NeurIPS 2025 Papers

Spatio-Temporal Graph Neural Networks (STGNNs) have emerged as a powerful tool for modeling dynamic graph-structured data across diverse domains. However, they often fail to generalize in Spatio-Temporal Out-of-Distribution (STOOD) scenarios, where both temporal dynamics and spatial structures evolve beyond the training distribution. To address this problem, we propose an innovative Spatio-Temporal Retrieval-Augmented Pattern Learning framework, STRAP, which enhances model generalization by integrating retrieval-augmented learning into the STGNN continue learning pipeline. The core of STRAP is a compact and expressive pattern library that stores representative spatio-temporal patterns enriched with historical, structural, and semantic information, which is obtained and optimized during the training phase. During inference, STRAP retrieves relevant patterns from this library based on similarity to the current input and injects them into the model via a plug-and-play prompting mechanism. This not only strengthens spatio-temporal representations but also mitigates catastrophic forgetting. Moreover, STRAP introduces a knowledge-balancing objective to harmonize new information with retrieved knowledge. Extensive experiments across multiple real-world streaming graph datasets show that STRAP consistently outperforms state-of-the-art STGNN baselines on STOOD tasks, demonstrating its robustness, adaptability, and strong generalization capability without task-specific fine-tuning.

Unsupervised domain adaptive hashing has emerged as a promising approach for efficient and memory-friendly cross-domain retrieval. It leverages the model learned on labeled source domains to generate compact binary codes for unlabeled target domain samples, ensuring that semantically similar samples are mapped to nearby points in the Hamming space. Existing methods typically apply domain adaptation techniques to the feature space or the Hamming space, especially pseudo-labeling and feature alignment. However, the inherent noise of pseudo-labels and the insufficient exploration of complementary knowledge across spaces hinder the ability of the adapted model. To address these challenges, we propose a Vision-language model assisted Pseudo-labeling and Dual Space adaptation (VPDS) method. Motivated by the strong zero-shot generalization capabilities of pre-trained vision-language models (VLMs), VPDS leverages VLMs to calibrate pseudo-labels, thereby mitigating pseudo-label bias. Furthermore, to simultaneously utilize the semantic richness of high-dimensional feature space and preserve discriminative efficiency of low-dimensional Hamming space, we introduce a dual space adaptation approach that performs independent alignment within each space. Extensive experiments on three benchmark datasets demonstrate that VPDS consistently outperforms existing methods in both cross-domain and single-domain retrieval tasks, highlighting its effectiveness and superiority.

High-content screening (HCS) assays based on high-throughput microscopy techniques such as Cell Painting have enabled the interrogation of cells' morphological responses to perturbations at an unprecedented scale. The collection of such data promises to facilitate a better understanding of the relationships between different perturbations and their effects on cellular state. Towards achieving this goal, recent advances in cross-modal contrastive learning could, in theory, be leveraged to learn a unified latent space that aligns perturbations with their corresponding morphological effects. However, the application of such methods to HCS data is not straightforward due to substantial differences in the semantics of Cell Painting images compared to natural images, and the difficulty of representing different classes of perturbations (e.g. small molecule vs CRISPR gene knockout) in a single latent space. In response to these challenges, here we introduce CellCLIP, a cross-modal contrastive learning framework for HCS data. CellCLIP leverages pre-trained image encoders coupled with a novel channel encoding scheme to better capture relationships between different microscopy channels in image embeddings, along with natural language encoders for representing perturbations. Our framework outperforms current open-source models, demonstrating the best performance in both cross-modal retrieval and biologically meaningful downstream tasks while also achieving significant reductions in computation time. Code for our reproducing our experiments is available at https://github.com/suinleelab/CellCLIP.

Despite their consistent performance improvements, cross-modal retrieval models (e.g., CLIP) show degraded performances with retrieving keys composed of fused image-text modality (e.g., Wikipedia pages with both images and text). To address this critical challenge, multimodal retrieval has been recently explored to develop a unified single retrieval model capable of retrieving keys across diverse modality combinations. A common approach involves constructing new composed sets of image-text triplets (e.g., retrieving a pair of image and text given a query image). However, such an approach requires careful curation to ensure the dataset quality and fails to generalize to unseen modality combinations. To overcome these limitations, this paper proposes Generalized Contrastive Learning (GCL), a novel loss formulation that improves multimodal retrieval performance without the burdensome need for new dataset curation. Specifically, GCL operates by enforcing contrastive learning across all modalities within a mini-batch, utilizing existing image-caption paired datasets to learn a unified representation space. We demonstrate the effectiveness of GCL by showing consistent performance improvements on off-the-shelf multimodal retrieval models (e.g., VISTA, CLIP, and TinyCLIP) using the M-BEIR, MMEB, and CoVR benchmarks.

