NeurIPS 2026 Papers

Conference on Neural Information Processing Systems

Decision breakdown

6,437papers

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

  • Oral
    991.5%
  • Spotlight
    2403.7%
  • Poster
    6,09894.7%

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Partition-Aware Unlearning for Removing Spurious Correlations in Large Vision-Language Models

Aditi Sarker, Nazreen Shah, Rafi Ibn Sultan, Rhongho Jang, Dongxiao Zhu, Prashant Khanduri

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Large Vision-Language Models (LVLMs) achieve strong performance across many multimodal tasks; however, they often exploit spurious object-background correlations, resulting in predictions driven by contextual shortcuts rather than object-relevant visual evidence. Despite growing interest in hallucination and robustness evaluation, existing benchmarks provide limited control over whether model predictions are grounded in the target object or induced by correlated background cues. In this work, we introduce PURGE (Partition-aware Unlearning for Removing spurious-correlation Generated Errors), a framework for constructing, benchmarking, and mitigating spurious-correlation-induced failures in LVLMs. The framework consists of two components: (1) Structured dataset construction, wherein we develop three complementary structured data construction strategies that partition examples by object-relevant evidence and spurious background cues, enabling controlled diagnosis of shortcut reliance; and (2) Partition-aware unlearning, which uses these partitions to selectively remove spurious object-background associations while preserving object-based reasoning. We evaluate the PURGE framework across multiple LVLMs, including LLaVA-1.6-7B, Qwen3-VL-8B-Instruct, and Qwen3.5-9B, together with CLIP as a vision-language encoder, on a diverse suite of benchmarks, including CHAIR, POPE, Causal-HalBench, MM-SpuBench, AMBER, MMHal, and Waterbirds. Our results show that PURGE consistently reduces hallucinations and spurious-correlation-driven errors while maintaining or improving overall performance, providing both a reusable evaluation protocol and an effective mitigation framework for more reliable LVLMs.

Poster
Participatory ML for Social Harm Should be Constructed, Validated and Reasoned Through First-Person Accounts

Atmadeep Ghoshal, Ankit Agarwal, Martim Brandão

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Participatory machine learning has improved who develops social harm evaluation resources but has left largely unexamined what kind of text serves as the raw signal for those resources. Researcher-generated stimuli fix the epistemic frame of harm before community participation begins, and the structured conditions of annotation prevent the richest forms of interpretive harm knowledge from entering the pipeline. We argue that participatory ML should construct, validate and reason about social harm pipelines through first-person accounts, by which we mean autobiography, memoir, testimony, and oral history authored by people describing their own experiences of discrimination and harm. Such accounts possess two epistemic properties that directly address these limitations. Authorial independence from research framing grounds what counts as harm, which contexts matter, and how discrimination is operationalised in experience rather than in researchers' prior conceptions of harm. Embedded rationale structure preserves the interpretive judgment through which harm becomes meaningful rather than reducing it to a label. We draw on existing archival corpora spanning multiple languages and harm domains and propose three concrete integration pathways across evaluation benchmarks, harm classifier training corpora, and safety preference datasets.

Poster
Partially Performative Prediction

Jaewook Lee, Tijana Zrnic

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Performative prediction studies feedback loops that arise when predictive models are deployed in consequential domains. In these settings, model updates can shape the population whose patterns they aim to predict, inducing a distribution shift that is *endogenous* to the learning system. This perspective departs from classical treatments of distribution shift, where shifts are typically modeled as *exogenous* changes in the data-generating process. Yet, in practice, distribution shift is rarely one or the other. Predictive models may influence future data through the decisions they support, while the world itself continues to drift for reasons beyond the learner’s control. We study *partially performative prediction*, a framework that captures both endogenous and exogenous sources of distribution shift. The framework generalizes performative prediction by allowing the data distribution to evolve both in response to the deployed model and according to an external, time-varying process. We extend the central notions of performative stability and performative optimality to this setting by defining online analogues that measure performance relative to the evolving partially performative environment. We analyze practical learning heuristics, including repeated retraining, and characterize when they successfully adapt to partially performative environments.

