GenAI4ELab/papercli-papers huggingface dataset:
Covering Multiple Objectives with a Small Set of Solutions Using Bayesian Optimization
Authors: Natalie Maus; Kyurae Kim; Yimeng Zeng; Haydn Thomas Jones; Fangping Wan; Marcelo Der Torossian Torres; Cesar de la Fuente-Nunez; Jacob R. Gardner
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: In multi-objective black-box optimization, the goal is typically to find solutions that optimize a set of $T$ black-box objective functions, $f_1, \ldots f_T$, simultaneously. Traditional approaches often seek a single Pareto-optimal set that balances trade-offs among all objectives. In contrast, we consider a problem setting that departs from this paradigm: finding a small set of $K < T$ solutions, that collectively "cover" the $T$ objectives. A set of solutions is defined as "covering" if, for each objective $f_1, \ldots f_T$, there is at least one good solution. A motivating example for this problem setting occurs in drug design. For example, we may have $T$ pathogens and aim to identify a set of $K < T$ antibiotics such that at least one antibiotic can be used to treat each pathogen. This problem, known as coverage optimization, has yet to be tackled with the Bayesian optimization (BO) framework. To fill this void, we develop Multi-Objective Coverage Bayesian Optimization (MOCOBO), a BO algorithm for solving coverage optimization. Our approach is based on a new acquisition function reminiscent of expected improvement in the vanilla BO setup. We demonstrate the performance of our method on high-dimensional black-box optimization tasks, including applications in peptide and molecular design. Results show that the coverage of the $K < T$ solutions found by MOCOBO matches or nearly matches the coverage of $T$ solutions obtained by optimizing each objective individually. Furthermore, in *in vitro* experiments, the peptides found by MOCOBO exhibited high potency against drug-resistant pathogens, further demonstrating the potential of MOCOBO for drug discovery. All of our code is publicly available at the following link: https://github.com/nataliemaus/mocobo.
Native Segmentation Vision Transformers
Authors: Guillem Braso; Aljosa Osep; Laura Leal-Taixé
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Uniform downsampling remains the de facto standard for reducing spatial resolution in vision backbones. In this work, we propose an alternative design built around a content-aware spatial grouping layer that dynamically assigns tokens to a reduced set based on image boundaries and their semantic content. Stacking our grouping layer across consecutive backbone stages results in hierarchical segmentation that arises *natively* in the feature extraction process, resulting in our coined Native Segmentation Vision Transformer.
We show that a careful design of our architecture enables the emergence of strong segmentation masks solely from grouping layers, that is, without additional segmentation-specific heads. This sets the foundation for a new paradigm of *native*, backbone-level segmentation, which enables strong zero-shot results without mask supervision, as well as a minimal and efficient standalone model design for downstream segmentation tasks.
System-Embedded Diffusion Bridge Models
Authors: Bartlomiej Sobieski; Matthew Tivnan; Yuang Wang; Siyeop yoon; Pengfei Jin; Dufan Wu; Quanzheng Li; Przemyslaw Biecek
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Solving inverse problems—recovering signals from incomplete or noisy measurements—is fundamental in science and engineering. Score-based generative models (SGMs) have recently emerged as a powerful framework for this task. Two main paradigms have formed: unsupervised approaches that adapt pretrained generative models to inverse problems, and supervised bridge methods that train stochastic processes conditioned on paired clean and corrupted data. While the former typically assume knowledge of the measurement model, the latter have largely overlooked this structural information. We introduce System-embedded Diffusion Bridge Models (SDBs), a new class of supervised bridge methods that explicitly embed the known linear measurement system into the coefficients of a matrix-valued SDE. This principled integration yields consistent improvements across diverse linear inverse problems and demonstrates robust generalization under system misspecification between training and deployment, offering a promising solution to real-world applications.
