Daily Papers

Microbes have a profound impact on our health and environment, but our understanding of the diversity and function of microbial communities is severely limited. Through DNA sequencing of microbial communities (metagenomics), DNA fragments (reads) of the individual microbes can be obtained, which through assembly graphs can be combined into long contiguous DNA sequences (contigs). Given the complexity of microbial communities, single contig microbial genomes are rarely obtained. Instead, contigs are eventually clustered into bins, with each bin ideally making up a full genome. This process is referred to as metagenomic binning. Current state-of-the-art techniques for metagenomic binning rely only on the local features for the individual contigs. These techniques therefore fail to exploit the similarities between contigs as encoded by the assembly graph, in which the contigs are organized. In this paper, we propose to use Graph Neural Networks (GNNs) to leverage the assembly graph when learning contig representations for metagenomic binning. Our method, VaeG-Bin, combines variational autoencoders for learning latent representations of the individual contigs, with GNNs for refining these representations by taking into account the neighborhood structure of the contigs in the assembly graph. We explore several types of GNNs and demonstrate that VaeG-Bin recovers more high-quality genomes than other state-of-the-art binners on both simulated and real-world datasets.

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.

This paper introduces a generative model designed for multimodal control over text-to-image foundation generative AI models such as Stable Diffusion, specifically tailored for engineering design synthesis. Our model proposes parametric, image, and text control modalities to enhance design precision and diversity. Firstly, it handles both partial and complete parametric inputs using a diffusion model that acts as a design autocomplete co-pilot, coupled with a parametric encoder to process the information. Secondly, the model utilizes assembly graphs to systematically assemble input component images, which are then processed through a component encoder to capture essential visual data. Thirdly, textual descriptions are integrated via CLIP encoding, ensuring a comprehensive interpretation of design intent. These diverse inputs are synthesized through a multimodal fusion technique, creating a joint embedding that acts as the input to a module inspired by ControlNet. This integration allows the model to apply robust multimodal control to foundation models, facilitating the generation of complex and precise engineering designs. This approach broadens the capabilities of AI-driven design tools and demonstrates significant advancements in precise control based on diverse data modalities for enhanced design generation.

Assistants on assembly tasks have a large potential to benefit humans from everyday tasks to industrial settings. However, no testbeds support application-oriented system evaluation in a practical setting, especially in assembly. To foster the development, we propose a new multimodal QA dataset on assembly activities. Our dataset, ProMQA-Assembly, consists of 391 QA pairs that require the multimodal understanding of human-activity recordings and their instruction manuals in an online-style manner. In the development, we adopt a semi-automated QA annotation approach, where LLMs generate candidates and humans verify them, as a cost-effective method, and further improve it by integrating fine-grained action labels to diversify question types. Furthermore, we create instruction task graphs for the target tasks of assembling toy vehicles. These newly created task graphs are used in our benchmarking experiment, as well as to facilitate the human verification process in the QA annotation. Utilizing our dataset, we benchmark models, including competitive proprietary multimodal models. Our results suggest great room for improvement for the current models. We believe our new evaluation dataset can contribute to the further development of procedural-activity assistants.

Generative models are now used to create a variety of high-quality digital artifacts. Yet their use in designing physical objects has received far less attention. In this paper, we advocate for the construction toy, LEGO, as a platform for developing generative models of sequential assembly. We develop a generative model based on graph-structured neural networks that can learn from human-built structures and produce visually compelling designs. Our code is released at: https://github.com/uoguelph-mlrg/GenerativeLEGO.

Shape primitive abstraction, which decomposes complex 3D shapes into simple geometric elements, plays a crucial role in human visual cognition and has broad applications in computer vision and graphics. While recent advances in 3D content generation have shown remarkable progress, existing primitive abstraction methods either rely on geometric optimization with limited semantic understanding or learn from small-scale, category-specific datasets, struggling to generalize across diverse shape categories. We present PrimitiveAnything, a novel framework that reformulates shape primitive abstraction as a primitive assembly generation task. PrimitiveAnything includes a shape-conditioned primitive transformer for auto-regressive generation and an ambiguity-free parameterization scheme to represent multiple types of primitives in a unified manner. The proposed framework directly learns the process of primitive assembly from large-scale human-crafted abstractions, enabling it to capture how humans decompose complex shapes into primitive elements. Through extensive experiments, we demonstrate that PrimitiveAnything can generate high-quality primitive assemblies that better align with human perception while maintaining geometric fidelity across diverse shape categories. It benefits various 3D applications and shows potential for enabling primitive-based user-generated content (UGC) in games. Project page: https://primitiveanything.github.io

While text-3D editing has made significant strides in leveraging score distillation sampling, emerging approaches still fall short in delivering separable, precise and consistent outcomes that are vital to content creation. In response, we introduce FocalDreamer, a framework that merges base shape with editable parts according to text prompts for fine-grained editing within desired regions. Specifically, equipped with geometry union and dual-path rendering, FocalDreamer assembles independent 3D parts into a complete object, tailored for convenient instance reuse and part-wise control. We propose geometric focal loss and style consistency regularization, which encourage focal fusion and congruent overall appearance. Furthermore, FocalDreamer generates high-fidelity geometry and PBR textures which are compatible with widely-used graphics engines. Extensive experiments have highlighted the superior editing capabilities of FocalDreamer in both quantitative and qualitative evaluations.

We present Assembler, a scalable and generalizable framework for 3D part assembly that reconstructs complete objects from input part meshes and a reference image. Unlike prior approaches that mostly rely on deterministic part pose prediction and category-specific training, Assembler is designed to handle diverse, in-the-wild objects with varying part counts, geometries, and structures. It addresses the core challenges of scaling to general 3D part assembly through innovations in task formulation, representation, and data. First, Assembler casts part assembly as a generative problem and employs diffusion models to sample plausible configurations, effectively capturing ambiguities arising from symmetry, repeated parts, and multiple valid assemblies. Second, we introduce a novel shape-centric representation based on sparse anchor point clouds, enabling scalable generation in Euclidean space rather than SE(3) pose prediction. Third, we construct a large-scale dataset of over 320K diverse part-object assemblies using a synthesis and filtering pipeline built on existing 3D shape repositories. Assembler achieves state-of-the-art performance on PartNet and is the first to demonstrate high-quality assembly for complex, real-world objects. Based on Assembler, we further introduce an interesting part-aware 3D modeling system that generates high-resolution, editable objects from images, demonstrating potential for interactive and compositional design. Project page: https://assembler3d.github.io

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.

The CAD design process includes a number of repetitive steps when creating assemblies. This issue is compounded when engineering whole product lines or design families, as steps like inserting parts common to all variations, such as fasteners and product-integral base parts, get repeated numerous times. This makes creating designs time-, and as a result, cost-intensive. While many CAD software packages have APIs, the effort of creating use-case specific plugins to automate creation of assemblies usually outweighs the benefit. We developed a plugin for the CAD software package "Fusion 360" which tackles this issue. The plugin adds several graphical interfaces to Fusion 360 that allow parts to be annotated with types, subtype hierarchies to be managed, and requests to synthesize assembly programs for assemblies to be posed. The plugin is use-case agnostic and is able to generate arbitrary open kinematic chain structures. We envision engineers working with CAD software being able to make designed parts reusable and automate the generation of different design alternatives as well as whole product lines.

As hardware design complexity escalates, there is an urgent need for advanced automation in electronic design automation (EDA). Traditional register transfer level (RTL) design methods are manual, time-consuming, and prone to errors. While commercial (instruction-tuned) large language models (LLMs) shows promising performance for automation, they pose security and privacy concerns. Open-source models offer alternatives; however, they frequently fall short in quality/correctness, largely due to limited, high-quality RTL code data essential for effective training and generalization. This paper proposes RTL++, a first-of-its-kind LLM-assisted method for RTL code generation that utilizes graph representations of code structures to enhance the quality of generated code. By encoding RTL code into a textualized control flowgraphs (CFG) and data flow graphs (DFG), RTL++ captures the inherent hierarchy, dependencies, and relationships within the code. This structured graph-based approach enhances the context available to LLMs, enabling them to better understand and generate instructions. By focusing on data generation through graph representations, RTL++ addresses the limitations of previous approaches that rely solely on code and suffer from lack of diversity. Experimental results demonstrate that RTL++ outperforms state-of-the-art models fine-tuned for RTL generation, as evaluated using the VerilogEval benchmark's Pass@1/5/10 metric, as well as the RTLLM1.1 model, which highlight the effectiveness of graph-enhanced context in advancing the capabilities of LLM-assisted RTL code generation.

Large Language Models (LLMs) have demonstrated their potential in hardware design tasks, such as Hardware Description Language (HDL) generation and debugging. Yet, their performance in real-world, repository-level HDL projects with thousands or even tens of thousands of code lines is hindered. To this end, we propose HDLxGraph, a novel framework that integrates Graph Retrieval Augmented Generation (Graph RAG) with LLMs, introducing HDL-specific graph representations by incorporating Abstract Syntax Trees (ASTs) and Data Flow Graphs (DFGs) to capture both code graph view and hardware graph view. HDLxGraph utilizes a dual-retrieval mechanism that not only mitigates the limited recall issues inherent in similarity-based semantic retrieval by incorporating structural information, but also enhances its extensibility to various real-world tasks by a task-specific retrieval finetuning. Additionally, to address the lack of comprehensive HDL search benchmarks, we introduce HDLSearch, a multi-granularity evaluation dataset derived from real-world repository-level projects. Experimental results demonstrate that HDLxGraph significantly improves average search accuracy, debugging efficiency and completion quality by 12.04%, 12.22% and 5.04% compared to similarity-based RAG, respectively. The code of HDLxGraph and collected HDLSearch benchmark are available at https://github.com/Nick-Zheng-Q/HDLxGraph.

Evaluating and enhancing the general capabilities of large language models (LLMs) has been an important research topic. Graph is a common data structure in the real world, and understanding graph data is a crucial part for advancing general intelligence. To evaluate and enhance the graph understanding abilities of LLMs, in this paper, we propose a benchmark named GraphInstruct, which comprehensively includes 21 classical graph reasoning tasks, providing diverse graph generation pipelines and detailed reasoning steps. Based on GraphInstruct, we further construct GraphLM through efficient instruction-tuning, which shows prominent graph understanding capability. In order to enhance the LLM with graph reasoning capability as well, we propose a step mask training strategy, and construct a model named GraphLM+. As one of the pioneering efforts to enhance the graph understanding and reasoning abilities of LLMs, extensive experiments have demonstrated the superiority of GraphLM and GraphLM+ over other LLMs. We look forward to more researchers exploring the potential of LLMs in the graph data mining domain through GraphInstruct. Our code for generating GraphInstruct is released publicly at: https://github.com/CGCL-codes/GraphInstruct.

Large language models (LLMs) are increasingly adopted for a variety of tasks with implicit graphical structures, such as planning in robotics, multi-hop question answering or knowledge probing, structured commonsense reasoning, and more. While LLMs have advanced the state-of-the-art on these tasks with structure implications, whether LLMs could explicitly process textual descriptions of graphs and structures, map them to grounded conceptual spaces, and perform structured operations remains underexplored. To this end, we propose NLGraph (Natural Language Graph), a comprehensive benchmark of graph-based problem solving designed in natural language. NLGraph contains 29,370 problems, covering eight graph reasoning tasks with varying complexity from simple tasks such as connectivity and shortest path up to complex problems such as maximum flow and simulating graph neural networks. We evaluate LLMs (GPT-3/4) with various prompting approaches on the NLGraph benchmark and find that 1) language models do demonstrate preliminary graph reasoning abilities, 2) the benefit of advanced prompting and in-context learning diminishes on more complex graph problems, while 3) LLMs are also (un)surprisingly brittle in the face of spurious correlations in graph and problem settings. We then propose Build-a-Graph Prompting and Algorithmic Prompting, two instruction-based approaches to enhance LLMs in solving natural language graph problems. Build-a-Graph and Algorithmic prompting improve the performance of LLMs on NLGraph by 3.07% to 16.85% across multiple tasks and settings, while how to solve the most complicated graph reasoning tasks in our setup with language models remains an open research question. The NLGraph benchmark and evaluation code are available at https://github.com/Arthur-Heng/NLGraph.

The need to analyze graphs is ubiquitous across various fields, from social networks to biological research and recommendation systems. Therefore, enabling the ability of large language models (LLMs) to process graphs is an important step toward more advanced general intelligence. However, current LLM benchmarks on graph analysis require models to directly reason over the prompts describing graph topology, and are thus limited to small graphs with only a few dozens of nodes. In contrast, human experts typically write programs based on popular libraries for task solving, and can thus handle graphs with different scales. To this end, a question naturally arises: can LLMs analyze graphs like professionals? In this paper, we introduce ProGraph, a manually crafted benchmark containing 3 categories of graph tasks. The benchmark expects solutions based on programming instead of directly reasoning over raw inputs. Our findings reveal that the performance of current LLMs is unsatisfactory, with the best model achieving only 36% accuracy. To bridge this gap, we propose LLM4Graph datasets, which include crawled documents and auto-generated codes based on 6 widely used graph libraries. By augmenting closed-source LLMs with document retrieval and fine-tuning open-source ones on the codes, we show 11-32% absolute improvements in their accuracies. Our results underscore that the capabilities of LLMs in handling structured data are still under-explored, and show the effectiveness of LLM4Graph in enhancing LLMs' proficiency of graph analysis. The benchmark, datasets and enhanced open-source models are available at https://github.com/BUPT-GAMMA/ProGraph.

