论文检索

Computer Vision · Segmentation

Conghui Li, Chern Hong Lim, Xin Wang

While deep neural networks possess the capability to perform semantic segmentation, producing a single deterministic output limits reliability in safety-critical applications, caused by uncertainty and annotation variability. To address this, stochastic segmentation models using Conditional Variational Autoencoders (CVAE), Bayesian networks, and diffusion have been explored. However, existing approaches suffer from limited latent expressiveness and interpretability. Furthermore, our experiments showed that models like Probabilistic U-Net rely excessively on high latent variance, leading to posterior collapse. This work propose a novel framework by integrating Gaussian Mixture Model (GMM) with Normalizing Flow (NF) in CVAE for stochastic segmentation. GMM structures the latent space into meaningful semantic clusters, while NF captures feature deformations with quantified uncertainty. Our method stabilizes latent distributions through constrained variance and mean ranges. Experiments on LIDC, Crack500, and Cityscapes datasets show that our approach outperformed state-of-the-art in curvilinear structure and medical image segmentation.

Computer Vision · Classification and Understanding

Xiaoyu Zhou, Jingqi Wang, Yuang Jia, Yongtao Wang, Deqing Sun, Ming-Hsuan Yang

Current 3D scene understanding methods are limited by offline-collected multi-view data or pre-constructed 3D geometry. In this paper, we present ExtractAnything3D (EA3D), a unified online framework for open-world 3D object extraction that enables simultaneous geometric reconstruction and holistic scene understanding. Given a streaming video, EA3D dynamically interprets each frame using vision-language and 2D vision foundation encoders to extract object-level knowledge. This knowledge is integrated and embedded into a Gaussian feature map via a feed-forward online update strategy. We then iteratively estimate visual odometry from historical frames and incrementally update online Gaussian features with new observations. A recurrent joint optimization module directs the model's attention to regions of interest, simultaneously enhancing both geometric reconstruction and semantic understanding. Extensive experiments across diverse benchmarks and tasks, including photo-realistic rendering, semantic and instance segmentation, 3D bounding box and semantic occupancy estimation, and 3D mesh generation, demonstrate the effectiveness of EA3D. Our method establishes a unified and efficient framework for joint online 3D reconstruction and holistic scene understanding, enabling a broad range of downstream tasks. The project webpage is available at \url{https://github.com/VDIGPKU/EA3D}.

Social Aspects · Accountability, Transparency and Interpretability

Adrian Hill, Neal McKee, Johannes Maeß, Stefan Bluecher, Klaus-Robert Müller

Explaining complex machine learning models is a fundamental challenge when developing safe and trustworthy deep learning applications. To date, a broad selection of explainable AI (XAI) algorithms exist. One popular choice is SmoothGrad, which has been conceived to alleviate the well-known shattered gradient problem by smoothing gradients through convolution. SmoothGrad proposes to solve this high-dimensional convolution integral by sampling -- typically approximating the convolution with limited precision. Higher numbers of samples would amount to higher precision in approximating the convolution but also to higher computing demand, therefore in practice only few samples are used in SmoothGrad. In this work we propose a well founded novel method _SmoothDiff_ to resolve this tradeoff yielding a _speedup of over two orders of magnitude_. Specifically, _SmoothDiff_ leverages automatic differentiation to decompose the expected values of Jacobians across a network architecture, directly targeting only the non-linearities responsible for shattered gradients and making it easy to implement. We demonstrate SmoothDiff's excellent speed and performance in a number of experiments and benchmarks. Thus, SmoothDiff greatly enhances the usability (quality and speed) of SmoothGrad -- a popular workhorse of XAI.

Applications · Physics

Jes Frellsen, Maher Kassem, Tone Bengtsen, Lars Olsen, Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg, Wouter Boomsma

Inverse folding models have proven to be highly effective zero-shot predictors of protein stability. Despite this success, the link between the amino acid preferences of an inverse folding model and the free-energy considerations underlying thermodynamic stability remains incompletely understood. A better understanding would be of interest not only from a theoretical perspective, but also potentially provide the basis for stronger zero-shot stability prediction. In this paper, we take steps to clarify the free-energy foundations of inverse folding models. Our derivation reveals the standard practice of likelihood ratios as a simplistic approximation and suggests several paths towards better estimates of the relative stability. We empirically assess these approaches and demonstrate that considerable gains in zero-shot performance can be achieved with fairly simple means.

