Daily Papers

In this paper, we aim to develop a large language model (LLM) with the reasoning ability on complex graph data. Currently, LLMs have achieved very impressive performance on various natural language learning tasks, extensions of which have also been applied to study the vision tasks with multi-modal data. However, when it comes to the graph learning tasks, existing LLMs present very serious flaws due to their several inherited weaknesses in performing {multi-step logic reasoning}, {precise mathematical calculation} and {perception about the spatial and temporal factors}. To address such challenges, in this paper, we will investigate the principles, methodologies and algorithms to empower existing LLMs with graph reasoning ability, which will have tremendous impacts on the current research of both LLMs and graph learning. Inspired by the latest ChatGPT and Toolformer models, we propose the Graph-ToolFormer (Graph Reasoning oriented Toolformer) framework to teach LLMs themselves with prompts augmented by ChatGPT to use external graph reasoning API tools. Specifically, we will investigate to teach Graph-ToolFormer to handle various graph data reasoning tasks in this paper, including both (1) very basic graph data loading and graph property reasoning tasks, ranging from simple graph order and size to the graph diameter and periphery, and (2) more advanced reasoning tasks on real-world graph data, such as bibliographic networks, protein molecules, sequential recommender systems, social networks and knowledge graphs.

Language models (LMs) exhibit remarkable abilities to solve new tasks from just a few examples or textual instructions, especially at scale. They also, paradoxically, struggle with basic functionality, such as arithmetic or factual lookup, where much simpler and smaller models excel. In this paper, we show that LMs can teach themselves to use external tools via simple APIs and achieve the best of both worlds. We introduce Toolformer, a model trained to decide which APIs to call, when to call them, what arguments to pass, and how to best incorporate the results into future token prediction. This is done in a self-supervised way, requiring nothing more than a handful of demonstrations for each API. We incorporate a range of tools, including a calculator, a Q\&A system, two different search engines, a translation system, and a calendar. Toolformer achieves substantially improved zero-shot performance across a variety of downstream tasks, often competitive with much larger models, without sacrificing its core language modeling abilities.

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

The Transformer architecture has become a dominant choice in many domains, such as natural language processing and computer vision. Yet, it has not achieved competitive performance on popular leaderboards of graph-level prediction compared to mainstream GNN variants. Therefore, it remains a mystery how Transformers could perform well for graph representation learning. In this paper, we solve this mystery by presenting Graphormer, which is built upon the standard Transformer architecture, and could attain excellent results on a broad range of graph representation learning tasks, especially on the recent OGB Large-Scale Challenge. Our key insight to utilizing Transformer in the graph is the necessity of effectively encoding the structural information of a graph into the model. To this end, we propose several simple yet effective structural encoding methods to help Graphormer better model graph-structured data. Besides, we mathematically characterize the expressive power of Graphormer and exhibit that with our ways of encoding the structural information of graphs, many popular GNN variants could be covered as the special cases of Graphormer.

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.

We propose a generalization of transformer neural network architecture for arbitrary graphs. The original transformer was designed for Natural Language Processing (NLP), which operates on fully connected graphs representing all connections between the words in a sequence. Such architecture does not leverage the graph connectivity inductive bias, and can perform poorly when the graph topology is important and has not been encoded into the node features. We introduce a graph transformer with four new properties compared to the standard model. First, the attention mechanism is a function of the neighborhood connectivity for each node in the graph. Second, the positional encoding is represented by the Laplacian eigenvectors, which naturally generalize the sinusoidal positional encodings often used in NLP. Third, the layer normalization is replaced by a batch normalization layer, which provides faster training and better generalization performance. Finally, the architecture is extended to edge feature representation, which can be critical to tasks s.a. chemistry (bond type) or link prediction (entity relationship in knowledge graphs). Numerical experiments on a graph benchmark demonstrate the performance of the proposed graph transformer architecture. This work closes the gap between the original transformer, which was designed for the limited case of line graphs, and graph neural networks, that can work with arbitrary graphs. As our architecture is simple and generic, we believe it can be used as a black box for future applications that wish to consider transformer and graphs.

We propose a recipe on how to build a general, powerful, scalable (GPS) graph Transformer with linear complexity and state-of-the-art results on a diverse set of benchmarks. Graph Transformers (GTs) have gained popularity in the field of graph representation learning with a variety of recent publications but they lack a common foundation about what constitutes a good positional or structural encoding, and what differentiates them. In this paper, we summarize the different types of encodings with a clearer definition and categorize them as being local, global or relative. The prior GTs are constrained to small graphs with a few hundred nodes, here we propose the first architecture with a complexity linear in the number of nodes and edges O(N+E) by decoupling the local real-edge aggregation from the fully-connected Transformer. We argue that this decoupling does not negatively affect the expressivity, with our architecture being a universal function approximator on graphs. Our GPS recipe consists of choosing 3 main ingredients: (i) positional/structural encoding, (ii) local message-passing mechanism, and (iii) global attention mechanism. We provide a modular framework GraphGPS that supports multiple types of encodings and that provides efficiency and scalability both in small and large graphs. We test our architecture on 16 benchmarks and show highly competitive results in all of them, show-casing the empirical benefits gained by the modularity and the combination of different strategies.