Dense image correspondence is central to many applications, such as visual odometry, 3D reconstruction, object association, and re-identification. Historically, dense correspondence has been tackled separately for wide-baseline scenarios and optical flow estimation, despite the common goal of matching content between two images. In this paper, we develop a Unified Flow \& Matching model (UFM), which is trained on unified data for pixels that are co-visible in both source and target images. UFM uses a simple, generic transformer architecture that directly regresses the $(u,v)$ flow. It is easier to train and more accurate for large flows compared to the typical coarse-to-fine cost volumes in prior work. UFM is 28\% more accurate than state-of-the-art flow methods (Unimatch), while also having 62\% less error and 6.7x faster than dense wide-baseline matchers (RoMa). UFM is the first to demonstrate that unified training can outperform specialized approaches across both domains. This result enables fast, general-purpose correspondence and opens new directions for multi-modal, long-range, and real-time correspondence tasks.

Hands are essential to human interaction, and exploring contact between hands and the world can promote comprehensive understanding of their function. Recently, there have been growing number of hand interaction datasets that cover interaction with object, other hand, scene, and body. Despite the significance of the task and increasing high-quality data, how to effectively learn dense hand contact estimation remains largely underexplored. There are two major challenges for learning dense hand contact estimation. First, there exists class imbalance issue from hand contact datasets where majority of regions are not in contact. Second, hand contact datasets contain spatial imbalance issue with most of hand contact exhibited in finger tips, resulting in challenges for generalization towards contacts in other hand regions. To tackle these issues, we present a framework that learns dense HAnd COntact estimation (HACO) from imbalanced data. To resolve the class imbalance issue, we introduce balanced contact sampling, which builds and samples from multiple sampling groups that fairly represent diverse contact statistics for both contact and non-contact vertices. Moreover, to address the spatial imbalance issue, we propose vertex-level class-balanced (VCB) loss, which incorporates spatially varying contact distribution by separately reweighting loss contribution of each vertex based on its contact frequency across dataset. As a result, we effectively learn to predict dense hand contact estimation with large-scale hand contact data without suffering from class and spatial imbalance issue. The codes are available at https://github.com/dqj5182/HACO_RELEASE.

Implicit Neural Representations (INRs) have recently shown impressive results, but their fundamental capacity, implicit biases, and scaling behavior remain poorly understood. We investigate the performance of diverse INRs across a suite of 2D and 3D real and synthetic signals with varying effective bandwidth, as well as both overfitting and generalization tasks including tomography, super-resolution, and denoising. By stratifying performance according to model size as well as signal type and bandwidth, our results shed light on how different INR and grid representations allocate their capacity. We find that, for most tasks and signals, a simple regularized grid with interpolation trains faster and to higher quality than any INR with the same number of parameters. We also find limited settings–namely fitting binary signals such as shape contours–where INRs outperform grids, to guide future development and use of INRs towards the most advantageous applications.

Linear recurrent neural networks (RNNs) and state-space models (SSMs) such as Mamba have become promising alternatives to softmax-attention as sequence mixing layers in Transformer architectures. Current models, however, do not exhibit the full state-tracking expressivity of RNNs because they rely on channel-wise (i.e. diagonal) sequence mixing. In this paper, we investigate parameterizations of a large class of dense linear RNNs as fixed-points of parallelizable diagonal linear RNNs. The resulting models can naturally trade expressivity for efficiency at a fixed number of parameters and achieve state-of-the-art results on the state-tracking benchmarks $A_5$ and $S_5$, while matching performance on copying and other tasks.

The meta-task of obtaining and aligning representations through contrastive pretraining is steadily gaining importance since its introduction in CLIP and ALIGN. In this paper we theoretically explain the advantages of synchronizing with trainable inverse temperature and bias under the sigmoid loss, as implemented in the recent SigLIP and SigLIP2 models of Google DeepMind. Temperature and bias can drive the loss function to zero for a rich class of configurations that we call $(\mathsf{m}, \mathsf{br})$ -Constellations. $(\mathsf{m}, \mathsf{br})$ -Constellations are a novel combinatorial object related to spherical codes and are parametrized by a margin $\mathsf{m}$ and relative bias $\mathsf{br}$. We use our characterization of constellations to theoretically justify the success of SigLIP on retrieval, to explain the modality gap present in SigLIP, and to identify the necessary dimension for producing high-quality representations. Finally, we propose a reparameterization of the sigmoid loss with explicit relative bias, which improves training dynamics in experiments with synthetic data.