Adaptive LoRA Experts Allocation and Selection for Federated Fine-Tuning
Authors: Lei Wang; Jieming Bian; Letian Zhang; Jie Xu
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Large Language Models (LLMs) have demonstrated impressive capabilities across various tasks, but fine-tuning them for domain-specific applications often requires substantial domain-specific data that may be distributed across multiple organizations. Federated Learning (FL) offers a privacy-preserving solution, but faces challenges with computational constraints when applied to LLMs. Low-Rank Adaptation (LoRA) has emerged as a parameter-efficient fine-tuning approach, though a single LoRA module often struggles with heterogeneous data across diverse domains. This paper addresses two critical challenges in federated LoRA fine-tuning: 1. determining the optimal number and allocation of LoRA experts across heterogeneous clients, and 2. enabling clients to selectively utilize these experts based on their specific data characteristics. We propose FedLEASE (Federated adaptive LoRA Expert Allocation and SElection), a novel framework that adaptively clusters clients based on representation similarity to allocate and train domain-specific LoRA experts. It also introduces an adaptive top-$M$ Mixture-of-Experts mechanism that allows each client to select the optimal number of utilized experts. Our extensive experiments on diverse benchmark datasets demonstrate that FedLEASE significantly outperforms existing federated fine-tuning approaches in heterogeneous client settings while maintaining communication efficiency.
Meta-Learning Objectives for Preference Optimization
Authors: Carlo Alfano; Silvia Sapora; Jakob Nicolaus Foerster; Patrick Rebeschini; Yee Whye Teh
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Evaluating preference optimization (PO) algorithms on LLM alignment is a challenging task that presents prohibitive costs, noise, and several variables like model size and hyper-parameters. In this work, we show that it is possible to gain insights on the efficacy of PO algorithm on simpler benchmarks. We design a diagnostic suite of MuJoCo tasks and datasets, which we use to systematically evaluate PO algorithms, establishing a more controlled and cheaper benchmark. We then propose a novel family of PO algorithms based on mirror descent, which we call Mirror Preference Optimization (MPO). Through evolutionary strategies, we search this class to discover algorithms specialized to specific properties of preference datasets, such as mixed-quality or noisy data. We demonstrate that our discovered PO algorithms outperform all known algorithms in the targeted MuJoCo settings. Finally, based on the insights gained from our MuJoCo experiments, we design a PO algorithm that significantly outperform existing baselines in an LLM alignment task.
RAD: Towards Trustworthy Retrieval-Augmented Multi-modal Clinical Diagnosis
Authors: Haolin Li; Tianjie Dai; Zhe Chen; Siyuan Du; Jiangchao Yao; Ya Zhang; Yanfeng Wang
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Clinical diagnosis is a highly specialized discipline requiring both domain expertise and strict adherence to rigorous guidelines. 
While current AI-driven medical research predominantly focuses on knowledge graphs or natural text pretraining paradigms to incorporate medical knowledge, these approaches primarily rely on implicitly encoded knowledge within model parameters, neglecting task-specific knowledge required by diverse downstream tasks.
To address this limitation, we propose **R**etrieval-**A**ugmented **D**iagnosis (RAD), a novel framework that explicitly injects external knowledge into multimodal models directly on downstream tasks.
Specifically, RAD operates through three key mechanisms: retrieval and refinement of disease-centered knowledge from multiple medical sources, a guideline-enhanced contrastive loss that constrains the latent distance between multi-modal features and guideline knowledge, and the dual transformer decoder that employs guidelines as queries to steer cross-modal fusion, aligning the models with clinical diagnostic workflows from guideline acquisition to feature extraction and decision-making.
Moreover, recognizing the lack of quantitative evaluation of interpretability for multimodal diagnostic models, we introduce a set of criteria to assess the interpretability from both image and text perspectives. Extensive evaluations across four datasets with different anatomies demonstrate RAD's generalizability, achieving state-of-the-art performance. Furthermore, RAD enables the model to concentrate more precisely on abnormal regions and critical indicators, ensuring evidence-based, trustworthy diagnosis. Our code is available at https://github.com/tdlhl/RAD.
