NeurIPS 2025 Papers

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.

One proposed mechanism to improve exploration in reinforcement learning is the use of macro-actions, a form of temporal abstractions over actions. Paradoxically though, in many scenarios the naive addition of macro-actions does not lead to better exploration, but rather the opposite. In this work, we argue that the difficulty stems from the trade-offs between reducing the average number of decisions per episode versus increasing the size of the action space. Namely, one typically treats each potential macro-action as independent and atomic, hence strictly increasing the search space and making typical exploration strategies inefficient. To address this problem we propose a novel regularization term that exploits the relationship between actions and macro-actions to improve the credit assignment mechanism reducing the effective dimension of the action space and therefore improving exploration. The term relies on a similarity matrix that is meta-learned jointly with learning the desired policy. We empirically validate our strategy looking at macro-actions in Atari games, and the StreetFighter II environment. Our results show significant improvements over the Rainbow-DQN baseline in all environments. Additionally, we show that the macro-action similarity is transferable to other environments with similar dynamics. We believe this work is a small but important step towards understanding how the similarity-imposed geometry on the action space can be exploited to improve credit assignment and exploration, therefore making learning more efficient.

Although RAW images offer advantages over sRGB by avoiding ISP-induced distortion and preserving more information in low-light conditions, their widespread use is limited due to high storage costs, transmission burdens, and the need for significant architectural changes for downstream tasks. To address the issues, this paper explores a new raw-based machine vision paradigm, termed Compact RAW Metadata-guided Image Refinement (CRM-IR). In particular, we propose a Machine Vision-oriented Image Refinement (MV-IR) module that refines sRGB images to better suit machine vision preferences, guided by learned raw metadata. Such a design allows the CRM-IR to focus on extracting the most essential metadata from raw images to support downstream machine vision tasks, while remaining plug-and-play and fully compatible with existing imaging pipelines, without any changes to model architectures or ISP modules. We implement our CRM-IR scheme on various object detection networks, and extensive experiments under low-light conditions demonstrate that it can significantly improve performance with an additional bitrate cost of less than $10^{-3}$ bits per pixel.

Predicting the 3D conformation of small molecules within protein binding sites is a key challenge in drug design. When a crystallized reference ligand (template) is available, it provides geometric priors that can guide 3D pose prediction. We present a two-stage method for ligand conformation generation guided by such templates. In the first stage, we introduce a molecular alignment approach based on flow-matching to generate 3D coordinates for the ligand, using the template structure as a reference. In the second stage, a differentiable pose optimization procedure refines this conformation based on shape and pharmacophore similarities, internal energy, and, optionally, the protein binding pocket. We introduce a new benchmark of ligand pairs co-crystallized with the same target to evaluate our approach and show that it outperforms standard docking tools and open-access alignment methods, especially in cases involving low similarity to the template or high ligand flexibility.

Diffusion models can be improved with additional guidance towards more effective representations of input. Indeed, prior empirical work has already shown that aligning internal representations of the diffusion model with those of pre-trained models improves generation quality. In this paper, we present a systematic framework for incorporating representation guidance into diffusion models. We provide alternative decompositions of denoising models along with their associated training criteria, where the decompositions determine when and how the auxiliary representations are incorporated. Guided by our theoretical insights, we introduce two new strategies for enhancing representation alignment in diffusion models. First, we pair examples with target representations either derived from themselves or arisen from different synthetic modalities, and subsequently learn a joint model over the multimodal pairs. Second, we design an optimal training curriculum that balances representation learning and data generation. Our experiments across image, protein sequence, and molecule generation tasks demonstrate superior performance as well as accelerated training. In particular, on the class-conditional ImageNet $256\times 256$ benchmark, our guidance results in $23.3$ times faster training than the original SiT-XL as well as four times speedup over the state-of-the-art method REPA.

Text-to-image diffusion models rely on text embeddings from a pre-trained text encoder, but these embeddings remain fixed across all diffusion timesteps, limiting their adaptability to the generative process. We propose Diffusion Adaptive Text Embedding (DATE), which dynamically updates text embeddings at each diffusion timestep based on intermediate perturbed data. We formulate an optimization problem and derive an update rule that refines the text embeddings at each sampling step to improve alignment and preference between the mean predicted image and the text. This allows DATE to dynamically adapts the text conditions to the reverse-diffused images throughout diffusion sampling without requiring additional model training. Through theoretical analysis and empirical results, we show that DATE maintains the generative capability of the model while providing superior text-image alignment over fixed text embeddings across various tasks, including multi-concept generation and text-guided image editing. Our code is available at https://github.com/aailab-kaist/DATE.

