Daily Papers

Graphs are essential data structures for modeling complex interactions in domains such as social networks, molecular structures, and biological systems. Graph-level tasks, which predict properties or classes for the entire graph, are critical for applications, such as molecular property prediction and subgraph counting. Graph Neural Networks (GNNs) have shown promise in these tasks, but their evaluations are often limited to narrow datasets, tasks, and inconsistent experimental setups, restricting their generalizability. To address these limitations, we propose a unified evaluation framework for graph-level GNNs. This framework provides a standardized setting to evaluate GNNs across diverse datasets, various graph tasks (e.g., graph classification and regression), and challenging scenarios, including noisy, imbalanced, and few-shot graphs. Additionally, we propose a novel GNN model with enhanced expressivity and generalization capabilities. Specifically, we enhance the expressivity of GNNs through a k-path rooted subgraph approach, enabling the model to effectively count subgraphs (e.g., paths and cycles). Moreover, we introduce a unified graph contrastive learning algorithm for graphs across diverse domains, which adaptively removes unimportant edges to augment graphs, thereby significantly improving generalization performance. Extensive experiments demonstrate that our model achieves superior performance against fourteen effective baselines across twenty-seven graph datasets, establishing it as a robust and generalizable model for graph-level tasks.

Graph Structure Learning (GSL) has recently garnered considerable attention due to its ability to optimize both the parameters of Graph Neural Networks (GNNs) and the computation graph structure simultaneously. Despite the proliferation of GSL methods developed in recent years, there is no standard experimental setting or fair comparison for performance evaluation, which creates a great obstacle to understanding the progress in this field. To fill this gap, we systematically analyze the performance of GSL in different scenarios and develop a comprehensive Graph Structure Learning Benchmark (GSLB) curated from 20 diverse graph datasets and 16 distinct GSL algorithms. Specifically, GSLB systematically investigates the characteristics of GSL in terms of three dimensions: effectiveness, robustness, and complexity. We comprehensively evaluate state-of-the-art GSL algorithms in node- and graph-level tasks, and analyze their performance in robust learning and model complexity. Further, to facilitate reproducible research, we have developed an easy-to-use library for training, evaluating, and visualizing different GSL methods. Empirical results of our extensive experiments demonstrate the ability of GSL and reveal its potential benefits on various downstream tasks, offering insights and opportunities for future research. The code of GSLB is available at: https://github.com/GSL-Benchmark/GSLB.

Graph Neural Networks (GNNs) have been widely adopted for drug discovery with molecular graphs. Nevertheless, current GNNs are mainly good at leveraging short-range interactions (SRI) but struggle to capture long-range interactions (LRI), both of which are crucial for determining molecular properties. To tackle this issue, we propose a method that implicitly projects all original atoms into a few Neural Atoms, which abstracts the collective information of atomic groups within a molecule. Specifically, we explicitly exchange the information among neural atoms and project them back to the atoms' representations as an enhancement. With this mechanism, neural atoms establish the communication channels among distant nodes, effectively reducing the interaction scope of arbitrary node pairs into a single hop. To provide an inspection of our method from a physical perspective, we reveal its connection with the traditional LRI calculation method, Ewald Summation. We conduct extensive experiments on three long-range graph benchmarks, covering both graph-level and link-level tasks on molecular graphs. We empirically justify that our method can be equipped with an arbitrary GNN and help to capture LRI.

Recent years have witnessed the great success of graph pre-training for graph representation learning. With hundreds of graph pre-training tasks proposed, integrating knowledge acquired from multiple pre-training tasks has become a popular research topic. In this paper, we identify two important collaborative processes for this topic: (1) select: how to select an optimal task combination from a given task pool based on their compatibility, and (2) weigh: how to weigh the selected tasks based on their importance. While there currently has been a lot of work focused on weighing, comparatively little effort has been devoted to selecting. This paper proposes a novel instance-level framework for integrating multiple graph pre-training tasks, Weigh And Select (WAS), where the two collaborative processes, weighing and selecting, are combined by decoupled siamese networks. Specifically, it first adaptively learns an optimal combination of tasks for each instance from a given task pool, based on which a customized instance-level task weighing strategy is learned. Extensive experiments on 16 graph datasets across node-level and graph-level downstream tasks have demonstrated that by combining a few simple but classical tasks, WAS can achieve comparable performance to other leading counterparts. The code is available at https://github.com/TianyuFan0504/WAS.

Graph representation learning is a fundamental research theme and can be generalized to benefit multiple downstream tasks from the node and link levels to the higher graph level. In practice, it is desirable to develop task-agnostic general graph representation learning methods that are typically trained in an unsupervised manner. Related research reveals that the power of graph representation learning methods depends on whether they can differentiate distinct graph structures as different embeddings and map isomorphic graphs to consistent embeddings (i.e., the isomorphic consistency of graph models). However, for task-agnostic general graph representation learning, existing unsupervised graph models, represented by the variational graph auto-encoders (VGAEs), can only keep the isomorphic consistency within the subgraphs of 1-hop neighborhoods and thus usually manifest inferior performance on the more difficult higher-level tasks. To overcome the limitations of existing unsupervised methods, in this paper, we propose the Isomorphic-Consistent VGAE (IsoC-VGAE) for multi-level task-agnostic graph representation learning. We first devise a decoding scheme to provide a theoretical guarantee of keeping the isomorphic consistency under the settings of unsupervised learning. We then propose the Inverse Graph Neural Network (Inv-GNN) decoder as its intuitive realization, which trains the model via reconstructing the GNN node embeddings with multi-hop neighborhood information, so as to maintain the high-order isomorphic consistency within the VGAE framework. We conduct extensive experiments on the representative graph learning tasks at different levels, including node classification, link prediction and graph classification, and the results verify that our proposed model generally outperforms both the state-of-the-art unsupervised methods and representative supervised methods.

Contrastive learning is an effective unsupervised method in graph representation learning, and the key component of contrastive learning lies in the construction of positive and negative samples. Previous methods usually utilize the proximity of nodes in the graph as the principle. Recently, the data-augmentation-based contrastive learning method has advanced to show great power in the visual domain, and some works extended this method from images to graphs. However, unlike the data augmentation on images, the data augmentation on graphs is far less intuitive and much harder to provide high-quality contrastive samples, which leaves much space for improvement. In this work, by introducing an adversarial graph view for data augmentation, we propose a simple but effective method, Adversarial Graph Contrastive Learning (ARIEL), to extract informative contrastive samples within reasonable constraints. We develop a new technique called information regularization for stable training and use subgraph sampling for scalability. We generalize our method from node-level contrastive learning to the graph level by treating each graph instance as a super-node. ARIEL consistently outperforms the current graph contrastive learning methods for both node-level and graph-level classification tasks on real-world datasets. We further demonstrate that ARIEL is more robust in the face of adversarial attacks.