Styl3R: Instant 3D Stylized Reconstruction for Arbitrary Scenes and Styles
Authors: Peng Wang; Xiang Liu; Peidong Liu
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Stylizing 3D scenes instantly while maintaining multi-view consistency and faithfully resembling a style image remains a significant challenge. Current state-of-the-art 3D stylization methods typically involve computationally intensive test-time optimization to transfer artistic features into a pretrained 3D representation, often requiring dense posed input images. In contrast, leveraging recent advances in feed-forward reconstruction models, we demonstrate a novel approach to achieve direct 3D stylization in less than a second using unposed sparse-view scene images and an arbitrary style image. To address the inherent decoupling between reconstruction and stylization, we introduce a branched architecture that separates structure modeling and appearance shading, effectively preventing stylistic transfer from distorting the underlying 3D scene structure. Furthermore, we adapt an identity loss to facilitate pre-training our stylization model through the novel view synthesis task. This strategy also allows our model to retain its original reconstruction capabilities while being fine-tuned for stylization. Comprehensive evaluations, using both in-domain and out-of-domain datasets, demonstrate that our approach produces high-quality stylized 3D content that achieve a superior blend of style and scene appearance, while also outperforming existing methods in terms of multi-view consistency and efficiency.
Stackelberg Self-Annotation: A Robust Approach to Data-Efficient LLM Alignment
Authors: Xu Chu; Zhixin Zhang; Tianyu Jia; Yujie Jin
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Aligning large language models (LLMs) with human preferences typically demands vast amounts of meticulously curated data, which is both expensive and prone to labeling noise. We propose Stackelberg Game Preference Optimization (SGPO), a robust alignment framework that models alignment as a two-player Stackelberg game between a policy (leader) and a worst-case preference distribution (follower). The proposed SGPO guarantees $\mathcal{O}(\epsilon)$-bounded regret within an $\epsilon$-Wasserstein ball, offering formal robustness to (self-)annotation noise. We instantiate SGPO with Stackelberg Self-Annotated Preference Optimization (SSAPO), which uses minimal human-labeled “seed” preferences and iteratively self-annotates new prompts. In each iteration, SSAPO applies a distributionally robust reweighting of synthetic annotations, ensuring that noisy or biased self-labels do not derail training. Remarkably, using only 2K seed preferences—about 1/30 of standard human labels—SSAPO achieves strong win rates against GPT-4 across multiple benchmarks within three iterations. These results highlight that a principled Stackelberg formulation yields data-efficient alignment for LLMs, significantly reducing reliance on costly human annotations.
Understand Before You Generate: Self-Guided Training for Autoregressive Image Generation
Authors: Xiaoyu Yue; ZiDong Wang; Yuqing Wang; Wenlong Zhang; Xihui Liu; Wanli Ouyang; LEI BAI; Luping Zhou
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Recent studies have demonstrated the importance of high-quality visual representations in image generation and have highlighted the limitations of generative models in image understanding. As a generative paradigm originally designed for natural language, autoregressive models face similar challenges. In this work, we present the first systematic investigation into the mechanisms of applying the next-token prediction paradigm to the visual domain. We identify three key properties that hinder the learning of high-level visual semantics: local and conditional dependence, inter-step semantic inconsistency, and spatial invariance deficiency. We show that these issues can be effectively addressed by introducing self-supervised objectives during training, leading to a novel training framework, Self-guided Training for AutoRegressive models (ST-AR). Without relying on pre-trained representation models, ST-AR significantly enhances the image understanding ability of autoregressive models and leads to improved generation quality. Specifically, ST-AR brings approximately 42% FID improvement for LlamaGen-L and 49% FID improvement for LlamaGen-XL, while maintaining the same sampling strategy.
