NeurIPS 2026 Papers

GANs are appealing because they generate sharp images in a single forward pass. Recent works have stabilized GAN training, but FID may still plateau on diverse datasets like ImageNet-256 because the discriminator's activation magnitudes increase through training. We trace this pathology to the discriminator's incentive to sharpen its decision boundary by rescaling activations rather than by finding better features. Then, building on R3GAN, we treat magnitude preservation as a first-class architectural target across the network: $\ell_2$ weight normalization with centering, magnitude-preserving LReLU and residuals, forced post-update normalization, and feed-forward classifier heads. Across a roadmap of configurations, we perform diagnostic ablations to clarify what does and does not work and why. The resulting models reach FIDs of 2.20 @ 17 M parameters, 1.63 @ 60 M, and 1.52 @ 130 M on class-conditional ImageNet-256. At 1 NFE, this is substantially more efficient than competing diffusion and autoregressive methods, and than prior GAN baselines too (e.g., 10$\times$ more efficient than StyleGAN-XL for similar FID). In sum, our work presents a new SOTA in FID/parameter efficiency derived from simple adversarial training with well-behaved magnitude preserving layers.

Visual Text Comprehension (VTC) renders text into images for a vision-language model (VLM) to read, sidestepping LLM context-window limits and powering applications from long-page OCR to multi-page memory QA. Yet existing VTC pipelines treat rendering and layout as a fixed, content-agnostic preprocessing step, and offer little mechanistic understanding of how VLMs internally process visualized text. Through a focused empirical study on VTC QA tasks, we find that VLMs exhibit a localization-without-utilization regime: evidence-localizing attention emerges sharply in the middle-to-late layers and is largely decoupled from answer correctness, yet simply enlarging the localized spans on the rendered page recovers a large fraction of the failures. Building on these observations, we propose AGAR (Attention-Guided Adaptive Rendering), a training-free, model-agnostic method that leverages a VLM's own middle-to-late layer attention to identify the top-K important visual patches, maps them back to word spans, and re-renders the page with those spans enlarged before re-inferring the answer. Extensive experiments across nine VTC benchmarks (short-form, long-context, and multi-page memory QA) and four VLM backbones show that AGAR (i) consistently improves off-the-shelf VLMs as a plug-and-play enhancement, (ii) composes with VLM post-training to yield further gains, and (iii) remains robust under both visual- and text-side input degradation.

Unpaired image translation is a critical preprocessing strategy for synthesizing missing sequences and harmonizing contrast variability in magnetic resonance (MR) imaging. However, in medical image processing, distribution-level translation is insufficient; it is vitally important that the anatomy is not distorted, corrupted, or lost after translation. Previous methods, like diffusion Schrödinger bridge matching (DSBM) achieve image translation, but do not preserve anatomy. We introduce the pseudometric Schrödinger bridge (PMSB), which trains two independent volume-preserving, isometry-regularized diffeomorphisms to map data from each domain to a latent anatomic pseudometric space. Then, DSBM is used within that space, explicitly minimizing the transport gap while preserving anatomy. Extensive experiments on the multi-contrast OASIS-3 dataset demonstrate that PMSB establishes a new state-of-the-art in structural consistency for cross-contrast synthesis. PMSB outperforms other leading methods and drastically reduces anatomical hallucinations, notably yielding a mean PSNR of 26.70 dB, a mean SSIM of 0.86, and a mean LNCC of 0.24.

Many scientific simulations are computationally expensive, limiting their use in simulation-based inference, uncertainty quantification, and decision making. We introduce *macrocanonical generator networks*, a framework for learning fast, data-efficient neural surrogates for *amortized* simulation of stationary physical processes by matching multiscale statistics of a target process. Inspired by microcanonical maximum-entropy synthesis, which matches feature statistics per sample by inner-loop optimization, our approach instead trains a neural generator to satisfy the same constraints in expectation, preserving physically realistic sample-to-sample fluctuations. We prove that gradient-descent training induces preconditioned gradient-descent dynamics in sample space that inherit the symmetry-preservation properties of the microcanonical gradient descent of Bruna and Mallat, amortizing its per-sample inner-loop optimization into a single training run after which every sample is generated in one forward pass. We further show that residual generator parameterizations initialized near the identity, trained with a small learning rate, preserve entropy locally during early optimization and mitigate mode collapse. Experiments on cosmology and fluid simulations show that macrocanonical generators recover realistic samples from extremely small training sets, in some cases a single training example, while generating new realizations more than $10^6$ times faster per sample than the reference simulator and more than $10^3$ times faster than microcanonical gradient descent. The trained generators can be reused for downstream pretraining, including simulation-based inference, providing a data-efficient route to multi-fidelity scientific machine learning workflows.