Poster
ParetoM$^3$: Learning on the Pareto Set under Preference Guidance via Min-Max-Min Optimization

Pei Tang, Songtao Lu

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Learning across multiple inherently conflicting objectives requires selecting desirable trade-offs from the Pareto set. In this work, we study preference-guided multi-objective optimization, where a predefined preference function is minimized over the weak Pareto set of multiple nonconvex objectives. Leveraging a merit function that vanishes on the weak Pareto set, we propose a penalty-based min-max-min formulation, termed the M$^3$ problem, which unifies preference optimization and the enforcement of weak Pareto optimality in a single objective. We further develop ParetoM$^3$, a single-loop first-order algorithm for computing stationary solutions of the resulting M$^3$ problem. Under a local Kurdyka-{\L}ojasiewicz assumption, we prove that ParetoM$^3$ finds an $\epsilon$-stationary point of the M$^3$ problem that is also approximately weakly Pareto optimal for the original multi-objective problem when the penalty parameter is sufficiently large, with explicit non-asymptotic convergence rates. We also show that this stationarity notion recovers existing optimality criteria, including approximate preference stationarity and approximate Karush-Kuhn-Tucker conditions, under the same assumptions used in prior works. Experiments on a synthetic benchmark, image classification, regression, and math reasoning demonstrate that ParetoM$^3$ reliably attains preferred weak Pareto optimal solutions while achieving strong practical performance.

Poster
Parasite Features: Causal Abstraction Through Spurious Pathways

Denis Sutter, Qing Yao, Sasha Boguraev, Julian Minder, Antonio Di Maio, Thomas Hofmann, Kyle Mahowald, Tiago Pimentel

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Causal Abstraction can be used to define a notion of equivalence between a neural network and an algorithm, thus serving as a powerful framework for mechanistic interpretability. In this paper, however, we show the existence of a class of spurious features which straightforwardly pass such equivalence tests. Suppose there are two directions in a model's representation space where: (i) one discriminates the input based on some specific feature, and (ii) the other steers the model towards a certain output. Causal Abstraction techniques can create a pathway leveraging these unrelated directions to simulate their combined behavior in the model, which thus spuriously appears to implement a certain feature. In such cases, we say the method discovered a parasite feature. Experimentally, we show that Distributed Alignment Search---a Causal Abstraction-based method---finds parasite features using linear alignment maps in two tasks: syntactic agreement and two-digit addition. Our paper highlights an important consideration for Causal Abstraction and contributes to the ongoing debate about best practices for mechanistic interpretability.

Poster
Parametric Meets Non-parametric: Bridging Dual Prediction Spaces for Semi-supervised Medical Image Segmentation

Zenggui Chen, Jianwei Ma

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Semi-supervised medical image segmentation leverages abundant unlabeled data to reduce the reliance on costly dense annotations, yet its dominant pseudo-labeling paradigm suffers from inevitable prediction noise, especially under scarce supervision. In this work, we observe that parametric network predictions and non-parametric prototype-based predictions exhibit complementary behaviors under pseudo-label noise: the former offers high expressiveness in capturing local structures but is sensitive to erroneous supervision, while the latter provides stable semantic guidance by aggregating class-level statistics but may lack spatial precision. Motivated by this observation, we propose a simple yet effective complementary learning framework that jointly exploits the parametric prediction space and the non-parametric prototype space for semi-supervised segmentation. Specifically, we introduce a confidence-aware selection mechanism that identifies reliable voxels from either prediction space, a prototype entropy minimization objective that sharpens the non-parametric semantic anchors, and a dual-space semantic alignment objective that encourages mutual enhancement between the two spaces. The unified objective enables reliability-aware mutual enhancement, where each space guides the other when confident and noisy alignment is suppressed when both are uncertain. Extensive experiments on multiple medical image segmentation benchmarks demonstrate that our method consistently outperforms existing approaches under various label-scarce settings.

