NeurIPS 2025 Papers

Conference on Neural Information Processing Systems

Decision breakdown

5,812papers

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

  • Oral
    931.6%
  • Spotlight
    73912.7%
  • Poster
    4,98085.7%

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Evaluating Program Semantics Reasoning with Type Inference in System $F$

Yifeng He, Luning Yang, Christopher Castro Gaw Gonzalo, Hao Chen

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Large Language Models (LLMs) are increasingly integrated into the software engineering ecosystem. Their test-time compute reasoning capabilities promise significant potential in understanding program logic and semantics beyond mere token recognition. However, current benchmarks evaluating reasoning LLMs for code lack a formal, program-centric deductive framework for the soundness of evaluation, incompetent in assessing of whether models genuinely reason about program semantics or merely associate superficial connections between natural language and code tokens. To bridge this gap, we introduce TF-Bench, a benchmark designed to evaluate LLM reasoning based on type inference in System F, a task we refer to as *program semantics reasoning*. By employing verified transformations to remove semantically irrelevant natural language, we construct TF-Bench_pure, a purely semantics-driven variant of TF-Bench. Our analysis reveals substantial limitations in state-of-the-art LLMs, with the best-performing LLM (Claude-3.7-sonnet) achieving only $55.85\%$ accuracy on TF-Bench_pure. Additionally, we propose two novel metrics to assess the robustness and effectiveness of extended reasoning, underscoring the critical limitation in current LLM capabilities and highlighting essential directions for future research.

Poster
Differentially Private Bilevel Optimization: Efficient Algorithms with Near-Optimal Rates

Andrew Lowy, Daogao Liu

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Bilevel optimization, in which one optimization problem is nested inside another, underlies many machine learning applications with a hierarchical structure---such as meta-learning and hyperparameter optimization. Such applications often involve sensitive training data, raising pressing concerns about individual privacy. Motivated by this, we study differentially private bilevel optimization. We first focus on settings where the outer-level objective is convex, and provide novel upper and lower bounds on the excess empirical risk for both pure and approximate differential privacy. These bounds are nearly tight and essentially match the optimal rates for standard single-level differentially private ERM, up to additional terms that capture the intrinsic complexity of the nested bilevel structure. We also provide population loss bounds for bilevel stochastic optimization. The bounds are achieved in polynomial time via efficient implementations of the exponential and regularized exponential mechanisms. A key technical contribution is a new method and analysis of log-concave sampling under inexact function evaluations, which may be of independent interest. In the non-convex setting, we develop novel algorithms with state-of-the-art rates for privately finding approximate stationary points. Notably, our bounds do not depend on the dimension of the inner problem.

Poster
PRESTO: Preimage-Informed Instruction Optimization for Prompting Black-Box LLMs

Jaewon Chu, Seunghun Lee, Hyunwoo J. Kim

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Large language models (LLMs) have achieved remarkable success across diverse domains, due to their strong instruction-following capabilities. This raised interest in optimizing instructions for black-box LLMs, whose internal parameters are inaccessible but popular for their strong performance and ease of use. Recent approaches leverage white-box LLMs to assist instruction optimization for black-box LLMs by generating instructions from soft prompts. However, white-box LLMs often map different soft prompts to the same instruction, leading to redundant queries to the black-box model. While previous studies regarded this many-to-one mapping as a redundancy to be avoided, we reinterpret it as useful prior knowledge that can enhance the optimization performance. To this end, we introduce PREimage-informed inSTruction Optimization (PRESTO), a novel framework that leverages the preimage structure of soft prompts to improve query efficiency. PRESTO consists of three key components: (1) score sharing, which shares the evaluation score with all soft prompts in a preimage; (2) preimage-based initialization, which select initial data points that maximize search space coverage using preimage information; and (3) score consistency regularization, which enforces prediction consistency within each preimage. By leveraging preimages, PRESTO observes 14 times more scored data under the same query budget, resulting in more efficient optimization. Experimental results on 33 instruction optimization tasks demonstrate the superior performance of PRESTO.