Machine unlearning (MU) aims to remove sensitive or undesired knowledge from a trained model without retraining from scratch. While MU has been widely studied for autoregressive large language models, its application to diffusion large language models (DLLMs) remains largely unexplored. In this paper, we present the first systematic study of MU in DLLMs and show that existing unlearning objectives transfer poorly to this setting due to sparse supervision and inaccurate forgetting localization. To address these challenges, we propose \textsc{DL-Eraser}, a DLLM-native unlearning framework that suppresses target recoverability under high-mask conditioning while constraining updates to a utility-preserving subspace. Extensive experiments show that \textsc{DL-Eraser} achieves stronger forgetting while better preserving model utility than existing baselines. To the best of our knowledge, this is the first work that systematically investigates MU in DLLMs.

Retrieval-Augmented Generation (RAG) has become a standard approach for grounding large language models in external knowledge, yet its performance depends critically on a large number of interacting design choices. Systematic optimization of these choices remains costly, as each configuration must be evaluated through full pipeline execution. In this work, we propose to treat RAG optimization as a prediction problem, using surrogate models to approximate the functional dependencies between configuration parameters and performance metrics. Using a stage-wise configurable RAG framework, we conduct large-scale experiments across three chemistry QA domains, systematically evaluating 648 configurations per domain and publicly releasing the resulting datasets of configurations and evaluation metrics. Surrogate models trained on this data achieve strong predictive accuracy ($R^2 \geq 0.84$ across all metrics and domains), and SHAP-IQ-based analysis of the learned models reveals consistent parameter interaction patterns across domains — despite substantial differences in corpus characteristics. We exploit this cross-domain regularity in transfer experiments: surrogate predictions generalize to unseen domains without target-domain training data on two transfer-robust metrics, and achieve full transfer across all six metrics with as little as 10\% of target-domain data. Finally, we apply surrogate models to optimize RAG configurations over an expanded search space of 61,152 candidates, recovering top-performing configurations in seconds rather than days, with gains of up to +0.09 in key retrieval and generation evaluation metrics. Together, these results demonstrate that RAG design spaces are structured, transferable, and efficiently optimizable via surrogate modeling.

Multimodal Large Language Models (MLLMs) show strong visual perception capabilities, but existing evaluations largely focus on single-view or multi-view settings with shared camera parameters, leaving the challenge of {multi-agent collaborative} scenarios underexplored. In such settings, multiple agents observe a shared environment from independent viewpoints, and reliable decisions require reasoning across these independent observations of the same environment. To study this problem, we introduce **MaRiO**, a benchmark for evaluating multi-agent collaborative reasoning, and evaluate 23 state-of-the-art MLLMs on it. Our analysis reveals three key findings: (1) spatial tasks are generally easier than geometric reasoning tasks; (2) most models struggle to resolve cross-agent correspondences, with errors increasing with scene complexity; and (3) models show limited ability to leverage geometric cues present in the scene. As an initial step toward addressing these challenges, we explore geometry-guided synthetic view augmentation that generates intermediate transition frames between agent observations, providing auxiliary spatial context that improves performance in certain categories. Overall, our results highlight that multi-agent collaborative reasoning remains an open challenge and an important direction for multimodal embodied systems.