Given a graph G and the desired size k in bits, how can we summarize G within k bits, while minimizing the information loss? Large-scale graphs have become omnipresent, posing considerable computational challenges. Analyzing such large graphs can be fast and easy if they are compressed sufficiently to fit in main memory or even cache. Graph summarization, which yields a coarse-grained summary graph with merged nodes, stands out with several advantages among graph compression techniques. Thus, a number of algorithms have been developed for obtaining a concise summary graph with little information loss or equivalently small reconstruction error. However, the existing methods focus solely on reducing the number of nodes, and they often yield dense summary graphs, failing to achieve better compression rates. Moreover, due to their limited scalability, they can be applied only to moderate-size graphs. In this work, we propose SSumM, a scalable and effective graph-summarization algorithm that yields a sparse summary graph. SSumM not only merges nodes together but also sparsifies the summary graph, and the two strategies are carefully balanced based on the minimum description length principle. Compared with state-of-the-art competitors, SSumM is (a) Concise: yields up to 11.2X smaller summary graphs with similar reconstruction error, (b) Accurate: achieves up to 4.2X smaller reconstruction error with similarly concise outputs, and (c) Scalable: summarizes 26X larger graphs while exhibiting linear scalability. We validate these advantages through extensive experiments on 10 real-world graphs.

Large Language Models (LLMs) have achieved impressive performance in text understanding and have become an essential tool for building smart assistants. Originally focusing on text, they have been enhanced with multimodal capabilities in recent works that successfully built visual instruction following assistants. As far as the graph modality goes, however, no such assistants have yet been developed. Graph structures are complex in that they represent relation between different features and are permutation invariant. Moreover, representing them in purely textual form does not always lead to good LLM performance even for finetuned models. As a result, there is a need to develop a new method to integrate graphs in LLMs for general graph understanding. This work explores the integration of the graph modality in LLM for general graph instruction following tasks. It aims at producing a deep learning model that enhances an underlying LLM with graph embeddings and trains it to understand them and to produce, given an instruction, an answer grounded in the graph representation. The approach performs significantly better than a graph to text approach and remains consistent even for larger graphs.

Methods that use Large Language Models (LLM) as planners for embodied instruction following tasks have become widespread. To successfully complete tasks, the LLM must be grounded in the environment in which the robot operates. One solution is to use a scene graph that contains all the necessary information. Modern methods rely on prebuilt scene graphs and assume that all task-relevant information is available at the start of planning. However, these approaches do not account for changes in the environment that may occur between the graph construction and the task execution. We propose LookPlanGraph - a method that leverages a scene graph composed of static assets and object priors. During plan execution, LookPlanGraph continuously updates the graph with relevant objects, either by verifying existing priors or discovering new entities. This is achieved by processing the agents egocentric camera view using a Vision Language Model. We conducted experiments with changed object positions VirtualHome and OmniGibson simulated environments, demonstrating that LookPlanGraph outperforms methods based on predefined static scene graphs. To demonstrate the practical applicability of our approach, we also conducted experiments in a real-world setting. Additionally, we introduce the GraSIF (Graph Scenes for Instruction Following) dataset with automated validation framework, comprising 514 tasks drawn from SayPlan Office, BEHAVIOR-1K, and VirtualHome RobotHow. Project page available at https://lookplangraph.github.io .

We introduce SPAFormer, an innovative model designed to overcome the combinatorial explosion challenge in the 3D Part Assembly (3D-PA) task. This task requires accurate prediction of each part's poses in sequential steps. As the number of parts increases, the possible assembly combinations increase exponentially, leading to a combinatorial explosion that severely hinders the efficacy of 3D-PA. SPAFormer addresses this problem by leveraging weak constraints from assembly sequences, effectively reducing the solution space's complexity. Since the sequence of parts conveys construction rules similar to sentences structured through words, our model explores both parallel and autoregressive generation. We further strengthen SPAFormer through knowledge enhancement strategies that utilize the attributes of parts and their sequence information, enabling it to capture the inherent assembly pattern and relationships among sequentially ordered parts. We also construct a more challenging benchmark named PartNet-Assembly covering 21 varied categories to more comprehensively validate the effectiveness of SPAFormer. Extensive experiments demonstrate the superior generalization capabilities of SPAFormer, particularly with multi-tasking and in scenarios requiring long-horizon assembly. Code is available at https://github.com/xuboshen/SPAFormer.

Graphs are a fundamental data structure for representing relationships in real-world scenarios. With the success of Large Language Models (LLMs) across various natural language processing (NLP) tasks, there has been growing interest in integrating LLMs for graph learning. However, applying LLMs to graph-related tasks poses significant challenges, as these models are not inherently designed to capture the complex structural information present in graphs. Existing approaches address this challenge through two strategies: the chain of tasks approach, which uses Graph Neural Networks (GNNs) to encode the graph structure so that LLMs are relieved from understanding spatial positions; and Graph-to-Text Conversion, which translates graph structures into semantic text representations that LLMs can process. Despite their progress, these methods often struggle to fully preserve the topological information of graphs or require extensive computational resources, limiting their practical applicability. In this work, we introduce Node Tokenizer for Large Language Models (NT-LLM), a novel framework that efficiently encodes graph structures by selecting key nodes as anchors and representing each node based on its relative distance to these anchors. This position-anchored encoding effectively captures the graph topology, enabling enhanced reasoning capabilities in LLMs over graph data. Additionally, we implement a task-specific tuning procedure to further improve structural understanding within LLMs. Through extensive empirical evaluations, NT-LLM demonstrates significant performance improvements across a variety of graph-related tasks.

Maintaining legacy software requires many software and systems engineering hours. Assembly code programs, which demand low-level control over the computer machine state and have no variable names, are particularly difficult for humans to analyze. Existing conventional program translators guarantee correctness, but are hand-engineered for the source and target programming languages in question. Learned transpilation, i.e. automatic translation of code, offers an alternative to manual re-writing and engineering efforts. Automated symbolic program translation approaches guarantee correctness but struggle to scale to longer programs due to the exponentially large search space. Their rigid rule-based systems also limit their expressivity, so they can only reason about a reduced space of programs. Probabilistic neural language models (LMs) produce plausible outputs for every input, but do so at the cost of guaranteed correctness. In this work, we leverage the strengths of LMs and symbolic solvers in a neurosymbolic approach to learned transpilation for assembly code. Assembly code is an appropriate setting for a neurosymbolic approach, since assembly code can be divided into shorter non-branching basic blocks amenable to the use of symbolic methods. Guess & Sketch extracts alignment and confidence information from features of the LM then passes it to a symbolic solver to resolve semantic equivalence of the transpilation input and output. We test Guess & Sketch on three different test sets of assembly transpilation tasks, varying in difficulty, and show that it successfully transpiles 57.6% more examples than GPT-4 and 39.6% more examples than an engineered transpiler. We also share a training and evaluation dataset for this task.

Assembly101 is a new procedural activity dataset featuring 4321 videos of people assembling and disassembling 101 "take-apart" toy vehicles. Participants work without fixed instructions, and the sequences feature rich and natural variations in action ordering, mistakes, and corrections. Assembly101 is the first multi-view action dataset, with simultaneous static (8) and egocentric (4) recordings. Sequences are annotated with more than 100K coarse and 1M fine-grained action segments, and 18M 3D hand poses. We benchmark on three action understanding tasks: recognition, anticipation and temporal segmentation. Additionally, we propose a novel task of detecting mistakes. The unique recording format and rich set of annotations allow us to investigate generalization to new toys, cross-view transfer, long-tailed distributions, and pose vs. appearance. We envision that Assembly101 will serve as a new challenge to investigate various activity understanding problems.

Text-to-image (T2I) generation has seen significant growth over the past few years. Despite this, there has been little work on generating diagrams with T2I models. A diagram is a symbolic/schematic representation that explains information using structurally rich and spatially complex visualizations (e.g., a dense combination of related objects, text labels, directional arrows, connection lines, etc.). Existing state-of-the-art T2I models often fail at diagram generation because they lack fine-grained object layout control when many objects are densely connected via complex relations such as arrows/lines and also often fail to render comprehensible text labels. To address this gap, we present DiagrammerGPT, a novel two-stage text-to-diagram generation framework that leverages the layout guidance capabilities of LLMs (e.g., GPT-4) to generate more accurate open-domain, open-platform diagrams. In the first stage, we use LLMs to generate and iteratively refine 'diagram plans' (in a planner-auditor feedback loop) which describe all the entities (objects and text labels), their relationships (arrows or lines), and their bounding box layouts. In the second stage, we use a diagram generator, DiagramGLIGEN, and a text label rendering module to generate diagrams following the diagram plans. To benchmark the text-to-diagram generation task, we introduce AI2D-Caption, a densely annotated diagram dataset built on top of the AI2D dataset. We show quantitatively and qualitatively that our DiagrammerGPT framework produces more accurate diagrams, outperforming existing T2I models. We also provide comprehensive analysis including open-domain diagram generation, vector graphic diagram generation in different platforms, human-in-the-loop diagram plan editing, and multimodal planner/auditor LLMs (e.g., GPT-4Vision). We hope our work can inspire further research on diagram generation via T2I models and LLMs.

Large Language Models (LLMs) have demonstrated exceptional abilities in reasoning for task planning. However, challenges remain under-explored for parallel schedules. This paper introduces a novel paradigm, plan-over-graph, in which the model first decomposes a real-life textual task into executable subtasks and constructs an abstract task graph. The model then understands this task graph as input and generates a plan for parallel execution. To enhance the planning capability of complex, scalable graphs, we design an automated and controllable pipeline to generate synthetic graphs and propose a two-stage training scheme. Experimental results show that our plan-over-graph method significantly improves task performance on both API-based LLMs and trainable open-sourced LLMs. By normalizing complex tasks as graphs, our method naturally supports parallel execution, demonstrating global efficiency. The code and data are available at https://github.com/zsq259/Plan-over-Graph.

Graph Neural Networks (GNNs) have advanced graph structure understanding via recursive information exchange and aggregation among graph nodes. To improve model robustness, self-supervised learning (SSL) has emerged as a promising approach for data augmentation. However, existing methods for generating pre-trained graph embeddings often rely on fine-tuning with specific downstream task labels, which limits their usability in scenarios where labeled data is scarce or unavailable. To address this, our research focuses on advancing the generalization capabilities of graph models in challenging zero-shot learning scenarios. Inspired by the success of large language models (LLMs), we aim to develop a graph-oriented LLM that can achieve high generalization across diverse downstream datasets and tasks, even without any information available from the downstream graph data. In this work, we present the GraphGPT framework that aligns LLMs with graph structural knowledge with a graph instruction tuning paradigm. Our framework incorporates a text-graph grounding component to establish a connection between textual information and graph structures. Additionally, we propose a dual-stage instruction tuning paradigm, accompanied by a lightweight graph-text alignment projector. This paradigm explores self-supervised graph structural signals and task-specific graph instructions, to guide LLMs in understanding complex graph structures and improving their adaptability across different downstream tasks. Our framework is evaluated on supervised and zero-shot graph learning tasks, demonstrating superior generalization and outperforming state-of-the-art baselines.

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.

Graphs or networks are a very convenient way to represent data with lots of interaction. Recently, Machine Learning on Graph data has gained a lot of traction. In particular, vertex classification and missing edge detection have very interesting applications, ranging from drug discovery to recommender systems. To achieve such tasks, tremendous work has been accomplished to learn embedding of nodes and edges into finite-dimension vector spaces. This task is called Graph Representation Learning. However, Graph Representation Learning techniques often display prohibitive time and memory complexities, preventing their use in real-time with business size graphs. In this paper, we address this issue by leveraging a degeneracy property of Graphs - the K-Core Decomposition. We present two techniques taking advantage of this decomposition to reduce the time and memory consumption of walk-based Graph Representation Learning algorithms. We evaluate the performances, expressed in terms of quality of embedding and computational resources, of the proposed techniques on several academic datasets. Our code is available at https://github.com/SBrandeis/kcore-embedding

Various human-designed prompt engineering techniques have been proposed to improve problem solvers based on Large Language Models (LLMs), yielding many disparate code bases. We unify these approaches by describing LLM-based agents as computational graphs. The nodes implement functions to process multimodal data or query LLMs, and the edges describe the information flow between operations. Graphs can be recursively combined into larger composite graphs representing hierarchies of inter-agent collaboration (where edges connect operations of different agents). Our novel automatic graph optimizers (1) refine node-level LLM prompts (node optimization) and (2) improve agent orchestration by changing graph connectivity (edge optimization). Experiments demonstrate that our framework can be used to efficiently develop, integrate, and automatically improve various LLM agents. The code can be found at https://github.com/metauto-ai/gptswarm.

Shape assembly is a ubiquitous task in daily life, integral for constructing complex 3D structures like IKEA furniture. While significant progress has been made in developing autonomous agents for shape assembly, existing datasets have not yet tackled the 4D grounding of assembly instructions in videos, essential for a holistic understanding of assembly in 3D space over time. We introduce IKEA Video Manuals, a dataset that features 3D models of furniture parts, instructional manuals, assembly videos from the Internet, and most importantly, annotations of dense spatio-temporal alignments between these data modalities. To demonstrate the utility of IKEA Video Manuals, we present five applications essential for shape assembly: assembly plan generation, part-conditioned segmentation, part-conditioned pose estimation, video object segmentation, and furniture assembly based on instructional video manuals. For each application, we provide evaluation metrics and baseline methods. Through experiments on our annotated data, we highlight many challenges in grounding assembly instructions in videos to improve shape assembly, including handling occlusions, varying viewpoints, and extended assembly sequences.

In medical and industrial domains, providing guidance for assembly processes can be critical to ensure efficiency and safety. Errors in assembly can lead to significant consequences such as extended surgery times and prolonged manufacturing or maintenance times in industry. Assembly scenarios can benefit from in-situ augmented reality visualization, i.e., augmentations in close proximity to the target object, to provide guidance, reduce assembly times, and minimize errors. In order to enable in-situ visualization, 6D pose estimation can be leveraged to identify the correct location for an augmentation. Existing 6D pose estimation techniques primarily focus on individual objects and static captures. However, assembly scenarios have various dynamics, including occlusion during assembly and dynamics in the appearance of assembly objects. Existing work focus either on object detection combined with state detection, or focus purely on the pose estimation. To address the challenges of 6D pose estimation in combination with assembly state detection, our approach ASDF builds upon the strengths of YOLOv8, a real-time capable object detection framework. We extend this framework, refine the object pose, and fuse pose knowledge with network-detected pose information. Utilizing our late fusion in our Pose2State module results in refined 6D pose estimation and assembly state detection. By combining both pose and state information, our Pose2State module predicts the final assembly state with precision. The evaluation of our ASDF dataset shows that our Pose2State module leads to an improved assembly state detection and that the improvement of the assembly state further leads to a more robust 6D pose estimation. Moreover, on the GBOT dataset, we outperform the pure deep learning-based network and even outperform the hybrid and pure tracking-based approaches.