Poster
Stable Part Diffusion 4D: Multi-View RGB and Kinematic Parts Video Generation

Hao Zhang, Chun-Han Yao, Simon Donné, Narendra Ahuja, Varun Jampani

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We present Stable Part Diffusion 4D (SP4D), a framework for generating paired RGB and kinematic part videos from monocular inputs. Unlike conventional part segmentation methods that rely on appearance-based semantic cues, SP4D learns to produce kinematic parts --- structural components aligned with object articulation and consistent across views and time. SP4D adopts a dual-branch diffusion model that jointly synthesizes RGB frames and corresponding part segmentation maps. To simplify architecture and flexibly enable different part counts, we introduce a spatial color encoding scheme that maps part masks to continuous RGB-like images. This encoding allows the segmentation branch to share the latents VAE from the RGB branch, while enabling part segmentation to be recovered via straightforward post-processing. A Bidirectional Diffusion Fusion (BiDiFuse) module enhances cross-branch consistency, supported by a contrastive part consistency loss to promote spatial and temporal alignment of part predictions. We demonstrate that the generated 2D part maps can be lifted to 3D to derive skeletal structures and harmonic skinning weights with few manual adjustments. To train and evaluate SP4D, we construct KinematicParts20K, a curated dataset of over 20K rigged objects selected and processed from Objaverse XL, each paired with multi-view RGB and part video sequences. Experiments show that SP4D generalizes strongly to diverse scenarios, including real-world videos, novel generated objects, and rare articulated poses, producing kinematic-aware outputs suitable for downstream animation and motion-related tasks.

Spotlight
Towards Robust Pseudo-Label Learning in Semantic Segmentation: An Encoding Perspective

Wangkai Li, Rui Sun, Zhaoyang Li, Tianzhu Zhang

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Pseudo-label learning is widely used in semantic segmentation, particularly in label-scarce scenarios such as unsupervised domain adaptation (UDA) and semi-supervised learning (SSL). Despite its success, this paradigm can generate erroneous pseudo-labels, which are further amplified during training due to utilization of one-hot encoding. To address this issue, we propose ECOCSeg, a novel perspective for segmentation models that utilizes error-correcting output codes (ECOC) to create a fine-grained encoding for each class. ECOCSeg offers several advantages. First, an ECOC-based classifier is introduced, enabling model to disentangle classes into attributes and handle partial inaccurate bits, improving stability and generalization in pseudo-label learning. Second, a bit-level label denoising mechanism is developed to generate higher-quality pseudo-labels, providing adequate and robust supervision for unlabeled images. ECOCSeg can be easily integrated with existing methods and consistently demonstrates significant improvements on multiple UDA and SSL benchmarks across different segmentation architectures. Code is available at https://github.com/Woof6/ECOCSeg.

Poster
Chain-of-Zoom: Extreme Super-Resolution via Scale Autoregression and Preference Alignment

Bryan Sangwoo Kim, Jeongsol Kim, Jong Chul Ye

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Modern single-image super-resolution (SISR) models deliver photo-realistic results at the scale factors on which they are trained, but collapse when asked to magnify far beyond that regime. We address this scalability bottleneck with Chain-of-Zoom (CoZ), a model-agnostic framework that factorizes SISR into an autoregressive chain of intermediate scale-states with multi-scale-aware prompts. CoZ repeatedly re-uses a backbone SR model, decomposing the conditional probability into tractable sub-problems to achieve extreme resolutions without additional training. Because visual cues diminish at high magnifications, we augment each zoom step with multi-scale-aware text prompts generated by a vision-language model (VLM). The prompt extractor itself is fine-tuned using Generalized Reward Policy Optimization (GRPO) with a critic VLM, aligning text guidance towards human preference. Experiments show that a standard $4\times$ diffusion SR model wrapped in CoZ attains beyond $256\times$ enlargement with high perceptual quality and fidelity.

Spotlight
Characterizing control between interacting subsystems with deep Jacobian estimation

Adam Joseph Eisen, Mitchell Ostrow, Sarthak Chandra, Leo Kozachkov, Earl K Miller, Ila R Fiete

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Biological function arises through the dynamical interactions of multiple subsystems, including those between brain areas, within gene regulatory networks, and more. A common approach to understanding these systems is to model the dynamics of each subsystem and characterize communication between them. An alternative approach is through the lens of control theory: how the subsystems control one another. This approach involves inferring the directionality, strength, and contextual modulation of control between subsystems. However, methods for understanding subsystem control are typically linear and cannot adequately describe the rich contextual effects enabled by nonlinear complex systems. To bridge this gap, we devise a data-driven nonlinear control-theoretic framework to characterize subsystem interactions via the Jacobian of the dynamics. We address the challenge of learning Jacobians from time-series data by proposing the JacobianODE, a deep learning method that leverages properties of the Jacobian to directly estimate it for arbitrary dynamical systems from data alone. We show that JacobianODE models outperform existing Jacobian estimation methods on challenging systems, including high-dimensional chaos. Applying our approach to a multi-area recurrent neural network (RNN) trained on a working memory selection task, we show that the “sensory” area gains greater control over the “cognitive” area over learning. Furthermore, we leverage the JacobianODE to directly control the trained RNN, enabling precise manipulation of its behavior. Our work lays the foundation for a theoretically grounded and data-driven understanding of interactions among biological subsystems.

