Multi-graph matching is a fundamental problem in computer vision. Our work is motivated by a challenging application in bioimaging, where dozens or even hundreds of 3D microscopy images of worms must be brought into correspondence. Existing datasets do not cover this large-scale regime, and virtually all existing methods are inapplicable because they assume a complete or dense problem setting. To support further research, our first contribution is a new large-scale dataset based on problem instances from bioimaging. Our second contribution is a comprehensive analysis of the two main multi-graph matching paradigms: direct and permutation synchronization-based formulations. We argue, in part by proof, that practical large-scale methods must explicitly address problem sparsity and incompleteness. Since standard permutation synchronization approaches fail in this setting, we further introduce a sparse permutation synchronization paradigm. Our final contribution is GREEDA, a general method for sparse and incomplete problems that can be instantiated across cost orders and paradigms. While our paper focuses on objective functions up to quadratic order, GREEDA is inherently generalizable to arbitrary orders. On larger, sparse instances, GREEDA outperforms competing methods in both objective value and runtime. For example, for moderately sized problems based on 30 worm images GREEDA produces a high-quality solution within 2 minutes, whereas competitors require at least an hour and yield far worse results. On smaller dense problems, GREEDA remains on par with leading methods while being an order of magnitude faster.
Probing large language models (LLMs) has yielded valuable insights into their internal mechanisms by linking neural representations to interpretable semantics. However, how neurons functionally co-activate with each other to give rise to emergent capabilities remains largely unknown, hindering a deeper understanding and safer development of LLMs. In this work, we introduce graph probing, a method for uncovering the functional connectivity topology of LLM neurons and relating it to language generation performance. By analyzing internal neural graphs across diverse LLM families and scales, we discover a universal predictability of next-token prediction performance using only neural topology. This predictability is robust even when retaining just 1% of neuron connections or probing models after only 8 pretraining steps, highlighting the sparsity and early emergence of topological patterns. Further graph matching analysis suggests that, despite significant distinctions in architectures, parameters, and training data, different LLMs develop intricate and consistent neural topological structures that may form the foundation for their language generation abilities. Codes and data for the graph probing toolbox are released at https://github.com/DavyMorgan/llm-graph-probing.
Anti-analysis techniques, particularly packing, challenge malware analysts, making packer identification fundamental. Existing packer identifiers have significant limitations: signature-based methods lack flexibility and struggle against dynamic evasion, while Machine Learning approaches require extensive training data, limiting scalability and adaptability. Consequently, achieving accurate and adaptable packer identification remains an open problem. This paper presents PackHero, a scalable and efficient methodology for identifying packers using a novel static approach. PackHero employs a Graph Matching Network and clustering to match and group Call Graphs from programs packed with known packers. We evaluate our approach on a public dataset of malware and benign samples packed with various packers, demonstrating its effectiveness and scalability across varying sample sizes. PackHero achieves a macro-average F1-score of 93.7% with just 10 samples per packer, improving to 98.3% with 100 samples. Notably, PackHero requires fewer samples to achieve stable performance compared to other Machine Learning-based tools. Overall, PackHero matches the performance of State-of-the-art signature-based tools, outperforming them in handling Virtualization-based packers such as Themida/Winlicense, with a recall of 100%.
Deep networks are prone to catastrophic forgetting during sequential task learning, i.e., losing the knowledge about old tasks upon learning new tasks. To this end, continual learning(CL) has emerged, whose existing methods focus mostly on regulating or protecting the parameters associated with the previous tasks. However, parameter protection is often impractical, since the size of parameters for storing the old-task knowledge increases linearly with the number of tasks, otherwise it is hard to preserve the parameters related to the old-task knowledge. In this work, we bring a dual opinion from neuroscience and physics to CL: in the whole networks, the pathways matter more than the parameters when concerning the knowledge acquired from the old tasks. Following this opinion, we propose a novel CL framework, learning without isolation(LwI), where model fusion is formulated as graph matching and the pathways occupied by the old tasks are protected without being isolated. Thanks to the sparsity of activation channels in a deep network, LwI can adaptively allocate available pathways for a new task, realizing pathway protection and addressing catastrophic forgetting in a parameter-efficient manner. Experiments on popular benchmark datasets demonstrate the superiority of the proposed LwI.