Graph representations of programs are commonly a central element of machine learning for code research. We introduce an open source Python library python_graphs that applies static analysis to construct graph representations of Python programs suitable for training machine learning models. Our library admits the construction of control-flow graphs, data-flow graphs, and composite ``program graphs'' that combine control-flow, data-flow, syntactic, and lexical information about a program. We present the capabilities and limitations of the library, perform a case study applying the library to millions of competitive programming submissions, and showcase the library's utility for machine learning research.

A 3D scene graph represents a compact scene model, storing information about the objects and the semantic relationships between them, making its use promising for robotic tasks. When interacting with a user, an embodied intelligent agent should be capable of responding to various queries about the scene formulated in natural language. Large Language Models (LLMs) are beneficial solutions for user-robot interaction due to their natural language understanding and reasoning abilities. Recent methods for creating learnable representations of 3D scenes have demonstrated the potential to improve the quality of LLMs responses by adapting to the 3D world. However, the existing methods do not explicitly utilize information about the semantic relationships between objects, limiting themselves to information about their coordinates. In this work, we propose a method 3DGraphLLM for constructing a learnable representation of a 3D scene graph. The learnable representation is used as input for LLMs to perform 3D vision-language tasks. In our experiments on popular ScanRefer, RIORefer, Multi3DRefer, ScanQA, Sqa3D, and Scan2cap datasets, we demonstrate the advantage of this approach over baseline methods that do not use information about the semantic relationships between objects. The code is publicly available at https://github.com/CognitiveAISystems/3DGraphLLM.

A proper scene representation is central to the pursuit of spatial intelligence where agents can robustly reconstruct and efficiently understand 3D scenes. A scene representation is either metric, such as landmark maps in 3D reconstruction, 3D bounding boxes in object detection, or voxel grids in occupancy prediction, or topological, such as pose graphs with loop closures in SLAM or visibility graphs in SfM. In this work, we propose to build Multiview Scene Graphs (MSG) from unposed images, representing a scene topologically with interconnected place and object nodes. The task of building MSG is challenging for existing representation learning methods since it needs to jointly address both visual place recognition, object detection, and object association from images with limited fields of view and potentially large viewpoint changes. To evaluate any method tackling this task, we developed an MSG dataset and annotation based on a public 3D dataset. We also propose an evaluation metric based on the intersection-over-union score of MSG edges. Moreover, we develop a novel baseline method built on mainstream pretrained vision models, combining visual place recognition and object association into one Transformer decoder architecture. Experiments demonstrate our method has superior performance compared to existing relevant baselines.

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.

Attention mechanisms are critical to the success of large language models (LLMs), driving significant advancements in multiple fields. However, for graph-structured data, which requires emphasis on topological connections, they fall short compared to message-passing mechanisms on fixed links, such as those employed by Graph Neural Networks (GNNs). This raises a question: ``Does attention fail for graphs in natural language settings?'' Motivated by these observations, we embarked on an empirical study from the perspective of attention mechanisms to explore how LLMs process graph-structured data. The goal is to gain deeper insights into the attention behavior of LLMs over graph structures. We uncovered unique phenomena regarding how LLMs apply attention to graph-structured data and analyzed these findings to improve the modeling of such data by LLMs. The primary findings of our research are: 1) While LLMs can recognize graph data and capture text-node interactions, they struggle to model inter-node relationships within graph structures due to inherent architectural constraints. 2) The attention distribution of LLMs across graph nodes does not align with ideal structural patterns, indicating a failure to adapt to graph topology nuances. 3) Neither fully connected attention nor fixed connectivity is optimal; each has specific limitations in its application scenarios. Instead, intermediate-state attention windows improve LLM training performance and seamlessly transition to fully connected windows during inference. Source code: https://github.com/millioniron/LLM_exploration{LLM4Exploration}

Shape assembly aims to reassemble parts (or fragments) into a complete object, which is a common task in our daily life. Different from the semantic part assembly (e.g., assembling a chair's semantic parts like legs into a whole chair), geometric part assembly (e.g., assembling bowl fragments into a complete bowl) is an emerging task in computer vision and robotics. Instead of semantic information, this task focuses on geometric information of parts. As the both geometric and pose space of fractured parts are exceptionally large, shape pose disentanglement of part representations is beneficial to geometric shape assembly. In our paper, we propose to leverage SE(3) equivariance for such shape pose disentanglement. Moreover, while previous works in vision and robotics only consider SE(3) equivariance for the representations of single objects, we move a step forward and propose leveraging SE(3) equivariance for representations considering multi-part correlations, which further boosts the performance of the multi-part assembly. Experiments demonstrate the significance of SE(3) equivariance and our proposed method for geometric shape assembly. Project page: https://crtie.github.io/SE-3-part-assembly/

Acceleration of graph applications on GPUs has found large interest due to the ubiquitous use of graph processing in various domains. The inherent irregularity in graph applications leads to several challenges for parallelization. A key challenge, which we address in this paper, is that of load-imbalance. If the work-assignment to threads uses node-based graph partitioning, it can result in skewed task-distribution, leading to poor load-balance. In contrast, if the work-assignment uses edge-based graph partitioning, the load-balancing is better, but the memory requirement is relatively higher. This makes it unsuitable for large graphs. In this work, we propose three techniques for improved load-balancing of graph applications on GPUs. Each technique brings in unique advantages, and a user may have to employ a specific technique based on the requirement. Using Breadth First Search and Single Source Shortest Paths as our processing kernels, we illustrate the effectiveness of each of the proposed techniques in comparison to the existing node-based and edge-based mechanisms.

Charts provide visual representations of data and are widely used for analyzing information, addressing queries, and conveying insights to others. Various chart-related downstream tasks have emerged recently, such as question-answering and summarization. A common strategy to solve these tasks is to fine-tune various models originally trained on vision tasks language. However, such task-specific models are not capable of solving a wide range of chart-related tasks, constraining their real-world applicability. To overcome these challenges, we introduce ChartInstruct: a novel chart-specific vision-language Instruction-following dataset comprising 191K instructions generated with 71K charts. We then present two distinct systems for instruction tuning on such datasets: (1) an end-to-end model that connects a vision encoder for chart understanding with a LLM; and (2) a pipeline model that employs a two-step approach to extract chart data tables and input them into the LLM. In experiments on four downstream tasks, we first show the effectiveness of our model--achieving a new set of state-of-the-art results. Further evaluation shows that our instruction-tuning approach supports a wide array of real-world chart comprehension and reasoning scenarios, thereby expanding the scope and applicability of our models to new kinds of tasks.

Recent developments in retrieval-augmented generation (RAG) for selecting relevant tools from a tool knowledge base enable LLM agents to scale their complex tool calling capabilities to hundreds or thousands of external tools, APIs, or agents-as-tools. However, traditional RAG-based tool retrieval fails to capture structured dependencies between tools, limiting the retrieval accuracy of a retrieved tool's dependencies. For example, among a vector database of tools, a "get stock price" API requires a "stock ticker" parameter from a "get stock ticker" API, and both depend on OS-level internet connectivity tools. In this paper, we address this limitation by introducing Graph RAG-Tool Fusion, a novel plug-and-play approach that combines the strengths of vector-based retrieval with efficient graph traversal to capture all relevant tools (nodes) along with any nested dependencies (edges) within the predefined tool knowledge graph. We also present ToolLinkOS, a new tool selection benchmark of 573 fictional tools, spanning over 15 industries, each with an average of 6.3 tool dependencies. We demonstrate that Graph RAG-Tool Fusion achieves absolute improvements of 71.7% and 22.1% over na\"ive RAG on ToolLinkOS and ToolSandbox benchmarks, respectively (mAP@10). ToolLinkOS dataset is available at https://github.com/EliasLumer/Graph-RAG-Tool-Fusion-ToolLinkOS

Biological neural networks define the brain function and intelligence of humans and other mammals, and form ultra-large, spatial, structured graphs. Their neuronal organization is closely interconnected with the spatial organization of the brain's microvasculature, which supplies oxygen to the neurons and builds a complementary spatial graph. This vasculature (or the vessel structure) plays an important role in neuroscience; for example, the organization of (and changes to) vessel structure can represent early signs of various pathologies, e.g. Alzheimer's disease or stroke. Recently, advances in tissue clearing have enabled whole brain imaging and segmentation of the entirety of the mouse brain's vasculature. Building on these advances in imaging, we are presenting an extendable dataset of whole-brain vessel graphs based on specific imaging protocols. Specifically, we extract vascular graphs using a refined graph extraction scheme leveraging the volume rendering engine Voreen and provide them in an accessible and adaptable form through the OGB and PyTorch Geometric dataloaders. Moreover, we benchmark numerous state-of-the-art graph learning algorithms on the biologically relevant tasks of vessel prediction and vessel classification using the introduced vessel graph dataset. Our work paves a path towards advancing graph learning research into the field of neuroscience. Complementarily, the presented dataset raises challenging graph learning research questions for the machine learning community, in terms of incorporating biological priors into learning algorithms, or in scaling these algorithms to handle sparse,spatial graphs with millions of nodes and edges. All datasets and code are available for download at https://github.com/jocpae/VesselGraph .

Graphs can be used to represent and reason about systems and a variety of metrics have been devised to quantify their global characteristics. However, little is currently known about how to construct a graph or improve an existing one given a target objective. In this work, we formulate the construction of a graph as a decision-making process in which a central agent creates topologies by trial and error and receives rewards proportional to the value of the target objective. By means of this conceptual framework, we propose an algorithm based on reinforcement learning and graph neural networks to learn graph construction and improvement strategies. Our core case study focuses on robustness to failures and attacks, a property relevant for the infrastructure and communication networks that power modern society. Experiments on synthetic and real-world graphs show that this approach can outperform existing methods while being cheaper to evaluate. It also allows generalization to out-of-sample graphs, as well as to larger out-of-distribution graphs in some cases. The approach is applicable to the optimization of other global structural properties of graphs.

Large language models (LLMs), while exhibiting exceptional performance, suffer from hallucinations, especially on knowledge-intensive tasks. Existing works propose to augment LLMs with individual text units retrieved from external knowledge corpora to alleviate the issue. However, in many domains, texts are interconnected (e.g., academic papers in a bibliographic graph are linked by citations and co-authorships) which form a (text-attributed) graph. The knowledge in such graphs is encoded not only in single texts/nodes but also in their associated connections. To facilitate the research of augmenting LLMs with graphs, we manually construct a Graph Reasoning Benchmark dataset called GRBench, containing 1,740 questions that can be answered with the knowledge from 10 domain graphs. Then, we propose a simple and effective framework called Graph Chain-of-thought (Graph-CoT) to augment LLMs with graphs by encouraging LLMs to reason on the graph iteratively. Each Graph-CoT iteration consists of three sub-steps: LLM reasoning, LLM-graph interaction, and graph execution. We conduct systematic experiments with three LLM backbones on GRBench, where Graph-CoT outperforms the baselines consistently. The code is available at https://github.com/PeterGriffinJin/Graph-CoT.

Attention mechanisms have been widely used to capture long-range dependencies among nodes in Graph Transformers. Bottlenecked by the quadratic computational cost, attention mechanisms fail to scale in large graphs. Recent improvements in computational efficiency are mainly achieved by attention sparsification with random or heuristic-based graph subsampling, which falls short in data-dependent context reasoning. State space models (SSMs), such as Mamba, have gained prominence for their effectiveness and efficiency in modeling long-range dependencies in sequential data. However, adapting SSMs to non-sequential graph data presents a notable challenge. In this work, we introduce Graph-Mamba, the first attempt to enhance long-range context modeling in graph networks by integrating a Mamba block with the input-dependent node selection mechanism. Specifically, we formulate graph-centric node prioritization and permutation strategies to enhance context-aware reasoning, leading to a substantial improvement in predictive performance. Extensive experiments on ten benchmark datasets demonstrate that Graph-Mamba outperforms state-of-the-art methods in long-range graph prediction tasks, with a fraction of the computational cost in both FLOPs and GPU memory consumption. The code and models are publicly available at https://github.com/bowang-lab/Graph-Mamba.

Verifying the reliability of complex, multi-step reasoning in Large Language Models (LLMs) remains a fundamental challenge, as existing methods often lack both faithfulness and precision. To address this issue, we propose the Graph of Verification (GoV) framework. GoV offers three key contributions: First, it explicitly models the underlying deductive process as a directed acyclic graph (DAG), whether this structure is implicit or explicitly constructed. Second, it enforces a topological order over the DAG to guide stepwise verification. Third, GoV introduces the notion of customizable node blocks, which flexibly define the verification granularity, from atomic propositions to full paragraphs, while ensuring that all requisite premises derived from the graph are provided as contextual input for each verification unit. We evaluate GoV on the Number Triangle Summation task and the ProcessBench benchmark with varying levels of reasoning complexity. Experimental results show that GoV substantially improves verification accuracy, faithfulness, and error localization when compared to conventional end-to-end verification approaches. Our code and data are available at https://github.com/Frevor/Graph-of-Verification.

Subgraph matching is vital in knowledge graph (KG) question answering, molecule design, scene graph, code and circuit search, etc. Neural methods have shown promising results for subgraph matching. Our study of recent systems suggests refactoring them into a unified design space for graph matching networks. Existing methods occupy only a few isolated patches in this space, which remains largely uncharted. We undertake the first comprehensive exploration of this space, featuring such axes as attention-based vs. soft permutation-based interaction between query and corpus graphs, aligning nodes vs. edges, and the form of the final scoring network that integrates neural representations of the graphs. Our extensive experiments reveal that judicious and hitherto-unexplored combinations of choices in this space lead to large performance benefits. Beyond better performance, our study uncovers valuable insights and establishes general design principles for neural graph representation and interaction, which may be of wider interest.

