NeurIPS 2025 Papers

The scarcity of annotated medical imaging data has driven significant progress in semi-supervised learning to alleviate reliance on expensive expert labeling. While foundational vision models such as the Segment Anything Model (SAM) exhibit robust generalization in generic segmentation tasks, their direct application to medical images often results in suboptimal performance. To address this challenge, in this work, we propose a novel fully SAM-based semi-supervised medical image segmentation framework and develop the corresponding knowledge distillation-based learning strategy. Specifically, we first employ an efficient SAM variant as the backbone network of the semi‑supervised framework and update the default prompt embedding of SAM to unleash its full potential. Then, we utilize an original SAM, which is rich in prior knowledge, as the teacher to optimize our efficient student SAM backbone through hierarchical knowledge distillation and a dynamic loss weighting strategy. Extensive experiments on various medical datasets demonstrate that our method outperforms state-of-the-art semi-supervised segmentation approaches. Especially, our model requires less than 10% of the parameter size of the original SAM, enabling substantially lower deployment and storage overhead in real-world clinical settings.

Speech tokenizers serve as foundational components for speech language models, yet current designs exhibit several limitations, including: (1) dependence on multi-layer residual vector quantization structures or high frame rates, (2) reliance on auxiliary pre-trained models for semantic distillation, and (3) requirements for complex two-stage training processes. In this work, we introduce the **T**ext-**a**ware **Di**ffusion Transformer Speech **Codec** (***TaDiCodec***), a novel approach designed to overcome these challenges. TaDiCodec employs end-to-end optimization for quantization and reconstruction through a diffusion autoencoder, while integrating text guidance into the diffusion decoder to enhance reconstruction quality and achieve optimal compression. TaDiCodec achieves an extremely low frame rate of **6.25 Hz** and a corresponding bitrate of **0.0875 kbps** with a **single-layer codebook** for 24 kHz speech, while maintaining superior performance on critical speech generation evaluation metrics such as Word Error Rate (WER), speaker similarity (SIM), and speech quality (UTMOS), Notably, TaDiCodec employs a single-stage, end-to-end training paradigm, and obviating the need for auxiliary pre-trained models. We also validate the compatibility of TaDiCodec in language model based zero-shot text-to-speech with both autoregressive modeling and masked generative modeling, demonstrating its effectiveness and efficiency for speech language modeling, as well as a significantly small *reconstruction-generation gap*. To facilitate reproducibility and further research, we will make our source code and pre-trained checkpoints publicly available. Audio samples are are available at https://tadicodec.github.io/. We release code and model checkpoints at https://github.com/AmphionTeam/TaDiCodec.

Recent generative data augmentation methods conditioned on both image and text prompts struggle to balance between fidelity and diversity, as it is challenging to preserve essential image details while aligning with varied text prompts. This challenge arises because representations in the synthesis process often become entangled with non-essential input image attributes such as environmental contexts, creating conflicts with text prompts intended to modify these elements. To address this, we propose a personalized image generation framework that uses a salient concept-aware image embedding model to reduce the influence of irrelevant visual details during the synthesis process, thereby maintaining intuitive alignment between image and text inputs. By generating images that better preserve class-discriminative features with additional controlled variations, our framework effectively enhances the diversity of training datasets and thereby improves the robustness of downstream models. Our approach demonstrates superior performance across eight fine-grained vision datasets, outperforming state-of-the-art augmentation methods with averaged classification accuracy improvements by 0.73\% and 6.5\% under conventional and long-tail settings, respectively.

Contrastive decoding strategies are widely used to reduce object hallucinations in multimodal large language models (MLLMs). These methods work by constructing contrastive samples to induce hallucinations and then suppressing them in the output distribution. However, this paper demonstrates that such approaches fail to effectively mitigate the hallucination problem. The performance improvements observed on POPE Benchmark are largely driven by two misleading factors: (1) crude, unidirectional adjustments to the model’s output distribution and (2) the adaptive plausibility constraint, which reduces the sampling strategy to greedy search. To further illustrate these issues, we introduce a series of spurious improvement methods and evaluate their performance against contrastive decoding techniques. Experimental results reveal that the observed performance gains in contrastive decoding are entirely unrelated to its intended goal of mitigating hallucinations. Our findings challenge common assumptions about the effectiveness of contrastive decoding strategies and pave the way for developing genuinely effective solutions to hallucinations in MLLMs.