Large language models (LLMs) are increasingly recognized as powerful tools for scientific discovery, particularly in molecular science. A fundamental requirement for these models is the ability to accurately understand molecular structures, commonly encoded in the SMILES representation. However, current LLMs struggle to interpret SMILES, even failing to carry out basic tasks such as counting molecular rings. To address this limitation, we introduce CLEANMOL, a novel framework that formulates SMILES parsing into a suite of clean and deterministic tasks explicitly designed to promote graph-level molecular comprehension. These tasks span from subgraph matching to global graph matching, providing structured supervision aligned with molecular structural properties. We construct a molecular pretraining dataset with adaptive difficulty scoring and pre-train open-source LLMs on these tasks. Our results show that CLEANMOL not only enhances structural comprehension but also achieves the best or competes with the baseline on the Mol-Instructions benchmark.
Transferring linguistic knowledge from a pretrained language model (PLM) to acoustic feature learning has proven effective in enhancing end-to-end automatic speech recognition (E2E-ASR). However, aligning representations between linguistic and acoustic modalities remains a challenge due to inherent modality gaps. Optimal transport (OT) has shown promise in mitigating these gaps by minimizing the Wasserstein distance (WD) between linguistic and acoustic feature distributions. However, previous OT-based methods overlook structural relationships, treating feature vectors as unordered sets. To address this, we propose Graph Matching Optimal Transport (GM-OT), which models linguistic and acoustic sequences as structured graphs. Nodes represent feature embeddings, while edges capture temporal and sequential relationships. GM-OT minimizes both WD (between nodes) and Gromov-Wasserstein distance (GWD) (between edges), leading to a fused Gromov-Wasserstein distance (FGWD) formulation. This enables structured alignment and more efficient knowledge transfer compared to existing OT-based approaches. Theoretical analysis further shows that prior OT-based methods in linguistic knowledge transfer can be viewed as a special case within our GM-OT framework. We evaluate GM-OT on Mandarin ASR using a CTC-based E2E-ASR system with a PLM for knowledge transfer. Experimental results demonstrate significant performance gains over state-of-the-art models, validating the effectiveness of our approach.
Reinforcement learning (RL) has been widely adopted to enhance the performance of large language models (LLMs) on Text-to-SQL tasks. However, existing methods often rely on execution-based or LLM-based Bradley-Terry reward models. The former suffers from high execution latency caused by repeated database calls, whereas the latter imposes substantial GPU memory overhead, both of which significantly hinder the efficiency and scalability of RL pipelines. To this end, we propose a novel Text-to-SQL RL fine-tuning framework named Graph-Reward-SQL, which employs the GMNScore outcome reward model. We leverage SQL graph representations to provide accurate reward signals while significantly reducing inference time and GPU memory usage. Building on this foundation, we further introduce StepRTM, a stepwise reward model that provides intermediate supervision over Common Table Expression (CTE) subqueries. This encourages both functional correctness and structural clarity of SQL. Extensive comparative and ablation experiments on standard benchmarks, including Spider and BIRD, demonstrate that our method consistently outperforms existing reward models.
Despite domain generalization (DG) has significantly addressed the performance degradation of pre-trained models caused by domain shifts, it often falls short in real-world deployment. Test-time adaptation (TTA), which adjusts a learned model using unlabeled test data, presents a promising solution. However, most existing TTA methods struggle to deliver strong performance in medical image segmentation, primarily because they overlook the crucial prior knowledge inherent to medical images. To address this challenge, we incorporate morphological information and propose a framework based on multi-graph matching. Specifically, we introduce learnable universe embeddings that integrate morphological priors during multi-source training, along with novel unsupervised test-time paradigms for domain adaptation. This approach guarantees cycle-consistency in multi-matching while enabling the model to more effectively capture the invariant priors of unseen data, significantly mitigating the effects of domain shifts. Extensive experiments demonstrate that our method outperforms other state-of-the-art approaches on two medical image segmentation benchmarks for both multi-source and single-source domain generalization tasks. The source code is available at https://github.com/Yore0/TTDG-MGM.