Deep Learning · Generative Models and Autoencoders

Andrej Leban

The Distributional Principal Autoencoder (DPA) combines distributionally correct reconstruction with principal-component-like interpretability of the encodings. In this work, we provide exact theoretical guarantees on both fronts. First, we derive a closed-form relation linking each optimal level-set geometry to the data-distribution score. This result explains DPA's empirical ability to disentangle factors of variation of the data, as well as allows the score to be recovered directly from samples. When the data follows the Boltzmann distribution, we demonstrate that this relation yields an approximation of the minimum free-energy path for the Müller–Brown potential in a single fit. Second, we prove that if the data lies on a manifold that can be approximated by the encoder, latent components beyond the manifold dimension are conditionally independent of the data distribution - carrying no additional information - and thus reveal the intrinsic dimension. Together, these results show that a single model can learn the data distribution and its intrinsic dimension with exact guarantees simultaneously, unifying two longstanding goals of unsupervised learning.

Social Aspects · Accountability, Transparency and Interpretability

Daniel Wurgaft, Ekdeep S Lubana, Core Francisco Park, Hidenori Tanaka, Gautam Reddy, Noah Goodman

Recent work analyzing in-context learning (ICL) has identified a broad set of strategies that describe model behavior in different experimental conditions. We aim to unify these findings by asking why a model learns these disparate strategies in the first place. Specifically, we start with the observation that when trained to learn a mixture of tasks, as is popular in the literature, the strategies learned by a model for performing ICL can be captured by a family of Bayesian predictors: a memorizing predictor, which assumes a discrete prior on the set of seen tasks, and a generalizing predictor, where the prior matches the underlying task distribution. Adopting the normative lens of rational analysis, where a learner’s behavior is explained as an optimal adaptation to data given computational constraints, we develop a hierarchical Bayesian framework that almost perfectly predicts Transformer next- token predictions throughout training—without assuming access to its weights. Under this framework, pretraining is viewed as a process of updating the posterior probability of different strategies, and inference-time behavior as a posterior- weighted average over these strategies’ predictions. Our framework draws on common assumptions about neural network learning dynamics, which make explicit a tradeoff between loss and complexity among candidate strategies: beyond how well it explains the data, a model’s preference towards implementing a strategy is dictated by its complexity. This helps explain well-known ICL phenomena, while offering novel predictions: e.g., we show a superlinear trend in the timescale for transitioning from generalization to memorization as task diversity increases. Overall, our work advances an explanatory and predictive account of ICL grounded in tradeoffs between strategy loss and complexity.

Computer Vision · Vision Models & Multimodal

Chun Wang, Xiaojun Ye, Xiaoran Pan, Zihao Pan, Haofan Wang, Yiren Song

Recent advances in Visual Language Models (VLMs) have demonstrated exceptional performance in visual reasoning tasks. However, geo-localization presents unique challenges, requiring the extraction of multigranular visual cues from images and their integration with external world knowledge for systematic reasoning. Current approaches to geo-localization tasks often lack robust reasoning mechanisms and explainability, limiting their effectiveness. To address these limitations, we propose the Geo Reason Enhancement (GRE) Suite, a novel framework that augments VLMs with structured reasoning chains for accurate and interpretable location inference. The GRE Suite is systematically developed across three key dimensions: dataset, model, and benchmark. First, we introduce GRE30K, a high-quality geo-localization reasoning dataset designed to facilitate fine-grained visual and contextual analysis. Next, we present the GRE model, which employs a multi-stage reasoning strategy to progressively infer scene attributes, local details, and semantic features, thereby narrowing down potential geographic regions with enhanced precision. Finally, we construct the Geo Reason Evaluation Benchmark (GREval-Bench), a comprehensive evaluation framework that assesses VLMs across diverse urban, natural, and landmark scenes to measure both coarse-grained (e.g., country, continent) and fine-grained (e.g., city, street) localization performance. Experimental results demonstrate that GRE significantly outperforms existing methods across all granularities of geo-localization tasks, underscoring the efficacy of reasoning-augmented VLMs in complex geographic inference. Code and data will be released at https://anonymous.4open.science/r/GRE-74C0.