This paper presents a novel approach to representation learning in recommender systems by integrating generative self-supervised learning with graph transformer architecture. We highlight the importance of high-quality data augmentation with relevant self-supervised pretext tasks for improving performance. Towards this end, we propose a new approach that automates the self-supervision augmentation process through a rationale-aware generative SSL that distills informative user-item interaction patterns. The proposed recommender with Graph TransFormer (GFormer) that offers parameterized collaborative rationale discovery for selective augmentation while preserving global-aware user-item relationships. In GFormer, we allow the rationale-aware SSL to inspire graph collaborative filtering with task-adaptive invariant rationalization in graph transformer. The experimental results reveal that our GFormer has the capability to consistently improve the performance over baselines on different datasets. Several in-depth experiments further investigate the invariant rationale-aware augmentation from various aspects. The source code for this work is publicly available at: https://github.com/HKUDS/GFormer.

Transformers for graph data are increasingly widely studied and successful in numerous learning tasks. Graph inductive biases are crucial for Graph Transformers, and previous works incorporate them using message-passing modules and/or positional encodings. However, Graph Transformers that use message-passing inherit known issues of message-passing, and differ significantly from Transformers used in other domains, thus making transfer of research advances more difficult. On the other hand, Graph Transformers without message-passing often perform poorly on smaller datasets, where inductive biases are more crucial. To bridge this gap, we propose the Graph Inductive bias Transformer (GRIT) -- a new Graph Transformer that incorporates graph inductive biases without using message passing. GRIT is based on several architectural changes that are each theoretically and empirically justified, including: learned relative positional encodings initialized with random walk probabilities, a flexible attention mechanism that updates node and node-pair representations, and injection of degree information in each layer. We prove that GRIT is expressive -- it can express shortest path distances and various graph propagation matrices. GRIT achieves state-of-the-art empirical performance across a variety of graph datasets, thus showing the power that Graph Transformers without message-passing can deliver.

Transformers have revolutionized machine learning, yet their inner workings remain opaque to many. We present Transformer Explainer, an interactive visualization tool designed for non-experts to learn about Transformers through the GPT-2 model. Our tool helps users understand complex Transformer concepts by integrating a model overview and enabling smooth transitions across abstraction levels of mathematical operations and model structures. It runs a live GPT-2 instance locally in the user's browser, empowering users to experiment with their own input and observe in real-time how the internal components and parameters of the Transformer work together to predict the next tokens. Our tool requires no installation or special hardware, broadening the public's education access to modern generative AI techniques. Our open-sourced tool is available at https://poloclub.github.io/transformer-explainer/. A video demo is available at https://youtu.be/ECR4oAwocjs.

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.

Temporal Graph Neural Networks have garnered substantial attention for their capacity to model evolving structural and temporal patterns while exhibiting impressive performance. However, it is known that these architectures are encumbered by issues that constrain their performance, such as over-squashing and over-smoothing. Meanwhile, Transformers have demonstrated exceptional computational capacity to effectively address challenges related to long-range dependencies. Consequently, we introduce Todyformer-a novel Transformer-based neural network tailored for dynamic graphs. It unifies the local encoding capacity of Message-Passing Neural Networks (MPNNs) with the global encoding of Transformers through i) a novel patchifying paradigm for dynamic graphs to improve over-squashing, ii) a structure-aware parametric tokenization strategy leveraging MPNNs, iii) a Transformer with temporal positional-encoding to capture long-range dependencies, and iv) an encoding architecture that alternates between local and global contextualization, mitigating over-smoothing in MPNNs. Experimental evaluations on public benchmark datasets demonstrate that Todyformer consistently outperforms the state-of-the-art methods for downstream tasks. Furthermore, we illustrate the underlying aspects of the proposed model in effectively capturing extensive temporal dependencies in dynamic graphs.

Information graphics are pivotal in effective information dissemination and storytelling. However, creating such graphics is extremely challenging for non-professionals, since the design process requires multifaceted skills and comprehensive knowledge. Thus, despite the many available authoring tools, a significant gap remains in enabling non-experts to produce compelling information graphics seamlessly, especially from scratch. Recent breakthroughs show that Large Language Models (LLMs), especially when tool-augmented, can autonomously engage with external tools, making them promising candidates for enabling innovative graphic design applications. In this work, we propose a LLM-centric interface with the agent GraphiMind for automatic generation, recommendation, and composition of information graphics design resources, based on user intent expressed through natural language. Our GraphiMind integrates a Textual Conversational Interface, powered by tool-augmented LLM, with a traditional Graphical Manipulation Interface, streamlining the entire design process from raw resource curation to composition and refinement. Extensive evaluations highlight our tool's proficiency in simplifying the design process, opening avenues for its use by non-professional users. Moreover, we spotlight the potential of LLMs in reshaping the domain of information graphics design, offering a blend of automation, versatility, and user-centric interactivity.

Graph Transformer (GT) recently has emerged as a new paradigm of graph learning algorithms, outperforming the previously popular Message Passing Neural Network (MPNN) on multiple benchmarks. Previous work (Kim et al., 2022) shows that with proper position embedding, GT can approximate MPNN arbitrarily well, implying that GT is at least as powerful as MPNN. In this paper, we study the inverse connection and show that MPNN with virtual node (VN), a commonly used heuristic with little theoretical understanding, is powerful enough to arbitrarily approximate the self-attention layer of GT. In particular, we first show that if we consider one type of linear transformer, the so-called Performer/Linear Transformer (Choromanski et al., 2020; Katharopoulos et al., 2020), then MPNN + VN with only O(1) depth and O(1) width can approximate a self-attention layer in Performer/Linear Transformer. Next, via a connection between MPNN + VN and DeepSets, we prove the MPNN + VN with O(n^d) width and O(1) depth can approximate the self-attention layer arbitrarily well, where d is the input feature dimension. Lastly, under some assumptions, we provide an explicit construction of MPNN + VN with O(1) width and O(n) depth approximating the self-attention layer in GT arbitrarily well. On the empirical side, we demonstrate that 1) MPNN + VN is a surprisingly strong baseline, outperforming GT on the recently proposed Long Range Graph Benchmark (LRGB) dataset, 2) our MPNN + VN improves over early implementation on a wide range of OGB datasets and 3) MPNN + VN outperforms Linear Transformer and MPNN on the climate modeling task.