Program source code contains complex structure information, which can be represented in structured data forms like trees or graphs. To acquire the structural information in source code, most existing researches use abstract syntax trees (AST). A group of works add additional edges to ASTs to convert source code into graphs and use graph neural networks to learn representations for program graphs. Although these works provide additional control or data flow information to ASTs for downstream tasks, they neglect an important aspect of structure information in AST itself: the different types of nodes and edges. In ASTs, different nodes contain different kinds of information like variables or control flow, and the relation between a node and all its children can also be different. To address the information of node and edge types, we bring the idea of heterogeneous graphs to learning on source code and present a new formula of building heterogeneous program graphs from ASTs with additional type information for nodes and edges. We use the ASDL grammar of programming language to define the node and edge types of program graphs. Then we use heterogeneous graph neural networks to learn on these graphs. We evaluate our approach on two tasks: code comment generation and method naming. Both tasks require reasoning on the semantics of complete code snippets. Experiment results show that our approach outperforms baseline models, including homogeneous graph-based models, showing that leveraging the type information of nodes and edges in program graphs can help in learning program semantics.

We propose a methodology that allows communication with Piping and Instrumentation Diagrams (P&IDs) using natural language. In particular, we represent P&IDs through the DEXPI data model as labeled property graphs and integrate them with Large Language Models (LLMs). The approach consists of three main parts: 1) P&IDs are cast into a graph representation from the DEXPI format using our pyDEXPI Python package. 2) A tool for generating P&ID knowledge graphs from pyDEXPI. 3) Integration of the P&ID knowledge graph to LLMs using graph-based retrieval augmented generation (graph-RAG). This approach allows users to communicate with P&IDs using natural language. It extends LLM's ability to retrieve contextual data from P&IDs and mitigate hallucinations. Leveraging the LLM's large corpus, the model is also able to interpret process information in PIDs, which could help engineers in their daily tasks. In the future, this work will also open up opportunities in the context of other generative Artificial Intelligence (genAI) solutions on P&IDs, and AI-assisted HAZOP studies.

Large language models (LLMs) have demonstrated strong capabilities across various language tasks, notably through instruction-tuning methods. However, LLMs face challenges in visualizing complex, real-world data through charts and plots. Firstly, existing datasets rarely cover a full range of chart types, such as 3D, volumetric, and gridded charts. Secondly, supervised fine-tuning methods do not fully leverage the intricate relationships within rich datasets, including text, code, and figures. To address these challenges, we propose a hierarchical pipeline and a new dataset for chart generation. Our dataset, Text2Chart31, includes 31 unique plot types referring to the Matplotlib library, with 11.1K tuples of descriptions, code, data tables, and plots. Moreover, we introduce a reinforcement learning-based instruction tuning technique for chart generation tasks without requiring human feedback. Our experiments show that this approach significantly enhances the model performance, enabling smaller models to outperform larger open-source models and be comparable to state-of-the-art proprietary models in data visualization tasks. We make the code and dataset available at https://github.com/fatemehpesaran310/Text2Chart31.

Recently, Large Language Models (LLMs) have demonstrated great potential in robotic applications by providing essential general knowledge for situations that can not be pre-programmed beforehand. Generally speaking, mobile robots need to understand maps to execute tasks such as localization or navigation. In this letter, we address the problem of enabling LLMs to comprehend Area Graph, a text-based map representation, in order to enhance their applicability in the field of mobile robotics. Area Graph is a hierarchical, topometric semantic map representation utilizing polygons to demark areas such as rooms, corridors or buildings. In contrast to commonly used map representations, such as occupancy grid maps or point clouds, osmAG (Area Graph in OpensStreetMap format) is stored in a XML textual format naturally readable by LLMs. Furthermore, conventional robotic algorithms such as localization and path planning are compatible with osmAG, facilitating this map representation comprehensible by LLMs, traditional robotic algorithms and humans. Our experiments show that with a proper map representation, LLMs possess the capability to understand maps and answer queries based on that understanding. Following simple fine-tuning of LLaMA2 models, it surpassed ChatGPT-3.5 in tasks involving topology and hierarchy understanding. Our dataset, dataset generation code, fine-tuned LoRA adapters can be accessed at https://github.com/xiefujing/LLM-osmAG-Comprehension.

A subgraph is constructed by using a subset of vertices and edges of a given graph. There exist many graph properties that are hereditary for subgraphs. Hence, researchers from different communities have paid a great deal of attention in studying numerous subgraph problems, on top of the ordinary graph problems. Many algorithms are proposed in studying subgraph problems, where one common approach is by extracting the patterns and structures of a given graph. Due to the complex structures of certain types of graphs and to improve overall performances of the existing frameworks, machine learning techniques have recently been employed in dealing with various subgraph problems. In this article, we present a comprehensive review on five well known subgraph problems that have been tackled by using machine learning methods. They are subgraph isomorphism (both counting and matching), maximum common subgraph, community detection and community search problems. We provide an outline of each proposed method, and examine its designs and performances. We also explore non-learning-based algorithms for each problem and a brief discussion is given. We then suggest some promising research directions in this area, hoping that relevant subgraph problems can be tackled by using a similar strategy. Since there is a huge growth in employing machine learning techniques in recent years, we believe that this survey will serve as a good reference point to relevant research communities.

This work explores the problem of generating task graphs of real-world activities. Different from prior formulations, we consider a setting where text transcripts of instructional videos performing a real-world activity (e.g., making coffee) are provided and the goal is to identify the key steps relevant to the task as well as the dependency relationship between these key steps. We propose a novel task graph generation approach that combines the reasoning capabilities of instruction-tuned language models along with clustering and ranking components to generate accurate task graphs in a completely unsupervised manner. We show that the proposed approach generates more accurate task graphs compared to a supervised learning approach on tasks from the ProceL and CrossTask datasets.

This paper introduces layout-aware graph modeling for multimodal RAG. Different from traditional RAG methods that mostly deal with flat text chunks, the proposed method takes into account the relationship of multimodalities by using a graph structure. To do that, a graph modeling structure is defined based on document layout parsing. The structure of an input document is retained with the connection of text chunks, tables, and figures. This representation allows the method to handle complex questions that require information from multimodalities. To confirm the efficiency of the graph modeling, a flexible RAG pipeline is developed using robust components. Experimental results on four benchmark test sets confirm the contribution of the layout-aware modeling for performance improvement of the RAG pipeline.

Understanding the various properties of glycans with machine learning has shown some preliminary promise. However, previous methods mainly focused on modeling the backbone structure of glycans as graphs of monosaccharides (i.e., sugar units), while they neglected the atomic structures underlying each monosaccharide, which are actually important indicators of glycan properties. We fill this blank by introducing the GlycanAA model for All-Atom-wise Glycan modeling. GlycanAA models a glycan as a heterogeneous graph with monosaccharide nodes representing its global backbone structure and atom nodes representing its local atomic-level structures. Based on such a graph, GlycanAA performs hierarchical message passing to capture from local atomic-level interactions to global monosaccharide-level interactions. To further enhance model capability, we pre-train GlycanAA on a high-quality unlabeled glycan dataset, deriving the PreGlycanAA model. We design a multi-scale mask prediction algorithm to endow the model about different levels of dependencies in a glycan. Extensive benchmark results show the superiority of GlycanAA over existing glycan encoders and verify the further improvements achieved by PreGlycanAA. We maintain all resources at https://github.com/kasawa1234/GlycanAA

A Harris Graph is a tough, Eulerian, non-Hamiltonian graph. Several approaches to creating new Harris graphs from existing ones are explored, including creating families of Harris graphs and combining Harris graphs. Pictures of all Harris Graphs through order 9 and the number of Harris graphs through order 12 are included. We also prove a result about barnacle-free Harris graphs.

Machine learning on graphs has been extensively studied in both academic and industry. However, as the literature on graph learning booms with a vast number of emerging methods and techniques, it becomes increasingly difficult to manually design the optimal machine learning algorithm for different graph-related tasks. To solve this critical challenge, automated machine learning (AutoML) on graphs which combines the strength of graph machine learning and AutoML together, is gaining attention from the research community. Therefore, we comprehensively survey AutoML on graphs in this paper, primarily focusing on hyper-parameter optimization (HPO) and neural architecture search (NAS) for graph machine learning. We further overview libraries related to automated graph machine learning and in-depth discuss AutoGL, the first dedicated open-source library for AutoML on graphs. In the end, we share our insights on future research directions for automated graph machine learning. This paper is the first systematic and comprehensive review of automated machine learning on graphs to the best of our knowledge.

Recently, multimodal large language models (MLLMs) have attracted increasing research attention due to their powerful visual understanding capabilities. While they have achieved impressive results on various vision tasks, their performance on chart-to-code generation remains suboptimal. This task requires MLLMs to generate executable code that can reproduce a given chart, demanding not only precise visual understanding but also accurate translation of visual elements into structured code. Directly prompting MLLMs to perform this complex task often yields unsatisfactory results. To address this challenge, we propose {ChartIR}, an iterative refinement method based on structured instruction. First, we distinguish two tasks: visual understanding and code translation. To accomplish the visual understanding component, we design two types of structured instructions: description and difference. The description instruction captures the visual elements of the reference chart, while the difference instruction characterizes the discrepancies between the reference chart and the generated chart. These instructions effectively transform visual features into language representations, thereby facilitating the subsequent code translation process. Second, we decompose the overall chart generation pipeline into two stages: initial code generation and iterative refinement, enabling progressive enhancement of the final output. Experimental results show that, compared to other method, our method achieves superior performance on both the open-source model Qwen2-VL and the closed-source model GPT-4o.

For large-scale and long-term simultaneous localization and mapping (SLAM), a robot has to deal with unknown initial positioning caused by either the kidnapped robot problem or multi-session mapping. This paper addresses these problems by tying the SLAM system with a global loop closure detection approach, which intrinsically handles these situations. However, online processing for global loop closure detection approaches is generally influenced by the size of the environment. The proposed graph-based SLAM system uses a memory management approach that only consider portions of the map to satisfy online processing requirements. The approach is tested and demonstrated using five indoor mapping sessions of a building using a robot equipped with a laser rangefinder and a Kinect.

Although Large Language Models (LLMs) have demonstrated potential in processing graphs, they struggle with comprehending graphical structure information through prompts of graph description sequences, especially as the graph size increases. We attribute this challenge to the uneven memory performance of LLMs across different positions in graph description sequences, known as ''positional biases''. To address this, we propose GraphInsight, a novel framework aimed at improving LLMs' comprehension of both macro- and micro-level graphical information. GraphInsight is grounded in two key strategies: 1) placing critical graphical information in positions where LLMs exhibit stronger memory performance, and 2) investigating a lightweight external knowledge base for regions with weaker memory performance, inspired by retrieval-augmented generation (RAG). Moreover, GraphInsight explores integrating these two strategies into LLM agent processes for composite graph tasks that require multi-step reasoning. Extensive empirical studies on benchmarks with a wide range of evaluation tasks show that GraphInsight significantly outperforms all other graph description methods (e.g., prompting techniques and reordering strategies) in understanding graph structures of varying sizes.

In the field of graphic design, automating the integration of design elements into a cohesive multi-layered artwork not only boosts productivity but also paves the way for the democratization of graphic design. One existing practice is Graphic Layout Generation (GLG), which aims to layout sequential design elements. It has been constrained by the necessity for a predefined correct sequence of layers, thus limiting creative potential and increasing user workload. In this paper, we present Hierarchical Layout Generation (HLG) as a more flexible and pragmatic setup, which creates graphic composition from unordered sets of design elements. To tackle the HLG task, we introduce Graphist, the first layout generation model based on large multimodal models. Graphist efficiently reframes the HLG as a sequence generation problem, utilizing RGB-A images as input, outputs a JSON draft protocol, indicating the coordinates, size, and order of each element. We develop new evaluation metrics for HLG. Graphist outperforms prior arts and establishes a strong baseline for this field. Project homepage: https://github.com/graphic-design-ai/graphist

We study the implications of the modeling choice to use a graph, instead of a hypergraph, to represent real-world interconnected systems whose constituent relationships are of higher order by nature. Such a modeling choice typically involves an underlying projection process that maps the original hypergraph onto a graph, and is common in graph-based analysis. While hypergraph projection can potentially lead to loss of higher-order relations, there exists very limited studies on the consequences of doing so, as well as its remediation. This work fills this gap by doing two things: (1) we develop analysis based on graph and set theory, showing two ubiquitous patterns of hyperedges that are root to structural information loss in all hypergraph projections; we also quantify the combinatorial impossibility of recovering the lost higher-order structures if no extra help is provided; (2) we still seek to recover the lost higher-order structures in hypergraph projection, and in light of (1)'s findings we propose to relax the problem into a learning-based setting. Under this setting, we develop a learning-based hypergraph reconstruction method based on an important statistic of hyperedge distributions that we find. Our reconstruction method is evaluated on 8 real-world datasets under different settings, and exhibits consistently good performance. We also demonstrate benefits of the reconstructed hypergraphs via use cases of protein rankings and link predictions.

Molecular structure recognition is the task of translating a molecular image into its graph structure. Significant variation in drawing styles and conventions exhibited in chemical literature poses a significant challenge for automating this task. In this paper, we propose MolScribe, a novel image-to-graph generation model that explicitly predicts atoms and bonds, along with their geometric layouts, to construct the molecular structure. Our model flexibly incorporates symbolic chemistry constraints to recognize chirality and expand abbreviated structures. We further develop data augmentation strategies to enhance the model robustness against domain shifts. In experiments on both synthetic and realistic molecular images, MolScribe significantly outperforms previous models, achieving 76-93% accuracy on public benchmarks. Chemists can also easily verify MolScribe's prediction, informed by its confidence estimation and atom-level alignment with the input image. MolScribe is publicly available through Python and web interfaces: https://github.com/thomas0809/MolScribe.