Poster
Parameterized Stripe Attention for Efficient Video Generation

xingyu jia, Baole Ai, Ang Wang, Kang Zhao, Yong Li

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Diffusion Transformers (DiTs) enable high-quality video generation but suffer from substantial inference latency, primarily attributable to the computationally expensive full spatio-temporal attention. While sparse attention methods offer potential solutions, existing approaches face an inherent flexibility--efficiency dilemma: predefined masks lack the flexibility to capture diverse attention patterns, while runtime-determined masks introduce overheads and sacrifice hardware efficiency. We identify the lack of a unified structural characterization of DiT attention as a key limitation of existing methods, and establish that video DiT attention exhibits periodic diagonal stripe structures along both temporal and spatial dimensions. To formally encode these structured patterns within a single efficient kernel, we present PSA, a parameterized stripe attention that formalizes the observed stripe regularity, unifying diverse attention patterns for efficient mask generation. This unified representation enables a single hardware-efficient CUDA kernel to process all sparse patterns, achieving FlashAttention-3-level Model FLOPs Utilization. To determine optimal sparsity configurations, we propose a training-free offline search algorithm that automatically maximizes sparsity under a specified error tolerance for each attention head. Experiments on HunyuanVideo and Wan 2.1 demonstrate that PSA achieves 1.57x and 1.37x end-to-end speedups over FlashAttention-3 baselines, with acceptable visual quality degradation.

Poster
Parameter symmetries determine representational geometry in overparameterized nonlinear networks

Marvin Theiss, Lukas Braun, Andrew Saxe, Erin Grant

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Representations are routinely used in machine learning, psychology, and neuroscience to probe the computations of biological and artificial systems. Yet it remains unclear to what extent computation constrains representation in artificial neural networks. Neural networks admit *parameter symmetries*: transformations of the parameters that preserve function exactly but reshape representational geometry. We show that known parameter symmetries act on representations through just three primitives: *addition*, *duplication*, and *scaling*, giving a closed-form descriptor of representational geometry as task-linked features plus symmetry-induced noise. This decomposition yields analytic bounds on representational similarity between networks related by parameter symmetry, which reveal when functionally equivalent networks become arbitrarily *dis*similar. Finally, we identify *privileged* representational geometries, which weight features by their computational importance and recover a stable link between representation and computation. Overall, our results delineate when representation can support inferences about computation, and when it cannot.

Poster
Parameter Exploration for RLVR via Variational Learning

Vatsal Venkatkrishna, Nico Carlsen Daheim, Iryna Gurevych

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Exploration has been a focus of reinforcement learning research for a long time. Recently, there has been growing evidence that encouraging exploration during LLM reinforcement learning can improve downstream performance. However, methods for controlling exploration often rely on heuristics like clipping or temperature scaling that are unable to fundamentally change token-level distributions, which might limit exploration. Here, we explore controlling exploration via variational learning, where a distribution over neural network parameters is learned via noisy optimization, with parameters sampled from an approximate posterior. We introduce Perturbed Parameter Policy Optimization (3PO), where the amount of noise that is added to model parameters functions as an additional control lever that can be tuned for exploration. We show that using multiple parameter samples within a batch performs better than using a single sample. When using multiple parameter samples in group-based methods like GRPO, we find that calculating advantages across rollouts from all parameter samples performs best. We call this Chunked Perturbed Parameter Policy Optimization (C3PO). We show empirically on a range of math reasoning benchmarks and LLMs that using multiple parameter samples can improve downstream performance, especially on harder benchmarks like AIME. Overall, our work presents evidence that parameter-space exploration can improve LLM reinforcement learning.