The integration of Large Language Models (LLMs) into diverse applications, ranging from interactive chatbots and cloud AIOps to intelligent agents, has introduced a wide spectrum of Service Level Objectives (SLOs) for responsiveness. These workloads include latency-sensitive requests focused on per-token latency in streaming chat, throughput-intensive requests that require rapid full responses to invoke tools, and collective requests with dynamic dependencies arising from self-reflection or agent-based reasoning. This workload diversity, amplified by unpredictable request information such as response lengths and runtime dependencies, makes existing schedulers inadequate even within their design envelopes. In this paper, we define service gain as the useful service delivered by completing requests. We observe that as SLO directly reflects the actual performance needs of requests, completing a request much faster than its SLO (e.g., deadline) yields limited additional service gain. Based on this insight, we introduce Tempo, the first systematic SLO-aware scheduler designed to maximize service gain across diverse LLM workloads. Tempo allocates just enough serving bandwidth to meet each SLO, maximizing residual capacity for others best-effort workloads. Instead of assuming request information or none at all, it adopts a hybrid scheduling strategy: using quantile-based response upper bounds and dependency-graph matching for conservative initial estimates, prioritizing requests by service gain density, and refining decisions online as generation progresses. Our evaluation across diverse workloads, including chat, reasoning, and agentic pipelines, shows that Tempo improves end-to-end service gain by up to 8.3$\times$ and achieves up to 10.3$\times$ SLO goodput compared to state-of-the-art designs
Human mobility analysis at urban-scale requires models to represent the complex nature of human movements, which in turn are affected by accessibility to nearby points of interest, underlying socioeconomic factors of a place, and local transport choices for people living in a geographic region. In this work, we represent human mobility and the associated flow of movements as a grapyh. Graph-based approaches for mobility analysis are still in their early stages of adoption and are actively being researched. The challenges of graph-based mobility analysis are multifaceted - the lack of sufficiently high-quality data to represent flows at high spatial and teporal resolution whereas, limited computational resources to translate large voluments of mobility data into a network structure, and scaling issues inherent in graph models etc. The current study develops a methodology by embedding graphs into a continuous space, which alleviates issues related to fast graph matching, graph time-series modeling, and visualization of mobility dynamics. Through experiments, we demonstrate how mobility data collected from taxicab trajectories could be transformed into network structures and patterns of mobility flow changes, and can be used for downstream tasks reporting approx 40% decrease in error on average in matched graphs vs unmatched ones.
Generalized zero-shot semantic segmentation (GZS3) aims to achieve the human-level capability of segmenting not only seen classes but also novel class regions unseen in the training data through introducing the bridge of semantic representations, e.g., word vector. While effective, the way of utilizing one semantic representation to associate the corresponding class and to enable the knowledge transfer from seen to unseen classes is insufficient as well as incompatible with human cognition. Inspired by the observation that humans often use some `part' and `state' information to comprehend the seen objects and imagine unseen classes, we decouple each class into detailed descriptions, including object parts and states. Based on the decoupling formulation, we propose a Decoupled Vision-Language Matching (DeVLMatch) framework, composed of spatial-part (SPMatch) and channel-state (CSMatch) matching modules, for GZS3. In SPMatch, we comprehend objects with spatial part information from both visual and linguistic perspectives and perform graph matching to bridge the gap. In CSMatch, states of objects from the linguistic perspective are matched to compatible channel information from the visual perspective. By decoupling and matching objects across visual and linguistic comprehension, we can explicitly introspect the relationship between seen and unseen classes in fine-grained object part and state levels, thereby facilitating the knowledge transfer from seen to unseen classes in visual space. The proposed DeVLMatch framework surpasses the previous GZS3 methods on standard benchmarks, including PASCAL VOC, COCO-Stuff, and CATARACTS, demonstrating its effectiveness.
The Graph Edit Distance (GED) problem, which aims to compute the minimum number of edit operations required to transform one graph into another, is a fundamental challenge in graph analysis with wide-ranging applications. However, due to its NP-hard nature, traditional A* approaches often suffer from scalability issue, making them computationally intractable for large graphs. Many recent deep learning frameworks address GED by formulating it as a regression task, which, while efficient, fails to recover the edit path -- a central interest in GED. Furthermore, recent hybrid approaches that combine deep learning with traditional methods to recover the edit path often yield poor solution quality. These methods also struggle to generate candidate solutions in parallel, resulting in increased running times.In this paper, we present a novel approach, DiffGED, that leverages generative diffusion model to solve GED and recover the corresponding edit path. Specifically, we first generate multiple diverse node matching matrices in parallel through a diffusion-based graph matching model. Next, node mappings are extracted from each generated matching matrices in parallel, and each extracted node mapping can be simply transformed into an edit path. Benefiting from the generative diversity provided by the diffusion model, DiffGED is less likely to fall into local sub-optimal solutions, thereby achieving superior overall solution quality close to the exact solution. Experimental results on real-world datasets demonstrate that DiffGED can generate multiple diverse edit paths with exceptionally high accuracy comparable to exact solutions while maintaining a running time shorter than most of hybrid approaches.