Recent advancements in Large Language Models (LLMs) have transformed code generation from natural language queries. However, despite their extensive knowledge and ability to produce high-quality code, LLMs often struggle with contextual accuracy, particularly in evolving codebases. Current code search and retrieval methods frequently lack robustness in both the quality and contextual relevance of retrieved results, leading to suboptimal code generation. This paper introduces a novel knowledge graph-based approach to improve code search and retrieval leading to better quality of code generation in the context of repository-level tasks. The proposed approach represents code repositories as graphs, capturing structural and relational information for enhanced context-aware code generation. Our framework employs a hybrid approach for code retrieval to improve contextual relevance, track inter-file modular dependencies, generate more robust code and ensure consistency with the existing codebase. We benchmark the proposed approach on the Evolutionary Code Benchmark (EvoCodeBench) dataset, a repository-level code generation benchmark, and demonstrate that our method significantly outperforms the baseline approach. These findings suggest that knowledge graph based code generation could advance robust, context-sensitive coding assistance tools.

The advent of the "pre-train, prompt" paradigm has recently extended its generalization ability and data efficiency to graph representation learning, following its achievements in Natural Language Processing (NLP). Initial graph prompt tuning approaches tailored specialized prompting functions for Graph Neural Network (GNN) models pre-trained with specific strategies, such as edge prediction, thus limiting their applicability. In contrast, another pioneering line of research has explored universal prompting via adding prompts to the input graph's feature space, thereby removing the reliance on specific pre-training strategies. However, the necessity to add feature prompts to all nodes remains an open question. Motivated by findings from prompt tuning research in the NLP domain, which suggest that highly capable pre-trained models need less conditioning signal to achieve desired behaviors, we advocate for strategically incorporating necessary and lightweight feature prompts to certain graph nodes to enhance downstream task performance. This introduces a combinatorial optimization problem, requiring a policy to decide 1) which nodes to prompt and 2) what specific feature prompts to attach. We then address the problem by framing the prompt incorporation process as a sequential decision-making problem and propose our method, RELIEF, which employs Reinforcement Learning (RL) to optimize it. At each step, the RL agent selects a node (discrete action) and determines the prompt content (continuous action), aiming to maximize cumulative performance gain. Extensive experiments on graph and node-level tasks with various pre-training strategies in few-shot scenarios demonstrate that our RELIEF outperforms fine-tuning and other prompt-based approaches in classification performance and data efficiency.

Recent advances in Large Language Models (LLMs) have shown promise in function-level code generation, yet repository-level software engineering tasks remain challenging. Current solutions predominantly rely on proprietary LLM agents, which introduce unpredictability and limit accessibility, raising concerns about data privacy and model customization. This paper investigates whether open-source LLMs can effectively address repository-level tasks without requiring agent-based approaches. We demonstrate this is possible by enabling LLMs to comprehend functions and files within codebases through their semantic information and structural dependencies. To this end, we introduce Code Graph Models (CGMs), which integrate repository code graph structures into the LLM's attention mechanism and map node attributes to the LLM's input space using a specialized adapter. When combined with an agentless graph RAG framework, our approach achieves a 43.00% resolution rate on the SWE-bench Lite benchmark using the open-source Qwen2.5-72B model. This performance ranks first among open weight models, second among methods with open-source systems, and eighth overall, surpassing the previous best open-source model-based method by 12.33%.

Large Language Models (LLMs) excel in code generation yet struggle with modern AI software engineering tasks. Unlike traditional function-level or file-level coding tasks, AI software engineering requires not only basic coding proficiency but also advanced skills in managing and interacting with code repositories. However, existing methods often overlook the need for repository-level code understanding, which is crucial for accurately grasping the broader context and developing effective solutions. On this basis, we present RepoGraph, a plug-in module that manages a repository-level structure for modern AI software engineering solutions. RepoGraph offers the desired guidance and serves as a repository-wide navigation for AI software engineers. We evaluate RepoGraph on the SWE-bench by plugging it into four different methods of two lines of approaches, where RepoGraph substantially boosts the performance of all systems, leading to a new state-of-the-art among open-source frameworks. Our analyses also demonstrate the extensibility and flexibility of RepoGraph by testing on another repo-level coding benchmark, CrossCodeEval. Our code is available at https://github.com/ozyyshr/RepoGraph.

Robots are increasingly being used in dynamic environments like workplaces, hospitals, and homes. As a result, interactions with robots must be simple and intuitive, with robots perception adapting efficiently to human-induced changes. This paper presents a robot control architecture that addresses key challenges in human-robot interaction, with a particular focus on the dynamic creation and continuous update of the robot state representation. The architecture uses Large Language Models to integrate diverse information sources, including natural language commands, robotic skills representation, real-time dynamic semantic mapping of the perceived scene. This enables flexible and adaptive robotic behavior in complex, dynamic environments. Traditional robotic systems often rely on static, pre-programmed instructions and settings, limiting their adaptability to dynamic environments and real-time collaboration. In contrast, this architecture uses LLMs to interpret complex, high-level instructions and generate actionable plans that enhance human-robot collaboration. At its core, the system Perception Module generates and continuously updates a semantic scene graph using RGB-D sensor data, providing a detailed and structured representation of the environment. A particle filter is employed to ensure accurate object localization in dynamic, real-world settings. The Planner Module leverages this up-to-date semantic map to break down high-level tasks into sub-tasks and link them to robotic skills such as navigation, object manipulation (e.g., PICK and PLACE), and movement (e.g., GOTO). By combining real-time perception, state tracking, and LLM-driven communication and task planning, the architecture enhances adaptability, task efficiency, and human-robot collaboration in dynamic environments.

Artificial General Intelligence (AGI) has revolutionized numerous fields, yet its integration with graph data, a cornerstone in our interconnected world, remains nascent. This paper presents a pioneering survey on the emerging domain of graph prompts in AGI, addressing key challenges and opportunities in harnessing graph data for AGI applications. Despite substantial advancements in AGI across natural language processing and computer vision, the application to graph data is relatively underexplored. This survey critically evaluates the current landscape of AGI in handling graph data, highlighting the distinct challenges in cross-modality, cross-domain, and cross-task applications specific to graphs. Our work is the first to propose a unified framework for understanding graph prompt learning, offering clarity on prompt tokens, token structures, and insertion patterns in the graph domain. We delve into the intrinsic properties of graph prompts, exploring their flexibility, expressiveness, and interplay with existing graph models. A comprehensive taxonomy categorizes over 100 works in this field, aligning them with pre-training tasks across node-level, edge-level, and graph-level objectives. Additionally, we present, ProG, a Python library, and an accompanying website, to support and advance research in graph prompting. The survey culminates in a discussion of current challenges and future directions, offering a roadmap for research in graph prompting within AGI. Through this comprehensive analysis, we aim to catalyze further exploration and practical applications of AGI in graph data, underlining its potential to reshape AGI fields and beyond. ProG and the website can be accessed by https://github.com/WxxShirley/Awesome-Graph-Prompt, and https://github.com/sheldonresearch/ProG, respectively.