Poster
Parallel Rollout Approximation for Pixel-Space Autoregressive Image Generation

Jiayi Xu, Di He, Guolin Ke

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Continuous-token autoregressive (AR) generation directly models continuous signals without discretizing them into vocabulary tokens, but suffers from a severe train--inference mismatch: teacher-forced training conditions on ground-truth prefixes, whereas inference conditions on model-generated continuous tokens. This mismatch becomes especially severe in pixel-space image generation, where each token is a high-dimensional raw pixel patch and autoregressive errors can accumulate over generation steps. Rollout-based training can reduce this mismatch but is prohibitively slow, especially when each token is produced by a multi-step diffusion head. We propose \emph{Parallel Rollout Approximation} (PRA), which approximates rollout-based training by constructing training inputs in parallel at all positions. PRA combines a shared one-step denoiser with an end-to-end learned low-dimensional intermediate state, aligning these constructed training inputs with inference-time generated outputs without relying on a separately pretrained tokenizer. On class-conditional ImageNet-1K generation at 256$\times$256 resolution, even PRA-S with 135M parameters achieves an FID of 2.58, surpassing the previous billion-scale pixel-space AR result of 3.60. Scaling to PRA-L (511M) further improves FID to 1.94, establishing a new state of the art among pixel-space AR models and substantially narrowing the gap to pixel-space diffusion models. Beyond generation, PRA achieves higher ImageNet classification probing accuracy than latent-space AR baselines, suggesting its potential for unified pixel-space image generation and understanding.

Poster
Parallel Computation Algorithms and Convergence Guarantees for Mean-Field Langevin Dynamics

Yoshihito Okamoto, Huanjian Zhou, Taiji Suzuki

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Entropy-regularized optimization problems arise in various areas of machine learning, including mean-field neural networks, variational inference, and reinforcement learning. Mean-field Langevin dynamics (MFLD) is a dynamics capable of sampling from the optimal solution of such problems under appropriate conditions, and has been the subject of extensive recent research. As machine learning models grow in scale and parameter dimension, computational efficiency becomes increasingly important, especially in reducing the adaptive complexity of computation of MFLD, that is, the number of sequential rounds they require. In this work, we initiate the study of the adaptive complexity of MFLD and provide the first theoretical evidence that MFLD can indeed be accelerated through parallelism. In particular, we provide polylogarithmic convergence guarantees for both the infinite-particle and finite-particle setting under the log-Sobolev inequality.

Poster
ParaVT: Taming the Tool Prior Paradox for Parallel Tool Use in Agentic Video Reinforcement Learning

Zuhao Yang, Kaichen Zhang, Sudong Wang, Keming Wu, Zhongyu Yang, Bo Li, Xiaojuan Qi, Shijian Lu, Xingxuan Li, Lidong Bing

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Training large multimodal models (LMMs) via reinforcement learning (RL) to natively invoke video-processing tools (e.g., cropping) has become a promising route to long-video understanding. However, existing native-RL methods dispatch tool calls sequentially (i.e., one per turn): a single wrong crop propagates errors without peer correction, multi-turn tool calls corrupt context, and inference cost scales linearly with the number of turns. We introduce **ParaVT**, the first multi-agent end-to-end RL-trained framework for **Para**llel **V**ideo **T**ool calling, dispatching multiple time-window crops in a single turn for cleaner context and better fault tolerance. Yet applying standard RL to ParaVT reveals an obstacle we term the *Tool Prior Paradox*: the pretrained tool priors that enable tool exploration also destabilize cold-started structural format and expose the skip-tool reward shortcut under temperature sampling. A cross-model contrast on a weaker-prior LMM supports this claim: format stays stable but RL elicits zero tool calls, indicating that prior strength is the shared driver of both format collapse and tool exploration. We propose **PARA-GRPO** (**P**arseability-**A**nchored and **R**atio-g**A**ted **GRPO**), which augments standard RL with two complementary mechanisms: (i) a *targeted format reward* applied only at the structural-token positions most prone to collapse, and (ii) a *per-prompt frame-budget randomization* that creates training prompts where calling the tool yields a measurable reward signal over skipping it. Across six long-video understanding benchmarks, ParaVT improves over the Qwen3-VL baseline by $+7.9\%$ on average, with PARA-GRPO lifting training-time format compliance from $0.13$ to $0.64$. As tool capabilities become increasingly internalized in modern LMMs, RL must cooperate with the resulting priors, and ParaVT offers a general recipe for agentic RL. Code, data, and model weights will be released.