Embodied agents operating in smart homes must understand human behavior through diverse sensory inputs and communicate via natural language. While Vision-Language Models (VLMs) have enabled impressive language-grounded perception, their reliance on visual data limits robustness in real-world scenarios with occlusions, poor lighting, or privacy constraints. In this paper, we introduce HoloLLM, a Multimodal Large Language Model (MLLM) that integrates uncommon but powerful sensing modalities, such as LiDAR, infrared, mmWave radar, and WiFi, to enable seamless human perception and reasoning across heterogeneous environments. We address two key challenges: (1) the scarcity of aligned modality-text data for rare sensors, and (2) the heterogeneity of their physical signal representations. To overcome these, we design a Universal Modality-Injection Projector (UMIP) that enhances pre-aligned modality embeddings with fine-grained, text-aligned features from tailored encoders via coarse-to-fine cross-attention without introducing significant alignment overhead. We further introduce a human-VLM collaborative data curation pipeline to generate paired textual annotations for sensing datasets. Extensive experiments on two newly constructed benchmarks show that HoloLLM significantly outperforms existing MLLMs, improving language-grounded human sensing accuracy by up to 30\%. This work establishes a new foundation for real-world, language-informed multisensory embodied intelligence.

Attention-based encoder decoder models remain a popular choice for state-of-the-art automatic speech recognition (ASR). These models combine a powerful audio encoder that extracts rich acoustic features with a decoder that autoregressively produces the ASR output. The decoder handles two critical tasks: (1) building rich text-only context and (2) merging acoustic information from the encoder to ensure the predictions remain faithful to the audio. We observe a systematic pattern across the attention distributions of decoder layers in prior architectures: the initial layers direct most attention towards building textual context, while the later layers largely focus on merging acoustic and textual information for the final predictions. Leveraging this key insight, we propose **BlockDecoder**, a novel decoder architecture comprising two distinct components: a text encoder that is purely text-based, and a **Merger** that combines information from the audio encoder and text encoder to generate output tokens. Unlike traditional decoders, the **Merger** autoregressively predicts a sequence of K tokens within a *block* of size K, while relying on the same precomputed contextual information from both text and audio encoders across the block. This design choice allows for the efficient reuse of encoder representations. The separation of the decoder into the text encoder and the **Merger** promotes modularity and more flexible control of parameters via the number of text encoder and **Merger** layers. As a result, **BlockDecoder** yields a significant speedup ($\sim2$x) compared to traditional decoders, across diverse datasets, languages, and speech tasks, without any degradation in performance. The code is available at https://github.com/csalt-research/blockdecoder.

Computation in recurrent networks of neurons has been hypothesized to occur at the level of low-dimensional latent dynamics, both in artificial systems and in the brain. This hypothesis seems at odds with evidence from large-scale neuronal recordings in mice showing that neuronal population activity is high-dimensional. To demonstrate that low-dimensional latent dynamics and high-dimensional activity can be two sides of the same coin, we present an analytically solvable recurrent neural network (RNN) model whose dynamics can be exactly reduced to a low-dimensional dynamical system, but generates an activity manifold that has a high linear embedding dimension. This raises the question: Do low-dimensional latents explain the high-dimensional activity observed in mouse visual cortex? Spectral theory tells us that the covariance eigenspectrum alone does not allow us to recover the dimensionality of the latents, which can be low or high, when neurons are nonlinear. To address this indeterminacy, we develop Neural Cross-Encoder (NCE), an interpretable, nonlinear latent variable modeling method for neuronal recordings, and find that high-dimensional neuronal responses to drifting gratings and spontaneous activity in visual cortex can be reduced to low-dimensional latents, while the responses to natural images cannot. We conclude that the high-dimensional activity measured in certain conditions, such as in the absence of a stimulus, is explained by low-dimensional latents that are nonlinearly processed by individual neurons.

Outcome‑reward reinforcement learning (RL) is a common—and increasingly significant—way to refine the step‑by‑step reasoning of multimodal large language models (MLLMs). In the multiple‑choice setting—a dominant format for multimodal reasoning benchmarks—the paradigm faces a significant yet often overlooked obstacle: unfaithful trajectories that guess the correct option after a faulty chain of thought receive the same reward as genuine reasoning, which is a flaw that cannot be ignored. We propose Self‑Consistency Sampling (SCS) to correct this issue. For each question, SCS (i) introduces small visual perturbations and (ii) performs repeated truncation‑and‑resampling of a reference trajectory; agreement among the resulting trajectories yields a differentiable consistency score that down‑weights unreliable traces during policy updates. Plugging SCS into RLOO, GRPO, REINFORCE++ series improves accuracy by up to 7.7 percentage points on six multimodal benchmarks with negligible extra computation, offering a simple, general remedy for outcome‑reward RL in MLLMs.