Spotlight
Learning Source-Free Domain Adaptation for Visible-Infrared Person Re-Identification

Yongxiang Li, Yanglin Feng, Yuan Sun, Dezhong Peng, Xi Peng, Peng Hu

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In this paper, we investigate source-free domain adaptation (SFDA) for visible-infrared person re-identification (VI-ReID), aiming to adapt a pre-trained source model to an unlabeled target domain without access to source data. To address this challenging setting, we propose a novel learning paradigm, termed Source-Free Visible-Infrared Person Re-Identification (SVIP), which fully exploits the prior knowledge embedded in the source model to guide target domain adaptation. The proposed framework comprises three key components specifically designed for the source-free scenario: 1) a Source-Guided Contrastive Learning (SGCL) module, which leverages the discriminative feature space of the frozen source model as a reference to perform contrastive learning on the unlabeled target data, thereby preserving discrimination without requiring source samples; 2) a Residual Transfer Learning (RTL) module, which learns residual mappings to adapt the target model’s representations while maintaining the knowledge from the source model; and 3) a Structural Consistency-Guided Cross-modal Alignment (SCCA) module, which enforces reciprocal structural constraints between visible and infrared modalities to identify reliable cross-modal pairs and achieve robust modality alignment without source supervision. Extensive experiments on benchmark datasets demonstrate that SVIP substantially enhances target domain performance and outperforms existing unsupervised VI-ReID methods under source-free settings.

Poster
Multimodal Causal Reasoning for UAV Object Detection

Nianxin Li, Mao Ye, Lihua Zhou, Shuaifeng Li, Song Tang, Luping Ji, Ce Zhu

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Unmanned Aerial Vehicle (UAV) object detection faces significant challenges due to complex environmental conditions and different imaging conditions. These factors introduce significant changes in scale and appearance, particularly for small objects that occupy limited pixels and exhibit limited information, complicating detection tasks. To address these challenges, we propose a Multimodel Causal Reasoning framework based on YOLO backbone for UAV Object Detection (MCR-UOD). The key idea is to use the backdoor adjustment to discover the condition-invariant object representation for easy detection. Specifically, the YOLO backbone is first adjusted to incorporate the pre-trained vision-language model. The original category labels are replaced with semantic text prompts, and the detection head is replaced with text-image contrastive learning. Based on this backbone, our method consists of two parts. The first part, named language guided region exploration, discovers the regions with high probability of object existence using text embeddings based on vision-language model such as CLIP. Another part is the backdoor adjustment casual reasoning module, which constructs a confounder dictionary tailored to different imaging conditions to capture global image semantics and derives a prior probability distribution of shooting conditions. During causal inference, we use the confounder dictionary and the prior to intervene on local instance features, disentangling condition variations, and obtaining condition-invariant representations. Experimental results on several public datasets confirm the state-of-the-art performance of our approach. The code, data and models will be released upon publication of this paper.

Poster
MaterialRefGS: Reflective Gaussian Splatting with Multi-view Consistent Material Inference

Wenyuan Zhang, Jimin Tang, Weiqi Zhang, Yi Fang, Yu-Shen Liu, Zhizhong Han

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Modeling reflections from 2D images is essential for photorealistic rendering and novel view synthesis. Recent approaches enhance Gaussian primitives with reflection-related material attributes to enable physically based rendering (PBR) with Gaussian Splatting. However, the material inference often lacks sufficient constraints, especially under limited environment modeling, resulting in illumination aliasing and reduced generalization. In this work, we revisit the problem from a multi-view perspective and show that multi-view consistent material inference with more physically-based environment modeling is key to learning accurate reflections with Gaussian Splatting. To this end, we enforce 2D Gaussians to produce multi-view consistent material maps during deferred shading. We also track photometric variations across views to identify highly reflective regions, which serve as strong priors for reflection strength terms. To handle indirect illumination caused by inter-object occlusions, we further introduce an environment modeling strategy through ray tracing with 2DGS, enabling photorealistic rendering of indirect radiance. Experiments on widely used benchmarks show that our method faithfully recovers both illumination and geometry, achieving state-of-the-art rendering quality in novel views synthesis. Project Page: https://wen-yuan-zhang.github.io/MaterialRefGS.