Unlocking Multimodal Mathematical Reasoning via Process Reward Model
Authors: Ruilin Luo; Zhuofan Zheng; Lei Wang; Yifan Wang; Xinzhe Ni; Zicheng Lin; Songtao Jiang; Yiyao Yu; Chufan Shi; Ruihang Chu; Jin zeng; Yujiu Yang
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Process Reward Models (PRMs) have shown promise in enhancing the mathematical reasoning capabilities of Large Language Models (LLMs) through Test-Time Scaling (TTS). However, their integration into multimodal reasoning remains largely unexplored. In this work, we take the first step toward unlocking the potential of PRMs in multimodal mathematical reasoning. We identify three key challenges: (i) the scarcity of high-quality reasoning data constrains the capabilities of foundation Multimodal Large Language Models (MLLMs), which imposes further limitations on the upper bounds of TTS and reinforcement learning (RL); (ii) a lack of automated methods for process labeling within multimodal contexts persists; (iii) the employment of process rewards in unimodal RL faces issues like reward hacking, which may extend to multimodal scenarios. To address these issues, we introduce URSA, a three-stage Unfolding multimodal pRocess-Supervision Aided training framework. We first construct MMathCoT-1M, a high-quality large-scale multimodal Chain-of-Thought (CoT) reasoning dataset, to build a stronger math reasoning foundation MLLM, URSA-8B. Subsequently, we go through an automatic process to synthesize process supervision data, which emphasizes both logical correctness and perceptual consistency. We introduce DualMath-1.1M to facilitate the training of URSA-8B-RM. Finally, we propose Process-Supervised Group-Relative-Policy-Optimization (PS-GRPO), pioneering a multimodal PRM-aided online RL method that outperforms vanilla GRPO. With PS-GRPO application, URSA-8B-PS-GRPO outperforms Gemma3-12B and GPT-4o by 8.4% and 2.7% on average across 6 benchmarks.
DOTA: Distributional Test-time Adaptation of Vision-Language Models
Authors: Zongbo Han; Jialong Yang; Guangyu Wang; Junfan Li; Qianli Xu; Mike Zheng Shou; Changqing Zhang
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Vision-language foundation models (VLMs), such as CLIP, exhibit remarkable performance across a wide range of tasks. However, deploying these models can be unreliable when significant distribution gaps exist between training and test data, while fine-tuning for diverse scenarios is often costly. Cache-based test-time adapters offer an efficient alternative by storing representative test samples to guide subsequent classifications. Yet, these methods typically employ naive cache management with limited capacity, leading to severe catastrophic forgetting when samples are inevitably dropped during updates. In this paper, we propose DOTA (DistributiOnal Test-time Adaptation), a simple yet effective method addressing this limitation. Crucially, instead of merely memorizing individual test samples, DOTA continuously estimates the underlying distribution of the test data stream. Test-time posterior probabilities are then computed using these dynamically estimated distributions via Bayes' theorem for adaptation. This distribution-centric approach enables the model to continually learn and adapt to the deployment environment. Extensive experiments validate that DOTA significantly mitigates forgetting and achieves state-of-the-art performance compared to existing methods.
Toward a Unified Geometry Understanding : Riemannian Diffusion Framework for Graph Generation and Prediction
Authors: Yisen Gao; Xingcheng Fu; Qingyun Sun; Jianxin Li; Xianxian LI
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Graph diffusion models have made significant progress in learning structured graph data and have demonstrated strong potential for predictive tasks. Existing approaches typically embed node, edge, and graph-level features into a unified latent space, modeling prediction tasks including classification and regression as a form of conditional generation.  However, due to the non-Euclidean nature of graph data, features of different curvatures are entangled in the same latent space without releasing their geometric potential. To address this issue, we aim to construt an ideal Riemannian diffusion model to capture distinct manifold signatures of complex graph data and learn their distribution.  This goal faces two challenges: numerical instability caused by exponential mapping during the encoding proces and manifold deviation during diffusion generation.  To address these challenges, we propose **GeoMancer**: a novel Riemannian graph diffusion framework for both generation and prediction tasks. To mitigate numerical instability, we replace exponential mapping with an isometric-invariant Riemannian gyrokernel approach and decouple multi-level features onto their respective task-specific manifolds to learn optimal representations.  To address manifold deviation, we introduce a manifold-constrained diffusion method and a self-guided strategy for unconditional generation, ensuring that the generated data remains aligned with the manifold signature. Extensive experiments validate the effectiveness of our approach, demonstrating superior performance across a variety of tasks.