Existing Moment retrieval (MR) methods focus on Single-Moment Retrieval (SMR). However, one query can correspond to multiple relevant moments in real-world applications. This makes the existing datasets and methods insufficient for video temporal grounding. By revisiting the gap between current MR tasks and real-world applications, we introduce a high-quality datasets called QVHighlights Multi-Moment Dataset (QV-M$^2$), along with new evaluation metrics tailored for multi-moment retrieval (MMR). QV-M$^2$ consists of 2,212 annotations covering 6,384 video segments. Building on existing efforts in MMR, we propose a framework called FlashMMR. Specifically, we propose a Multi-moment Post-verification module to refine the moment boundaries. We introduce constrained temporal adjustment and subsequently leverage a verification module to re-evaluate the candidate segments. Through this sophisticated filtering pipeline, low-confidence proposals are pruned, and robust multi-moment alignment is achieved. We retrain and evaluate 6 existing MR methods on QV-M$^2$ and QVHighlights under both SMR and MMR settings. Results show that QV-M$^2$ serves as an effective benchmark for training and evaluating MMR models, while FlashMMR provides a strong baseline. Specifically, on QV-M$^2$, it achieves improvements over prior SOTA method by 3.00% on G-mAP, 2.70% on mAP@3+tgt, and 2.56% on mR@3. The proposed benchmark and method establish a foundation for advancing research in more realistic and challenging video temporal grounding scenarios. Code is released at https://github.com/Zhuo-Cao/QV-M2.

Foundation Vision Encoders have become indispensable across a wide range of dense vision tasks. However, their operation at low spatial feature resolutions necessitates subsequent feature decompression to enable full-resolution processing. To address this limitation, we introduce JAFAR, a lightweight and flexible feature upsampler designed to enhance the spatial resolution of visual features from any Foundation Vision Encoder to any target resolution. JAFAR features an attention-based upsampling module that aligns the spatial representations of high-resolution queries with semantically enriched low-resolution keys via Spatial Feature Transform modulation. Despite the absence of high-resolution feature ground truth; we find that learning at low upsampling ratios and resolutions generalizes surprisingly well to much higher scales. Extensive experiments demonstrate that JAFAR recovers intricate pixel-level details and consistently outperforms existing feature upsampling techniques across a diverse set of dense downstream applications.

Retrieving graphs from a large corpus, that contain a subgraph isomorphic to a given query graph, is a core operation in many real-world applications. While recent multi-vector graph representations and scores based on set alignment and containment can provide accurate subgraph isomorphism tests, their use in retrieval remains limited by their need to score corpus graphs exhaustively. We introduce CoRGII (COntextual Representation of Graphs for Inverted Indexing), a graph indexing framework in which, starting with a contextual dense graph representation, a differentiable discretization module computes sparse binary codes over a learned latent vocabulary. This text document-like representation allows us to leverage classic, highly optimized inverted indexes, while supporting soft (vector) set containment scores. Improving on this paradigm further, we replace the classical impact score of a `word' on a graph (such as defined by TFIDF or BM25) with a data-driven, trainable impact score. Crucially, CoRGII is trained end-to-end using only binary relevance labels, without fine-grained supervision of query-to-document set alignments. Extensive experiments show that CoRGII provides better trade-offs between efficiency and accuracy, compared to several baselines.

Competitive programming is widely used to evaluate the coding and reasoning abilities of large language models. However, the growing presence of duplicate or highly similar problems raises concerns not only about competition fairness, but also about the validity of competitive programming as a benchmark for model evaluation. We introduce a retrieval-oriented benchmark suite for competitive programming, covering four retrieval tasks—two code-centric (Text-to-Code, Code-to-Code) and two newly proposed problem-centric tasks (Problem-to-Duplicate, Simplified-to-Full)—built from a combination of automatically crawled problem–solution data and manually curated annotations. Our contribution includes both high-quality training data and temporally separated test sets for reliable evaluation. We develop two task-specialized retrievers based on this dataset: CPRetriever-Code, trained with a novel Group-InfoNCE loss for problem–code alignment, and CPRetriever-Prob, fine-tuned for problem-level similarity. Both models achieve strong results and are open-sourced for local use. Finally, we analyze LiveCodeBench and find that high-similarity problems inflate model pass rates and reduce differentiation, underscoring the need for similarity-aware evaluation in future benchmarks.

We present VGGT-SLAM, a dense RGB SLAM system constructed by incrementally and globally aligning submaps created from the feed-forward scene reconstruction approach VGGT using only uncalibrated monocular cameras. While related works align submaps using similarity transforms (i.e., translation, rotation, and scale), we show that such approaches are inadequate in the case of uncalibrated cameras. In particular, we revisit the idea of reconstruction ambiguity, where given a set of uncalibrated cameras with no assumption on the camera motion or scene structure, the scene can only be reconstructed up to a 15-degrees-of-freedom projective transformation of the true geometry. This inspires us to recover a consistent scene reconstruction across submaps by optimizing over the SL(4) manifold, thus estimating 15-degrees-of-freedom homography transforms between sequential submaps while accounting for potential loop closure constraints. As verified by extensive experiments, we demonstrate that VGGT-SLAM achieves improved map quality using long video sequences that are infeasible for VGGT due to its high GPU requirements. Our code is available at https://github.com/MIT-SPARK/VGGT-SLAM.