Recent advances in 3D point cloud transformers have led to state-of-the-art results in tasks such as semantic segmentation and reconstruction. However, these models typically rely on dense token representations, incurring high computational and memory costs during training and inference. In this work, we present the finding that tokens are remarkably redundant, leading to substantial inefficiency. We introduce an efficient token merging method and illustrate that it can reduce the token count by up to 90–95% while maintaining competitive performance. This finding challenges the prevailing assumption that more tokens inherently yield better performance and highlights that many current models are over-tokenized and under-optimized for scalability. We validate our method across multiple 3D vision tasks and show consistent improvements in computational efficiency. This work is the first to assess redundancy in large-scale 3D transformer models, providing insights into the development of more efficient 3D foundation architectures. Our code and checkpoints are publicly available at https://gitmerge3d.github.io.

Pruning is a widely used technique to reduce the size and inference cost of large language models (LLMs), but it often causes performance degradation. To mitigate this, existing restoration methods typically employ parameter-efficient fine-tuning (PEFT), such as LoRA, to recover the pruned model's performance. However, most PEFT methods are designed for dense models and overlook the distinct properties of pruned models, often resulting in suboptimal recovery. In this work, we propose a targeted restoration strategy for pruned models that restores performance while preserving their low cost and high efficiency. We observe that pruning-induced information loss is reflected in attention activations, and selectively reintroducing components of this information can significantly recover model performance. Based on this insight, we introduce RestoreLCC (Restoring Pruned LLMs via Lost Component Compensation), a plug-and-play method that contrastively probes critical attention heads via activation editing, extracts lost components from activation differences, and finally injects them back into the corresponding pruned heads for compensation and recovery. RestoreLCC is compatible with structured, semi-structured, and unstructured pruning schemes. Extensive experiments demonstrate that RestoreLCC consistently outperforms state-of-the-art baselines in both general and task-specific performance recovery, without compromising the sparsity or inference efficiency of pruned models.

Simulated tempering is a widely used strategy for sampling from multimodal distributions. In this paper, we consider simulated tempering combined with an arbitrary local Markov chain Monte Carlo sampler and present a new decomposition theorem that provides a lower bound on the restricted spectral gap of the algorithm for sampling from mixture distributions. By working with the restricted spectral gap, the applicability of our results is extended to broader settings such as when the usual spectral gap is difficult to bound or becomes degenerate. We demonstrate the application of our theoretical results by analyzing simulated tempering combined with random walk Metropolis--Hastings for sampling from mixtures of Gaussian distributions. Our complexity bound scales polynomially with the separation between modes, logarithmically with $1/\varepsilon$, where $\varepsilon$ denotes the target accuracy in total variation distance, and exponentially with the dimension $d$.

We study the complexity of learning real-valued Multi-Index Models (MIMs) under the Gaussian distribution. A $K$-MIM is a function $f:\mathbb{R}^d\to \mathbb{R}$ that depends only on the projection of its input onto a $K$-dimensional subspace. We give a general algorithm for PAC learning a broad class of MIMs with respect to the square loss, even in the presence of adversarial label noise. Moreover, we establish a nearly matching Statistical Query (SQ) lower bound, providing evidence that the complexity of our algorithm is qualitatively optimal as a function of the dimension. Specifically, we consider the class of bounded variation MIMs with the property that degree at most $m$ distinguishing moments exist with respect to projections onto any subspace. In the presence of adversarial label noise, the complexity of our learning algorithm is $d^{O(m)}2^{\mathrm{poly}(K/\epsilon)}$. For the realizable and independent noise settings, our algorithm incurs complexity $d^{O(m)}2^{\mathrm{poly}(K)}(1/\epsilon)^{O(K)}$. To complement our upper bound, we show that if for some subspace degree-$m$ distinguishing moments do not exist, then any SQ learner for the corresponding class of MIMs requires complexity $d^{\Omega(m)}$. As an application, we give the first efficient learner for the class of positive-homogeneous $L$-Lipschitz $K$-MIMs. The resulting algorithm has complexity $\mathrm{poly}(d) 2^{\mathrm{poly}(KL/\epsilon)}$. This gives a new PAC learning algorithm for Lipschitz homogeneous ReLU networks with complexity independent of the network size, removing the exponential dependence incurred in prior work.