In this paper, we propose the first framework that enables solving graph learning tasks of all levels (node, edge and graph) and all types (generation, regression and classification) with one model. We first propose Latent Graph Diffusion (LGD), a generative model that can generate node, edge, and graph-level features of all categories simultaneously. We achieve this goal by embedding the graph structures and features into a latent space leveraging a powerful encoder which can also be decoded, then training a diffusion model in the latent space. LGD is also capable of conditional generation through a specifically designed cross-attention mechanism. Then we formulate prediction tasks including regression and classification as (conditional) generation, which enables our LGD to solve tasks of all levels and all types with provable guarantees. We verify the effectiveness of our framework with extensive experiments, where our models achieve state-of-the-art or highly competitive results across generation and regression tasks.

Graph neural networks (GNNs) are one of the most popular approaches to using deep learning on graph-structured data, and they have shown state-of-the-art performances on a variety of tasks. However, according to a recent study, a careful choice of pooling functions, which are used for the aggregation and readout operations in GNNs, is crucial for enabling GNNs to extrapolate. Without proper choices of pooling functions, which varies across tasks, GNNs completely fail to generalize to out-of-distribution data, while the number of possible choices grows exponentially with the number of layers. In this paper, we present GNP, a L^p norm-like pooling function that is trainable end-to-end for any given task. Notably, GNP generalizes most of the widely-used pooling functions. We verify experimentally that simply using GNP for every aggregation and readout operation enables GNNs to extrapolate well on many node-level, graph-level, and set-related tasks; and GNP sometimes performs even better than the best-performing choices among existing pooling functions.

Point clouds provide a flexible geometric representation suitable for countless applications in computer graphics; they also comprise the raw output of most 3D data acquisition devices. While hand-designed features on point clouds have long been proposed in graphics and vision, however, the recent overwhelming success of convolutional neural networks (CNNs) for image analysis suggests the value of adapting insight from CNN to the point cloud world. Point clouds inherently lack topological information so designing a model to recover topology can enrich the representation power of point clouds. To this end, we propose a new neural network module dubbed EdgeConv suitable for CNN-based high-level tasks on point clouds including classification and segmentation. EdgeConv acts on graphs dynamically computed in each layer of the network. It is differentiable and can be plugged into existing architectures. Compared to existing modules operating in extrinsic space or treating each point independently, EdgeConv has several appealing properties: It incorporates local neighborhood information; it can be stacked applied to learn global shape properties; and in multi-layer systems affinity in feature space captures semantic characteristics over potentially long distances in the original embedding. We show the performance of our model on standard benchmarks including ModelNet40, ShapeNetPart, and S3DIS.

While most network embedding techniques model the relative positions of nodes in a network, recently there has been significant interest in structural embeddings that model node role equivalences, irrespective of their distances to any specific nodes. We present PhUSION, a proximity-based unified framework for computing structural and positional node embeddings, which leverages well-established methods for calculating node proximity scores. Clarifying a point of contention in the literature, we show which step of PhUSION produces the different kinds of embeddings and what steps can be used by both. Moreover, by aggregating the PhUSION node embeddings, we obtain graph-level features that model information lost by previous graph feature learning and kernel methods. In a comprehensive empirical study with over 10 datasets, 4 tasks, and 35 methods, we systematically reveal successful design choices for node and graph-level machine learning with embeddings.

Privacy restrictions hinder the sharing of real-world Water Distribution Network (WDN) models, limiting the application of emerging data-driven machine learning, which typically requires extensive observations. To address this challenge, we propose the dataset DiTEC-WDN that comprises 36,000 unique scenarios simulated over either short-term (24 hours) or long-term (1 year) periods. We constructed this dataset using an automated pipeline that optimizes crucial parameters (e.g., pressure, flow rate, and demand patterns), facilitates large-scale simulations, and records discrete, synthetic but hydraulically realistic states under standard conditions via rule validation and post-hoc analysis. With a total of 228 million generated graph-based states, DiTEC-WDN can support a variety of machine-learning tasks, including graph-level, node-level, and link-level regression, as well as time-series forecasting. This contribution, released under a public license, encourages open scientific research in the critical water sector, eliminates the risk of exposing sensitive data, and fulfills the need for a large-scale water distribution network benchmark for study comparisons and scenario analysis.

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.

We present the Temporal Graph Benchmark (TGB), a collection of challenging and diverse benchmark datasets for realistic, reproducible, and robust evaluation of machine learning models on temporal graphs. TGB datasets are of large scale, spanning years in duration, incorporate both node and edge-level prediction tasks and cover a diverse set of domains including social, trade, transaction, and transportation networks. For both tasks, we design evaluation protocols based on realistic use-cases. We extensively benchmark each dataset and find that the performance of common models can vary drastically across datasets. In addition, on dynamic node property prediction tasks, we show that simple methods often achieve superior performance compared to existing temporal graph models. We believe that these findings open up opportunities for future research on temporal graphs. Finally, TGB provides an automated machine learning pipeline for reproducible and accessible temporal graph research, including data loading, experiment setup and performance evaluation. TGB will be maintained and updated on a regular basis and welcomes community feedback. TGB datasets, data loaders, example codes, evaluation setup, and leaderboards are publicly available at https://tgb.complexdatalab.com/.

Large Language Models (LLMs) have demonstrated remarkable generalization and instruction-following capabilities with instruction tuning. The advancements in LLMs and instruction tuning have led to the development of Large Vision-Language Models (LVLMs). However, the competency of the LLMs and instruction tuning have been less explored in the molecular domain. Thus, we propose LLaMo: Large Language Model-based Molecular graph assistant, which is an end-to-end trained large molecular graph-language model. To bridge the discrepancy between the language and graph modalities, we present the multi-level graph projector that transforms graph representations into graph tokens by abstracting the output representations of each GNN layer and motif representations with the cross-attention mechanism. We also introduce machine-generated molecular graph instruction data to instruction-tune the large molecular graph-language model for general-purpose molecule and language understanding. Our extensive experiments demonstrate that LLaMo shows the best performance on diverse tasks, such as molecular description generation, property prediction, and IUPAC name prediction. The code of LLaMo is available at https://github.com/mlvlab/LLaMo.