Poster
ParaPC-FM: Accelerating Parallel Sampling via Principled Initialization

Bangwei Li, Chuan Gou, Jianrong Lu, Guoyao Yu, Jianhai Chen

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Flow matching and diffusion models achieve high-quality generation by solving continuous-time generative dynamics, but their sampling remains inherently sequential and costly. Parallel sampling reduces wall-clock latency, yet often requires many function evaluations (NFEs) due to inaccurate future-state initialization and repeated correction. We propose ParaPC-FM, a fixed-point predictor--corrector framework that unifies high-order solver correction and future-state initialization, enabling both components to be incorporated into different parallel samplers. In particular, our UniP-based truncated initialization reuses past velocity predictions to estimate future states more accurately, reducing correction iterations and NFEs with almost no additional overhead. On a ParaDiGMS-style framework, ParaPC-FM achieves up to $1.25\times$ and $1.49\times$ speedups on FLUX.1-dev at $50$ and $100$ steps, and up to $1.22\times$ and $1.16\times$ speedups on Stable Diffusion 3 and Stable Diffusion 3.5 at $50$ steps. When integrated into ParaTAA, the proposed initialization further achieves up to $1.17\times$ speedup at $50$ steps. Importantly, these acceleration gains are obtained while keeping image quality nearly unchanged.

Poster
PaperLens: How Predictable Is Paper Acceptance?

Sachin Konan, Jonathan Liu, Zhuang Liu

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Peer review is sometimes seen as noisy and difficult to predict. How much of the final accept/reject decision is recoverable from the paper itself? We investigate this question with PaperLens, text and vision models trained to predict binary acceptance from anonymized paper artifacts. For a clean evaluation, we construct balanced, shortcut-controlled OpenReview and source-derived arXiv datasets that remove deanonymization artifacts and majority-class shortcuts. Supervised binary decision training is surprisingly strong. PaperLens outperforms frontier prompting and review-trained baselines on decision accuracy and ranking, while its acceptance probability remains well calibrated after validation-set scaling and correlates better to ratings than baselines. Vision consistently improves over markdown text, showing that layout, figures, and visual presentation carry reviewer-relevant signal. Scaling from 3B to 14B parameters yields only modest gains, with clean supervision and faithful paper representations mattering more than model size. Together, our results show that decision prediction provides a powerful signal for paper assessment and can even improve the alignment of AI reviewing agents.

Poster
Panoptic Scene Program Diffusion Transformer

Chika Maduabuchi

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Modern text-to-image models produce high-fidelity images but still struggle with compositional prompts that require instance identity, attribute ownership, counting, spatial ordering, and role-sensitive relations. We introduce *Panoptic Scene Program Diffusion Transformer* (PSP-DiT), a diffusion-transformer architecture that treats a panoptic scene program as a first-class latent variable rather than an external control signal or post-hoc parse. PSP-DiT jointly denoises image latents and scene-program latents through coupled transformer streams, while panoptic grounding and cycle-consistency objectives tie object instances, attributes, relations, and counts to visual support in the generated image. Under matched training and inference settings, PSP-DiT improves over a strong flat-text baseline across GenEval 2, SANEval-Simple, PSG-Score, and DetailMaster, with the largest gains on counting, attribute binding, role-sensitive relations, and long structured prompts. The method preserves image quality, adds modest inference overhead, and remains robust to imperfect scene programs.