Graph Transformers (GTs) have achieved impressive results on various graph-related tasks. However, the huge computational cost of GTs hinders their deployment and application, especially in resource-constrained environments. Therefore, in this paper, we explore the feasibility of sparsifying GTs, a significant yet under-explored topic. We first discuss the redundancy of GTs based on the characteristics of existing GT models, and then propose a comprehensive Graph Transformer SParsification (GTSP) framework that helps to reduce the computational complexity of GTs from four dimensions: the input graph data, attention heads, model layers, and model weights. Specifically, GTSP designs differentiable masks for each individual compressible component, enabling effective end-to-end pruning. We examine our GTSP through extensive experiments on prominent GTs, including GraphTrans, Graphormer, and GraphGPS. The experimental results substantiate that GTSP effectively cuts computational costs, accompanied by only marginal decreases in accuracy or, in some cases, even improvements. For instance, GTSP yields a reduction of 30\% in Floating Point Operations while contributing to a 1.8\% increase in Area Under the Curve accuracy on OGBG-HIV dataset. Furthermore, we provide several insights on the characteristics of attention heads and the behavior of attention mechanisms, all of which have immense potential to inspire future research endeavors in this domain.

Transformers serve as the backbone architectures of Foundational Models, where a domain-specific tokenizer helps them adapt to various domains. Graph Transformers (GTs) have recently emerged as a leading model in geometric deep learning, outperforming Graph Neural Networks (GNNs) in various graph learning tasks. However, the development of tokenizers for graphs has lagged behind other modalities, with existing approaches relying on heuristics or GNNs co-trained with Transformers. To address this, we introduce GQT (Graph Quantized Tokenizer), which decouples tokenizer training from Transformer training by leveraging multi-task graph self-supervised learning, yielding robust and generalizable graph tokens. Furthermore, the GQT utilizes Residual Vector Quantization (RVQ) to learn hierarchical discrete tokens, resulting in significantly reduced memory requirements and improved generalization capabilities. By combining the GQT with token modulation, a Transformer encoder achieves state-of-the-art performance on 16 out of 18 benchmarks, including large-scale homophilic and heterophilic datasets. The code is available at: https://github.com/limei0307/graph-tokenizer

Graph transformers have emerged as a promising architecture for a variety of graph learning and representation tasks. Despite their successes, though, it remains challenging to scale graph transformers to large graphs while maintaining accuracy competitive with message-passing networks. In this paper, we introduce Exphormer, a framework for building powerful and scalable graph transformers. Exphormer consists of a sparse attention mechanism based on two mechanisms: virtual global nodes and expander graphs, whose mathematical characteristics, such as spectral expansion, pseduorandomness, and sparsity, yield graph transformers with complexity only linear in the size of the graph, while allowing us to prove desirable theoretical properties of the resulting transformer models. We show that incorporating Exphormer into the recently-proposed GraphGPS framework produces models with competitive empirical results on a wide variety of graph datasets, including state-of-the-art results on three datasets. We also show that Exphormer can scale to datasets on larger graphs than shown in previous graph transformer architectures. Code can be found at https://github.com/hamed1375/Exphormer.

Language models (LMs) are powerful yet mostly for text generation tasks. Tools have substantially enhanced their performance for tasks that require complex skills. However, many works adopt the term "tool" in different ways, raising the question: What is a tool anyway? Subsequently, where and how do tools help LMs? In this survey, we provide a unified definition of tools as external programs used by LMs, and perform a systematic review of LM tooling scenarios and approaches. Grounded on this review, we empirically study the efficiency of various tooling methods by measuring their required compute and performance gains on various benchmarks, and highlight some challenges and potential future research in the field.

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.

Transformers have revolutionized performance in Natural Language Processing and Vision, paving the way for their integration with Graph Neural Networks (GNNs). One key challenge in enhancing graph transformers is strengthening the discriminative power of distinguishing isomorphisms of graphs, which plays a crucial role in boosting their predictive performances. To address this challenge, we introduce 'Topology-Informed Graph Transformer (TIGT)', a novel transformer enhancing both discriminative power in detecting graph isomorphisms and the overall performance of Graph Transformers. TIGT consists of four components: A topological positional embedding layer using non-isomorphic universal covers based on cyclic subgraphs of graphs to ensure unique graph representation: A dual-path message-passing layer to explicitly encode topological characteristics throughout the encoder layers: A global attention mechanism: And a graph information layer to recalibrate channel-wise graph features for better feature representation. TIGT outperforms previous Graph Transformers in classifying synthetic dataset aimed at distinguishing isomorphism classes of graphs. Additionally, mathematical analysis and empirical evaluations highlight our model's competitive edge over state-of-the-art Graph Transformers across various benchmark datasets.