Poster
GSO: Challenging Software Optimization Tasks for Evaluating SWE-Agents

Manish Shetty, Naman Jain, Jinjian Liu, Vijay Kethanaboyina, Koushik Sen, Ion Stoica

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Developing high-performance software is a complex task that requires specialized expertise. We introduce GSO, a benchmark for evaluating language models' capabilities in developing high-performance software. We develop an automated pipeline that generates and executes performance tests to analyze repository commit histories to identify 102 challenging optimization tasks across 10 codebases, spanning diverse domains and programming languages. An agent is provided with a codebase and performance test as a precise specification, and tasked to improve the runtime efficiency, which is measured against the expert developer optimization. Our quantitative evaluation reveals that leading SWE-Agents struggle significantly, achieving less than 5% success rate, with limited improvements even with inference-time scaling. Our qualitative analysis identifies key failure modes, including difficulties with low-level languages, practicing lazy optimization strategies, and challenges in accurately localizing bottlenecks. We release the code and artifacts of our benchmark along with agent trajectories to enable future research.

Poster
Focus-Then-Reuse: Fast Adaptation in Visual Perturbation Environments

Jiahui Wang, Chao Chen, Jiacheng Xu, Zongzhang Zhang, Yang Yu

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Visual reinforcement learning has shown promise in various real-world applications. However, deploying policies in complex real-world environments with visual perturbations remains a significant challenge. We notice that humans tend to filter information at the object level prior to decision-making, facilitating efficient skill transfer across different contexts. Inspired by this, we introduce Focus-Then-Reuse (FTR), a method utilizing a novel object selection mechanism to focus on task-relevant objects, and directly reuse the simulation-trained policy on them. The training of the object selection mechanism integrates prior knowledge from a vision-language model and feedback from the environment. Experimental results on challenging tasks based on DeepMind Control Suite and Franka Emika Robotics demonstrate that FTR enables rapid adaptation in visual perturbation environments and achieves state-of-the-art performance. The source code is available at https://github.com/LAMDA-RL/FTR.

Poster
Your Pre-trained LLM is Secretly an Unsupervised Confidence Calibrator

Beier Luo, Shuoyuan Wang, Sharon Li, Hongxin Wei

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Post-training of large language models is essential for adapting pre-trained language models (PLMs) to align with human preferences and downstream tasks. While PLMs typically exhibit well-calibrated confidence, post-trained language models (PoLMs) often suffer from over-confidence, assigning high confidence to both correct and incorrect outputs, which can undermine reliability in critical applications. A major obstacle in calibrating PoLMs is the scarcity of labeled data for individual downstream tasks. To address this, we propose Disagreement-Aware Confidence Alignment (DACA), a novel unsupervised method to optimize the parameters (e.g., temperature $\tau$) in post-hoc confidence calibration. Our method is motivated by the under-confidence issue caused by prediction disagreement between the PLM and PoLM while aligning their confidence via temperature scaling. Theoretically, the PLM's confidence underestimates PoLM's prediction accuracy on disagreement examples, causing a larger $\tau$ and producing under-confident predictions. DACA mitigates this by selectively using only agreement examples for calibration, effectively decoupling the influence of disagreement. In this manner, our method avoids an overly large $\tau$ in temperature scaling caused by disagreement examples, improving calibration performance. Extensive experiments demonstrate the effectiveness of our method, improving the average ECE of open-sourced and API-based LLMs (e.g. GPT-4o) by up to 15.08$\%$ on common benchmarks.