Poster
Panoptic Saliency Ranking

Zhenyu Wu, Min Li, Chong Ma, Xun Gong, Wei Wang, Chenglizhao Chen, Aimin Hao, Shuo Li

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We introduce Panoptic Saliency Ranking (PSR), a new task that aims to estimate the visual saliency of all objects within a scene. Unlike salient object ranking, which focuses only on ranking salient regions, PSR extends the problem to the entire scene, providing a holistic and fine-grained understanding of visual saliency. To facilitate this task, we construct PSR18K, the first large-scale benchmark for panoptic saliency ranking. It contains 17,861 images with 146,460 annotated object instances spanning 13 superclasses and 376 fine-grained categories. In addition, PSR18K provides relation graph annotations to explicitly model semantic and spatial relationships among objects. We further propose an efficient Intrinsic Relation Graph Network (IRGNet), which reinterprets Transformer self-attention as an implicit relational matrix and seamlessly transforms it into an explicit relation graph, thereby obviating the need for additional relation modeling and significantly improving inference speed. Extensive experiments on PSR18K and three widely used SOR benchmarks demonstrate that our IRGNet achieves new state-of-the-art performance and faster inference with fewer parameters. The dataset and code are publicly available at https://sites.google.com/view/PSR18K.

Poster
PanoWorld: Towards Spatial Supersensing in 360◦ Panorama World

Changpeng Wang, Xin Lin, Junhan Liu, Yuheng Liu, Zhen Wang, Donglian Qi, Yunfeng Yan, Xi Chen

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Multimodal large language models (MLLMs) still struggle with spatial understanding under the dominant perspective-image paradigm, which inherits the narrow field of view of human-like perception. For navigation, robotic search, and 3D scene understanding, 360$^\circ$ panoramic sensing offers a form of supersensing by capturing the entire surrounding environment at once. However, existing MLLM pipelines typically decompose panoramas into multiple perspective views, leaving the spherical structure of equirectangular projection (ERP) largely implicit. In this paper, we study pano-native understanding, which requires an MLLM to reason over an ERP panorama as a continuous, observer-centered space. To this end, we first define the key abilities for pano-native understanding, including semantic anchoring, spherical localization, reference-frame transformation, and depth-aware 3D spatial reasoning. We then build a large-scale metadata construction pipeline that converts mixed-source ERP panoramas into geometry-aware, language-grounded, and depth-aware supervision, and instantiate these signals as capability-aligned instruction tuning data. On the model side, we introduce PanoWorld with Spherical Spatial Cross-Attention, which injects spherical geometry into the visual stream. We further construct PanoSpace-Bench, a diagnostic benchmark for evaluating ERP-native spatial reasoning. Experiments show that PanoWorld substantially outperforms both proprietary and open-source baselines on PanoSpace-Bench, H$^\ast$Bench, and R2R-CE Val-Unseen benchmarks. These results demonstrate that robust panoramic reasoning requires dedicated pano-native supervision and geometry-aware model adaptation. All source code and proposed data will be publicly released.

Poster
PanoWorld: Geometry-Consistent Panoramic Video World Modeling

Le Jiang, Xiangyu Bai, Bishoy Galoaa, Shayda Moezzi, Caleb J Lee, Tooba Imtiaz, Edmund Yeh, Jennifer Dy, Yanzhi Wang, Sarah Ostadabbas