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.

Recent advancements in function calling and tool use have significantly enhanced the capabilities of large language models (LLMs) by enabling them to interact with external information sources and execute complex tasks. However, the limited context window of LLMs presents challenges when a large number of tools are available, necessitating efficient methods to manage prompt length and maintain accuracy. Existing approaches, such as fine-tuning LLMs or leveraging their reasoning capabilities, either require frequent retraining or incur significant latency overhead. A more efficient solution involves training smaller models to retrieve the most relevant tools for a given query, although this requires high quality, domain-specific data. To address those challenges, we present a novel framework for generating synthetic data for tool retrieval applications and an efficient data-driven tool retrieval strategy using small encoder models. Empowered by LLMs, we create ToolBank, a new tool retrieval dataset that reflects real human user usages. For tool retrieval methodologies, we propose novel approaches: (1) Tool2Vec: usage-driven tool embedding generation for tool retrieval, (2) ToolRefiner: a staged retrieval method that iteratively improves the quality of retrieved tools, and (3) MLC: framing tool retrieval as a multi-label classification problem. With these new methods, we achieve improvements of up to 27.28 in Recall@K on the ToolBench dataset and 30.5 in Recall@K on ToolBank. Additionally, we present further experimental results to rigorously validate our methods. Our code is available at https://github.com/SqueezeAILab/Tool2Vec

Large language models (LLMs) have shown promising capabilities in using external tools to solve complex problems. However, existing approaches either involve fine-tuning on tool demonstrations, which do not generalize to new tools without additional training, or providing tool documentation in context, limiting the number of tools. Both approaches often generate syntactically invalid tool calls. In this paper, we propose ToolDec, a finite-state machine-guided decoding algorithm for tool-augmented LLMs. ToolDec eliminates tool-related errors for any tool-augmented LLMs by ensuring valid tool names and type-conforming arguments. Furthermore, ToolDec enables LLM to effectively select tools using only the information contained in their names, with no need for fine-tuning or in-context documentation. We evaluated multiple prior methods and their ToolDec-enhanced versions on a variety of tasks involving tools like math functions, knowledge graph relations, and complex real-world RESTful APIs. Our experiments show that ToolDec reduces syntactic errors to zero, consequently achieving significantly better performance and as much as a 2x speedup. We also show that ToolDec achieves superior generalization performance on unseen tools, performing up to 8x better than the baselines.

Graph generation is a critical task in numerous domains, including molecular design and social network analysis, due to its ability to model complex relationships and structured data. While most modern graph generative models utilize adjacency matrix representations, this work revisits an alternative approach that represents graphs as sequences of node set and edge set. We advocate for this approach due to its efficient encoding of graphs and propose a novel representation. Based on this representation, we introduce the Graph Generative Pre-trained Transformer (G2PT), an auto-regressive model that learns graph structures via next-token prediction. To further exploit G2PT's capabilities as a general-purpose foundation model, we explore fine-tuning strategies for two downstream applications: goal-oriented generation and graph property prediction. We conduct extensive experiments across multiple datasets. Results indicate that G2PT achieves superior generative performance on both generic graph and molecule datasets. Furthermore, G2PT exhibits strong adaptability and versatility in downstream tasks from molecular design to property prediction.

In this work, instead of directly predicting the pixel-level segmentation masks, the problem of referring image segmentation is formulated as sequential polygon generation, and the predicted polygons can be later converted into segmentation masks. This is enabled by a new sequence-to-sequence framework, Polygon Transformer (PolyFormer), which takes a sequence of image patches and text query tokens as input, and outputs a sequence of polygon vertices autoregressively. For more accurate geometric localization, we propose a regression-based decoder, which predicts the precise floating-point coordinates directly, without any coordinate quantization error. In the experiments, PolyFormer outperforms the prior art by a clear margin, e.g., 5.40% and 4.52% absolute improvements on the challenging RefCOCO+ and RefCOCOg datasets. It also shows strong generalization ability when evaluated on the referring video segmentation task without fine-tuning, e.g., achieving competitive 61.5% J&F on the Ref-DAVIS17 dataset.

Contextual Text Block Detection (CTBD) is the task of identifying coherent text blocks within the complexity of natural scenes. Previous methodologies have treated CTBD as either a visual relation extraction challenge within computer vision or as a sequence modeling problem from the perspective of natural language processing. We introduce a new framework that frames CTBD as a graph generation problem. This methodology consists of two essential procedures: identifying individual text units as graph nodes and discerning the sequential reading order relationships among these units as graph edges. Leveraging the cutting-edge capabilities of DQ-DETR for node detection, our framework innovates further by integrating a novel mechanism, a Dynamic Relation Transformer (DRFormer), dedicated to edge generation. DRFormer incorporates a dual interactive transformer decoder that deftly manages a dynamic graph structure refinement process. Through this iterative process, the model systematically enhances the graph's fidelity, ultimately resulting in improved precision in detecting contextual text blocks. Comprehensive experimental evaluations conducted on both SCUT-CTW-Context and ReCTS-Context datasets substantiate that our method achieves state-of-the-art results, underscoring the effectiveness and potential of our graph generation framework in advancing the field of CTBD.

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.