Uncovering cause-effect relationships from observational time series is fundamental to understanding complex systems. While many methods infer static causal graphs, real-world systems often exhibit *dynamic causality*—where relationships evolve over time. Accurately capturing these temporal dynamics requires time-resolved causal graphs. We propose UnCLe, a novel deep learning method for scalable dynamic causal discovery. UnCLe employs a pair of Uncoupler and Recoupler networks to disentangle input time series into semantic representations and learns inter-variable dependencies via auto-regressive Dependency Matrices. It estimates dynamic causal influences by analyzing datapoint-wise prediction errors induced by temporal perturbations. Extensive experiments demonstrate that UnCLe not only outperforms state-of-the-art baselines on static causal discovery benchmarks but, more importantly, exhibits a unique capability to accurately capture and represent evolving temporal causality in both synthetic and real-world dynamic systems (e.g., human motion). UnCLe offers a promising approach for revealing the underlying, time-varying mechanisms of complex phenomena.

Regression trees have emerged as a preeminent tool for solving real-world regression problems due to their ability to deal with nonlinearities, interaction effects and sharp discontinuities. In this article, we rather study regression trees applied to well-behaved, differentiable functions, and determine the relationship between node parameters and the local gradient of the function being approximated. We find a simple estimate of the gradient which can be efficiently computed using quantities exposed by popular tree learning libraries. This allows tools developed in the context of differentiable algorithms, like neural nets and Gaussian processes, to be deployed to tree-based models. To demonstrate this, we study measures of model sensitivity defined in terms of integro-differential quantities and demonstrate how to compute them for regression trees using the proposed gradient estimates. Quantitative and qualitative numerical experiments reveal the capability of gradients estimated by regression trees to improve predictive analysis, solve tasks in uncertainty quantification, and provide interpretation of model behavior.

Variational inference often struggles with the posterior geometry exhibited by complex hierarchical Bayesian models. Recent advances in flow‐based variational families and Variationally Inferred Parameters (VIP) each address aspects of this challenge, but their formal relationship is unexplored. Here, we prove that the combination of VIP and a full-rank Gaussian can be represented exactly as a forward autoregressive flow augmented with a translation term and input from the model’s prior. Guided by this theoretical insight, we introduce the Model‐Informed Flow (MIF) architecture, which adds the necessary translation mechanism, prior information, and hierarchical ordering. Empirically, MIF delivers tighter posterior approximations and matches or exceeds state‐of‐the‐art performance across a suite of hierarchical and non‐hierarchical benchmarks.

Recent advancements in 3D object detection and novel category detection have made significant progress, yet research on learning generalized 3D objectness remains insufficient. In this paper, we delve into learning open-world 3D objectness, which focuses on detecting all objects in a 3D scene, including novel objects unseen during training. Traditional closed-set 3D detectors struggle to generalize to open-world scenarios, while directly incorporating 3D open-vocabulary models for open-world ability struggles with vocabulary expansion and semantic overlap. To achieve generalized 3D object discovery, We propose OP3Det, a class-agnostic Open-World Prompt-free 3D Detector to detect any objects within 3D scenes without relying on hand-crafted text prompts. We introduce the strong generalization and zero-shot capabilities of 2D foundation models, utilizing both 2D semantic priors and 3D geometric priors for class-agnostic proposals to broaden 3D object discovery. Then, by integrating complementary information from point cloud and RGB image in the cross-modal mixture of experts, OP3Det dynamically routes uni-modal and multi-modal features to learn generalized 3D objectness. Extensive experiments demonstrate the extraordinary performance of OP3Det, which significantly surpasses existing open-world 3D detectors by up to 16.0% in AR and achieves a 13.5% improvement compared to closed-world 3D detectors.