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We present PanoWorld, a panoramic video world model that generates geometry-consistent 360$\degree$ video from a single image and a caption. Existing panoramic video methods optimize primarily for visual realism and do not explicitly constrain the underlying 3D scene state, producing outputs that appear plausible yet exhibit inconsistent depth, broken correspondences, and implausible motion across the spherical surface. We address this gap by framing panoramic video generation as a geometry- and dynamics-consistent latent state modeling problem rather than pure visual synthesis. Building on a pre-trained perspective video world model, we introduce two lightweight regularizers: a depth consistency loss against pseudo ground-truth panoramic depth, and a trajectory consistency loss that supervises the 3D world-frame positions of tracked points across time. We further apply spherical-geometry-aware adaptation to the conditioning and positional encoding. We additionally introduce PanoGeo, a unified geometry-aware panoramic video dataset with consistent depth, trajectory, and prompt annotations across diverse real and synthetic sources, used for both training and stratified evaluation. Experiments show that PanoWorld improves geometric consistency over prior panoramic generation methods while maintaining competitive visual realism, establishing that panoramic video generation must be treated as a geometric modeling problem to support the holistic spatial understanding requirements of embodied AI applications.

Poster
Pandora's AI Model Routing Box: Efficient Allocation with Costly Value Estimation

Adam Fisch, Shubhendu Trivedi, Fantine Huot, William Cohen, Michael Kaisers, Mirella Lapata, Kate Larson, Jacob Eisenstein

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Heterogeneous AI systems composed of multiple models, architectures, harnesses, or inference-time settings can improve quality and efficiency by routing queries to the \emph{specialist} who can answer most effectively at the lowest cost. Routing requires estimating each specialist's expected return, but this value estimation has a cost. Cheap estimators (e.g., embedding-based predictors) are fast but noisy, while accurate estimators (e.g., fine-tuned models with access to retrieval results or partial reasoning traces) are expensive. We formalize this tradeoff as an instance of Pandora's Box, the classical problem of optimal search with costly inspection. Under a Gaussian signal model, the resulting policies have closed-form value-of-information expressions that determine, for each specialist and input, whether refining the value estimate is worth its cost. We call the centralized policy Pandora's Router. We extend this to a decentralized setting, Pandora's Bidder, where specialists independently decide whether to invest in self-assessment before accepting an offered price to claim a query. Experiments across three domains---a standard multi-LLM benchmark, retrieval-augmented specialists, and LLMs with variable inference-time reasoning---show that Pandora's Router matches the routing quality of exhaustive estimation, while querying the expensive estimator far less often. In the decentralized setting, value-of-information reasoning improves allocative efficiency when competing estimates are accurate; when competing estimates are noisy, however, it can increase the strategic specialist's utility at the expense of

Poster
Pan-FM: A Pan-Organ Foundation Model with Saliency-Guided Masking for Missing Robustness

Qiangqiang Wu, Grace McIlvain, Zhou Yu, Junhao Wen

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Foundation models (FMs) have shown great promise in medical imaging, but most FMs are trained on unimodal data within isolated domains, such as brain MRI alone. Human aging and disease arise through coordinated biological processes across organs, therefore motivating multimodal FMs that learn whole-body representations. A key challenge, however, is that real-world multimodal biomedical data are often missing not at random, which can reduce power, limit generalizability, and introduce bias. We propose Pan-FM, a pan-organ foundation model pre-trained on imaging from seven organs (Brain, Heart, Adipose, Liver, Kidney, Spleen, and Pancreas) under realistic missing-organ scenarios. Pan-FM uses a unified backbone that handles organ missingness during both training and inference, and is pre-trained with masking-based self-distillation. We find that naive multimodal pre-training leads to dominant-organ shortcut learning bias, with the model over-relying on dominant organs such as adipose and heart. To address this, we introduce Saliency-Guided Masking (SGM), which uses the model attention distribution to adaptively mask dominant organs during pre-training, thus encouraging more balanced cross-organ, whole-body learning. Notably, SGM introduces negligible computational overhead and can be seamlessly integrated into existing self-supervised learning frameworks to improve multi-organ representation learning. On the UK Biobank, Pan-FM achieves stronger prediction across 13 disease categories and 14 single disease entities than single-organ and multi-organ baselines, with improved robustness under missing-organ settings. Pan-FM serves as a scalable solution to realistic modality-missingness in multimodal learning in system neuroscience and as a step toward more generalizable whole-body FMs.

Poster