While Transformers have enabled tremendous progress in various application settings, such architectures still lag behind traditional symbolic planners for solving complex decision making tasks. In this work, we demonstrate how to train Transformers to solve complex planning tasks and present Searchformer, a Transformer model that optimally solves previously unseen Sokoban puzzles 93.7% of the time, while using up to 26.8% fewer search steps than standard A^* search. Searchformer is an encoder-decoder Transformer model trained to predict the search dynamics of A^*. This model is then fine-tuned via expert iterations to perform fewer search steps than A^* search while still generating an optimal plan. In our training method, A^*'s search dynamics are expressed as a token sequence outlining when task states are added and removed into the search tree during symbolic planning. In our ablation studies on maze navigation, we find that Searchformer significantly outperforms baselines that predict the optimal plan directly with a 5-10times smaller model size and a 10times smaller training dataset. We also demonstrate how Searchformer scales to larger and more complex decision making tasks like Sokoban with improved percentage of solved tasks and shortened search dynamics.

Transformers have recently emerged as powerful neural networks for graph learning, showcasing state-of-the-art performance on several graph property prediction tasks. However, these results have been limited to small-scale graphs, where the computational feasibility of the global attention mechanism is possible. The next goal is to scale up these architectures to handle very large graphs on the scale of millions or even billions of nodes. With large-scale graphs, global attention learning is proven impractical due to its quadratic complexity w.r.t. the number of nodes. On the other hand, neighborhood sampling techniques become essential to manage large graph sizes, yet finding the optimal trade-off between speed and accuracy with sampling techniques remains challenging. This work advances representation learning on single large-scale graphs with a focus on identifying model characteristics and critical design constraints for developing scalable graph transformer (GT) architectures. We argue such GT requires layers that can adeptly learn both local and global graph representations while swiftly sampling the graph topology. As such, a key innovation of this work lies in the creation of a fast neighborhood sampling technique coupled with a local attention mechanism that encompasses a 4-hop reception field, but achieved through just 2-hop operations. This local node embedding is then integrated with a global node embedding, acquired via another self-attention layer with an approximate global codebook, before finally sent through a downstream layer for node predictions. The proposed GT framework, named LargeGT, overcomes previous computational bottlenecks and is validated on three large-scale node classification benchmarks. We report a 3x speedup and 16.8% performance gain on ogbn-products and snap-patents, while we also scale LargeGT on ogbn-papers100M with a 5.9% performance improvement.

Despite that going deep has proven successful in many neural architectures, the existing graph transformers are relatively shallow. In this work, we explore whether more layers are beneficial to graph transformers, and find that current graph transformers suffer from the bottleneck of improving performance by increasing depth. Our further analysis reveals the reason is that deep graph transformers are limited by the vanishing capacity of global attention, restricting the graph transformer from focusing on the critical substructure and obtaining expressive features. To this end, we propose a novel graph transformer model named DeepGraph that explicitly employs substructure tokens in the encoded representation, and applies local attention on related nodes to obtain substructure based attention encoding. Our model enhances the ability of the global attention to focus on substructures and promotes the expressiveness of the representations, addressing the limitation of self-attention as the graph transformer deepens. Experiments show that our method unblocks the depth limitation of graph transformers and results in state-of-the-art performance across various graph benchmarks with deeper models.

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.

This paper studies how to keep a vision backbone effective while removing token mixers in its basic building blocks. Token mixers, as self-attention for vision transformers (ViTs), are intended to perform information communication between different spatial tokens but suffer from considerable computational cost and latency. However, directly removing them will lead to an incomplete model structure prior, and thus brings a significant accuracy drop. To this end, we first develop an RepIdentityFormer base on the re-parameterizing idea, to study the token mixer free model architecture. And we then explore the improved learning paradigm to break the limitation of simple token mixer free backbone, and summarize the empirical practice into 5 guidelines. Equipped with the proposed optimization strategy, we are able to build an extremely simple vision backbone with encouraging performance, while enjoying the high efficiency during inference. Extensive experiments and ablative analysis also demonstrate that the inductive bias of network architecture, can be incorporated into simple network structure with appropriate optimization strategy. We hope this work can serve as a starting point for the exploration of optimization-driven efficient network design. Project page: https://techmonsterwang.github.io/RIFormer/.

Search is an ability foundational in many important tasks, and recent studies have shown that large language models (LLMs) struggle to perform search robustly. It is unknown whether this inability is due to a lack of data, insufficient model parameters, or fundamental limitations of the transformer architecture. In this work, we use the foundational graph connectivity problem as a testbed to generate effectively limitless high-coverage data to train small transformers and test whether they can learn to perform search. We find that, when given the right training distribution, the transformer is able to learn to search. We analyze the algorithm that the transformer has learned through a novel mechanistic interpretability technique that enables us to extract the computation graph from the trained model. We find that for each vertex in the input graph, transformers compute the set of vertices reachable from that vertex. Each layer then progressively expands these sets, allowing the model to search over a number of vertices exponential in the number of layers. However, we find that as the input graph size increases, the transformer has greater difficulty in learning the task. This difficulty is not resolved even as the number of parameters is increased, suggesting that increasing model scale will not lead to robust search abilities. We also find that performing search in-context (i.e., chain-of-thought) does not resolve this inability to learn to search on larger graphs.

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

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.