Recent years have witnessed significant advancements in industrial anomaly detection (IAD) thanks to existing anomaly detection datasets. However, the large performance gap between these benchmarks and real industrial practice reveals critical limitations in existing datasets. We argue that the mismatch between current datasets and real industrial scenarios becomes the primary barrier to practical IAD deployment. To this end, we propose ReinAD dataset, a comprehensive contrastive dataset towards Real-world industrial Anomaly Detection. Our dataset prioritizes three critical real-world requirements: 1) Contrast-based anomaly definition that is essential for industrial practice, 2) Fine-grained unaligned image pairs reflecting real inspections, and 3) Large-scale data from active production lines spanning multiple industrial categories. Based on our dataset, we introduce the ReinADNet. It takes both normal reference and test images as inputs, achieving anomaly detection through normal-anomaly comparison. To address the fine-grained and unaligned properties of real industrial scenes, our method integrates pyramidal similarity aggregation for comprehensive anomaly characterization and global-local feature fusion for spatial misalignment tolerance. Our method outperforms all baselines on the ReinAD dataset (e.g., 64.5% v.s. 59.5% in 1-shot image-level AP) under all settings. Extensive experiments across several datasets demonstrate our dataset's challenging nature and our method's superior generalization. This work provides a solid foundation for practical industrial anomaly detection. Dataset and code are available at https://tocmac.github.io/ReinAD.

Recent advances in inference-time compute have significantly improved performance on complex tasks by generating long chains of thought (CoTs) using Large Reasoning Models (LRMs). However, this improved accuracy comes at the cost of high inference latency due to the length of generated reasoning sequences and the autoregressive nature of decoding. Our key insight in tackling these overheads is that LRM inference, and the reasoning that it embeds, is highly tolerant of approximations: complex tasks are typically broken down into simpler steps, each of which brings utility based on the semantic insight it provides for downstream steps rather than the exact tokens it generates. Accordingly, we introduce SpecReason, a system that automatically accelerates LRM inference by using a lightweight model to (speculatively) carry out simpler intermediate reasoning steps and reserving the costly base model only to efficiently assess (and potentially correct) the speculated outputs. Importantly, SpecReason's focus on exploiting the semantic flexibility of thinking tokens in preserving final-answer accuracy is complementary to prior speculation techniques, most notably speculative decoding, which demands token-level equivalence at each step. Across a variety of cross-domain reasoning benchmarks, SpecReason achieves 1.4-3.0$\times$ speedup over vanilla LRM inference while improving accuracy by 0.4-9.0%. Compared to speculative decoding without SpecReason, their combination yields an additional 8.8-58.0% latency reduction. We open-source SpecReason at \url{https://anonymous.4open.science/r/specreason/}.

Flow-based latent generative models such as Stable Diffusion 3 are able to generate images with remarkable quality, even enabling photorealistic text-to-image generation. Their impressive performance suggests that these models should also constitute powerful priors for inverse imaging problems, but that approach has not yet led to comparable fidelity. There are several key obstacles: (i) the data likelihood term is usually intractable; (ii) learned generative models cannot be directly conditioned on the distorted observations, leading to conflicting objectives between data likelihood and prior; and (iii) the reconstructions can deviate from the observed data. We present FLAIR, a novel, training-free variational framework that leverages flow-based generative models as prior for inverse problems. To that end, we introduce a variational objective for flow matching that is agnostic to the type of degradation, and combine it with deterministic trajectory adjustments to guide the prior towards regions which are more likely under the posterior. To enforce exact consistency with the observed data, we decouple the optimization of the data fidelity and regularization terms. Moreover, we introduce a time-dependent calibration scheme in which the strength of the regularization is modulated according to off-line accuracy estimates. Results on standard imaging benchmarks demonstrate that FLAIR consistently outperforms existing diffusion- and flow-based methods in terms of reconstruction quality and sample diversity. Source code is available at https://inverseflair.github.io/.

Vision-language models (VLMs) like CLIP exhibit strong zero-shot capabilities but often fail to generalize under distribution shifts. Test-time adaptation (TTA) allows models to update at inference time without labeled data, typically via entropy minimization. However, this objective is fundamentally misaligned with the contrastive image-text training of VLMs, limiting adaptation performance and introducing failure modes such as pseudo-label drift and class collapse. We propose CLIPTTA, a new gradient-based TTA method for vision-language models that leverages a soft contrastive loss aligned with CLIP’s pre-training objective. We provide a theoretical analysis of CLIPTTA’s gradients, showing how its batch-aware design mitigates the risk of collapse. We further extend CLIPTTA to the open-set setting, where both in-distribution (ID) and out-of-distribution (OOD) samples are encountered, using an Outlier Contrastive Exposure (OCE) loss to improve OOD detection. Evaluated on 75 datasets spanning diverse distribution shifts, CLIPTTA consistently outperforms entropy-based objectives and is highly competitive with state-of-the-art TTA methods, outperforming them on a large number of datasets and exhibiting more stable performance across diverse shifts.