Poster
Scalable Neural Incentive Design with Parameterized Mean-Field Approximation

Nathan Corecco, Batuhan Yardim, Vinzenz Thoma, Zebang Shen, Niao He

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Designing incentives for a multi-agent system to induce a desirable Nash equilibrium is both a crucial and challenging problem appearing in many decision-making domains, especially for a large number of agents $N$. Under the exchangeability assumption, we formalize this incentive design (ID) problem as a parameterized mean-field game (PMFG), aiming to reduce complexity via an infinite-population limit. We first show that when dynamics and rewards are Lipschitz, the finite-$N$ ID objective is approximated by the PMFG at rate $\mathcal{O}(\frac{1}{\sqrt{N}})$. Moreover, beyond the Lipschitz-continuous setting, we prove the same $\mathcal{O}(\frac{1}{\sqrt{N}})$ decay for the important special case of sequential auctions, despite discontinuities in dynamics, through a tailored auction-specific analysis. Built on our novel approximation results, we further introduce our Adjoint Mean-Field Incentive Design (AMID) algorithm, which uses explicit differentiation of iterated equilibrium operators to compute gradients efficiently. By uniting approximation bounds with optimization guarantees, AMID delivers a powerful, scalable algorithmic tool for many-agent (large $N$) ID. Across diverse auction settings, the proposed AMID method substantially increases revenue over first-price formats and outperforms existing benchmark methods.

Poster
Sekai: A Video Dataset towards World Exploration

Zhen Li, Chuanhao Li, Xiaofeng Mao, Shaoheng Lin, Ming Li, Shitian Zhao, xu Zhao Pan, Xinyue Li, Yukang Feng, Jianwen Sun, Zizhen Li, Fanrui Zhang, Jiaxin Ai, Zhixiang Wang, Yuwei Wu, Tong He, Yunde Jia, Kaipeng Zhang

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Video generation techniques have made remarkable progress, promising to be the foundation of interactive world exploration. However, existing video generation datasets are not well-suited for world exploration training as they suffer from some limitations: limited locations, short duration, static scenes, and a lack of annotations about exploration and the world. In this paper, we introduce Sekai (meaning "world" in Japanese), a high-quality first-person view worldwide video dataset with rich annotations for world exploration. It consists of over 5,000 hours of walking or drone view (FPV and UVA) videos from over 100 countries and regions across 750 cities. We develop an efficient and effective toolbox to collect, pre-process and annotate videos with location, scene, weather, crowd density, captions, and camera trajectories. Comprehensive analyses and experiments demonstrate the dataset’s scale, diversity, annotation quality, and effectiveness for training video generation models. We believe Sekai will benefit the area of video generation and world exploration, and motivate valuable applications.

Poster
DSRF: A Dynamic and Scalable Reasoning Framework for Solving RPMs

Chengtai Li, Yuting He, Jianfeng Ren, Ruibin Bai, Yitian Zhao, Xudong Jiang

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Abstract Visual Reasoning (AVR) entails discerning latent patterns in visual data and inferring underlying rules. Existing solutions often lack scalability and adaptability, as deep architectures tend to overfit training data, and static neural networks fail to dynamically capture diverse rules. To tackle the challenges, we propose a Dynamic and Scalable Reasoning Framework (DSRF) that greatly enhances the reasoning ability by widening the network instead of deepening it, and dynamically adjusting the reasoning network to better fit novel samples instead of a static network. Specifically, we design a Multi-View Reasoning Pyramid (MVRP) to capture complex rules through layered reasoning to focus features at each view on distinct combinations of attributes, widening the reasoning network to cover more attribute combinations analogous to complex reasoning rules. Additionally, we propose a Dynamic Domain-Contrast Prediction (DDCP) block to handle varying task-specific relationships dynamically by introducing a Gram matrix to model feature distributions, and a gate matrix to capture subtle domain differences between context and target features. Extensive experiments on six AVR tasks demonstrate DSRF’s superior performance, achieving state-of-the-art results under various settings. Code is available here: https://github.com/UNNCRoxLi/DSRF.

Poster
Reward-oriented Causal Representation Learning

Zirui Yan, Emre Acartürk, Ali Tajer

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Causal representation learning (CRL) is the process of disentangling the *latent* low-dimensional causally-related generating factors underlying high-dimensional observable data. Extensive recent studies have characterized CRL identifiability and *perfect* recovery of the latent variables and their attendant causal graph. This paper introduces the notion of *reward-oriented* CRL, the purpose of which is to move away from perfectly learning the latent representation and instead learning it to the extent needed for optimizing a desired downstream task (reward). In reward-oriented CRL, perfectly learning the latent representation can be excessive; instead, it must be learned at the *coarsest* level sufficient for optimizing the desired task. Reward-oriented CRL is formalized as the optimization of a desired function of the observable data over the space of all possible interventions and focuses on linear causal and transformation models. To sequentially identify the optimal subset of interventions, an adaptive exploration algorithm is designed that learns the latent causal graph and the variables needed to identify the best intervention. It is shown that for an $n$-dimensional latent space and a $d$-dimensional observation space, over a horizon $T$ the algorithm's regret scales as $\tilde O(d^{\frac{1}{3}}n^{\frac{1}{3}}u^{\frac{2}{3}}T^{\frac{2}{3}} + u\sqrt{T})$, where $u$ measures total uncertainty in the graph estimates. Furthermore, an almost-matching lower bound is shown to scale as $\Omega(d^{\frac{1}{3}}n^{\frac{1}{3}}p^{\frac{2}{3}}T^{\frac{2}{3}} + p\sqrt{T})$, in which $u$ is replaced by $p$ that counts the number of causal paths in the graph.