Today, large language models (LLMs) are taught to use new tools by providing a few demonstrations of the tool's usage. Unfortunately, demonstrations are hard to acquire, and can result in undesirable biased usage if the wrong demonstration is chosen. Even in the rare scenario that demonstrations are readily available, there is no principled selection protocol to determine how many and which ones to provide. As tasks grow more complex, the selection search grows combinatorially and invariably becomes intractable. Our work provides an alternative to demonstrations: tool documentation. We advocate the use of tool documentation, descriptions for the individual tool usage, over demonstrations. We substantiate our claim through three main empirical findings on 6 tasks across both vision and language modalities. First, on existing benchmarks, zero-shot prompts with only tool documentation are sufficient for eliciting proper tool usage, achieving performance on par with few-shot prompts. Second, on a newly collected realistic tool-use dataset with hundreds of available tool APIs, we show that tool documentation is significantly more valuable than demonstrations, with zero-shot documentation significantly outperforming few-shot without documentation. Third, we highlight the benefits of tool documentations by tackling image generation and video tracking using just-released unseen state-of-the-art models as tools. Finally, we highlight the possibility of using tool documentation to automatically enable new applications: by using nothing more than the documentation of GroundingDino, Stable Diffusion, XMem, and SAM, LLMs can re-invent the functionalities of the just-released Grounded-SAM and Track Anything models.

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.

As large language models (LLMs) advance, their inability to autonomously execute tasks by directly interacting with external tools remains a critical limitation. Traditional methods rely on inputting tool descriptions as context, which is constrained by context length and requires separate, often inefficient, retrieval mechanisms. We introduce ToolGen, a paradigm shift that integrates tool knowledge directly into the LLM's parameters by representing each tool as a unique token. This enables the LLM to generate tool calls and arguments as part of its next token prediction capabilities, seamlessly blending tool invocation with language generation. Our framework allows the LLM to access and utilize a vast amount of tools with no additional retrieval step, significantly enhancing both performance and scalability. Experimental results with over 47,000 tools show that ToolGen not only achieves superior results in both tool retrieval and autonomous task completion but also sets the stage for a new era of AI agents that can adapt to tools across diverse domains. By fundamentally transforming tool retrieval into a generative process, ToolGen paves the way for more versatile, efficient, and autonomous AI systems. ToolGen enables end-to-end tool learning and opens opportunities for integration with other advanced techniques such as chain-of-thought and reinforcement learning, thereby expanding the practical capabilities of LLMs.

In recent years, graph pre-training has gained significant attention, focusing on acquiring transferable knowledge from unlabeled graph data to improve downstream performance. Despite these recent endeavors, the problem of negative transfer remains a major concern when utilizing graph pre-trained models to downstream tasks. Previous studies made great efforts on the issue of what to pre-train and how to pre-train by designing a variety of graph pre-training and fine-tuning strategies. However, there are cases where even the most advanced "pre-train and fine-tune" paradigms fail to yield distinct benefits. This paper introduces a generic framework W2PGNN to answer the crucial question of when to pre-train (i.e., in what situations could we take advantage of graph pre-training) before performing effortful pre-training or fine-tuning. We start from a new perspective to explore the complex generative mechanisms from the pre-training data to downstream data. In particular, W2PGNN first fits the pre-training data into graphon bases, each element of graphon basis (i.e., a graphon) identifies a fundamental transferable pattern shared by a collection of pre-training graphs. All convex combinations of graphon bases give rise to a generator space, from which graphs generated form the solution space for those downstream data that can benefit from pre-training. In this manner, the feasibility of pre-training can be quantified as the generation probability of the downstream data from any generator in the generator space. W2PGNN offers three broad applications: providing the application scope of graph pre-trained models, quantifying the feasibility of pre-training, and assistance in selecting pre-training data to enhance downstream performance. We provide a theoretically sound solution for the first application and extensive empirical justifications for the latter two applications.

We introduce SynFormer, a generative modeling framework designed to efficiently explore and navigate synthesizable chemical space. Unlike traditional molecular generation approaches, we generate synthetic pathways for molecules to ensure that designs are synthetically tractable. By incorporating a scalable transformer architecture and a diffusion module for building block selection, SynFormer surpasses existing models in synthesizable molecular design. We demonstrate SynFormer's effectiveness in two key applications: (1) local chemical space exploration, where the model generates synthesizable analogs of a reference molecule, and (2) global chemical space exploration, where the model aims to identify optimal molecules according to a black-box property prediction oracle. Additionally, we demonstrate the scalability of our approach via the improvement in performance as more computational resources become available. With our code and trained models openly available, we hope that SynFormer will find use across applications in drug discovery and materials science.

Transformers for time series forecasting mainly model time series from limited or fixed scales, making it challenging to capture different characteristics spanning various scales. We propose Pathformer, a multi-scale Transformer with adaptive pathways. It integrates both temporal resolution and temporal distance for multi-scale modeling. Multi-scale division divides the time series into different temporal resolutions using patches of various sizes. Based on the division of each scale, dual attention is performed over these patches to capture global correlations and local details as temporal dependencies. We further enrich the multi-scale Transformer with adaptive pathways, which adaptively adjust the multi-scale modeling process based on the varying temporal dynamics of the input, improving the accuracy and generalization of Pathformer. Extensive experiments on eleven real-world datasets demonstrate that Pathformer not only achieves state-of-the-art performance by surpassing all current models but also exhibits stronger generalization abilities under various transfer scenarios. The code is made available at https://github.com/decisionintelligence/pathformer.