Graph Structure Learning (GSL) focuses on capturing intrinsic dependencies and interactions among nodes in graph-structured data by generating novel graph structures. Graph Neural Networks (GNNs) have emerged as promising GSL solutions, utilizing recursive message passing to encode node-wise inter-dependencies. However, many existing GSL methods heavily depend on explicit graph structural information as supervision signals, leaving them susceptible to challenges such as data noise and sparsity. In this work, we propose GraphEdit, an approach that leverages large language models (LLMs) to learn complex node relationships in graph-structured data. By enhancing the reasoning capabilities of LLMs through instruction-tuning over graph structures, we aim to overcome the limitations associated with explicit graph structural information and enhance the reliability of graph structure learning. Our approach not only effectively denoises noisy connections but also identifies node-wise dependencies from a global perspective, providing a comprehensive understanding of the graph structure. We conduct extensive experiments on multiple benchmark datasets to demonstrate the effectiveness and robustness of GraphEdit across various settings. We have made our model implementation available at: https://github.com/HKUDS/GraphEdit.

For a graph G with n vertices and m edges, Lin et al. Lin define the atom--bond sum-connectivity (ABS) matrix of G such that the (i,j)^{th} entry is \[ 1 - \frac{2{d_i + d_j}} \] if vertex v_i is adjacent to the vertex v_j, and 0 otherwise. In this article, we determine the characteristic polynomial of the ABS matrix for certain specific classes of graphs. Furthermore, we compute the ABS eigenvalues and the ABS energy for these classes.

Recently, there has been a surge of interest in employing neural networks for graph generation, a fundamental statistical learning problem with critical applications like molecule design and community analysis. However, most approaches encounter significant limitations when generating large-scale graphs. This is due to their requirement to output the full adjacency matrices whose size grows quadratically with the number of nodes. In response to this challenge, we introduce a new, simple, and scalable graph representation named gap encoded edge list (GEEL) that has a small representation size that aligns with the number of edges. In addition, GEEL significantly reduces the vocabulary size by incorporating the gap encoding and bandwidth restriction schemes. GEEL can be autoregressively generated with the incorporation of node positional encoding, and we further extend GEEL to deal with attributed graphs by designing a new grammar. Our findings reveal that the adoption of this compact representation not only enhances scalability but also bolsters performance by simplifying the graph generation process. We conduct a comprehensive evaluation across ten non-attributed and two molecular graph generation tasks, demonstrating the effectiveness of GEEL.

This paper presents a novel framework for automated code generation and debugging, designed to improve accuracy, efficiency, and scalability in software development. The proposed system integrates three core components LangGraph, GLM4 Flash, and ChromaDB within a four step iterative workflow to deliver robust performance and seamless functionality. LangGraph serves as a graph-based library for orchestrating tasks, providing precise control and execution while maintaining a unified state object for dynamic updates and consistency. It supports multi-agent, hierarchical, and sequential processes, making it highly adaptable to complex software engineering workflows. GLM4 Flash, a large language model, leverages its advanced capabilities in natural language understanding, contextual reasoning, and multilingual support to generate accurate code snippets based on user prompts. ChromaDB acts as a vector database for semantic search and contextual memory storage, enabling the identification of patterns and the generation of context-aware bug fixes based on historical data. The system operates through a structured four-step process: (1) Code Generation, which translates natural language descriptions into executable code; (2) Code Execution, which validates the code by identifying runtime errors and inconsistencies; (3) Code Repair, which iteratively refines buggy code using ChromaDB's memory capabilities and LangGraph's state tracking; and (4) Code Update, which ensures the code meets functional and performance requirements through iterative modifications.

Graphs are ubiquitous structures found in numerous real-world applications, such as drug discovery, recommender systems, and social network analysis. To model graph-structured data, graph neural networks (GNNs) have become a popular tool. However, existing GNN architectures encounter challenges in cross-graph learning where multiple graphs have different feature spaces. To address this, recent approaches introduce text-attributed graphs (TAGs), where each node is associated with a textual description, which can be projected into a unified feature space using textual encoders. While promising, this method relies heavily on the availability of text-attributed graph data, which is difficult to obtain in practice. To bridge this gap, we propose a novel method named Topology-Aware Node description Synthesis (TANS), leveraging large language models (LLMs) to convert existing graphs into text-attributed graphs. The key idea is to integrate topological information into LLMs to explain how graph topology influences node semantics. We evaluate our TANS on text-rich, text-limited, and text-free graphs, demonstrating its applicability. Notably, on text-free graphs, our method significantly outperforms existing approaches that manually design node features, showcasing the potential of LLMs for preprocessing graph-structured data in the absence of textual information. The code and data are available at https://github.com/Zehong-Wang/TANS.

The advancement of Large Language Models (LLMs) has remarkably pushed the boundaries towards artificial general intelligence (AGI), with their exceptional ability on understanding diverse types of information, including but not limited to images and audio. Despite this progress, a critical gap remains in empowering LLMs to proficiently understand and reason on graph data. Recent studies underscore LLMs' underwhelming performance on fundamental graph reasoning tasks. In this paper, we endeavor to unearth the obstacles that impede LLMs in graph reasoning, pinpointing the common practice of converting graphs into natural language descriptions (Graph2Text) as a fundamental bottleneck. To overcome this impediment, we introduce GraphLLM, a pioneering end-to-end approach that synergistically integrates graph learning models with LLMs. This synergy equips LLMs with the ability to proficiently interpret and reason on graph data, harnessing the superior expressive power of graph learning models. Our empirical evaluations across four fundamental graph reasoning tasks validate the effectiveness of GraphLLM. The results exhibit a substantial average accuracy enhancement of 54.44%, alongside a noteworthy context reduction of 96.45% across various graph reasoning tasks.

Large language models (LLMs) have demonstrated remarkable success across a wide range of tasks; however, they still encounter challenges in reasoning tasks that require understanding and inferring relationships between distinct pieces of information within text sequences. This challenge is particularly pronounced in tasks involving multi-step processes, such as logical reasoning and multi-hop question answering, where understanding implicit relationships between entities and leveraging multi-hop connections in the given context are crucial. Graphs, as fundamental data structures, explicitly represent pairwise relationships between entities, thereby offering the potential to enhance LLMs' reasoning capabilities. External graphs have proven effective in supporting LLMs across multiple tasks. However, in many reasoning tasks, no pre-existing graph structure is provided. Can we structure implicit knowledge derived from context into graphs to assist LLMs in reasoning? In this paper, we propose Reasoning with Graphs (RwG) by first constructing explicit graphs from the context and then leveraging these graphs to enhance LLM reasoning performance on reasoning tasks. Extensive experiments demonstrate the effectiveness of the proposed method in improving both logical reasoning and multi-hop question answering tasks.

Knowledge graphs have been proven extremely useful in powering diverse applications in semantic search and natural language understanding. In this paper, we present GraphGen4Code, a toolkit to build code knowledge graphs that can similarly power various applications such as program search, code understanding, bug detection, and code automation. GraphGen4Code uses generic techniques to capture code semantics with the key nodes in the graph representing classes, functions, and methods. Edges indicate function usage (e.g., how data flows through function calls, as derived from program analysis of real code), and documentation about functions (e.g., code documentation, usage documentation, or forum discussions such as StackOverflow). Our toolkit uses named graphs in RDF to model graphs per program, or can output graphs as JSON. We show the scalability of the toolkit by applying it to 1.3 million Python files drawn from GitHub, 2,300 Python modules, and 47 million forum posts. This results in an integrated code graph with over 2 billion triples. We make the toolkit to build such graphs as well as the sample extraction of the 2 billion triples graph publicly available to the community for use.

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.

Scene graph generation has emerged as a prominent research field in computer vision, witnessing significant advancements in the recent years. However, despite these strides, precise and thorough definitions for the metrics used to evaluate scene graph generation models are lacking. In this paper, we address this gap in the literature by providing a review and precise definition of commonly used metrics in scene graph generation. Our comprehensive examination clarifies the underlying principles of these metrics and can serve as a reference or introduction to scene graph metrics. Furthermore, to facilitate the usage of these metrics, we introduce a standalone Python package called SGBench that efficiently implements all defined metrics, ensuring their accessibility to the research community. Additionally, we present a scene graph benchmarking web service, that enables researchers to compare scene graph generation methods and increase visibility of new methods in a central place. All of our code can be found at https://lorjul.github.io/sgbench/.

We introduce rLLM (relationLLM), a PyTorch library designed for Relational Table Learning (RTL) with Large Language Models (LLMs). The core idea is to decompose state-of-the-art Graph Neural Networks, LLMs, and Table Neural Networks into standardized modules, to enable the fast construction of novel RTL-type models in a simple "combine, align, and co-train" manner. To illustrate the usage of rLLM, we introduce a simple RTL method named BRIDGE. Additionally, we present three novel relational tabular datasets (TML1M, TLF2K, and TACM12K) by enhancing classic datasets. We hope rLLM can serve as a useful and easy-to-use development framework for RTL-related tasks. Our code is available at: https://github.com/rllm-project/rllm.

Graph-structured data are the commonly used and have wide application scenarios in the real world. For these diverse applications, the vast variety of learning tasks, graph domains, and complex graph learning procedures present challenges for human experts when designing versatile graph learning approaches. Facing these challenges, large language models (LLMs) offer a potential solution due to the extensive knowledge and the human-like intelligence. This paper proposes a novel conceptual prototype for designing versatile graph learning methods with LLMs, with a particular focus on the "where" and "how" perspectives. From the "where" perspective, we summarize four key graph learning procedures, including task definition, graph data feature engineering, model selection and optimization, deployment and serving. We then explore the application scenarios of LLMs in these procedures across a wider spectrum. In the "how" perspective, we align the abilities of LLMs with the requirements of each procedure. Finally, we point out the promising directions that could better leverage the strength of LLMs towards versatile graph learning methods.

Neural inductive program synthesis is a task generating instructions that can produce desired outputs from given inputs. In this paper, we focus on the generation of a chunk of assembly code that can be executed to match a state change inside the CPU and RAM. We develop a neural program synthesis algorithm, AutoAssemblet, learned via self-learning reinforcement learning that explores the large code space efficiently. Policy networks and value networks are learned to reduce the breadth and depth of the Monte Carlo Tree Search, resulting in better synthesis performance. We also propose an effective multi-entropy policy sampling technique to alleviate online update correlations. We apply AutoAssemblet to basic programming tasks and show significant higher success rates compared to several competing baselines.

Mobile manipulators in households must both navigate and manipulate. This requires a compact, semantically rich scene representation that captures where objects are, how they function, and which parts are actionable. Scene graphs are a natural choice, yet prior work often separates spatial and functional relations, treats scenes as static snapshots without object states or temporal updates, and overlooks information most relevant for accomplishing the current task. To address these limitations, we introduce MomaGraph, a unified scene representation for embodied agents that integrates spatial-functional relationships and part-level interactive elements. However, advancing such a representation requires both suitable data and rigorous evaluation, which have been largely missing. We thus contribute MomaGraph-Scenes, the first large-scale dataset of richly annotated, task-driven scene graphs in household environments, along with MomaGraph-Bench, a systematic evaluation suite spanning six reasoning capabilities from high-level planning to fine-grained scene understanding. Built upon this foundation, we further develop MomaGraph-R1, a 7B vision-language model trained with reinforcement learning on MomaGraph-Scenes. MomaGraph-R1 predicts task-oriented scene graphs and serves as a zero-shot task planner under a Graph-then-Plan framework. Extensive experiments demonstrate that our model achieves state-of-the-art results among open-source models, reaching 71.6% accuracy on the benchmark (+11.4% over the best baseline), while generalizing across public benchmarks and transferring effectively to real-robot experiments.

This paper presents a novel approach for source code similarity detection that integrates an additional output feature into the classification process with the goal of improving model performance. Our approach is based on the GraphCodeBERT model, extended with a custom output feature layer and a concatenation mechanism for improved feature representation. The model was trained and evaluated, achieving promising results in terms of precision, recall, and f-measure. The implementation details, including model architecture and training strategies are discussed. The source code that illustrates our approach can be downloaded from https://www.github.com/jorge-martinez-gil/graphcodebert-feature-integration.

Many graph representation learning (GRL) problems are dynamic, with millions of edges added or removed per second. A fundamental workload in this setting is dynamic link prediction: using a history of graph updates to predict whether a given pair of vertices will become connected. Recent schemes for link prediction in such dynamic settings employ Transformers, modeling individual graph updates as single tokens. In this work, we propose HOT: a model that enhances this line of works by harnessing higher-order (HO) graph structures; specifically, k-hop neighbors and more general subgraphs containing a given pair of vertices. Harnessing such HO structures by encoding them into the attention matrix of the underlying Transformer results in higher accuracy of link prediction outcomes, but at the expense of increased memory pressure. To alleviate this, we resort to a recent class of schemes that impose hierarchy on the attention matrix, significantly reducing memory footprint. The final design offers a sweetspot between high accuracy and low memory utilization. HOT outperforms other dynamic GRL schemes, for example achieving 9%, 7%, and 15% higher accuracy than - respectively - DyGFormer, TGN, and GraphMixer, for the MOOC dataset. Our design can be seamlessly extended towards other dynamic GRL workloads.

Understanding causal relationships between machines is crucial for fault diagnosis and optimization in manufacturing processes. Real-world datasets frequently exhibit up to 90% missing data and high dimensionality from hundreds of sensors. These datasets also include domain-specific expert knowledge and chronological order information, reflecting the recording order across different machines, which is pivotal for discerning causal relationships within the manufacturing data. However, previous methods for handling missing data in scenarios akin to real-world conditions have not been able to effectively utilize expert knowledge. Conversely, prior methods that can incorporate expert knowledge struggle with datasets that exhibit missing values. Therefore, we propose COKE to construct causal graphs in manufacturing datasets by leveraging expert knowledge and chronological order among sensors without imputing missing data. Utilizing the characteristics of the recipe, we maximize the use of samples with missing values, derive embeddings from intersections with an initial graph that incorporates expert knowledge and chronological order, and create a sensor ordering graph. The graph-generating process has been optimized by an actor-critic architecture to obtain a final graph that has a maximum reward. Experimental evaluations in diverse settings of sensor quantities and missing proportions demonstrate that our approach compared with the benchmark methods shows an average improvement of 39.9% in the F1-score. Moreover, the F1-score improvement can reach 62.6% when considering the configuration similar to real-world datasets, and 85.0% in real-world semiconductor datasets. The source code is available at https://github.com/OuTingYun/COKE.