Poster
Tree-Guided Diffusion Planner

Hyeonseong Jeon, Cheolhong Min, Jaesik Park

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Planning with pretrained diffusion models has emerged as a promising approach for solving test-time guided control problems. Standard gradient guidance typically performs optimally under convex, differentiable reward landscapes. However, it shows substantially reduced effectiveness in real-world scenarios with non-convex objectives, non-differentiable constraints, and multi-reward structures. Furthermore, recent supervised planning approaches require task-specific training or value estimators, which limits test-time flexibility and zero-shot generalization. We propose a Tree-guided Diffusion Planner (TDP), a zero-shot test-time planning framework that balances exploration and exploitation through structured trajectory generation. We frame test-time planning as a tree search problem using a bi-level sampling process: (1) diverse parent trajectories are produced via training-free particle guidance to encourage broad exploration, and (2) sub-trajectories are refined through fast conditional denoising guided by task objectives. TDP addresses the limitations of gradient guidance by exploring diverse trajectory regions and harnessing gradient information across this expanded solution space using only pretrained models and test-time reward signals. We evaluate TDP on three diverse tasks: maze gold-picking, robot arm block manipulation, and AntMaze multi-goal exploration. TDP consistently outperforms state-of-the-art approaches on all tasks. The project page can be found at: https://tree-diffusion-planner.github.io

Poster
Aligning What Matters: Masked Latent Adaptation for Text-to-Audio-Video Generation

Jiyang Zheng, Siqi Pan, Yu Yao, Zhaoqing Wang, Dadong Wang, Tongliang Liu

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Text-to-Audio-Video (T2AV) generation aims to produce temporally and semantically aligned visual and auditory content from natural language descriptions. While recent progress in text-to-audio and text-to-video models has improved generation quality within each modality, jointly modeling them remains challenging due to incomplete and asymmetric correspondence: audio often reflects only a subset of the visual scene, and vice versa. Naively enforcing full alignment introduces semantic noise and temporal mismatches. To address this, we propose a novel framework that performs selective cross-modal alignment through a learnable masking mechanism, enabling the model to isolate and align only the shared latent components relevant to both modalities. This mechanism is integrated into an adaptation module that interfaces with pretrained encoders and decoders from latent video and audio diffusion models, preserving their generative capacity with reduced training overhead. Theoretically, we show that our masked objective provably recovers the minimal set of shared latent variables across modalities. Empirically, our method achieves state-of-the-art performance on standard T2AV benchmarks, demonstrating significant improvements in audiovisual synchronization and semantic consistency.

Poster
Position: Biology is the Challenge Physics-Informed ML Needs to Evolve

Julien Martinelli

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Physics-Informed Machine Learning (PIML) has successfully integrated mechanistic understanding into machine learning, particularly in domains governed by well-known physical laws. This success has motivated efforts to apply PIML to biology, a field rich in dynamical systems but shaped by different constraints. Biological modeling, however, presents unique challenges: multi-faceted and uncertain prior knowledge, heterogeneous and noisy data, partial observability, and complex, high-dimensional networks. \textbf{In this position paper, we argue that these challenges should not be seen as obstacles to PIML, but as catalysts for its evolution. We propose Biology-Informed Machine Learning (BIML): a principled extension of PIML that retains its structural grounding while adapting to the practical realities of biology.} Rather than replacing PIML, BIML retools its methods to operate under softer, probabilistic forms of prior knowledge. We outline four foundational pillars as a roadmap for this transition: uncertainty quantification, contextualization, constrained latent structure inference, and scalability. Foundation Models and Large Language Models will be key enablers, bridging human expertise with computational modeling. We conclude with concrete recommendations to build the BIML ecosystem and channel PIML-inspired innovation toward challenges of high scientific and societal relevance.

Poster