State Space Models (SSMs) offer an efficient alternative to Transformers for sequence modeling, yet conditioning pre-trained SSMs for iterative generation typically operates outside the recurrent operator, through input injection or activation modulation. While such mechanisms expose the model to conditioning information, they leave the underlying temporal dynamics fixed. We introduce MaRK (Markov-adapted Recurrent Kernels), a dynamic operator-conditioning framework that maps context vectors directly into bounded modulations of a frozen SSM's recurrence ($A$), read-in ($B$), read-out ($C$), skip ($D$), and discretization ($\Delta$) parameters. Viewed through the lens of Linear Parameter-Varying systems, MaRK induces a context-indexed family of Markov parameter sequences, allowing each diffusion timestep to reshape the model's input-output memory kernel. We instantiate MaRK on a frozen 111M-parameter Hydra SSM backbone and study three adapter geometries: Hypernet, Chebyshev polynomial, and Discrete Cosine Transform kernels. Since these adapters modify the Markov parameter sequence through low-rank auxiliary maps on the frozen backbone, parameter-efficient fine-tuning arises as a structural consequence of the adaptation mechanism itself, requiring only 7.5--13M trainable auxiliary parameters to transition from a bidirectional objective to an iterative diffusion regime. The bounded recurrence parameterization further yields an analytic Affine Quadratic Stability certificate for the modulated recurrence. Through synthetic LPV recovery experiments and Markov-operator diagnostics, we show that MaRK recovers coordinate-invariant temporal operators under matched assumptions and produces distinct, stable timestep-conditioned memory profiles. Empirically, the Chebyshev variant yields the strongest performance, achieving an average validation loss of 2.63, followed by the DCT (2.66) and Hypernet (3.60) geometries. Together, these results provide initial evidence that dynamic operator modulation is a principled operator-level conditioning mechanism for adapting SSMs beyond input-stream injection and adaptive normalization.

As the era of large language models (LLMs) unfolds, Preference Optimization (PO) methods have become a central approach to aligning LLMs with human preferences and improving performance. We propose Maximum a Posteriori Preference Optimization (MaPPO), a methodology for learning from preferences that explicitly incorporates prior reward knowledge into the optimization objective. Building on the paradigm employed by Direct Preference Optimization (DPO) and its variants of treating preference learning as a Maximum Likelihood Estimation (MLE) problem, MaPPO integrates prior reward estimates into a principled Maximum a Posteriori (MaP) objective. This not only generalizes DPO and its variants, but also enhances alignment by mitigating the oversimplified binary classification of responses. Additionally, MaPPO introduces no additional hyperparameters, and supports preference optimization in both offline and online settings. In addition, MaPPO can be used as a plugin for DPO variants, including widely used SimPO, IPO and CPO, and produce consistent improvements. Extensive empirical evaluations of different model sizes and model series on three standard benchmarks (MT-Bench, AlpacaEval 2.0, and Arena-Hard) demonstrate consistent improvements in alignment performance without sacrificing computational efficiency.

Reinforcement learning with verifiable rewards (RLVR) enhances the reasoning capabilities of large language models (LLMs), but at the expense of significant computational overhead due to compute-intensive rollout processes and frequent policy updates. Online prompt selection, a widely adopted strategy for improving training efficiency, maintains per-prompt Bayesian posteriors to predict prompt difficulty and prioritize informative prompts before committing rollout budget. However, these methods assess prompt informativeness without accounting for how reliably learning signal is extracted from sampled responses. In GRPO-based RL algorithms, the realized advantage of a response depends not only on its own outcome, but also on the randomly sampled outcomes of its peers through group normalization. Our experimental and theoretical analysis show that the resulting uncertainty in group composition induces composition noise, a non-vanishing variance component that creates an irreducible lower bound on gradient estimation error. Consequently, the standard group-relative advantage fails to faithfully characterize response-level utility, degrading gradient estimation and thereby impairing downstream prompt selection. To address this issue, we propose a unified Marginalized Posterior-Predictive framework, MaPP, for data-efficient RLVR, which first denoises response-level advantage estimation and then improves prompt selection using a shared Beta posterior. Specifically, for each response, MaPP replaces the standard group-relative advantage with a composition-invariant intrinsic advantage via closed-form Beta-Binomial marginalization. This yields a closed-form posterior-predictive advantage estimator whose error provably diminishes as the posterior concentrates. Then, building on the same posterior, MaPP derives an uncertainty-aware prompt selection score that more faithfully characterizes prompt informativeness, improving data efficiency without additional rollout cost. Experiments across mathematics, planning, and visual geometry on five model backbones show that MaPP consistently outperforms GRPO and strong selection baselines, achieving up to +2.45 average accuracy improvement over the strongest baseline under the same rollout budget, a new state-of-the-art.