Rapidly improving large language models (LLMs) have the potential to assist in scientific progress. One critical skill in this endeavor is the ability to faithfully reproduce existing work. To evaluate the capability of AI agents to reproduce complex code in an active research area, we introduce the Automated LLM Speedrunning Benchmark, leveraging the research community's contributions to the $\textit{NanoGPT speedrun}$, a competition to train a GPT-2 model in the shortest time. Each of the 19 speedrun tasks provides the agent with the previous record's training script, optionally paired with one of three hint formats, ranging from pseudocode to paper-like descriptions of the new record's improvements. Records execute quickly by design and speedrun improvements encompass diverse code-level changes, ranging from high-level algorithmic advancements to hardware-aware optimizations. These features make the benchmark both accessible and realistic for the frontier problem of improving LLM training. We find that recent frontier reasoning LLMs combined with SoTA scaffolds struggle to reimplement already-known innovations in our benchmark, even when given detailed hints. Our benchmark thus provides a simple, non-saturated measure of an LLM's ability to automate scientific reproduction, a necessary (but not sufficient) skill for an autonomous research agent.

Evaluating the scientific discovery capabilities of large language model based agents, particularly how they cope with varying environmental complexity and utilize prior knowledge, requires specialized benchmarks currently lacking in the landscape. To address this gap, we introduce PhysGym, a novel benchmark suite and simulation platform for rigorously assessing LLM-based scientific reasoning in interactive physics environments. PhysGym's primary contribution lies in its sophisticated control over the level of prior knowledge provided to the agent. This allows researchers to dissect agent performance along axes including the complexity of the problem and the prior knowledge levels. The benchmark comprises a suite of interactive simulations, where agents must actively probe environments, gather data sequentially under constraints and formulate hypotheses about underlying physical laws. PhysGym provides standardized evaluation protocols and metrics for assessing hypothesis accuracy and model fidelity. We demonstrate the benchmark's utility by presenting results from baseline LLMs, showcasing its ability to differentiate capabilities based on varying priors and task complexity.

In-silico prediction of protein mutant stability, measured by the difference in Gibbs free energy change ($\Delta \Delta G$), is fundamental for protein engineering. Current sequence-to-label methods typically employ two-stage pipelines: (i) encoding mutant sequences using neural networks (e.g., transformers), followed by (ii) the $\Delta \Delta G$ regression from the latent representations. Although these methods have demonstrated promising performance, their dependence on specialized neural network encoders significantly increases the complexity. Additionally, the requirement to compute latent representations individually for each mutant sequence negatively impacts computational efficiency and poses the risk of overfitting. This work proposes the Venus-MAXWELL framework, which reformulates mutation $\Delta \Delta G$ prediction as a sequence-to-landscape task. In Venus-MAXWELL, mutations of a protein and their corresponding $\Delta \Delta G$ values are organized into a landscape matrix, allowing our framework to learn the $\Delta \Delta G$ landscape of a protein with a single forward and backward pass during training. To this end, we curated a new $\Delta \Delta G$ benchmark dataset with strict controls on data leakage and redundancy to ensure robust evaluation. Leveraging the zero-shot scoring capability of protein language models (PLMs), Venus-MAXWELL effectively utilizes the evolutionary patterns learned by PLMs during pre-training. More importantly, Venus-MAXWELL is compatible with multiple protein language models. For example, when integrated with the ESM-IF, Venus-MAXWELL achieves higher accuracy than ThermoMPNN with 10$\times$ faster in inference speed (despite having 50$\times$ more parameters than ThermoMPNN). The training codes, model weights, and datasets are publicly available at https://github.com/ai4protein/Venus-MAXWELL.