Robotic assembly tasks are open challenges due to the long task horizon and complex part relations. Behavior trees (BTs) are increasingly used in robot task planning for their modularity and flexibility, but manually designing them can be effort-intensive. Large language models (LLMs) have recently been applied in robotic task planning for generating action sequences, but their ability to generate BTs has not been fully investigated. To this end, We propose LLM as BT-planner, a novel framework to leverage LLMs for BT generation in robotic assembly task planning and execution. Four in-context learning methods are introduced to utilize the natural language processing and inference capabilities of LLMs to produce task plans in BT format, reducing manual effort and ensuring robustness and comprehensibility. We also evaluate the performance of fine-tuned, fewer-parameter LLMs on the same tasks. Experiments in simulated and real-world settings show that our framework enhances LLMs' performance in BT generation, improving success rates in BT generation through in-context learning and supervised fine-tuning.

Recent studies in using deep reinforcement learning (DRL) to solve Job-shop scheduling problems (JSSP) focus on construction heuristics. However, their performance is still far from optimality, mainly because the underlying graph representation scheme is unsuitable for modelling partial solutions at each construction step. This paper proposes a novel DRL-guided improvement heuristic for solving JSSP, where graph representation is employed to encode complete solutions. We design a Graph Neural-Network-based representation scheme, consisting of two modules to effectively capture the information of dynamic topology and different types of nodes in graphs encountered during the improvement process. To speed up solution evaluation during improvement, we present a novel message-passing mechanism that can evaluate multiple solutions simultaneously. We prove that the computational complexity of our method scales linearly with problem size. Experiments on classic benchmarks show that the improvement policy learned by our method outperforms state-of-the-art DRL-based methods by a large margin.

G-code (Geometric code) or RS-274 is the most widely used computer numerical control (CNC) and 3D printing programming language. G-code provides machine instructions for the movement of the 3D printer, especially for the nozzle, stage, and extrusion of material for extrusion-based additive manufacturing. Currently there does not exist a large repository of curated CAD models along with their corresponding G-code files for additive manufacturing. To address this issue, we present SLICE-100K, a first-of-its-kind dataset of over 100,000 G-code files, along with their tessellated CAD model, LVIS (Large Vocabulary Instance Segmentation) categories, geometric properties, and renderings. We build our dataset from triangulated meshes derived from Objaverse-XL and Thingi10K datasets. We demonstrate the utility of this dataset by finetuning GPT-2 on a subset of the dataset for G-code translation from a legacy G-code format (Sailfish) to a more modern, widely used format (Marlin). SLICE-100K will be the first step in developing a multimodal foundation model for digital manufacturing.

3D indoor scenes are widely used in computer graphics, with applications ranging from interior design to gaming to virtual and augmented reality. They also contain rich information, including room layout, as well as furniture type, geometry, and placement. High-quality 3D indoor scenes are highly demanded while it requires expertise and is time-consuming to design high-quality 3D indoor scenes manually. Existing research only addresses partial problems: some works learn to generate room layout, and other works focus on generating detailed structure and geometry of individual furniture objects. However, these partial steps are related and should be addressed together for optimal synthesis. We propose SCENEHGN, a hierarchical graph network for 3D indoor scenes that takes into account the full hierarchy from the room level to the object level, then finally to the object part level. Therefore for the first time, our method is able to directly generate plausible 3D room content, including furniture objects with fine-grained geometry, and their layout. To address the challenge, we introduce functional regions as intermediate proxies between the room and object levels to make learning more manageable. To ensure plausibility, our graph-based representation incorporates both vertical edges connecting child nodes with parent nodes from different levels, and horizontal edges encoding relationships between nodes at the same level. Extensive experiments demonstrate that our method produces superior generation results, even when comparing results of partial steps with alternative methods that can only achieve these. We also demonstrate that our method is effective for various applications such as part-level room editing, room interpolation, and room generation by arbitrary room boundaries.

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%.

Crystal structures are characterized by atomic bases within a primitive unit cell that repeats along a regular lattice throughout 3D space. The periodic and infinite nature of crystals poses unique challenges for geometric graph representation learning. Specifically, constructing graphs that effectively capture the complete geometric information of crystals and handle chiral crystals remains an unsolved and challenging problem. In this paper, we introduce a novel approach that utilizes the periodic patterns of unit cells to establish the lattice-based representation for each atom, enabling efficient and expressive graph representations of crystals. Furthermore, we propose ComFormer, a SE(3) transformer designed specifically for crystalline materials. ComFormer includes two variants; namely, iComFormer that employs invariant geometric descriptors of Euclidean distances and angles, and eComFormer that utilizes equivariant vector representations. Experimental results demonstrate the state-of-the-art predictive accuracy of ComFormer variants on various tasks across three widely-used crystal benchmarks. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS).

Decompilation aims to restore compiled code to human-readable source code, but struggles with details like names and structure. Large language models (LLMs) show promise for programming tasks, motivating their application to decompilation. However, there does not exist any open-source LLM for decompilation. Moreover, existing decompilation evaluation systems mainly consider token-level accuracy and largely ignore code executability, which is the most important feature of any program. Therefore, we release the first open-access decompilation LLMs ranging from 1B to 33B pre-trained on 4 billion tokens of C source code and the corresponding assembly code. The open-source LLMs can serve as baselines for further development in the field. To ensure practical program evaluation, we introduce Decompile-Eval, the first dataset that considers re-compilability and re-executability for decompilation. The benchmark emphasizes the importance of evaluating the decompilation model from the perspective of program semantics. Experiments indicate that our LLM4Decompile has demonstrated the capability to accurately decompile 21% of the assembly code, which achieves a 50% improvement over GPT-4. Our code, dataset, and models are released at https://github.com/albertan017/LLM4Decompile

Deep graph generative modeling has proven capable of learning the distribution of complex, multi-scale structures characterizing real-world graphs. However, one of the main limitations of existing methods is their large output space, which limits generation scalability and hinders accurate modeling of the underlying distribution. To overcome these limitations, we propose a novel approach that significantly reduces the output space of existing graph generative models. Specifically, starting from the observation that many real-world graphs have low graph bandwidth, we restrict graph bandwidth during training and generation. Our strategy improves both generation scalability and quality without increasing architectural complexity or reducing expressiveness. Our approach is compatible with existing graph generative methods, and we describe its application to both autoregressive and one-shot models. We extensively validate our strategy on synthetic and real datasets, including molecular graphs. Our experiments show that, in addition to improving generation efficiency, our approach consistently improves generation quality and reconstruction accuracy. The implementation is made available.

We present a unified representation for actionable spatial perception: 3D Dynamic Scene Graphs. Scene graphs are directed graphs where nodes represent entities in the scene (e.g. objects, walls, rooms), and edges represent relations (e.g. inclusion, adjacency) among nodes. Dynamic scene graphs (DSGs) extend this notion to represent dynamic scenes with moving agents (e.g. humans, robots), and to include actionable information that supports planning and decision-making (e.g. spatio-temporal relations, topology at different levels of abstraction). Our second contribution is to provide the first fully automatic Spatial PerceptIon eNgine(SPIN) to build a DSG from visual-inertial data. We integrate state-of-the-art techniques for object and human detection and pose estimation, and we describe how to robustly infer object, robot, and human nodes in crowded scenes. To the best of our knowledge, this is the first paper that reconciles visual-inertial SLAM and dense human mesh tracking. Moreover, we provide algorithms to obtain hierarchical representations of indoor environments (e.g. places, structures, rooms) and their relations. Our third contribution is to demonstrate the proposed spatial perception engine in a photo-realistic Unity-based simulator, where we assess its robustness and expressiveness. Finally, we discuss the implications of our proposal on modern robotics applications. 3D Dynamic Scene Graphs can have a profound impact on planning and decision-making, human-robot interaction, long-term autonomy, and scene prediction. A video abstract is available at https://youtu.be/SWbofjhyPzI

Large language models (LLMs) like ChatGPT, exhibit powerful zero-shot and instruction-following capabilities, have catalyzed a revolutionary transformation across diverse fields, especially for open-ended tasks. While the idea is less explored in the graph domain, despite the availability of numerous powerful graph models (GMs), they are restricted to tasks in a pre-defined form. Although several methods applying LLMs to graphs have been proposed, they fail to simultaneously handle the pre-defined and open-ended tasks, with LLM as a node feature enhancer or as a standalone predictor. To break this dilemma, we propose to bridge the pretrained GM and LLM by a Translator, named GraphTranslator, aiming to leverage GM to handle the pre-defined tasks effectively and utilize the extended interface of LLMs to offer various open-ended tasks for GM. To train such Translator, we propose a Producer capable of constructing the graph-text alignment data along node information, neighbor information and model information. By translating node representation into tokens, GraphTranslator empowers an LLM to make predictions based on language instructions, providing a unified perspective for both pre-defined and open-ended tasks. Extensive results demonstrate the effectiveness of our proposed GraphTranslator on zero-shot node classification. The graph question answering experiments reveal our GraphTranslator potential across a broad spectrum of open-ended tasks through language instructions. Our code is available at: https://github.com/alibaba/GraphTranslator.

The issue localization task aims to identify the locations in a software repository that requires modification given a natural language issue description. This task is fundamental yet challenging in automated software engineering due to the semantic gap between issue description and source code implementation. This gap manifests as two mismatches:(1) symptom-to-cause mismatches, where descriptions do not explicitly reveal underlying root causes; (2) one-to-many mismatches, where a single issue corresponds to multiple interdependent code entities. To address these two mismatches, we propose GraphLocator, an approach that mitigates symptom-to-cause mismatches through causal structure discovering and resolves one-to-many mismatches via dynamic issue disentangling. The key artifact is the causal issue graph (CIG), in which vertices represent discovered sub-issues along with their associated code entities, and edges encode the causal dependencies between them. The workflow of GraphLocator consists of two phases: symptom vertices locating and dynamic CIG discovering; it first identifies symptom locations on the repository graph, then dynamically expands the CIG by iteratively reasoning over neighboring vertices. Experiments on three real-world datasets demonstrates the effectiveness of GraphLocator: (1) Compared with baselines, GraphLocator achieves more accurate localization with average improvements of +19.49% in function-level recall and +11.89% in precision. (2) GraphLocator outperforms baselines on both symptom-to-cause and one-to-many mismatch scenarios, achieving recall improvement of +16.44% and +19.18%, precision improvement of +7.78% and +13.23%, respectively. (3) The CIG generated by GraphLocator yields the highest relative improvement, resulting in a 28.74% increase in performance on downstream resolving task.

We introduce the task of text-to-diagram generation, which focuses on creating structured visual representations directly from textual descriptions. Existing approaches in text-to-image and text-to-code generation lack the logical organization and flexibility needed to produce accurate, editable diagrams, often resulting in outputs that are either unstructured or difficult to modify. To address this gap, we introduce DiagramGenBenchmark, a comprehensive evaluation framework encompassing eight distinct diagram categories, including flowcharts, model architecture diagrams, and mind maps. Additionally, we present DiagramAgent, an innovative framework with four core modules-Plan Agent, Code Agent, Check Agent, and Diagram-to-Code Agent-designed to facilitate both the generation and refinement of complex diagrams. Our extensive experiments, which combine objective metrics with human evaluations, demonstrate that DiagramAgent significantly outperforms existing baseline models in terms of accuracy, structural coherence, and modifiability. This work not only establishes a foundational benchmark for the text-to-diagram generation task but also introduces a powerful toolset to advance research and applications in this emerging area.

Large Language Models (LLMs) have gained the ability to assimilate human knowledge and facilitate natural language interactions with both humans and other LLMs. However, despite their impressive achievements, LLMs have not made significant advancements in the realm of graph machine learning. This limitation arises because graphs encapsulate distinct relational data, making it challenging to transform them into natural language that LLMs understand. In this paper, we bridge this gap with a novel framework, GraphText, that translates graphs into natural language. GraphText derives a graph-syntax tree for each graph that encapsulates both the node attributes and inter-node relationships. Traversal of the tree yields a graph text sequence, which is then processed by an LLM to treat graph tasks as text generation tasks. Notably, GraphText offers multiple advantages. It introduces training-free graph reasoning: even without training on graph data, GraphText with ChatGPT can achieve on par with, or even surpassing, the performance of supervised-trained graph neural networks through in-context learning (ICL). Furthermore, GraphText paves the way for interactive graph reasoning, allowing both humans and LLMs to communicate with the model seamlessly using natural language. These capabilities underscore the vast, yet-to-be-explored potential of LLMs in the domain of graph machine learning.

Existing visual parsers for molecule diagrams translate pixel-based raster images such as PNGs to chemical structure representations (e.g., SMILES). However, PDFs created by word processors including LaTeX and Word provide explicit locations and shapes for characters, lines, and polygons. We extract symbols from born-digital PDF molecule images and then apply simple graph transformations to capture both visual and chemical structure in editable ChemDraw files (CDXML). Our fast ( PDF rightarrow visual graph rightarrow chemical graph ) pipeline does not require GPUs, Optical Character Recognition (OCR) or vectorization. We evaluate on standard benchmarks using SMILES strings, along with a novel evaluation that provides graph-based metrics and error compilation using LgEval. The geometric information in born-digital PDFs produces a highly accurate parser, motivating generating training data for visual parsers that recognize from raster images, with extracted graphics, visual structure, and chemical structure as annotations. To do this we render SMILES strings in Indigo, parse molecule structure, and then validate recognized structure to select correct files.