Knowledge distillation is a powerful technique for transferring knowledge from a pre-trained teacher model to a student model. However, the true potential of knowledge transfer has not been fully explored. Existing approaches primarily focus on distilling individual information or instance-level relationships, overlooking the valuable information embedded in token-level relationships, which may be particularly affected by the long-tail effects. To address the above limitations, we propose a novel method called Knowledge Distillation with Token-level Relationship Graph (TRG) that leverages the token-wise relational knowledge to enhance the performance of knowledge distillation. By employing TRG, the student model can effectively emulate higher-level semantic information from the teacher model, resulting in improved distillation results. To further enhance the learning process, we introduce a token-wise contextual loss called contextual loss, which encourages the student model to capture the inner-instance semantic contextual of the teacher model. We conduct experiments to evaluate the effectiveness of the proposed method against several state-of-the-art approaches. Empirical results demonstrate the superiority of TRG across various visual classification tasks, including those involving imbalanced data. Our method consistently outperforms the existing baselines, establishing a new state-of-the-art performance in the field of knowledge distillation.

Remote Sensing Large Multi-Modal Models (RSLMMs) are developing rapidly and showcase significant capabilities in remote sensing imagery (RSI) comprehension. However, due to the limitations of existing datasets, RSLMMs have shortcomings in understanding the rich semantic relations among objects in complex remote sensing scenes. To unlock RSLMMs' complex comprehension ability, we propose a large-scale instruction tuning dataset FIT-RS, containing 1,800,851 instruction samples. FIT-RS covers common interpretation tasks and innovatively introduces several complex comprehension tasks of escalating difficulty, ranging from relation reasoning to image-level scene graph generation. Based on FIT-RS, we build the FIT-RSFG benchmark. Furthermore, we establish a new benchmark to evaluate the fine-grained relation comprehension capabilities of LMMs, named FIT-RSRC. Based on combined instruction data, we propose SkySenseGPT, which achieves outstanding performance on both public datasets and FIT-RSFG, surpassing existing RSLMMs. We hope the FIT-RS dataset can enhance the relation comprehension capability of RSLMMs and provide a large-scale fine-grained data source for the remote sensing community. The dataset will be available at https://github.com/Luo-Z13/SkySenseGPT

While many EDA tasks already involve graph-based data, existing LLMs in EDA primarily either represent graphs as sequential text, or simply ignore graph-structured data that might be beneficial like dataflow graphs of RTL code. Recent studies have found that LLM performance suffers when graphs are represented as sequential text, and using additional graph information significantly boosts performance. To address these challenges, we introduce BRIDGES, a framework designed to incorporate graph modality into LLMs for EDA tasks. BRIDGES integrates an automated data generation workflow, a solution that combines graph modality with LLM, and a comprehensive evaluation suite. First, we establish an LLM-driven workflow to generate RTL and netlist-level data, converting them into dataflow and netlist graphs with function descriptions. This workflow yields a large-scale dataset comprising over 500,000 graph instances and more than 1.5 billion tokens. Second, we propose a lightweight cross-modal projector that encodes graph representations into text-compatible prompts, enabling LLMs to effectively utilize graph data without architectural modifications. Experimental results demonstrate 2x to 10x improvements across multiple tasks compared to text-only baselines, including accuracy in design retrieval, type prediction and perplexity in function description, with negligible computational overhead (<1% model weights increase and <30% additional runtime overhead). Even without additional LLM finetuning, our results outperform text-only by a large margin. We plan to release BRIDGES, including the dataset, models, and training flow.

Recent studies on Graph Convolutional Networks (GCNs) reveal that the initial node representations (i.e., the node representations before the first-time graph convolution) largely affect the final model performance. However, when learning the initial representation for a node, most existing work linearly combines the embeddings of node features, without considering the interactions among the features (or feature embeddings). We argue that when the node features are categorical, e.g., in many real-world applications like user profiling and recommender system, feature interactions usually carry important signals for predictive analytics. Ignoring them will result in suboptimal initial node representation and thus weaken the effectiveness of the follow-up graph convolution. In this paper, we propose a new GCN model named CatGCN, which is tailored for graph learning when the node features are categorical. Specifically, we integrate two ways of explicit interaction modeling into the learning of initial node representation, i.e., local interaction modeling on each pair of node features and global interaction modeling on an artificial feature graph. We then refine the enhanced initial node representations with the neighborhood aggregation-based graph convolution. We train CatGCN in an end-to-end fashion and demonstrate it on semi-supervised node classification. Extensive experiments on three tasks of user profiling (the prediction of user age, city, and purchase level) from Tencent and Alibaba datasets validate the effectiveness of CatGCN, especially the positive effect of performing feature interaction modeling before graph convolution.

We introduceGraphGPT, a novel self-supervised generative pre-trained model for graph learning based on the Graph Eulerian Transformer (GET). First, we propose GET, which combines a standard transformer encoder or decoder architecture with an innovative graph-to-sequence transformation method. This method converts graphs or sampled subgraphs into sequences of tokens representing nodes, edges, and attributes in a reversible manner using Eulerian paths. We pre-train GET using either of the two self-supervised tasks: next-token prediction (NTP) and scheduled masked-token prediction (SMTP). The pre-trained model is then fine-tuned for downstream tasks such as graph-, edge-, and node-level prediction. Despite its simplicity, GraphGPT achieves performance comparable to or surpassing state-of-the-art methods on multiple large-scale Open Graph Benchmark (OGB) datasets. It demonstrates exceptional results on the molecular property prediction dataset PCQM4Mv2 and the protein-protein interaction dataset ogbl-ppa. Notably, generative pre-training enables scaling GraphGPT to 2 billion parameters while maintaining performance gains - a breakthrough that overcomes the scalability limitations of traditional Graph Neural Networks (GNNs) and prior graph transformers (GTs). To advance research in graph foundation models and facilitate scientific discovery in chemistry, materials science, and related fields, we will release the source code (https://github.com/alibaba/graph-gpt) and pre-trained checkpoints.

Given the recent impressive accomplishments of language models (LMs) for code generation, we explore the use of LMs as adaptive mutation and crossover operators for an evolutionary neural architecture search (NAS) algorithm. While NAS still proves too difficult a task for LMs to succeed at solely through prompting, we find that the combination of evolutionary prompt engineering with soft prompt-tuning, a method we term EvoPrompting, consistently finds diverse and high performing models. We first demonstrate that EvoPrompting is effective on the computationally efficient MNIST-1D dataset, where EvoPrompting produces convolutional architecture variants that outperform both those designed by human experts and naive few-shot prompting in terms of accuracy and model size. We then apply our method to searching for graph neural networks on the CLRS Algorithmic Reasoning Benchmark, where EvoPrompting is able to design novel architectures that outperform current state-of-the-art models on 21 out of 30 algorithmic reasoning tasks while maintaining similar model size. EvoPrompting is successful at designing accurate and efficient neural network architectures across a variety of machine learning tasks, while also being general enough for easy adaptation to other tasks beyond neural network design.