In this paper, we propose a general framework for universal zero-shot goal-oriented navigation. Existing zero-shot methods build inference framework upon large language models (LLM) for specific tasks, which differs a lot in overall pipeline and fails to generalize across different types of goal. Towards the aim of universal zero-shot navigation, we propose a uniform graph representation to unify different goals, including object category, instance image and text description. We also convert the observation of agent into an online maintained scene graph. With this consistent scene and goal representation, we preserve most structural information compared with pure text and are able to leverage LLM for explicit graph-based reasoning. Specifically, we conduct graph matching between the scene graph and goal graph at each time instant and propose different strategies to generate long-term goal of exploration according to different matching states. The agent first iteratively searches subgraph of goal when zero-matched. With partial matching, the agent then utilizes coordinate projection and anchor pair alignment to infer the goal location. Finally scene graph correction and goal verification are applied for perfect matching. We also present a blacklist mechanism to enable robust switch between stages. Extensive experiments on several benchmarks show that our UniGoal achieves state-of-the-art zero-shot performance on three studied navigation tasks with a single model, even outperforming task-specific zero-shot methods and supervised universal methods.
Graph similarity learning (GSL), also referred to as graph matching in many scenarios, is a fundamental problem in computer vision, pattern recognition, and graph learning. However, previous GSL methods assume that graphs are homogeneous and struggle to maintain their performance on heterogeneous graphs. To address this problem, this paper proposes a Heterogeneous Graph Matching Network (HeGMN), which is an end-to-end graph similarity learning framework composed of a two-tier matching mechanism. Firstly, a heterogeneous graph isomorphism network is proposed as the encoder, which reinvents graph isomorphism network for heterogeneous graphs by perceiving different semantic relationships during aggregation. Secondly, a graph-level and node-level matching modules are designed, both employing type-aligned matching principles. The former conducts graph-level matching by node type alignment, and the latter computes the interactions between the cross-graph nodes with the same type thus reducing noise interference and computational overhead. Finally, the graph-level and node-level matching features are combined and fed into fully connected layers for predicting graph similarity scores. In experiments, we propose a heterogeneous graph resampling method to construct heterogeneous graph pairs and define the corresponding heterogeneous graph edit distance, filling the gap in missing datasets. Extensive experiments demonstrate that HeGMN consistently achieves advanced performance on graph similarity prediction across all datasets.
In this work we present a novel approach for unsupervised multi-graph matching, which applies to problems for which a Gaussian distribution of keypoint features can be assumed. We leverage cycle consistency as loss for self-supervised learning, and determine Gaussian parameters through Bayesian Optimization, yielding a highly efficient approach that scales to large datasets. Our fully unsupervised approach enables us to reach the accuracy of state-of-the-art supervised methodology for the use case of annotating cell nuclei in 3D microscopy images of the worm C. elegans. To this end, our approach yields the first unsupervised atlas of C. elegans, i.e. a model of the joint distribution of all of its cell nuclei, without the need for any ground truth cell annotation. This advancement enables highly efficient annotation of cell nuclei in large microscopy datasets of C. elegans. Beyond C. elegans, our approach offers fully unsupervised construction of cell-level atlases for any model organism with a stereotyped cell lineage, and thus bears the potential to catalyze respective comparative developmental studies in a range of further species.
We propose a method for accurately detecting bioacoustic sound events that is robust to overlapping events, a common issue in domains such as ethology, ecology and conservation. While standard methods employ a frame-based, multi-label approach, we introduce an onset-based detection method which we name Voxaboxen. It takes inspiration from object detection methods in computer vision, but simultaneously takes advantage of recent advances in self-supervised audio encoders. For each time window, Voxaboxen predicts whether it contains the start of a vocalization and how long the vocalization is. It also does the same in reverse, predicting whether each window contains the end of a vocalization, and how long ago it started. The two resulting sets of bounding boxes are then fused using a graph-matching algorithm. We also release a new dataset designed to measure performance on detecting overlapping vocalizations. This consists of recordings of zebra finches annotated with temporally-strong labels and showing frequent overlaps. We test Voxaboxen on seven existing data sets and on our new data set. We compare Voxaboxen to natural baselines and existing sound event detection methods and demonstrate SotA results. Further experiments show that improvements are robust to frequent vocalization overlap.