Social Aspects · Accountability, Transparency and Interpretability

Yazheng Liu, Xi Zhang, Sihong Xie, Hui Xiong

Explaining graph neural networks (GNNs) is a key approach to improve the trustworthiness of GNN in high-stakes applications, such as finance and healthcare. However, existing methods are vulnerable to perturbations, raising concerns about explanation reliability. Prior methods enhance explanation robustness using model retraining or explanation ensemble, with certain weaknesses. Retraining leads to models that are different from the original target model and misleading explanations, while ensemble can produce contradictory results due to different inputs or models. To improve explanation robustness without the above weaknesses, we take an unexplored route and exploit the two edge geometry properties curvature and resistance to enhance explanation robustness. We are the first to prove that these geometric notions can be used to bound explanation robustness. We design a general optimization algorithm to incorporate these geometric properties into a wide spectrum of base GNN explanation methods to enhance the robustness of base explanations. We empirically show that our method outperforms six base explanation methods in robustness across nine datasets spanning node classification, link prediction, and graph classification tasks, improving fidelity in 80\% of the cases and achieving up to a 10\% relative improvement in robust performance. The code is available at [https://github.com/yazhengliu/Robust_explanation_curvature](https://github.com/yazhengliu/Robust_explanation_curvature).

Applications · Time Series

Felix Draxler, Yang Meng, Kai Nelson, Lukas Laskowski, Yibo Yang, Theofanis Karaletsos, Stephan Mandt

Event sequences appear widely in domains such as medicine, finance, and remote sensing, yet modeling them is challenging due to their heterogeneity: sequences often contain multiple event types with diverse structures—for example, electronic health records that mix discrete events like medical procedures with continuous lab measurements. Existing approaches either tokenize all entries, violating natural inductive biases, or ignore parts of the data to enforce a consistent structure. In this work, we propose a simple yet powerful Marked Temporal Point Process (MTPP) framework for modeling event sequences with flexible structure, using a single unified model. Our approach employs a single autoregressive transformer with discrete and continuous prediction heads, capable of modeling variable-length, mixed-type event sequences. The continuous head leverages an expressive normalizing flow to model continuous event attributes, avoiding the numerical integration required for inter-event times in most competing methods. Empirically, our model excels on both discrete-only and mixed-type sequences, improving prediction quality and enabling interpretable uncertainty quantification. We make our code public at https://github.com/czi-ai/FlexTPP.

Applications · Health

Yulong Li, Xiwei Liu, feilong tang, Ming Hu, Jionglong Su, Zongyuan Ge, Imran Razzak, Eran Segal

Causal mediation analysis is crucial for deconstructing complex mechanisms of action. However, in current mediation analysis, complex structures derived from causal discovery lack direct interpretation of mediation pathways, while traditional mediation analysis and effect estimation are limited by the reliance on pre-specified pathways, leading to a disconnection between structure discovery and causal mechanism understanding. Therefore, a unified framework integrating structure discovery, pathway identification, and effect estimation systematically quantifies mediation pathways under structural uncertainty, enabling automated identification and inference of mediation pathways. To this end, we propose Structure-Informed Guided Mediation Analysis (SIGMA), which guides automated mediation pathway identification through probabilistic causal structure discovery and uncertainty quantification, enabling end-to-end propagation of structural uncertainty from structure learning to effect estimation. Specifically, SIGMA employs differentiable Flow-Structural Equation Models to learn structural posteriors, generating diverse Directed Acyclic Graphs (DAGs) to quantify structural uncertainty. Based on these DAGs, we introduce the Path Stability Score to evaluate the marginal probability of pathways, identifying high-confidence mediation paths. For identified mediation pathways, we integrate Efficient Influence Functions with Bayesian model averaging to fuse within-structure estimation uncertainty and between-structure effect variation, propagating uncertainty to the final effect estimates. In synthetic data experiments, SIGMA achieves state-of-the-art performance in pathway identification accuracy and effect quantification precision under structures uncertainty, concurrent multiple pathways, and nonlinear scenarios. In real-world applications using Human Phenotype Project data, SIGMA identifies mediation effects of sleep quality on cardiovascular health through inflammatory and metabolic pathways, uncovering previously unspecified multiple mediation paths.

