility in high-throughput protein screening. Speculative decoding accelerates generation by employing a lightweight draft model to sample tokens, which a larger target model then verifies and refines. Yet in protein sequence generation, draft models are typically agnostic to the structural and functional constraints of the target protein, leading to biologically implausible outputs and a shift in the likelihood distribution of generated sequences. We introduce SpecMER (Speculative Decoding via k-mer Guidance), a novel framework that incorporates biological, structural, and functional priors using k-mer motifs extracted from multiple sequence alignments. By scoring candidate sequences in parallel and selecting those most consistent with known biological patterns, SpecMER significantly improves sequence plausibility while retaining the efficiency of speculative decoding. SpecMER achieves 24–32% speedup over standard autoregressive decoding, along with higher acceptance rates and improved sequence likelihoods.

Programming assistants powered by large language models have transformed software development, yet most benchmarks focus narrowly on code generation tasks. Recent efforts like InfiBench and StackEval attempt to address this gap using Stack Overflow data but remain limited to single-turn interactions in isolated contexts, require significant manual curation, and fail to represent complete project environments. We introduce CodeAssistBench (CAB), the first benchmark framework for evaluating multi-turn programming assistance in realistic settings that address questions grounded in actual codebases. Unlike existing programming Q&A benchmarks, CAB automatically generates scalable datasets from GitHub issues tagged with questions using configurable parameters (e.g., repository creation date, star count, programming languages), and includes automatic containerization of codebases for evaluation. It then evaluates models through simulated users in these containerized environments with full codebase access. Using this framework, we constructed a test set of 3,286 real-world programming questions across 214 repositories, spanning seven programming languages and diverse problem domains. Our evaluation of leading LLMs reveals a substantial capability gap: while models perform well on Stack Overflow questions with success rates of 70-83%, they resolve only up to 16.49% of CAB's issues from recent repositories (post-training cutoff). This discrepancy highlights the challenges of providing assistance in complex, project-specific contexts versus answering standalone questions. Our fully automated framework enables continuous benchmark expansion and is available at https://github.com/amazon-science/CodeAssistBench/.

The rise of Large Language Models (LLMs) has driven progress in reasoning tasks, from program synthesis to scientific hypothesis generation, yet their ability to handle ranked preferences and structured algorithms in combinatorial domains remains underexplored. We study matching markets, a core framework behind applications like resource allocation and ride-sharing, which require reconciling individual ranked preferences to ensure stable outcomes. We evaluate seven state‐of‐the‐art models on a hierarchy of preference‐based reasoning tasks---ranging from stable‐matching generation to instability detection, instability resolution, and fine-grained preference queries---to systematically expose their logical and algorithmic limitations in handling ranked inputs. Surprisingly, even top-performing models with advanced reasoning struggle to resolve instability in large markets, often failing to identify blocking pairs or execute algorithms iteratively. We further show that parameter-efficient fine-tuning (LoRA) significantly improves performance in small markets, but fails to bring about a similar improvement on large instances, suggesting the need for more sophisticated strategies to improve LLMs' reasoning with larger-context inputs.

Despite remarkable advances in coding capabilities, language models (LMs) still struggle with simple syntactic tasks such as generating balanced parentheses. In this study, we investigate the underlying mechanisms behind the persistence of these errors across LMs of varying sizes (124M–7B) to both understand and mitigate the errors. Our study reveals that LMs rely on a number of components (attention heads and FF neurons) that independently make their own predictions. While some components reliably promote correct answers across a generalized range of inputs (i.e., implementing "sound mechanisms''), others are less reliable and introduce noise by promoting incorrect tokens (i.e., implementing "faulty mechanisms''). Errors occur when the faulty mechanisms overshadow the sound ones and dominantly affect the predictions. Motivated by this insight, we introduce RASteer, a steering method to systematically identify and increase the contribution of reliable components for improving model performance. RASteer substantially improves performance on balanced parentheses tasks, boosting accuracy of some models from $0$\% to around $100$\% without impairing the models' general coding ability. We further demonstrate its broader applicability in arithmetic reasoning tasks, achieving performance gains of up to around $20$\%.

We argue that diffusion models' success in modeling complex distributions is, for the most part, coming from their conditioning. This paper investigates the representation used to condition diffusion models from the perspective that ideal representations should improve modeling the data distribution, be easy to generate, and be compositional to allow generalizing outside the training distribution. We introduce Discrete Latent Code (DLC), an image representation derived from Simplicial Embeddings trained with a self-supervised learning objective. DLCs are sequences of discrete tokens, as opposed to the standard continuous image embeddings. They are easy to generate and their compositionality enables sampling of novel images beyond the training distribution. Diffusion models trained with DLCs improve generation fidelity, establishing a new state-of-the-art for unconditional image generation on ImageNet. Additionally, we show that composing DLCs allows the image generator to produce interesting out-of-distribution samples that coherently combine the semantics of images in diverse ways. Finally, we showcase how DLCs can enable text-to-image generation by leveraging large-scale pretrained language models. Using only 9M image-caption pairs, we efficiently finetune a text diffusion model to generate novel DLCs that produces samples outside of the data distribution used to train the image generator.

Chain-of-Thought (CoT) enhances the performance of Large Language Models (LLMs) on reasoning tasks by encouraging step-by-step solutions. However, the verbosity of CoT reasoning hinders its mass deployment in efficiency-critical applications. Recently, implicit CoT approaches have emerged, which encode reasoning steps within LLM's hidden embeddings (termed ``implicit reasoning'') rather than explicit tokens. This approach accelerates CoT reasoning by reducing the reasoning length and bypassing some LLM components. However, existing implicit CoT methods face two significant challenges: (1) they fail to preserve the semantic alignment between the implicit reasoning (when transformed to natural language) and the ground-truth reasoning, resulting in a significant CoT performance degradation, and (2) they focus on reducing the length of the implicit reasoning; however, they neglect the considerable time cost for an LLM to generate one individual implicit reasoning token. To tackle these challenges, we propose a novel semantically-aligned implicit CoT framework termed **SemCoT**. In particular, for the first challenge, we design a contrastively trained sentence transformer that evaluates semantic alignment between implicit and explicit reasoning, which is used to enforce semantic preservation during implicit reasoning optimization. To address the second challenge, we introduce an efficient implicit reasoning generator by finetuning a lightweight language model using knowledge distillation. This generator is guided by our sentence transformer to distill ground-truth reasoning into semantically aligned implicit reasoning, while also optimizing for accuracy. SemCoT is the first approach that enhances CoT efficiency by jointly optimizing token-level generation speed and preserving semantic alignment with ground-truth reasoning. Extensive experiments demonstrate the superior performance of SemCoT compared to state-of-the-art methods in both efficiency and effectiveness. Our code can be found at https://github.com/YinhanHe123/SemCoT/.