Language models have been effective in a wide range of applications, yet the most sophisticated models are often proprietary. For example, GPT-4 by OpenAI and various models by Anthropic are expensive and consume substantial energy. In contrast, the open-source community has produced competitive models, like Llama3. Furthermore, niche-specific smaller language models, such as those tailored for legal, medical or financial tasks, have outperformed their proprietary counterparts. This paper introduces a novel approach that employs functional tokens to integrate multiple open-source models, each optimized for particular tasks. Our newly developed Octopus v4 model leverages functional tokens to intelligently direct user queries to the most appropriate vertical model and reformat the query to achieve the best performance. Octopus v4, an evolution of the Octopus v1, v2, and v3 models, excels in selection and parameter understanding and reformatting. Additionally, we explore the use of graph as a versatile data structure that effectively coordinates multiple open-source models by harnessing the capabilities of the Octopus model and functional tokens. Use our open-sourced GitHub (https://www.nexa4ai.com/) to try Octopus v4 models (https://huggingface.co/NexaAIDev/Octopus-v4), and contrite to a larger graph of language models. By activating models less than 10B parameters, we achieved SOTA MMLU score of 74.8 among the same level models.

Large language models (LLMs), such as ChatGPT and LLaMA, are creating significant advancements in natural language processing, due to their strong text encoding/decoding ability and newly found emergent capability (e.g., reasoning). While LLMs are mainly designed to process pure texts, there are many real-world scenarios where text data are associated with rich structure information in the form of graphs (e.g., academic networks, and e-commerce networks) or scenarios where graph data are paired with rich textual information (e.g., molecules with descriptions). Besides, although LLMs have shown their pure text-based reasoning ability, it is underexplored whether such ability can be generalized to graph scenarios (i.e., graph-based reasoning). In this paper, we provide a systematic review of scenarios and techniques related to large language models on graphs. We first summarize potential scenarios of adopting LLMs on graphs into three categories, namely pure graphs, text-rich graphs, and text-paired graphs. We then discuss detailed techniques for utilizing LLMs on graphs, including LLM as Predictor, LLM as Encoder, and LLM as Aligner, and compare the advantages and disadvantages of different schools of models. Furthermore, we mention the real-world applications of such methods and summarize open-source codes and benchmark datasets. Finally, we conclude with potential future research directions in this fast-growing field. The related source can be found at https://github.com/PeterGriffinJin/Awesome-Language-Model-on-Graphs.

Graphs are widely used for modeling relational data in real-world scenarios, such as social networks and urban computing. Existing LLM-based graph analysis approaches either integrate graph neural networks (GNNs) for specific machine learning tasks, limiting their transferability, or rely solely on LLMs' internal reasoning ability, resulting in suboptimal performance. To address these limitations, we take advantage of recent advances in LLM-based agents, which have shown capabilities of utilizing external knowledge or tools for problem solving. By simulating human problem-solving strategies such as analogy and collaboration, we propose a multi-agent system based on LLMs named GraphTeam, for graph analysis. GraphTeam consists of five LLM-based agents from three modules, and the agents with different specialities can collaborate with each other to address complex problems. Specifically, (1) input-output normalization module: the question agent extracts and refines four key arguments from the original question, facilitating the problem understanding, and the answer agent organizes the results to meet the output requirement; (2) external knowledge retrieval module: we first build a knowledge base consisting of relevant documentation and experience information, and then the search agent retrieves the most relevant entries for each question. (3) problem-solving module: given the retrieved information from search agent, the coding agent uses established algorithms via programming to generate solutions, and in case the coding agent does not work, the reasoning agent will directly compute the results without programming. Extensive experiments on six graph analysis benchmarks demonstrate that GraphTeam achieves state-of-the-art performance with an average 25.85% improvement over the best baseline in terms of accuracy. The code and data are available at https://github.com/BUPT-GAMMA/GraphTeam.

In recent years, Graph Neural Networks (GNNs) have made significant advances in processing structured data. However, most of them primarily adopted a model-centric approach, which simplifies graphs by converting them into undirected formats and emphasizes model designs. This approach is inherently limited in real-world applications due to the unavoidable information loss in simple undirected graphs and the model optimization challenges that arise when exceeding the upper bounds of this sub-optimal data representational capacity. As a result, there has been a shift toward data-centric methods that prioritize improving graph quality and representation. Specifically, various types of graphs can be derived from naturally structured data, including heterogeneous graphs, hypergraphs, and directed graphs. Among these, directed graphs offer distinct advantages in topological systems by modeling causal relationships, and directed GNNs have been extensively studied in recent years. However, a comprehensive survey of this emerging topic is still lacking. Therefore, we aim to provide a comprehensive review of directed graph learning, with a particular focus on a data-centric perspective. Specifically, we first introduce a novel taxonomy for existing studies. Subsequently, we re-examine these methods from the data-centric perspective, with an emphasis on understanding and improving data representation. It demonstrates that a deep understanding of directed graphs and their quality plays a crucial role in model performance. Additionally, we explore the diverse applications of directed GNNs across 10+ domains, highlighting their broad applicability. Finally, we identify key opportunities and challenges within the field, offering insights that can guide future research and development in directed graph learning.

Large Language Models (LLMs) have garnered considerable interest within both academic and industrial. Yet, the application of LLMs to graph data remains under-explored. In this study, we evaluate the capabilities of four LLMs in addressing several analytical problems with graph data. We employ four distinct evaluation metrics: Comprehension, Correctness, Fidelity, and Rectification. Our results show that: 1) LLMs effectively comprehend graph data in natural language and reason with graph topology. 2) GPT models can generate logical and coherent results, outperforming alternatives in correctness. 3) All examined LLMs face challenges in structural reasoning, with techniques like zero-shot chain-of-thought and few-shot prompting showing diminished efficacy. 4) GPT models often produce erroneous answers in multi-answer tasks, raising concerns in fidelity. 5) GPT models exhibit elevated confidence in their outputs, potentially hindering their rectification capacities. Notably, GPT-4 has demonstrated the capacity to rectify responses from GPT-3.5-turbo and its own previous iterations. The code is available at: https://github.com/Ayame1006/LLMtoGraph.

The notion of shortcut partition, introduced recently by Chang, Conroy, Le, Milenkovi\'c, Solomon, and Than [CCLMST23], is a new type of graph partition into low-diameter clusters. Roughly speaking, the shortcut partition guarantees that for every two vertices u and v in the graph, there exists a path between u and v that intersects only a few clusters. They proved that any planar graph admits a shortcut partition and gave several applications, including a construction of tree cover for arbitrary planar graphs with stretch 1+varepsilon and O(1) many trees for any fixed varepsilon in (0,1). However, the construction heavily exploits planarity in multiple steps, and is thus inherently limited to planar graphs. In this work, we breach the "planarity barrier" to construct a shortcut partition for K_r-minor-free graphs for any r. To this end, we take a completely different approach -- our key contribution is a novel deterministic variant of the cop decomposition in minor-free graphs [And86, AGG14]. Our shortcut partition for K_r-minor-free graphs yields several direct applications. Most notably, we construct the first optimal distance oracle for K_r-minor-free graphs, with 1+varepsilon stretch, linear space, and constant query time for any fixed varepsilon in (0,1). The previous best distance oracle [AG06] uses O(nlog n) space and O(log n) query time, and its construction relies on Robertson-Seymour structural theorem and other sophisticated tools. We also obtain the first tree cover of O(1) size for minor-free graphs with stretch 1+varepsilon, while the previous best (1+varepsilon)-tree cover has size O(log^2 n) [BFN19].

Designing a single model to address multiple tasks has been a long-standing objective in artificial intelligence. Recently, large language models have demonstrated exceptional capability in solving different tasks within the language domain. However, a unified model for various graph tasks remains underexplored, primarily due to the challenges unique to the graph learning domain. First, graph data from different areas carry distinct attributes and follow different distributions. Such discrepancy makes it hard to represent graphs in a single representation space. Second, tasks on graphs diversify into node, link, and graph tasks, requiring distinct embedding strategies. Finally, an appropriate graph prompting paradigm for in-context learning is unclear. We propose One for All (OFA), the first general framework that can use a single graph model to address the above challenges. Specifically, OFA proposes text-attributed graphs to unify different graph data by describing nodes and edges with natural language and uses language models to encode the diverse and possibly cross-domain text attributes to feature vectors in the same embedding space. Furthermore, OFA introduces the concept of nodes-of-interest to standardize different tasks with a single task representation. For in-context learning on graphs, OFA introduces a novel graph prompting paradigm that appends prompting substructures to the input graph, which enables it to address varied tasks without fine-tuning. We train the OFA model using graph data from multiple domains (including citation networks, molecular graphs, knowledge graphs, etc.) simultaneously and evaluate its ability in supervised, few-shot, and zero-shot learning scenarios. OFA performs well across different tasks, making it the first general-purpose across-domains classification model on graphs.

The transition from x86 to ARM architecture is becoming increasingly common across various domains, primarily driven by ARM's energy efficiency and improved performance across traditional sectors. However, this ISA shift poses significant challenges, mainly due to the extensive legacy ecosystem of x86 software and lack of portability across proprietary ecosystems and software stacks. This paper introduces CRT, a lightweight LLM-based transpiler that automatically converts x86 assembly to ARM assembly. Our approach bridges the fundamental architectural gap between x86's CISC-based and ARM's RISC-based computing paradigms while preserving program semantics and optimizing performance. We evaluate CRT on diverse real-world applications, achieving 79.25% translation accuracy from x86 to ARMv5 on our comprehensive test suite, and an 88.68% accuracy from x86 to RISC-V. In practical deployments on Apple M2 hardware (ARMv8), our transpiled code achieves 1.73times speedup compared to Apple's Rosetta 2 virtualization engine, while delivering 2.41times memory efficiency and 1.47times better energy consumption. Through testing and analysis, we show that CRT successfully navigates the CISC/RISC divide and generates correctly executable RISC code despite machine ``language'' barriers. We release our code, models, training datasets, and benchmarks at: https://ahmedheakl.github.io/asm2asm/.

The use of graph neural networks has produced significant advances in point cloud problems, such as those found in high energy physics. The question of how to produce a graph structure in these problems is usually treated as a matter of heuristics, employing fully connected graphs or K-nearest neighbors. In this work, we elevate this question to utmost importance as the Topology Problem. We propose an attention mechanism that allows a graph to be constructed in a learned space that handles geometrically the flow of relevance, providing one solution to the Topology Problem. We test this architecture, called GravNetNorm, on the task of top jet tagging, and show that it is competitive in tagging accuracy, and uses far fewer computational resources than all other comparable models.

This tutorial serves as a comprehensive guide for understanding graph databases, focusing on the fundamentals of graph theory while showcasing practical applications across various fields. It starts by introducing foundational concepts and delves into the structure of graphs through nodes and edges, covering different types such as undirected, directed, weighted, and unweighted graphs. Key graph properties, terminologies, and essential algorithms for network analysis are outlined, including Dijkstras shortest path algorithm and methods for calculating node centrality and graph connectivity. The tutorial highlights the advantages of graph databases over traditional relational databases, particularly in efficiently managing complex, interconnected data. It examines leading graph database systems such as Neo4j, Amazon Neptune, and ArangoDB, emphasizing their unique features for handling large datasets. Practical instructions on graph operations using NetworkX and Neo4j are provided, covering node and edge creation, attribute assignment, and advanced queries with Cypher. Additionally, the tutorial explores common graph visualization techniques using tools like Plotly and Neo4j Bloom, which enhance the interpretation and usability of graph data. It also delves into community detection algorithms, including the Louvain method, which facilitates clustering in large networks. Finally, the paper concludes with recommendations for researchers interested in exploring the vast potential of graph technologies.

Relational databases (RDBs) are composed of interconnected tables, where relationships between them are defined through foreign keys. Recent research on applying machine learning to RDBs has explored graph-based representations of RDBs, where rows of tables are modeled as nodes, and foreign key relationships are modeled as edges. RDB-to-graph modeling helps capture cross-table dependencies, ultimately leading to enhanced performance across diverse tasks. However, there are numerous ways to model RDBs as graphs, and performance varies significantly depending on the chosen graph model. In our analysis, applying a common heuristic rule for graph modeling leads to up to a 10% drop in performance compared to the best-performing graph model, which remains non-trivial to identify. To foster research on intelligent RDB-to-graph modeling, we introduce RDB2G-Bench, the first benchmark framework for evaluating such methods. We construct extensive datasets covering 5 real-world RDBs and 12 predictive tasks, resulting in around 50k graph-performance pairs for efficient and reproducible evaluations. Thanks to our precomputed datasets, we were able to benchmark 9 automatic RDB-to-graph modeling methods on the 12 tasks over 600x faster than on-the-fly evaluation, which requires repeated model training. Our analysis of the datasets and benchmark results reveals key structural patterns affecting graph model effectiveness, along with practical implications for effective graph modeling.

Machine learning (ML) and deep learning (DL) techniques have gained significant attention as reduced order models (ROMs) to computationally expensive structural analysis methods, such as finite element analysis (FEA). Graph neural network (GNN) is a particular type of neural network which processes data that can be represented as graphs. This allows for efficient representation of complex geometries that can change during conceptual design of a structure or a product. In this study, we propose a novel graph embedding technique for efficient representation of 3D stiffened panels by considering separate plate domains as vertices. This approach is considered using Graph Sampling and Aggregation (GraphSAGE) to predict stress distributions in stiffened panels with varying geometries. A comparison between a finite-element-vertex graph representation is conducted to demonstrate the effectiveness of the proposed approach. A comprehensive parametric study is performed to examine the effect of structural geometry on the prediction performance. Our results demonstrate the immense potential of graph neural networks with the proposed graph embedding method as robust reduced-order models for 3D structures.