Hongbin Zhang, Kehai Chen, Xuefeng Bai, Xiucheng Li, Yang Xiang, Min Zhang

While large language models (LLMs) demonstrate remarkable success in multilingual translation, their internal core translation mechanisms, even at the fundamental word level, remain insufficiently understood. To address this critical gap, this work introduces a systematic framework for interpreting the mechanism behind LLM translation from the perspective of computational components. This paper first proposes subspace-intervened path patching for precise, fine-grained causal analysis, enabling the detection of components crucial to translation tasks and subsequently characterizing their behavioral patterns in human-interpretable terms. Comprehensive experiments reveal that translation is predominantly driven by a sparse subset of components: specialized attention heads serve critical roles in extracting source language, translation indicators, and positional features, which are then integrated and processed by specific multi-layer perceptrons (MLPs) into intermediary English-centric latent representations before ultimately yielding the final translation. The significance of these findings is underscored by the empirical demonstration that targeted fine-tuning a minimal parameter subset (<5%) enhances translation performance while preserving general capabilities. This result further indicates that these crucial components generalize effectively to sentence-level translation and are instrumental in elucidating more intricate translation tasks.

General Machine Learning · Representation Learning

Giordano Cicchetti, Eleonora Grassucci, Danilo Comminiello

Multimodal learning plays a pivotal role in advancing artificial intelligence systems by incorporating information from multiple modalities to build a more comprehensive representation. Despite its importance, current state-of-the-art models still suffer from severe limitations that prevent the successful development of a fully multimodal model. Such methods do not provide indicators that all the involved modalities are effectively aligned. As a result, a set of modalities may not be aligned, undermining the effectiveness of the model in downstream tasks where multiple modalities should provide additional information that the model fails to exploit. In this paper, we present TRIANGLE: TRI-modAl Neural Geometric LEarning, the novel proposed similarity measure that is directly computed in the higher-dimensional space spanned by the modality embeddings. TRIANGLE improves the joint alignment of three modalities via a triangle‑area similarity, avoiding additional fusion layers. When incorporated in contrastive losses replacing cosine similarity, TRIANGLE significantly boosts the performance of multimodal modeling, while yielding interpretable alignment rationales. Extensive evaluation in three-modal tasks such as video-text and audio-text retrieval or audio-video classification, demonstrates that TRIANGLE achieves state-of-the-art results across different datasets improving the performance of cosine-based methods up to 9 points of Recall@1.

Deep Learning · Attention Mechanisms

Baran Hashemi, Kurt Pasque, Chris Teska, Ruriko Yoshida

*Can algebraic geometry enhance the sharpness, robustness, and interpretability of modern neural reasoning models by equipping them with a mathematically grounded inductive bias?* To answer this, we introduce Tropical Attention, an attention mechanism grounded in tropical geometry that lifts the attention kernel into tropical projective space, where reasoning is piecewise-linear and 1-Lipschitz, thus preserving the polyhedral decision structure inherent to combinatorial reasoning. We prove that multi-head Tropical Attention (MHTA) stacks universally approximate tropical circuits and realize tropical transitive closure through composition, achieving polynomial resource bounds without invoking recurrent mechanisms. These guarantees explain why the induced polyhedral decision boundaries remain sharp and scale-invariant, rather than smoothed by Softmax. Empirically, we show that Tropical Attention delivers stronger out-of-distribution generalization in both length and value, with high robustness against perturbative noise, and substantially faster inference with fewer parameters compared to Softmax-based and recurrent attention baselines, respectively. For the first time, we push the domain of neural algorithmic reasoning beyond **PTIME** problems to **NP-hard/complete** problems, paving the way toward sharper and more expressive Large Reasoning Models (LRMs) capable of tackling complex combinatorial challenges in Phylogenetics, Cryptography, Particle Physics, and Mathematical Discovery. The code is available at https://github.com/Baran-phys/Tropical-Attention/.

Optimization

Matias Cattaneo, Boris Shigida

In modern optimization methods used in deep learning, each update depends on the history of previous iterations, often referred to as memory, and this dependence decays fast as the iterates go further into the past. For example, gradient descent with momentum has exponentially decaying memory through exponentially averaged past gradients. We introduce a general technique for identifying a memoryless algorithm that approximates an optimization algorithm with memory. It is obtained by replacing all past iterates in the update by the current one, and then adding a correction term arising from memory (also a function of the current iterate). This correction term can be interpreted as a perturbation of the loss, and the nature of this perturbation can inform how memory implicitly (anti-)regularizes the optimization dynamics. As an application of our theory, we find that Lion does not have the kind of implicit anti-regularization induced by memory that AdamW does, providing a theory-based explanation for Lion’s better generalization performance recently documented. Empirical evaluations confirm our theoretical findings.