Molecular machine learning has gained popularity with the advancements of geometric deep learning. In parallel, retrieval-augmented generation has become a principled approach commonly used with language models. However, the optimal integration of retrieval augmentation into molecular machine learning remains unclear. Graph neural networks stand to benefit from clever matching to understand the structural alignment of retrieved molecules to a query molecule. Neural graph matching offers a compelling solution by explicitly modeling node and edge affinities between two structural graphs while employing a noise-robust, end-to-end neural network to learn affinity metrics. We apply this approach to mass spectrum simulation and introduce MARASON, a novel model that incorporates neural graph matching to enhance a fragmentation-based neural network. Experimental results highlight the effectiveness of our design, with MARASON achieving 28% top-1 accuracy, a substantial improvement over the non-retrieval state-of-the-art accuracy of 19%. Moreover, MARASON outperforms both naive retrieval-augmented generation methods and traditional graph matching approaches.
Semantic join discovery, which aims to find columns in a table repository with high semantic joinabilities to a query column, is crucial for dataset discovery. Existing methods can be divided into two categories: cell-level methods and column-level methods. However, neither of them ensures both effectiveness and efficiency simultaneously. Cell-level methods, which compute the joinability by counting cell matches between columns, enjoy ideal effectiveness but suffer poor efficiency. In contrast, column-level methods, which determine joinability only by computing the similarity of column embeddings, enjoy proper efficiency but suffer poor effectiveness due to the issues occurring in their column embeddings: (i) semantics-joinability-gap, (ii) size limit, and (iii) permutation sensitivity. To address these issues, this paper proposes to compute column embeddings via proxy columns; furthermore, a novel column-level semantic join discovery framework, Snoopy, is presented, leveraging proxy-column-based embeddings to bridge effectiveness and efficiency. Specifically, the proposed column embeddings are derived from the implicit column-to-proxy-column relationships, which are captured by the lightweight approximate-graph-matching-based column projection.To acquire good proxy columns for guiding the column projection, we introduce a rank-aware contrastive learning paradigm. Extensive experiments on four real-world datasets demonstrate that Snoopy outperforms SOTA column-level methods by 16% in Recall@25 and 10% in NDCG@25, and achieves superior efficiency--being at least 5 orders of magnitude faster than cell-level solutions, and 3.5x faster than existing column-level methods.
Ontology, and more broadly, Knowledge Graph Matching is a challenging task in which expressiveness has not been fully addressed. Despite the increasing use of embeddings and language models for this task, approaches for generating expressive correspondences still do not take full advantage of these models, in particular, large language models (LLMs). This paper proposes to integrate LLMs into an approach for generating expressive correspondences based on alignment need and ABox-based relation discovery. The generation of correspondences is performed by matching similar surroundings of instance sub-graphs. The integration of LLMs results in different architectural modifications, including label similarity, sub-graph matching, and entity matching. The performance word embeddings, sentence embeddings, and LLM-based embeddings, was compared. The results demonstrate that integrating LLMs surpasses all other models, enhancing the baseline version of the approach with a 45\% increase in F-measure.
We study community detection in multiple networks whose nodes and edges are jointly correlated. This setting arises naturally in applications such as social platforms, where a shared set of users may exhibit both correlated friendship patterns and correlated attributes across different platforms. Extending the classical Stochastic Block Model (SBM) and its contextual counterpart (CSBM), we introduce the correlated CSBM, which incorporates structural and attribute correlations across graphs. To build intuition, we first analyze correlated Gaussian Mixture Models, wherein only correlated node attributes are available without edges, and identify the conditions under which an estimator minimizing the distance between attributes achieves exact matching of nodes across the two databases. For correlated CSBMs, we develop a two-step procedure that first applies $k$-core matching to most nodes using edge information, then refines the matching for the remaining unmatched nodes by leveraging their attributes with a distance-based estimator. We identify the conditions under which the algorithm recovers the exact node correspondence, enabling us to merge the correlated edges and average the correlated attributes for enhanced community detection. Crucially, by aligning and combining graphs, we identify regimes in which community detection is impossible in a single graph but becomes feasible when side information from correlated graphs is incorporated. Our results illustrate how the interplay between graph matching and community recovery can boost performance, broadening the scope of multi-graph, attribute-based community detection.