Artificial general intelligence on graphs has shown significant advancements across various applications, yet the traditional 'Pre-train & Fine-tune' paradigm faces inefficiencies and negative transfer issues, particularly in complex and few-shot settings. Graph prompt learning emerges as a promising alternative, leveraging lightweight prompts to manipulate data and fill the task gap by reformulating downstream tasks to the pretext. However, several critical challenges still remain: how to unify diverse graph prompt models, how to evaluate the quality of graph prompts, and to improve their usability for practical comparisons and selection. In response to these challenges, we introduce the first comprehensive benchmark for graph prompt learning. Our benchmark integrates SIX pre-training methods and FIVE state-of-the-art graph prompt techniques, evaluated across FIFTEEN diverse datasets to assess performance, flexibility, and efficiency. We also present 'ProG', an easy-to-use open-source library that streamlines the execution of various graph prompt models, facilitating objective evaluations. Additionally, we propose a unified framework that categorizes existing graph prompt methods into two main approaches: prompts as graphs and prompts as tokens. This framework enhances the applicability and comparison of graph prompt techniques. The code is available at: https://github.com/sheldonresearch/ProG.

We explore the effects of various plasticity functions on assemblies of neurons. To bridge the gap between experimental and computational theories we make use of a conceptual framework, the Assembly Calculus, which is a formal system for the description of brain function based on assemblies of neurons. The Assembly Calculus includes operations for projecting, associating, and merging assemblies of neurons. Our research is focused on simulating different plasticity functions with Assembly Calculus. Our main contribution is the modification and evaluation of the projection operation. We experiment with Oja's and Spike Time-Dependent Plasticity (STDP) rules and test the effect of various hyper-parameters.

This paper aims to design a unified Computer-Aided Design (CAD) generation system that can easily generate CAD models based on the user's inputs in the form of textual description, images, point clouds, or even a combination of them. Towards this goal, we introduce the CAD-MLLM, the first system capable of generating parametric CAD models conditioned on the multimodal input. Specifically, within the CAD-MLLM framework, we leverage the command sequences of CAD models and then employ advanced large language models (LLMs) to align the feature space across these diverse multi-modalities data and CAD models' vectorized representations. To facilitate the model training, we design a comprehensive data construction and annotation pipeline that equips each CAD model with corresponding multimodal data. Our resulting dataset, named Omni-CAD, is the first multimodal CAD dataset that contains textual description, multi-view images, points, and command sequence for each CAD model. It contains approximately 450K instances and their CAD construction sequences. To thoroughly evaluate the quality of our generated CAD models, we go beyond current evaluation metrics that focus on reconstruction quality by introducing additional metrics that assess topology quality and surface enclosure extent. Extensive experimental results demonstrate that CAD-MLLM significantly outperforms existing conditional generative methods and remains highly robust to noises and missing points. The project page and more visualizations can be found at: https://cad-mllm.github.io/

WebAssembly enables near-native execution in web applications and is increasingly adopted for tasks that demand high performance and robust security. However, its assembly-like syntax, implicit stack machine, and low-level data types make it extremely difficult for human developers to understand, spurring the need for effective WebAssembly reverse engineering techniques. In this paper, we propose StackSight, a novel neurosymbolic approach that combines Large Language Models (LLMs) with advanced program analysis to decompile complex WebAssembly code into readable C++ snippets. StackSight visualizes and tracks virtual stack alterations via a static analysis algorithm and then applies chain-of-thought prompting to harness LLM's complex reasoning capabilities. Evaluation results show that StackSight significantly improves WebAssembly decompilation. Our user study also demonstrates that code snippets generated by StackSight have significantly higher win rates and enable a better grasp of code semantics.

In this paper, we presented GraphOmni, a comprehensive benchmark framework for systematically evaluating the graph reasoning capabilities of LLMs. By analyzing critical dimensions, including graph types, serialization formats, and prompt schemes, we provided extensive insights into the strengths and limitations of current LLMs. Our empirical findings emphasize that no single serialization or prompting strategy consistently outperforms others. Motivated by these insights, we propose a reinforcement learning-based approach that dynamically selects the best serialization-prompt pairings, resulting in significant accuracy improvements. GraphOmni's modular and extensible design establishes a robust foundation for future research, facilitating advancements toward general-purpose graph reasoning models.

Despite impressive advances in agent systems, multi-turn tool-use scenarios remain challenging. It is mainly because intent is clarified progressively and the environment evolves with each tool call. While reusing past experience is natural, current LLM agents either treat entire trajectories or pre-defined subtasks as indivisible units, or solely exploit tool-to-tool dependencies, hindering adaptation as states and information evolve across turns. In this paper, we propose a State Integrated Tool Graph (SIT-Graph), which enhances multi-turn tool use by exploiting partially overlapping experience. Inspired by human decision-making that integrates episodic and procedural memory, SIT-Graph captures both compact state representations (episodic-like fragments) and tool-to-tool dependencies (procedural-like routines) from historical trajectories. Specifically, we first build a tool graph from accumulated tool-use sequences, and then augment each edge with a compact state summary of the dialog and tool history that may shape the next action. At inference time, SIT-Graph enables a human-like balance between episodic recall and procedural execution: when the next decision requires recalling prior context, the agent retrieves the state summaries stored on relevant edges and uses them to guide its next action; when the step is routine, it follows high-confidence tool dependencies without explicit recall. Experiments across multiple stateful multi-turn tool-use benchmarks show that SIT-Graph consistently outperforms strong memory- and graph-based baselines, delivering more robust tool selection and more effective experience transfer.

Graph Neural Architecture Search (GNAS) facilitates the automatic design of Graph Neural Networks (GNNs) tailored to specific downstream graph learning tasks. However, existing GNAS approaches often require manual adaptation to new graph search spaces, necessitating substantial code optimization and domain-specific knowledge. To address this challenge, we present LLM4GNAS, a toolkit for GNAS that leverages the generative capabilities of Large Language Models (LLMs). LLM4GNAS includes an algorithm library for graph neural architecture search algorithms based on LLMs, enabling the adaptation of GNAS methods to new search spaces through the modification of LLM prompts. This approach reduces the need for manual intervention in algorithm adaptation and code modification. The LLM4GNAS toolkit is extensible and robust, incorporating LLM-enhanced graph feature engineering, LLM-enhanced graph neural architecture search, and LLM-enhanced hyperparameter optimization. Experimental results indicate that LLM4GNAS outperforms existing GNAS methods on tasks involving both homogeneous and heterogeneous graphs.

Programming languages possess rich semantic information such as data flow that is represented by graphs and not available from the surface form of source code. Recent code language models have scaled to billions of parameters, but model source code solely as text tokens while ignoring any other structural information. Conversely, models that do encode structural information of code make modifications to the Transformer architecture, limiting their scale and compatibility with pretrained LLMs. In this work, we take the best of both worlds with GALLa - Graph Aligned Large Language Model. GALLa utilizes graph neural networks and cross-modal alignment technologies to inject the structural information of code into LLMs as an auxiliary task during finetuning. This framework is both model-agnostic and task-agnostic, as it can be applied to any code LLM for any code downstream task, and requires the structural graph data only at training time from a corpus unrelated to the finetuning data, while incurring no cost at inference time over the baseline LLM. Experiments on five code tasks with four different baseline LLMs ranging in size from 350M to 8B validate the effectiveness of GALLa, demonstrating consistent improvement over the baseline, even for powerful models such as LLaMA3.

As part of its scholarly data efforts, the Internet Archive (IA) releases a first version of a citation graph dataset, named refcat, derived from scholarly publications and additional data sources. It is composed of data gathered by the fatcat cataloging project (the catalog that underpins IA Scholar), related web-scale crawls targeting primary and secondary scholarly outputs, as well as metadata from the Open Library project and Wikipedia. This first version of the graph consists of over 1.3B citations. We release this dataset under a CC0 Public Domain Dedication, accessible through Internet Archive. The source code used for the derivation process, including exact and fuzzy citation matching, is released under an MIT license. The goal of this report is to describe briefly the current contents and the derivation of the dataset.

The mainstream image captioning models rely on Convolutional Neural Network (CNN) image features to generate captions via recurrent models. Recently, image scene graphs have been used to augment captioning models so as to leverage their structural semantics, such as object entities, relationships and attributes. Several studies have noted that the naive use of scene graphs from a black-box scene graph generator harms image captioning performance and that scene graph-based captioning models have to incur the overhead of explicit use of image features to generate decent captions. Addressing these challenges, we propose SG2Caps, a framework that utilizes only the scene graph labels for competitive image captioning performance. The basic idea is to close the semantic gap between the two scene graphs - one derived from the input image and the other from its caption. In order to achieve this, we leverage the spatial location of objects and the Human-Object-Interaction (HOI) labels as an additional HOI graph. SG2Caps outperforms existing scene graph-only captioning models by a large margin, indicating scene graphs as a promising representation for image captioning. Direct utilization of scene graph labels avoids expensive graph convolutions over high-dimensional CNN features resulting in 49% fewer trainable parameters. Our code is available at: https://github.com/Kien085/SG2Caps

Structured representations like graphs and parse trees play a crucial role in many Natural Language Processing systems. In recent years, the advancements in multi-turn user interfaces necessitate the need for controlling and updating these structured representations given new sources of information. Although there have been many efforts focusing on improving the performance of the parsers that map text to graphs or parse trees, very few have explored the problem of directly manipulating these representations. In this paper, we explore the novel problem of graph modification, where the systems need to learn how to update an existing scene graph given a new user's command. Our novel models based on graph-based sparse transformer and cross attention information fusion outperform previous systems adapted from the machine translation and graph generation literature. We further contribute our large graph modification datasets to the research community to encourage future research for this new problem.

Systems that support users in the automatic creation of visualizations must address several subtasks - understand the semantics of data, enumerate relevant visualization goals and generate visualization specifications. In this work, we pose visualization generation as a multi-stage generation problem and argue that well-orchestrated pipelines based on large language models (LLMs) such as ChatGPT/GPT-4 and image generation models (IGMs) are suitable to addressing these tasks. We present LIDA, a novel tool for generating grammar-agnostic visualizations and infographics. LIDA comprises of 4 modules - A SUMMARIZER that converts data into a rich but compact natural language summary, a GOAL EXPLORER that enumerates visualization goals given the data, a VISGENERATOR that generates, refines, executes and filters visualization code and an INFOGRAPHER module that yields data-faithful stylized graphics using IGMs. LIDA provides a python api, and a hybrid user interface (direct manipulation and multilingual natural language) for interactive chart, infographics and data story generation. Learn more about the project here - https://microsoft.github.io/lida/

Large language models (LLMs) such as GPT-4 have emerged as frontrunners, showcasing unparalleled prowess in diverse applications, including answering queries, code generation, and more. Parallelly, graph-structured data, an intrinsic data type, is pervasive in real-world scenarios. Merging the capabilities of LLMs with graph-structured data has been a topic of keen interest. This paper bifurcates such integrations into two predominant categories. The first leverages LLMs for graph learning, where LLMs can not only augment existing graph algorithms but also stand as prediction models for various graph tasks. Conversely, the second category underscores the pivotal role of graphs in advancing LLMs. Mirroring human cognition, we solve complex tasks by adopting graphs in either reasoning or collaboration. Integrating with such structures can significantly boost the performance of LLMs in various complicated tasks. We also discuss and propose open questions for integrating LLMs with graph-structured data for the future direction of the field.

Graph-based retrieval-augmented generation (Graph-based RAG) has demonstrated significant potential in enhancing Large Language Models (LLMs) with structured knowledge. However, existing methods face three critical challenges: Inaccurate Graph Construction, caused by LLM hallucination; Poor Reasoning Ability, caused by failing to generate explicit reasons telling LLM why certain chunks were selected; and Inadequate Answering, which only partially answers the query due to the inadequate LLM reasoning, making their performance lag behind NaiveRAG on certain tasks. To address these issues, we propose AGRAG, an advanced graph-based retrieval-augmented generation framework. When constructing the graph, AGRAG substitutes the widely used LLM entity extraction method with a statistics-based method, avoiding hallucination and error propagation. When retrieval, AGRAG formulates the graph reasoning procedure as the Minimum Cost Maximum Influence (MCMI) subgraph generation problem, where we try to include more nodes with high influence score, but with less involving edge cost, to make the generated reasoning paths more comprehensive. We prove this problem to be NP-hard, and propose a greedy algorithm to solve it. The MCMI subgraph generated can serve as explicit reasoning paths to tell LLM why certain chunks were retrieved, thereby making the LLM better focus on the query-related part contents of the chunks, reducing the impact of noise, and improving AGRAG's reasoning ability. Furthermore, compared with the simple tree-structured reasoning paths, our MCMI subgraph can allow more complex graph structures, such as cycles, and improve the comprehensiveness of the generated reasoning paths.

The shift towards electrification and autonomous driving in the automotive industry results in more and more automotive wire harnesses being installed in modern automobiles, which stresses the great significance of guaranteeing the quality of automotive wire harness assembly. The mating of connectors is essential in the final assembly of automotive wire harnesses due to the importance of connectors on wire harness connection and signal transmission. However, the current manual operation of mating connectors leads to severe problems regarding assembly quality and ergonomics, where the robotized assembly has been considered, and different vision-based solutions have been proposed to facilitate a better perception of the robot control system on connectors. Nonetheless, there has been a lack of deep learning-based solutions for detecting automotive wire harness connectors in previous literature. This paper presents a deep learning-based connector detection for robotized automotive wire harness assembly. A dataset of twenty automotive wire harness connectors was created to train and evaluate a two-stage and a one-stage object detection model, respectively. The experiment results indicate the effectiveness of deep learning-based connector detection for automotive wire harness assembly but are limited by the design of the exteriors of connectors.

We seek to automate the design of molecules based on specific chemical properties. In computational terms, this task involves continuous embedding and generation of molecular graphs. Our primary contribution is the direct realization of molecular graphs, a task previously approached by generating linear SMILES strings instead of graphs. Our junction tree variational autoencoder generates molecular graphs in two phases, by first generating a tree-structured scaffold over chemical substructures, and then combining them into a molecule with a graph message passing network. This approach allows us to incrementally expand molecules while maintaining chemical validity at every step. We evaluate our model on multiple tasks ranging from molecular generation to optimization. Across these tasks, our model outperforms previous state-of-the-art baselines by a significant margin.