SpiderSolver: A Geometry-Aware Transformer for Solving PDEs on Complex Geometries
Authors: Kai Qi; Fan Wang; Zhewen Dong; Jian Sun
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Transformers have demonstrated effectiveness in solving partial differential equations (PDEs). However, extending them to solve PDEs on complex geometries remains a challenge. In this work, we propose SpiderSolver, a geometry-aware transformer that introduces spiderweb tokenization for handling complex domain geometry and irregularly discretized points. Our method partitions the irregular spatial domain into spiderweb-like patches, guided by the domain boundary geometry. SpiderSolver leverages a coarse-grained attention mechanism to capture global interactions across spiderweb tokens and a fine-grained attention mechanism to refine feature interactions between the domain boundary and its neighboring interior points. We evaluate SpiderSolver on PDEs with diverse domain geometries across seven datasets, including cars, airfoils, blood flow in the human thoracic aorta, as well as canonical cases governed by the Navier-Stokes, Darcy flow, elasticity, and plasticity equations. Experimental results demonstrate that SpiderSolver consistently achieves state-of-the-art performance across different datasets and metrics, with better generalization ability in the OOD setting. The code is available at https://github.com/Kai-Qi/SpiderSolver.
Delving into RL for Image Generation with CoT: A Study on DPO vs. GRPO
Authors: Chengzhuo Tong; Ziyu Guo; Renrui Zhang; Wenyu Shan; Xinyu Wei; Zhenghao Xing; Hongsheng Li; Pheng-Ann Heng
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Recent advancements underscore the significant role of Reinforcement Learning (RL) in enhancing the Chain-of-Thought (CoT) reasoning capabilities of large language models (LLMs). Two prominent RL algorithms, Direct Preference Optimization (DPO) and Group Relative Policy Optimization (GRPO), are central to these developments, showcasing different pros and cons. Autoregressive image generation, also interpretable as a sequential CoT reasoning process, presents unique challenges distinct from LLM-based CoT reasoning. These encompass ensuring text-image consistency, improving image aesthetic quality, and designing sophisticated reward models, rather than relying on simpler rule-based rewards. While recent efforts have extended RL to this domain, these explorations typically lack an in-depth analysis of the domain-specific challenges and the characteristics of different RL strategies. To bridge this gap, we provide the first comprehensive investigation of the GRPO and DPO algorithms in autoregressive image generation, evaluating their ***in-domain*** performance and ***out-of-domain*** generalization, while scrutinizing the impact of ***different reward models*** on their respective capabilities. Our findings reveal that GRPO and DPO exhibit distinct advantages, and crucially, that reward models possessing stronger intrinsic generalization capabilities potentially enhance the generalization potential of the applied RL algorithms. Furthermore, we systematically explore ***three prevalent scaling strategies*** to enhance both their in-domain and out-of-domain proficiency, deriving unique insights into efficiently scaling performance for each paradigm. We hope our study paves a new path for inspiring future work on developing more effective RL algorithms to achieve robust CoT reasoning in the realm of autoregressive image generation.
Safety Depth in Large Language Models: A Markov Chain Perspective
Authors: Ching-Chia Kao; Chia-Mu Yu; Chun-Shien Lu; Chu-Song Chen
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Large Language Models (LLMs) are increasingly adopted in high-stakes scenarios, yet their safety mechanisms often remain fragile. Simple jailbreak prompts or even benign fine-tuning can bypass internal safeguards, underscoring the need to understand the failure modes of current safety strategies.  Recent findings suggest that vulnerabilities emerge when alignment is confined to only the initial output tokens. To address this, we introduce the notion of safety depth, a designated output position where the model refuses to generate harmful content. While deeper alignment appears promising, identifying the optimal safety depth remains an open and underexplored challenge.

We leverage the equivalence between autoregressive language models and Markov chains to derive the first theoretical result on identifying the optimal safety depth. To reach this safety depth effectively, we propose a cyclic group augmentation strategy that improves safety scores across six LLMs. In addition, we uncover a critical interaction between safety depth and ensemble width, demonstrating that larger ensembles can offset shallower alignments. These results suggest that test-time computation, often overlooked in safety alignment, can play a key role. Our approach provides actionable insights for building safer LLMs.