We present a novel edge-level ego-network encoding for learning on graphs that can boost Message Passing Graph Neural Networks (MP-GNNs) by providing additional node and edge features or extending message-passing formats. The proposed encoding is sufficient to distinguish Strongly Regular Graphs, a family of challenging 3-WL equivalent graphs. We show theoretically that such encoding is more expressive than node-based sub-graph MP-GNNs. In an empirical evaluation on four benchmarks with 10 graph datasets, our results match or improve previous baselines on expressivity, graph classification, graph regression, and proximity tasks -- while reducing memory usage by 18.1x in certain real-world settings.

Graph Neural Networks (GNNs) have been extensively used for mining graph-structured data with impressive performance. However, because these traditional GNNs do not distinguish among various downstream tasks, embeddings embedded by them are not always effective. Intuitively, paths in a graph imply different semantics for different downstream tasks. Inspired by this, we design a novel GNN solution, namely Customized Graph Neural Network with Path Reweighting (CustomGNN for short). Specifically, the proposed CustomGNN can automatically learn the high-level semantics for specific downstream tasks to highlight semantically relevant paths as well to filter out task-irrelevant noises in a graph. Furthermore, we empirically analyze the semantics learned by CustomGNN and demonstrate its ability to avoid the three inherent problems in traditional GNNs, i.e., over-smoothing, poor robustness, and overfitting. In experiments with the node classification task, CustomGNN achieves state-of-the-art accuracies on three standard graph datasets and four large graph datasets. The source code of the proposed CustomGNN is available at https://github.com/cjpcool/CustomGNN.

We report a flexible language-model based deep learning strategy, applied here to solve complex forward and inverse problems in protein modeling, based on an attention neural network that integrates transformer and graph convolutional architectures in a causal multi-headed graph mechanism, to realize a generative pretrained model. The model is applied to predict secondary structure content (per-residue level and overall content), protein solubility, and sequencing tasks. Further trained on inverse tasks, the model is rendered capable of designing proteins with these properties as target features. The model is formulated as a general framework, completely prompt-based, and can be adapted for a variety of downstream tasks. We find that adding additional tasks yields emergent synergies that the model exploits in improving overall performance, beyond what would be possible by training a model on each dataset alone. Case studies are presented to validate the method, yielding protein designs specifically focused on structural proteins, but also exploring the applicability in the design of soluble, antimicrobial biomaterials. While our model is trained to ultimately perform 8 distinct tasks, with available datasets it can be extended to solve additional problems. In a broader sense, this work illustrates a form of multiscale modeling that relates a set of ultimate building blocks (here, byte-level utf8 characters) to complex output. This materiomic scheme captures complex emergent relationships between universal building block and resulting properties via a synergizing learning capacity to express a set of potentialities embedded in the knowledge used in training, via the interplay of universality and diversity.

Graph representation learning nowadays becomes fundamental in analyzing graph-structured data. Inspired by recent success of contrastive methods, in this paper, we propose a novel framework for unsupervised graph representation learning by leveraging a contrastive objective at the node level. Specifically, we generate two graph views by corruption and learn node representations by maximizing the agreement of node representations in these two views. To provide diverse node contexts for the contrastive objective, we propose a hybrid scheme for generating graph views on both structure and attribute levels. Besides, we provide theoretical justification behind our motivation from two perspectives, mutual information and the classical triplet loss. We perform empirical experiments on both transductive and inductive learning tasks using a variety of real-world datasets. Experimental experiments demonstrate that despite its simplicity, our proposed method consistently outperforms existing state-of-the-art methods by large margins. Moreover, our unsupervised method even surpasses its supervised counterparts on transductive tasks, demonstrating its great potential in real-world applications.

Existing visual place recognition (VPR) datasets predominantly rely on vehicle-mounted imagery, lack multimodal diversity and underrepresent dense, mixed-use street-level spaces, especially in non-Western urban contexts. To address these gaps, we introduce MMS-VPR, a large-scale multimodal dataset for street-level place recognition in complex, pedestrian-only environments. The dataset comprises 78,575 annotated images and 2,512 video clips captured across 207 locations in a ~70,800 m^2 open-air commercial district in Chengdu, China. Each image is labeled with precise GPS coordinates, timestamp, and textual metadata, and covers varied lighting conditions, viewpoints, and timeframes. MMS-VPR follows a systematic and replicable data collection protocol with minimal device requirements, lowering the barrier for scalable dataset creation. Importantly, the dataset forms an inherent spatial graph with 125 edges, 81 nodes, and 1 subgraph, enabling structure-aware place recognition. We further define two application-specific subsets -- Dataset_Edges and Dataset_Points -- to support fine-grained and graph-based evaluation tasks. Extensive benchmarks using conventional VPR models, graph neural networks, and multimodal baselines show substantial improvements when leveraging multimodal and structural cues. MMS-VPR facilitates future research at the intersection of computer vision, geospatial understanding, and multimodal reasoning. The dataset is publicly available at https://huggingface.co/datasets/Yiwei-Ou/MMS-VPR.

Recently, pre-trained foundation models have enabled significant advancements in multiple fields. In molecular machine learning, however, where datasets are often hand-curated, and hence typically small, the lack of datasets with labeled features, and codebases to manage those datasets, has hindered the development of foundation models. In this work, we present seven novel datasets categorized by size into three distinct categories: ToyMix, LargeMix and UltraLarge. These datasets push the boundaries in both the scale and the diversity of supervised labels for molecular learning. They cover nearly 100 million molecules and over 3000 sparsely defined tasks, totaling more than 13 billion individual labels of both quantum and biological nature. In comparison, our datasets contain 300 times more data points than the widely used OGB-LSC PCQM4Mv2 dataset, and 13 times more than the quantum-only QM1B dataset. In addition, to support the development of foundational models based on our proposed datasets, we present the Graphium graph machine learning library which simplifies the process of building and training molecular machine learning models for multi-task and multi-level molecular datasets. Finally, we present a range of baseline results as a starting point of multi-task and multi-level training on these datasets. Empirically, we observe that performance on low-resource biological datasets show improvement by also training on large amounts of quantum data. This indicates that there may be potential in multi-task and multi-level training of a foundation model and fine-tuning it to resource-constrained downstream tasks.