Deep Learning · Generative Models and Autoencoders

Ahmed Masry, Juan Rodriguez, Tianyu Zhang, Suyuchen Wang, Chao Wang, Aarash Feizi, Akshay Kalkunte Suresh, Abhay Puri, Xiangru Jian, Pierre-André Noël 等

Aligning visual features with language embeddings is a key challenge in vision-language models (VLMs). The performance of such models hinges on having a good connector that maps visual features generated by a vision encoder to a shared embedding space with the LLM while preserving semantic similarity. Existing connectors, such as multilayer perceptrons (MLPs), lack inductive bias to constrain visual features within the linguistic structure of the LLM’s embedding space, making them data-hungry and prone to cross-modal misalignment. In this work, we propose a novel vision-text alignment method, AlignVLM, that maps visual features to a weighted average of LLM text embeddings. Our approach leverages the linguistic priors encoded by the LLM to ensure that visual features are mapped to regions of the space that the LLM can effectively interpret. AlignVLM is particularly effective for document understanding tasks, where visual and textual modalities are highly correlated. Our extensive experiments show that AlignVLM achieves state-of-the-art performance compared to prior alignment methods, with larger gains on document understanding and under low-resource setups. We provide further analysis demonstrating its efficiency and robustness to noise.

Computer Vision · Image and Video Generation

Juan Rodriguez, Haotian Zhang, Abhay Puri, Rishav Pramanik, Aarash Feizi, Pascal Wichmann, Arnab Mondal, Mohammad R. Samsami, Rabiul Awal, Perouz Taslakian 等

Scalable Vector Graphics (SVG) offer a powerful format for representing visual designs as interpretable code. Recent advances in vision-language models (VLMs) have enabled high-quality SVG generation by framing the problem as a code generation task and leveraging large-scale pretraining. VLMs are particularly suitable for this task as they capture both global semantics and fine-grained visual patterns, while transferring knowledge across vision, natural language, and code domains. However, existing VLM approaches often struggle to produce faithful and efficient SVGs because they never observe the rendered images during training. Although differentiable rendering for autoregressive SVG code generation remains unavailable, rendered outputs can still be compared to original inputs, enabling evaluative feedback suitable for reinforcement learning (RL). We introduce Reinforcement Learning from Rendering Feedback, an RL method that enhances SVG generation in autoregressive VLMs by leveraging feedback from rendered SVG outputs. Given an input image, the model generates SVG roll-outs that are rendered and compared to the original image to compute a reward. This visual fidelity feedback guides the model toward producing more accurate, efficient, and semantically coherent SVGs. \method significantly outperforms supervised fine-tuning, addressing common failure modes and enabling precise, high-quality SVG generation with strong structural understanding and generalization.

Theory · Everything Else

Etienne Gauthier, Francis Bach, Michael Jordan

We introduce *Backward Conformal Prediction*, a method that guarantees conformal coverage while providing flexible control over the size of prediction sets. Unlike standard conformal prediction, which fixes the coverage level and allows the conformal set size to vary, our approach defines a rule that constrains how prediction set sizes behave based on the observed data, and adapts the coverage level accordingly. Our method builds on two key foundations: (i) recent results by Gauthier et al. [2025] on post-hoc validity using e-values, which ensure marginal coverage of the form $\mathbb{P}(Y_{\rm test} \in \hat C_n^{\tilde{\alpha}}(X_{\rm test})) \ge 1 - \mathbb{E}[\tilde{\alpha}]$ up to a first-order Taylor approximation for any data-dependent miscoverage $\tilde{\alpha}$, and (ii) a novel leave-one-out estimator $\hat{\alpha}^{\rm LOO}$ of the marginal miscoverage $\mathbb{E}[\tilde{\alpha}]$ based on the calibration set, ensuring that the theoretical guarantees remain computable in practice. This approach is particularly useful in applications where large prediction sets are impractical such as medical diagnosis. We provide theoretical results and empirical evidence supporting the validity of our method, demonstrating that it maintains computable coverage guarantees while ensuring interpretable, well-controlled prediction set sizes.