3D Gaussian Splatting (3DGS) achieves real-time photorealistic novel-view synthesis but is vulnerable to adversarial perturbations of its training images. Recent attacks inflate the Gaussian count to exhaust GPU memory or corrupt rendered scenes to mislead downstream classifiers. We find that both attacks have the same structural signature: 2D image adversarial perturbations are not 3D-consistent by design. The Gaussians generated to match them provide erroneous contributions in some views while making significant contributions in others. We propose Multi-View Photometric Inconsistency (MVPI) Defense that scores each Gaussian by the variance of its opacity-weighted local $\mathcal{L}_1$ contribution across a stratified set of training views. The most inconsistent are soft-pruned via 3DGS's existing opacity threshold method. We evalute our approach on two different datasets. MVPI reduces peak Gaussian count by up to $1.90\times$ and training time by $1.22{-}1.50\times$ under Poison-Splat attack. It also restores top-1 classification accuracy on adversarially perturbed renders from $57.4\%$ to $66.5\%$. Our code is available at https://anonymous.4open.science/r/PruneDefense-2876/README.md.

Language models solve complex problems by articulating intermediate reasoning steps in natural language. While effective, this process is computationally bottlenecked: each reasoning step conveys only a single subword, and many are spent expressing a thought instead of carrying out computation. We propose MUX, a simple method for high-bandwidth and compact reasoning based on distillation of discrete reasoning into continuous multiplexed tokens in a latent space. Each latent token is trained to represent a weighted linear superposition (multiplexing) of a span of discrete reasoning subwords, where this superposition is lossless by construction and the span can be fully recovered (demultiplexing). We prove that simple position-dependent weightings, such as suitable geometric decay, support lossless multiplexing and prevent latent collapse. We further show that multiplexed reasoning can perform parallel exploration in problems that require search. Across 32 evaluation settings spanning four language models, MUX outperforms strong latent reasoning baselines. Our results suggest that properly chosen learning targets can make continuous latent reasoning efficient and interpretable.

Talking-head generation models, which synthesize realistic facial animations from audio, are increasingly vulnerable to misuse in multimodal deepfake scenarios. Protecting such systems remains challenging, as talking-head models fundamentally rely on precise audio–visual alignment, while effective audio protection methods remain largely underexplored. In this work, we propose MUTE, an audio protection framework that uncouples the underlying audio–visual alignment through a multi-level strategy. Specifically, MUTE combines (1) Representation-level Degradation, which perturbs temporal audio embeddings to degrade their representations, and (2) Alignment-level Disruption, which directly perturbs cross-modal attention to disrupt structural alignment. To improve robustness, perturbations are constrained in the STFT domain to high-energy regions, making them resistant to post-processing and denoising. An optional speaker-level objective further mitigates potential bypass via TTS-based resynthesis. Extensive experiments demonstrate that MUTE consistently degrades lip synchronization across both white-box and black-box talking-head models while preserving perceptual audio quality. The proposed method remains effective under real-world transformations and can be combined with image-based approaches to provide stronger multimodal protection.

Test-time scaling (TTS) improves reasoning by allocating additional inference compute, but in multimodal large language models (MLLMs), more compute is not always reliable. Longer reasoning may amplify visual misperception, induce answer drift, reinforce majority traps, or turn initially correct predictions into overthought failures. We propose MUST, a training-free framework that recasts multimodal TTS as stage-conditioned stability control. MUST separates inference into reasoning and verification stages and assigns each stage a different reliability criterion. During reasoning, Contrastive Answer-Manifold Stability (CAMS) selects answers whose supporting trajectories form compact and separable latent groups. During verification, Attention-Free Support-Chain Stability (AF-SCS) evaluates whether explicit visual evidence and subsequent reasoning form a stable latent support chain, without relying on token-to-patch attention maps. Experiments on multimodal reasoning benchmarks show that MUST improves the accuracy-compute trade-off and reduces overthinking-induced errors. These results suggest that reliable MLLM test-time scaling should adaptively control when and how extra compute is trusted, rather than simply increasing inference budget.