We tackle real-world problems with complex structures beyond the pixel-based game or simulator. We formulate it as a few-shot reinforcement learning problem where a task is characterized by a subtask graph that defines a set of subtasks and their dependencies that are unknown to the agent. Different from the previous meta-rl methods trying to directly infer the unstructured task embedding, our multi-task subtask graph inferencer (MTSGI) first infers the common high-level task structure in terms of the subtask graph from the training tasks, and use it as a prior to improve the task inference in testing. Our experiment results on 2D grid-world and complex web navigation domains show that the proposed method can learn and leverage the common underlying structure of the tasks for faster adaptation to the unseen tasks than various existing algorithms such as meta reinforcement learning, hierarchical reinforcement learning, and other heuristic agents.

Graph Neural Networks (GNNs) have demonstrated superior performance on various graph learning tasks, including recommendation, where they leverage user-item collaborative filtering signals in graphs. However, theoretical formulations of their capability are scarce, despite their empirical effectiveness in state-of-the-art recommender models. Recently, research has explored the expressiveness of GNNs in general, demonstrating that message passing GNNs are at most as powerful as the Weisfeiler-Lehman test, and that GNNs combined with random node initialization are universal. Nevertheless, the concept of "expressiveness" for GNNs remains vaguely defined. Most existing works adopt the graph isomorphism test as the metric of expressiveness, but this graph-level task may not effectively assess a model's ability in recommendation, where the objective is to distinguish nodes of different closeness. In this paper, we provide a comprehensive theoretical analysis of the expressiveness of GNNs in recommendation, considering three levels of expressiveness metrics: graph isomorphism (graph-level), node automorphism (node-level), and topological closeness (link-level). We propose the topological closeness metric to evaluate GNNs' ability to capture the structural distance between nodes, which aligns closely with the objective of recommendation. To validate the effectiveness of this new metric in evaluating recommendation performance, we introduce a learning-less GNN algorithm that is optimal on the new metric and can be optimal on the node-level metric with suitable modification. We conduct extensive experiments comparing the proposed algorithm against various types of state-of-the-art GNN models to explore the explainability of the new metric in the recommendation task. For reproducibility, implementation codes are available at https://github.com/HKUDS/GTE.

Graph representation learning on Analog-Mixed Signal (AMS) circuits is crucial for various downstream tasks, e.g., parasitic estimation. However, the scarcity of design data, the unbalanced distribution of labels, and the inherent diversity of circuit implementations pose significant challenges to learning robust and transferable circuit representations. To address these limitations, we propose CircuitGCL, a novel graph contrastive learning framework that integrates representation scattering and label rebalancing to enhance transferability across heterogeneous circuit graphs. CircuitGCL employs a self-supervised strategy to learn topology-invariant node embeddings through hyperspherical representation scattering, eliminating dependency on large-scale data. Simultaneously, balanced mean squared error (BMSE) and balanced softmax cross-entropy (BSCE) losses are introduced to mitigate label distribution disparities between circuits, enabling robust and transferable parasitic estimation. Evaluated on parasitic capacitance estimation (edge-level task) and ground capacitance classification (node-level task) across TSMC 28nm AMS designs, CircuitGCL outperforms all state-of-the-art (SOTA) methods, with the R^2 improvement of 33.64% sim 44.20% for edge regression and F1-score gain of 0.9times sim 2.1times for node classification. Our code is available at https://github.com/ShenShan123/CircuitGCL.

Representation learning is a critical ingredient for natural language processing systems. Recent Transformer language models like BERT learn powerful textual representations, but these models are targeted towards token- and sentence-level training objectives and do not leverage information on inter-document relatedness, which limits their document-level representation power. For applications on scientific documents, such as classification and recommendation, the embeddings power strong performance on end tasks. We propose SPECTER, a new method to generate document-level embedding of scientific documents based on pretraining a Transformer language model on a powerful signal of document-level relatedness: the citation graph. Unlike existing pretrained language models, SPECTER can be easily applied to downstream applications without task-specific fine-tuning. Additionally, to encourage further research on document-level models, we introduce SciDocs, a new evaluation benchmark consisting of seven document-level tasks ranging from citation prediction, to document classification and recommendation. We show that SPECTER outperforms a variety of competitive baselines on the benchmark.

While great success has been achieved in building vision models with Contrastive Language-Image Pre-training (CLIP) over internet-scale image-text pairs, building transferable Graph Neural Networks (GNNs) with CLIP pipeline is challenging because of the scarcity of labeled data and text supervision, different levels of downstream tasks, and the conceptual gaps between domains. In this work, to address these issues, we propose a multi-modal prompt learning paradigm to effectively adapt pre-trained GNN to downstream tasks and data, given only a few semantically labeled samples, each with extremely weak text supervision. Our new paradigm embeds the graphs directly in the same space as the Large Language Models (LLMs) by learning both graph prompts and text prompts simultaneously. We demonstrate the superior performance of our paradigm in few-shot, multi-task-level, and cross-domain settings. Moreover, we build the first CLIP-style zero-shot classification prototype that can generalize GNNs to unseen classes with extremely weak text supervision. The code is available at https://github.com/Violet24K/Morpher.

This paper presents DWIE, the 'Deutsche Welle corpus for Information Extraction', a newly created multi-task dataset that combines four main Information Extraction (IE) annotation subtasks: (i) Named Entity Recognition (NER), (ii) Coreference Resolution, (iii) Relation Extraction (RE), and (iv) Entity Linking. DWIE is conceived as an entity-centric dataset that describes interactions and properties of conceptual entities on the level of the complete document. This contrasts with currently dominant mention-driven approaches that start from the detection and classification of named entity mentions in individual sentences. Further, DWIE presented two main challenges when building and evaluating IE models for it. First, the use of traditional mention-level evaluation metrics for NER and RE tasks on entity-centric DWIE dataset can result in measurements dominated by predictions on more frequently mentioned entities. We tackle this issue by proposing a new entity-driven metric that takes into account the number of mentions that compose each of the predicted and ground truth entities. Second, the document-level multi-task annotations require the models to transfer information between entity mentions located in different parts of the document, as well as between different tasks, in a joint learning setting. To realize this, we propose to use graph-based neural message passing techniques between document-level mention spans. Our experiments show an improvement of up to 5.5 F1 percentage points when incorporating neural graph propagation into our joint model. This demonstrates DWIE's potential to stimulate further research in graph neural networks for representation learning in multi-task IE. We make DWIE publicly available at https://github.com/klimzaporojets/DWIE.

We present the Power Law Graph Transformer, a transformer model with well defined deductive and inductive tasks for prediction and representation learning. The deductive task learns the dataset level (global) and instance level (local) graph structures in terms of learnable power law distribution parameters. The inductive task outputs the prediction probabilities using the deductive task output, similar to a transductive model. We trained our model with Turkish-English and Portuguese-English datasets from TED talk transcripts for machine translation and compared the model performance and characteristics to a transformer model with scaled dot product attention trained on the same experimental setup. We report BLEU scores of 17.79 and 28.33 on the Turkish-English and Portuguese-English translation tasks with our model, respectively. We also show how a duality between a quantization set and N-dimensional manifold representation can be leveraged to transform between local and global deductive-inductive outputs using successive application of linear and non-linear transformations end-to-end.