Social Aspects · Trustworthy Machine Learning

Zhe Tao, Aditya V Thakur

In explainable AI, DNN gradients are used to interpret the prediction; in safety-critical control systems, gradients could encode safety constraints; in scientific-computing applications, gradients could encode physical invariants. While recent work on provable editing of DNNs has focused on input-output constraints, the problem of enforcing hard constraints on DNN gradients remains unaddressed. We present ProGrad, the first efficient approach for editing the parameters of a DNN to provably enforce hard constraints on the DNN gradients. Given a DNN $\mathcal{N}$ with parameters $\theta$, and a set $\mathcal{S}$ of pairs $(\mathrm{x}, \mathrm{Q})$ of input $\mathrm{x}$ and corresponding linear gradient constraints $\mathrm{Q}$, ProGrad finds new parameters $\theta'$ such that $\bigwedge_{(\mathrm{x}, \mathrm{Q}) \in \mathcal{S}} \frac{\partial}{\partial \mathrm{x}}\mathcal{N}(\mathrm{x}; \theta') \in \mathrm{Q}$ while minimizing the changes $\lVert\theta' - \theta\rVert$. The key contribution is a novel *conditional variable gradient* of DNNs, which relaxes the NP-hard provable gradient editing problem to a linear program (LP), enabling ProGrad to use an LP solver to efficiently and effectively enforce the gradient constraints. We experimentally evaluated ProGrad via enforcing (i) hard Grad-CAM constraints on ImageNet ResNet DNNs; (ii) hard Integrated Gradients constraints on Llama 3 and Qwen 3 LLMs; (iii) hard gradient constraints in training a DNN to approximate a target function as a proxy for safety constraints in control systems and physical invariants in scientific applications. The results highlight the unique capability of ProGrad in enforcing hard constraints on DNN gradients.

Deep Learning · Algorithms

Ejafa Bassam, Dawei Zhu, Kaigui Bian

Knowledge distillation is a model compression technique in which a compact "student" network is trained to replicate the predictive behavior of a larger "teacher" network. In logit-based knowledge distillation, it has become the de facto approach to augment cross-entropy with a distillation term. Typically, this term is either a KL divergence that matches marginal probabilities or a correlation-based loss that captures intra- and inter-class relationships. In every case, it acts as an additional term to cross-entropy. This term has its own weight, which must be carefully tuned. In this paper, we adopt a choice-theoretic perspective and recast knowledge distillation under the Plackett–Luce model by interpreting teacher logits as "worth" scores. We introduce *Plackett-Luce Distillation (PLD)*, a weighted list-wise ranking loss. In PLD, the teacher model transfers knowledge of its full ranking of classes, weighting each ranked choice by its own confidence. PLD directly optimizes a single "teacher-optimal" ranking. The true label is placed first, followed by the remaining classes in descending teacher confidence. This process yields a convex and translation-invariant surrogate that subsumes weighted cross-entropy. Empirically, across CIFAR-100, ImageNet-1K, and MS-COCO, PLD achieves consistent gains across diverse architectures and distillation objectives, including divergence-based, correlation-based, and feature-based methods, in both homogeneous and heterogeneous teacher–student pairs.

Deep Learning · Attention Mechanisms

Xinnan Dai, Kai Yang, Jay Revolinsky, Kai Guo, Aoran Wang, Bohang Zhang, Jiliang Tang

Recent studies suggest that large language models (LLMs) possess the capability to solve graph reasoning tasks. Notably, even when graph structures are embedded within textual descriptions, LLMs can still effectively answer related questions. This raises a fundamental question: How can a decoder-only Transformer architecture understand underlying graph structures? To address this, we start with the substructure extraction task, interpreting the inner mechanisms inside the transformers and analyzing the impact of the input queries. Specifically, through both empirical results and theoretical analysis, we present Induced Substructure Filtration (ISF), a perspective that captures the substructure identification in the multi-layer transformers. We further validate the ISF process in LLMs, revealing consistent internal dynamics across layers. Building on these insights, we explore the broader capabilities of Transformers in handling diverse graph types. Specifically, we introduce the concept of thinking in substructures to efficiently extract complex composite patterns, and demonstrate that decoder-only Transformers can successfully extract substructures from attributed graphs, such as molecular graphs. Together, our findings offer a new insight on how sequence-based Transformers perform the substructure extraction task over graph data.