Modeling gene regulation in single cells requires jointly representing DNA sequence, chromatin accessibility, and gene expression across regulatory scales. Sequence-based models capture DNA-level regulatory grammar but typically lack cell-level resolution, whereas single-cell omics models capture cell-state semantics but treat genes and peaks as fixed vocabulary tokens, and thus lack a unified sequence-based view of regulation. Here, we present MUSS, a sequence-based multi-scale model for single-cell gene regulation that preserves both DNA-level and cell-level resolution. MUSS derives peak- and gene-level representations from DNA using a frozen pre-trained sequence encoder, integrates them with a multi-scale encoder combining peak-peak self-attention and distance-biased peak-gene interaction, and trains on paired scATAC-seq and scRNA-seq to align sequence-derived representations with cell-specific regulatory states. Across gene expression prediction, enhancer-gene linking, TF-target gene recovery, and zero-shot cell clustering, MUSS outperforms both sequence-based and single-cell omics baselines, and further generalizes to genes and peaks unseen during training. Together, these results demonstrate that MUSS learns biologically meaningful and broadly generalizable regulatory representations for decoding cell-type-specific regulatory programs from DNA sequence.

We introduce $\texttt{MUNI}$, an end-to-end multimodal latent diffusion framework for any-to-any generation that unifies subset-conditioned cross-modal generation and unconditional joint sampling through a shared stochastic latent. Existing multimodal generative models are largely LLM-based, which limits leveraging modality-specific generators and requires text-paired data for training. Recent diffusion- and flow-based any-to-any extensions take a different direction but still rely on text-aligned embeddings, fully-paired training, or matched-dimensionality deterministic mappings. $\texttt{MUNI}$ rests on two complementary contributions, one architectural and one in the training objective. First, we extend latent diffusion to multimodal any-to-any generation *end-to-end*: instead of the standard two-stage recipe that precomputes a frozen latent space and then fits a prior over it, $\texttt{MUNI}$ jointly trains modality-specific encoders, expressive decoders, and a single shared flow-based prior under one objective. Second, we identify that the standard aggregation rules of multimodal variational inference are insufficient once coupled with a learned prior and expressive decoders. A suitable shared latent must simultaneously satisfy *coherence* across generated modalities, *predictive sufficiency* of subset latents, and *minimality* of the latent content. We propose a routed training objective whose structural choices align the latent with these criteria and admit a minimal-sufficiency characterization in the realizable setting. Experiments on PolyMNIST-Quadrant-Labels and a large-scale image-text-audio benchmark show $\texttt{MUNI}$ matching or exceeding the strongest baselines on conditional generation while opening its largest margins on unconditional coherence.

3DGS-based open-vocabulary 3D scene understanding requires identifying reconstructed 3D instances that correspond to a natural-language query. Existing methods typically compress multi-view observations of an instance into a single semantic descriptor, which is insufficient to represent a complete 3D instance. To retain rich semantic information across diverse viewpoints, we propose MSR-3D, a framework built around a Multi-Mode Semantic Representation. Specifically, MSR-3D derives multi-view observations from both 2D segmentation masks and rendered masks of each segmented 3D instance. These observations are organized into groups. Each group is summarized as a semantic mode through a representative feature and associated statistical attributes. Based on the multi-mode semantic representation, we further introduce a lightweight learnable mode-aware matcher for querying. The matcher employs linear scoring modules to project the multi-mode representation of each query-instance pair into a three-dimensional score space. Calibrated decision boundaries are then learned in the resulting score space to separate true query-instance matches from semantically related distractors. This structured and decomposable design further improves the interpretability and generalization of MSR-3D. Experiments on open-vocabulary scene-understanding benchmarks show that MSR-3D achieves state-of-the-art results, improving mIoU on LERF-OVS by 7.52% over the baseline and achieving the best overall performance on 3DOVS.