In the midst of widespread misinformation and disinformation through social media and the proliferation of AI-generated texts, it has become increasingly difficult for people to validate and trust information they encounter. Many fact-checking approaches and tools have been developed, but they often lack appropriate explainability or granularity to be useful in various contexts. A text validation method that is easy to use, accessible, and can perform fine-grained evidence attribution has become crucial. More importantly, building user trust in such a method requires presenting the rationale behind each prediction, as research shows this significantly influences people's belief in automated systems. It is also paramount to localize and bring users' attention to the specific problematic content, instead of providing simple blanket labels. In this paper, we present ClaimVer, a human-centric framework tailored to meet users' informational and verification needs by generating rich annotations and thereby reducing cognitive load. Designed to deliver comprehensive evaluations of texts, it highlights each claim, verifies it against a trusted knowledge graph (KG), presents the evidence, and provides succinct, clear explanations for each claim prediction. Finally, our framework introduces an attribution score, enhancing applicability across a wide range of downstream tasks.

Graphs are a powerful tool for representing and analyzing complex relationships in real-world applications such as social networks, recommender systems, and computational finance. Reasoning on graphs is essential for drawing inferences about the relationships between entities in a complex system, and to identify hidden patterns and trends. Despite the remarkable progress in automated reasoning with natural text, reasoning on graphs with large language models (LLMs) remains an understudied problem. In this work, we perform the first comprehensive study of encoding graph-structured data as text for consumption by LLMs. We show that LLM performance on graph reasoning tasks varies on three fundamental levels: (1) the graph encoding method, (2) the nature of the graph task itself, and (3) interestingly, the very structure of the graph considered. These novel results provide valuable insight on strategies for encoding graphs as text. Using these insights we illustrate how the correct choice of encoders can boost performance on graph reasoning tasks inside LLMs by 4.8% to 61.8%, depending on the task.

In numerous artificial intelligence applications, the collaborative efforts of multiple intelligent agents are imperative for the successful attainment of target objectives. To enhance coordination among these agents, a distributed communication framework is often employed. However, indiscriminate information sharing among all agents can be resource-intensive, and the adoption of manually pre-defined communication architectures imposes constraints on inter-agent communication, thus limiting the potential for effective collaboration. Moreover, the communication framework often remains static during inference, which may result in sustained high resource consumption, as in most cases, only key decisions necessitate information sharing among agents. In this study, we introduce a novel approach wherein we conceptualize the communication architecture among agents as a learnable graph. We formulate this problem as the task of determining the communication graph while enabling the architecture parameters to update normally, thus necessitating a bi-level optimization process. Utilizing continuous relaxation of the graph representation and incorporating attention units, our proposed approach, CommFormer, efficiently optimizes the communication graph and concurrently refines architectural parameters through gradient descent in an end-to-end manner. Additionally, we introduce a temporal gating mechanism for each agent, enabling dynamic decisions on whether to receive shared information at a given time, based on current observations, thus improving decision-making efficiency. Extensive experiments on a variety of cooperative tasks substantiate the robustness of our model across diverse cooperative scenarios, where agents are able to develop more coordinated and sophisticated strategies regardless of changes in the number of agents.

Despite the recent advancements of vision-language-action (VLA) models on a variety of robotics tasks, they suffer from critical issues such as poor generalizability to unseen tasks, due to their reliance on behavior cloning exclusively from successful rollouts. Furthermore, they are typically fine-tuned to replicate demonstrations collected by experts under different settings, thus introducing distribution bias and limiting their adaptability to diverse manipulation objectives, such as efficiency, safety, and task completion. To bridge this gap, we introduce GRAPE: Generalizing Robot Policy via Preference Alignment. Specifically, GRAPE aligns VLAs on a trajectory level and implicitly models reward from both successful and failure trials to boost generalizability to diverse tasks. Moreover, GRAPE breaks down complex manipulation tasks to independent stages and automatically guides preference modeling through customized spatiotemporal constraints with keypoints proposed by a large vision-language model. Notably, these constraints are flexible and can be customized to align the model with varying objectives, such as safety, efficiency, or task success. We evaluate GRAPE across a diverse array of tasks in both real-world and simulated environments. Experimental results demonstrate that GRAPE enhances the performance of state-of-the-art VLA models, increasing success rates on in-domain and unseen manipulation tasks by 51.79% and 60.36%, respectively. Additionally, GRAPE can be aligned with various objectives, such as safety and efficiency, reducing collision rates by 44.31% and rollout step-length by 11.15%, respectively. All code, models, and data are available at https://grape-vla.github.io/

Towards building comprehensive real-world visual perception systems, we propose and study a new problem called panoptic scene graph generation (PVSG). PVSG relates to the existing video scene graph generation (VidSGG) problem, which focuses on temporal interactions between humans and objects grounded with bounding boxes in videos. However, the limitation of bounding boxes in detecting non-rigid objects and backgrounds often causes VidSGG to miss key details crucial for comprehensive video understanding. In contrast, PVSG requires nodes in scene graphs to be grounded by more precise, pixel-level segmentation masks, which facilitate holistic scene understanding. To advance research in this new area, we contribute the PVSG dataset, which consists of 400 videos (289 third-person + 111 egocentric videos) with a total of 150K frames labeled with panoptic segmentation masks as well as fine, temporal scene graphs. We also provide a variety of baseline methods and share useful design practices for future work.

This report introduces Aquarius, a family of industry-level video generation models for marketing scenarios designed for thousands-xPU clusters and models with hundreds of billions of parameters. Leveraging efficient engineering architecture and algorithmic innovation, Aquarius demonstrates exceptional performance in high-fidelity, multi-aspect-ratio, and long-duration video synthesis. By disclosing the framework's design details, we aim to demystify industrial-scale video generation systems and catalyze advancements in the generative video community. The Aquarius framework consists of five components: Distributed Graph and Video Data Processing Pipeline: Manages tens of thousands of CPUs and thousands of xPUs via automated task distribution, enabling efficient video data processing. Additionally, we are about to open-source the entire data processing framework named "Aquarius-Datapipe". Model Architectures for Different Scales: Include a Single-DiT architecture for 2B models and a Multimodal-DiT architecture for 13.4B models, supporting multi-aspect ratios, multi-resolution, and multi-duration video generation. High-Performance infrastructure designed for video generation model training: Incorporating hybrid parallelism and fine-grained memory optimization strategies, this infrastructure achieves 36% MFU at large scale. Multi-xPU Parallel Inference Acceleration: Utilizes diffusion cache and attention optimization to achieve a 2.35x inference speedup. Multiple marketing-scenarios applications: Including image-to-video, text-to-video (avatar), video inpainting and video personalization, among others. More downstream applications and multi-dimensional evaluation metrics will be added in the upcoming version updates.