The rapid proliferation of domain-specialized machine learning models presents a challenge: while individual models excel in specific domains, their performance varies significantly across diverse applications. This makes selecting the optimal model when faced with an unknown mixture of tasks, especially with limited or no data to estimate the mixture, a difficult problem. We address this challenge by formulating it as a multiple-source domain adaptation (MSA) problem. We introduce a novel, scalable algorithm that effectively routes each input to the best-suited model from a pool of available models. Our approach provides a strong performance guarantee: remarkably, for any mixture domain, the accuracy achieved by the best source model is maintained. This guarantee is established through a theoretical bound on the regret for new domains, expressed as a convex combination of the best regrets in the source domains, plus a concentration term that diminishes as the amount of source data increases. While our primary contributions are theoretical and algorithmic, we also present empirical results demonstrating the effectiveness of our approach.

Visual captioning benchmarks have become outdated with the emergence of modern multimodal large language models (MLLMs), as the brief ground-truth sentences and traditional metrics fail to assess detailed captions effectively. While recent benchmarks attempt to address this by focusing on keyword extraction or object-centric evaluation, they remain limited to vague-view or object-view analyses and incomplete visual element coverage. In this paper, we introduce CAPability, a comprehensive multi-view benchmark for evaluating visual captioning across 12 dimensions spanning six critical views. We curate nearly 11K human-annotated images and videos with visual element annotations to evaluate the generated captions. CAPability stably assesses both the correctness and thoroughness of captions with \textit{precision} and \textit{hit} metrics. By converting annotations to QA pairs, we further introduce a heuristic metric, \textit{know but cannot tell} ($K\bar{T}$), indicating a significant performance gap between QA and caption capabilities. Our work provides a holistic analysis of MLLMs' captioning abilities, as we identify their strengths and weaknesses across various dimensions, guiding future research to enhance specific aspects of their capabilities.

Ultra-High Definition (UHD) image restoration struggles to balance computational efficiency and detail retention. While Variational Autoencoders (VAEs) offer improved efficiency by operating in the latent space, with the Gaussian variational constraint, this compression preserves semantics but sacrifices critical high-frequency attributes specific to degradation and thus compromises reconstruction fidelity. % This compromises reconstruction fidelity, even when global semantics are preserved. Consequently, a VAE redesign is imperative to foster a robust semantic representation conducive to generalization and perceptual quality, while simultaneously enabling effective high-frequency information processing crucial for reconstruction fidelity. To address this, we propose \textit{Latent Harmony}, a two-stage framework that reinvigorates VAEs for UHD restoration by concurrently regularizing the latent space and enforcing high-frequency-aware reconstruction constraints. Specifically, Stage One introduces the LH-VAE, which fortifies its latent representation through visual semantic constraints and progressive degradation perturbation for enhanced semantics robustness; meanwhile, it incorporates latent equivariance to bolster its high-frequency reconstruction capabilities. Then, Stage Two facilitates joint training of this refined VAE with a dedicated restoration model. This stage integrates High-Frequency Low-Rank Adaptation (HF-LoRA), featuring two distinct modules: an encoder LoRA, guided by a fidelity-oriented high-frequency alignment loss, tailored for the precise extraction of authentic details from degradation-sensitive high-frequency components; and a decoder LoRA, driven by a perception-oriented loss, designed to synthesize perceptually superior textures. These LoRA modules are meticulously trained via alternating optimization with selective gradient propagation to preserve the integrity of the pre-trained latent structure. This methodology culminates in a flexible fidelity-perception trade-off at inference, managed by an adjustable parameter $\alpha$. Extensive experiments demonstrate that \textit{Latent Harmony} effectively balances perceptual and reconstructive objectives with efficiency, achieving superior restoration performance across diverse UHD and standard-resolution scenarios.

Recent multimodal large language models (MLLMs) marry modality-specific vision or audio encoders with a shared text decoder. While the encoder is compute- intensive but memory-light, the decoder is the opposite, yet state-of-the-art serving stacks still time-multiplex these complementary kernels, idling SMs or HBM in turn. We introduce SpaceServe, a serving system that space-multiplexes MLLMs: it decouples all modality encoders from the decoder, and co-locates them on the same GPU using fine-grained SM partitioning available in modern runtimes. A cost-model-guided Space-Inference Scheduler (SIS) dynamically assigns SM slices, while a Time-Windowed Shortest-Remaining-First (TWSRFT) policy batches en- coder requests to minimise completion latency and smooth decoder arrivals. Evaluation shows that SpaceServe reduces time-per-output-token by 4.81× on average and up to 28.9× on Nvidia A100 GPUs. SpaceServe is available at https://github.com/gofreelee/SpaceServe