Recent research shows the potential of enhancing the problem-solving ability of large language models (LLMs) through the use of external tools. However, prior work along this line depends on the availability of existing tools. In this work, we take an initial step towards removing this dependency by proposing a closed-loop framework, referred to as LLMs As Tool Makers (LATM), where LLMs create their own reusable tools for problem-solving. Our approach consists of two key phases: 1) tool making: an LLM acts as the tool maker that crafts tools for given tasks, where a tool is implemented as a Python utility function. 2) tool using: an LLM acts as the tool user, which applies the tool built by the tool maker for problem-solving. The tool user can be either the same or a different LLM from the tool maker. Tool-making enables an LLM to continually generate tools that can be applied to different requests so that future requests can call the corresponding APIs when beneficial for solving the tasks. Furthermore, the division of labor among LLMs for tool-making and tool-using phases introduces the opportunity to achieve cost effectiveness without degrading the quality of generated tools and problem solutions. For example, recognizing that tool-making demands more sophisticated capabilities than tool-using, we can apply a powerful yet resource-intensive model as the tool maker, and a lightweight while cost-effective model as the tool user. We validate the effectiveness of our approach across a variety of complex reasoning tasks, including Big-Bench tasks. With GPT-4 as the tool maker and GPT-3.5 as the tool user, LATM can achieve performance that is on par with using GPT-4 for both tool making and tool using, while the inference cost is significantly reduced.

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.

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.

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).

Transformers were originally proposed as a sequence-to-sequence model for text but have become vital for a wide range of modalities, including images, audio, video, and undirected graphs. However, transformers for directed graphs are a surprisingly underexplored topic, despite their applicability to ubiquitous domains including source code and logic circuits. In this work, we propose two direction- and structure-aware positional encodings for directed graphs: (1) the eigenvectors of the Magnetic Laplacian - a direction-aware generalization of the combinatorial Laplacian; (2) directional random walk encodings. Empirically, we show that the extra directionality information is useful in various downstream tasks, including correctness testing of sorting networks and source code understanding. Together with a data-flow-centric graph construction, our model outperforms the prior state of the art on the Open Graph Benchmark Code2 relatively by 14.7%.

With the goal of understanding the visual concepts that CLIP associates with text prompts, we show that the latent space of CLIP can be visualized solely in terms of linear transformations on simple geometric primitives like circles and straight lines. Although existing approaches achieve this by sketch-synthesis-through-optimization, they do so on the space of B\'ezier curves, which exhibit a wastefully large set of structures that they can evolve into, as most of them are non-essential for generating meaningful sketches. We present CLIPDrawX, an algorithm that provides significantly better visualizations for CLIP text embeddings, using only simple primitive shapes like straight lines and circles. This constrains the set of possible outputs to linear transformations on these primitives, thereby exhibiting an inherently simpler mathematical form. The synthesis process of CLIPDrawX can be tracked end-to-end, with each visual concept being explained exclusively in terms of primitives. Implementation will be released upon acceptance. Project Page: https://clipdrawx.github.io/{https://clipdrawx.github.io/}.

In recent years, the use of multi-modal pre-trained Transformers has led to significant advancements in visually-rich document understanding. However, existing models have mainly focused on features such as text and vision while neglecting the importance of layout relationship between text nodes. In this paper, we propose GraphLayoutLM, a novel document understanding model that leverages the modeling of layout structure graph to inject document layout knowledge into the model. GraphLayoutLM utilizes a graph reordering algorithm to adjust the text sequence based on the graph structure. Additionally, our model uses a layout-aware multi-head self-attention layer to learn document layout knowledge. The proposed model enables the understanding of the spatial arrangement of text elements, improving document comprehension. We evaluate our model on various benchmarks, including FUNSD, XFUND and CORD, and achieve state-of-the-art results among these datasets. Our experimental results demonstrate that our proposed method provides a significant improvement over existing approaches and showcases the importance of incorporating layout information into document understanding models. We also conduct an ablation study to investigate the contribution of each component of our model. The results show that both the graph reordering algorithm and the layout-aware multi-head self-attention layer play a crucial role in achieving the best performance.

Tools serve as pivotal interfaces that enable humans to understand and reshape the world. With the advent of foundational models, AI systems can utilize tools to expand their capabilities and interact with the world. Existing tool learning methodologies, encompassing supervised fine-tuning and prompt engineering approaches, often induce language models to utilize tools indiscriminately, as complex problems often exceed their own competencies. However, introducing tools for simple tasks, which the models themselves can readily resolve, can inadvertently propagate errors rather than enhance performance. This leads to the research question: can we teach language models when and how to use tools? To meet this need, we propose Tool leaRning wIth exeCution fEedback (TRICE), a two-stage end-to-end framework that enables the model to continually learn through feedback derived from tool execution, thereby learning when and how to use tools effectively. Experimental results, backed by further analysis, show that TRICE can make the language model to selectively use tools by decreasing the model's dependency on tools while enhancing the performance. Code and datasets will be available in https://github.com/zjunlp/trice.

The execution of graph algorithms using neural networks has recently attracted significant interest due to promising empirical progress. This motivates further understanding of how neural networks can replicate reasoning steps with relational data. In this work, we study the ability of transformer networks to simulate algorithms on graphs from a theoretical perspective. The architecture that we utilize is a looped transformer with extra attention heads that interact with the graph. We prove by construction that this architecture can simulate algorithms such as Dijkstra's shortest path algorithm, Breadth- and Depth-First Search, and Kosaraju's strongly connected components algorithm. The width of the network does not increase with the size of the input graph, which implies that the network can simulate the above algorithms for any graph. Despite this property, we show that there is a limit to simulation in our solution due to finite precision. Finally, we show a Turing Completeness result with constant width when the extra attention heads are utilized.