MSConsensus: A Hundred-Million-Scale, Batch-Effect–Suppressed Dataset and Benchmark for Proteomics Machine Learning Machine learning for proteomics is bottlenecked by three coupled and under-explored challenges: (i) noisy mass-spectrometry (MS) data dominated by instrument- and protocol-specific batch effects, (ii) slow data loading from legacy XML- and text-based file formats, and (iii) a fragmented evaluation landscape that prevents meaningful cross-study comparison. Each silently constrains what proteomics models learn, how efficiently they train, and how reliably they are compared. We address all three with MSConsensus, a multi-task dataset and benchmark built natively for proteomics ML. MSConsensus contains 110,209,043 consensus spectra distilled from 1.01 PB of public PRIDE data spanning 1,500 repositories and all major Orbitrap and timsTOF platforms, with per-peak ion annotations and stratified ML splits across instruments, species, and post-translational modifications. Unlike single-representative spectral libraries (MassIVE-KB v2, NIST, ProteomeTools), MSConsensus uses a new Weighted-Score Binning (WSBIN) algorithm that emits multiple consensus spectra per (peptide, charge) cluster, preserving intra-cluster variance required by contrastive and representation-learning objectives while suppressing context-specific artifacts. Across five held-out PRIDE repositories and four search engines (Comet, MetaMorpheus, MSFragger, Sage), WSBIN improves signal-to-noise ratio by an average of +3.86 dB (range +0.57 to +10.47 dB) without sacrificing protein, peptide, or PSM identification counts. To eliminate the I/O bottleneck during model training, we pair MSConsensus with MSCompress and a new msz binary container. msz compresses to 45% of mzML size losslessly and supports 25,378 random-access spectra/sec — 3.2× HDF5 — through a drop-in PyTorch / JAX dataloader. A unified public leaderboard standardizes evaluation across three core tasks—spectrum embedding, intensity prediction, and de novo peptide identification—and we report results for ten widely used systems (Casanovo, InstaNovo, Prosit, MS²PIP, GLEAMS, Spec2Vec, Comet, MetaMorpheus, MSFragger, Sage). Replacing raw training data with MSConsensus stabilizes Prosit's spectral angle on a never-before-seen 2025 instrument (PXD053296) from 0.6964 to 0.8137 and improves Spec2Vec top-1 retrieval from 39.2% to 46.7% (+19.0% relative). By jointly addressing scale, batch-effect suppression, I/O efficiency, and standardized evaluation, MSConsensus provides foundational infrastructure for training, evaluating, and comparing future proteomics models. The dataset is released on Harvard Dataverse (doi:10.7910/DVN/NUCT4N) under CC BY 4.0; MSCompress, MSDatasets, preprocessing pipelines, and baseline scripts are released on GitHub under Apache 2.0, with Docker containers for reproducibility.

Accurately identifying metabolites (small molecules) from mass spectrometry data remains a core challenge in metabolomics, with broad applications in drug discovery, environmental analysis, and clinical research. We address the Molecule Retrieval task, which consists in recovering the chemical structure of a metabolite from its MS/MS spectrum given a set of candidate molecules. While the recent release of benchmark datasets such as MassSpecGym and Spectraverse has considerably accelerated the development of novel machine learning approaches, the complexity of data preprocessing pipelines and the lack of unified implementations make methods and results difficult to reproduce and compare. We make three contributions. First, we propose a unified framework encompassing recent approaches based on representation alignment and contrastive learning. Second, we introduce MSAlign, inspired by multimodal alignment in vision-language models, which learns a shared representation space by aligning two frozen foundation models (DreaMS for mass spectra and ChemBERTa for molecules) through lightweight MLP projections trained with a candidate-based contrastive objective. MSAlign is simple to implement, fast to train and consistently outperforms existing approaches across all benchmarks. Third, we investigate a long-standing evaluation problem: data splitting strategies in molecule retrieval implicitly trade off data leakage against domain shift. We formalize this tension by introducing a quantitative measure of distribution shift, and use it to evaluate splitting strategies in existing benchmarks. All datasets, splits, candidate sets, and a unified implementation of MSAlign and baselines are publicly released to support reproducible research.