Low-rank pre-training and fine-tuning have recently emerged as promising techniques for reducing the computational and storage costs of large neural networks. Training low-rank parameterizations typically relies on conventional optimizers such as heavy ball momentum methods or Adam. In this work, we identify and analyze potential difficulties that these training methods encounter when used to train low-rank parameterizations of weights. In particular, we show that classical momentum methods can struggle to converge to a local optimum due to the geometry of the underlying optimization landscape. To address this, we introduce novel training strategies derived from dynamical low-rank approximation, which explicitly account for the underlying geometric structure. Our approach leverages and combines tools from dynamical low-rank approximation and momentum-based optimization to design optimizers that respect the intrinsic geometry of the parameter space. We validate our methods through numerical experiments, demonstrating faster convergence, and stronger validation metrics at given parameter budgets.

We introduce Oxford Day-and-Night, a large-scale, egocentric dataset for novel view synthesis (NVS) and visual relocalisation under challenging lighting conditions. Existing datasets often lack crucial combinations of features such as ground-truth 3D geometry, wide-ranging lighting variation, and full 6DoF motion. Oxford Day-and-Night addresses these gaps by leveraging Meta ARIA glasses to capture egocentric video and applying multi-session SLAM to estimate camera poses, reconstruct 3D point clouds, and align sequences captured under varying lighting conditions, including both day and night. The dataset spans over 30 km of recorded trajectories and covers an area of $40{,}000\mathrm{m}^2$, offering a rich foundation for egocentric 3D vision research. It supports two core benchmarks, NVS and relocalisation, providing a unique platform for evaluating models in realistic and diverse environments. Project page: https://oxdan.active.vision/

Post-training plays a crucial role in refining and aligning large language models to meet specific tasks and human preferences. While recent advancements in post-training techniques, such as Group Relative Policy Optimization (GRPO), leverage increased sampling with relative reward scoring to achieve superior performance, these methods often suffer from training instability that limits their practical adoption. As a next step, we present Group Variance Policy Optimization (GVPO). GVPO incorporates the analytical solution to KL-constrained reward maximization directly into its gradient weights, ensuring alignment with the optimal policy. The method provides intuitive physical interpretations: its gradient mirrors the mean squared error between the central distance of implicit rewards and that of actual rewards. GVPO offers two key advantages: (1) it guarantees a unique optimal solution, exactly the KL-constrained reward maximization objective, (2) it supports flexible sampling distributions that avoids on-policy and importance sampling limitations. By unifying theoretical guarantees with practical adaptability, GVPO establishes a new paradigm for reliable and versatile LLM post-training.

Recent advancements in large reasoning models (LRMs) have introduced an intermediate "thinking" process prior to generating final answers, improving their reasoning capabilities on complex downstream tasks. However, the potential of LRMs as evaluators for machine translation (MT) quality remains underexplored. We provides the first systematic analysis of LRM-as-a-judge in MT evaluation. We identify key challenges, revealing LRMs require tailored evaluation materials, tend to "overthink" simpler instances and have issues with scoring mechanisms leading to overestimation. To address these, we propose to calibrate LRM thinking by training them on synthetic, human-like thinking trajectories. Our experiments on WMT24 Metrics benchmarks demonstrate that this approach largely reduces thinking budgets by ~35x while concurrently improving evaluation performance across different LRM scales from 7B to 32B (e.g., R1-Distill-Qwen-7B achieves a +8.7 correlation point improvement). These findings highlight the potential of efficiently calibrated LRMs to advance fine-grained automatic MT evaluation.

The remarkable progress in text-to-video diffusion models enables the generation of photorealistic videos, although the content of these generated videos often includes unnatural movement or deformation, reverse playback, and motionless scenes. Recently, an alignment problem has attracted huge attention, where we steer the output of diffusion models based on some measure of the content's goodness. Because there is a large room for improvement of perceptual quality along the frame direction, we should address which metrics we should optimize and how we can optimize them in the video generation. In this paper, we propose diffusion latent beam search with lookahead estimator, which can select a better diffusion latent to maximize a given alignment reward at inference time. We then point out that improving perceptual video quality with respect to alignment to prompts requires reward calibration by weighting existing metrics. This is because when humans or vision language models evaluate outputs, many previous metrics to quantify the naturalness of video do not always correlate with the evaluation. We demonstrate that our method improves the perceptual quality evaluated on the calibrated reward, VLMs, and human assessment, without model parameter update, and outputs the best generation compared to greedy search and best-of-N sampling under much more efficient computational cost. The experiments highlight that our method is beneficial to many capable generative models, and provide a practical guideline: we should prioritize the inference-time compute allocation into enabling the lookahead estimator and increasing the search budget, rather than expanding the denoising steps.