Recent developments in Large Language Model (LLM)-based agents have shown impressive capabilities spanning multiple domains, exemplified by deep research systems that demonstrate superior performance on complex information-seeking and synthesis tasks. While general-purpose deep research agents have shown impressive capabilities, they struggle significantly with medical domain challenges, as evidenced by leading proprietary systems achieving limited accuracy on complex medical benchmarks. The key limitations are: (1) the model lacks sufficient dense medical knowledge for clinical reasoning, and (2) the framework is constrained by the absence of specialized retrieval tools tailored for medical contexts.We present a medical deep research agent that addresses these challenges through two core innovations. First, we develop a novel data synthesis framework using medical knowledge graphs, extracting the longest chains from subgraphs around rare medical entities to generate complex multi-hop question-answer pairs. Second, we integrate a custom-built private medical retrieval engine alongside general-purpose tools, enabling accurate medical information synthesis. Our approach generates 2100+ diverse trajectories across 12 medical specialties, each averaging 4.2 tool interactions.Through a two-stage training paradigm combining supervised fine-tuning and online reinforcement learning with composite rewards, our MedResearcher-R1-32B model demonstrates exceptional performance, establishing new state-of-the-art results on medical benchmarks while maintaining competitive performance on general deep research tasks. Our work demonstrates that strategic domain-specific innovations in architecture, tool design, and training data construction can enable smaller open-source models to outperform much larger proprietary systems in specialized domains.

Zero-shot learning relies on semantic class representations such as hand-engineered attributes or learned embeddings to predict classes without any labeled examples. We propose to learn class representations by embedding nodes from common sense knowledge graphs in a vector space. Common sense knowledge graphs are an untapped source of explicit high-level knowledge that requires little human effort to apply to a range of tasks. To capture the knowledge in the graph, we introduce ZSL-KG, a general-purpose framework with a novel transformer graph convolutional network (TrGCN) for generating class representations. Our proposed TrGCN architecture computes non-linear combinations of node neighbourhoods. Our results show that ZSL-KG improves over existing WordNet-based methods on five out of six zero-shot benchmark datasets in language and vision.

Large language models (LLMs) have achieved impressive success across several fields, but their proficiency in understanding and resolving complex graph problems is less explored. To bridge this gap, we introduce GraphInstruct, a novel and comprehensive instruction-tuning dataset designed to equip language models with the ability to tackle a broad spectrum of graph problems using explicit reasoning paths. Utilizing GraphInstruct, we build GraphWiz, an open-source language model capable of resolving various graph problem types while generating clear reasoning processes. To enhance the model's capability and reliability, we incorporate the Direct Preference Optimization (DPO) framework into the graph problem-solving context. The enhanced model, GraphWiz-DPO, achieves an average accuracy of 65% across nine tasks with different complexity levels, surpassing GPT-4 which has an average accuracy of 43.8%. Moreover, our research delves into the delicate balance between training data volume and model performance, highlighting the potential for overfitting with increased data. We also explore the transferability of the model's reasoning ability across different graph tasks, indicating the model's adaptability and practical application potential. Our investigation offers a new blueprint and valuable insights for developing LLMs specialized in graph reasoning and problem-solving.

Transformer large language models (LLMs) have sparked admiration for their exceptional performance on tasks that demand intricate multi-step reasoning. Yet, these models simultaneously show failures on surprisingly trivial problems. This begs the question: Are these errors incidental, or do they signal more substantial limitations? In an attempt to demystify Transformers, we investigate the limits of these models across three representative compositional tasks -- multi-digit multiplication, logic grid puzzles, and a classic dynamic programming problem. These tasks require breaking problems down into sub-steps and synthesizing these steps into a precise answer. We formulate compositional tasks as computation graphs to systematically quantify the level of complexity, and break down reasoning steps into intermediate sub-procedures. Our empirical findings suggest that Transformers solve compositional tasks by reducing multi-step compositional reasoning into linearized subgraph matching, without necessarily developing systematic problem-solving skills. To round off our empirical study, we provide theoretical arguments on abstract multi-step reasoning problems that highlight how Transformers' performance will rapidly decay with increased task complexity.

Humans possess an extraordinary ability to understand and execute complex manipulation tasks by interpreting abstract instruction manuals. For robots, however, this capability remains a substantial challenge, as they cannot interpret abstract instructions and translate them into executable actions. In this paper, we present Manual2Skill, a novel framework that enables robots to perform complex assembly tasks guided by high-level manual instructions. Our approach leverages a Vision-Language Model (VLM) to extract structured information from instructional images and then uses this information to construct hierarchical assembly graphs. These graphs represent parts, subassemblies, and the relationships between them. To facilitate task execution, a pose estimation model predicts the relative 6D poses of components at each assembly step. At the same time, a motion planning module generates actionable sequences for real-world robotic implementation. We demonstrate the effectiveness of Manual2Skill by successfully assembling several real-world IKEA furniture items. This application highlights its ability to manage long-horizon manipulation tasks with both efficiency and precision, significantly enhancing the practicality of robot learning from instruction manuals. This work marks a step forward in advancing robotic systems capable of understanding and executing complex manipulation tasks in a manner akin to human capabilities.

Although Large Language Models (LLMs) have demonstrated remarkable progress, their proficiency in graph-related tasks remains notably limited, hindering the development of truly general-purpose models. Previous attempts, including pretraining graph foundation models or employing supervised fine-tuning, often face challenges such as the scarcity of large-scale, universally represented graph data. We introduce G1, a simple yet effective approach demonstrating that Reinforcement Learning (RL) on synthetic graph-theoretic tasks can significantly scale LLMs' graph reasoning abilities. To enable RL training, we curate Erd\~os, the largest graph reasoning dataset to date comprising 50 diverse graph-theoretic tasks of varying difficulty levels, 100k training data and 5k test data, all drived from real-world graphs. With RL on Erd\~os, G1 obtains substantial improvements in graph reasoning, where our finetuned 3B model even outperforms Qwen2.5-72B-Instruct (24x size). RL-trained models also show strong zero-shot generalization to unseen tasks, domains, and graph encoding schemes, including other graph-theoretic benchmarks as well as real-world node classification and link prediction tasks, without compromising general reasoning abilities. Our findings offer an efficient, scalable path for building strong graph reasoners by finetuning LLMs with RL on graph-theoretic tasks, which combines the strengths of pretrained LLM capabilities with abundant, automatically generated synthetic data, suggesting that LLMs possess graph understanding abilities that RL can elicit successfully.