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.

Graph learning has become indispensable for interpreting and harnessing relational data in diverse fields, ranging from recommendation systems to social network analysis. In this context, a variety of GNNs have emerged as promising methodologies for encoding the structural information of graphs. By effectively capturing the graph's underlying structure, these GNNs have shown great potential in enhancing performance in graph learning tasks, such as link prediction and node classification. However, despite their successes, a significant challenge persists: these advanced methods often face difficulties in generalizing to unseen graph data that significantly differs from the training instances. In this work, our aim is to advance the graph learning paradigm by developing a general graph foundation model. This model is designed to understand the complex topological patterns present in diverse graph data, enabling it to excel in zero-shot graph learning tasks across different downstream datasets. To achieve this goal, we address several key technical challenges in our OpenGraph model. Firstly, we propose a unified graph tokenizer to adapt our graph model to generalize well on unseen graph data, even when the underlying graph properties differ significantly from those encountered during training. Secondly, we develop a scalable graph transformer as the foundational encoder, which effectively captures node-wise dependencies within the global topological context. Thirdly, we introduce a data augmentation mechanism enhanced by a LLM to alleviate the limitations of data scarcity in real-world scenarios. Extensive experiments validate the effectiveness of our framework. By adapting our OpenGraph to new graph characteristics and comprehending the nuances of diverse graphs, our approach achieves remarkable zero-shot graph learning performance across various settings and domains.

Methane emissions from livestock, particularly cattle, significantly contribute to climate change. Effective methane emission mitigation strategies are crucial as the global population and demand for livestock products increase. We introduce Gasformer, a novel semantic segmentation architecture for detecting low-flow rate methane emissions from livestock, and controlled release experiments using optical gas imaging. We present two unique datasets captured with a FLIR GF77 OGI camera. Gasformer leverages a Mix Vision Transformer encoder and a Light-Ham decoder to generate multi-scale features and refine segmentation maps. Gasformer outperforms other state-of-the-art models on both datasets, demonstrating its effectiveness in detecting and segmenting methane plumes in controlled and real-world scenarios. On the livestock dataset, Gasformer achieves mIoU of 88.56%, surpassing other state-of-the-art models. Materials are available at: github.com/toqitahamid/Gasformer.

Retrieval-augmented generation (RAG) is a powerful technique that enhances downstream task execution by retrieving additional information, such as knowledge, skills, and tools from external sources. Graph, by its intrinsic "nodes connected by edges" nature, encodes massive heterogeneous and relational information, making it a golden resource for RAG in tremendous real-world applications. As a result, we have recently witnessed increasing attention on equipping RAG with Graph, i.e., GraphRAG. However, unlike conventional RAG, where the retriever, generator, and external data sources can be uniformly designed in the neural-embedding space, the uniqueness of graph-structured data, such as diverse-formatted and domain-specific relational knowledge, poses unique and significant challenges when designing GraphRAG for different domains. Given the broad applicability, the associated design challenges, and the recent surge in GraphRAG, a systematic and up-to-date survey of its key concepts and techniques is urgently desired. Following this motivation, we present a comprehensive and up-to-date survey on GraphRAG. Our survey first proposes a holistic GraphRAG framework by defining its key components, including query processor, retriever, organizer, generator, and data source. Furthermore, recognizing that graphs in different domains exhibit distinct relational patterns and require dedicated designs, we review GraphRAG techniques uniquely tailored to each domain. Finally, we discuss research challenges and brainstorm directions to inspire cross-disciplinary opportunities. Our survey repository is publicly maintained at https://github.com/Graph-RAG/GraphRAG/.

This paper presents a new tool learning dataset Seal-Tools, which contains self-instruct API-like tools. Seal-Tools not only offers a large number of tools, but also includes instances which demonstrate the practical application of tools. Seeking to generate data on a large scale while ensuring reliability, we propose a self-instruct method to generate tools and instances, allowing precise control over the process. Moreover, our Seal-Tools contains hard instances that call multiple tools to complete the job, among which some are nested tool callings. For precise and comprehensive evaluation, we use strict format control and design three metrics from different dimensions. Therefore, Seal-Tools can serve as a new benchmark to evaluate the tool-calling ability of LLMs. Finally, we evaluate several prevalent LLMs and our finetuned model on Seal-Tools. The results show that current systems are far from perfect. The code, data and experiment results are available at https://github.com/fairyshine/Seal-Tools .

Self-supervised learning (SSL) has been extensively explored in recent years. Particularly, generative SSL has seen emerging success in natural language processing and other AI fields, such as the wide adoption of BERT and GPT. Despite this, contrastive learning-which heavily relies on structural data augmentation and complicated training strategies-has been the dominant approach in graph SSL, while the progress of generative SSL on graphs, especially graph autoencoders (GAEs), has thus far not reached the potential as promised in other fields. In this paper, we identify and examine the issues that negatively impact the development of GAEs, including their reconstruction objective, training robustness, and error metric. We present a masked graph autoencoder GraphMAE that mitigates these issues for generative self-supervised graph pretraining. Instead of reconstructing graph structures, we propose to focus on feature reconstruction with both a masking strategy and scaled cosine error that benefit the robust training of GraphMAE. We conduct extensive experiments on 21 public datasets for three different graph learning tasks. The results manifest that GraphMAE-a simple graph autoencoder with careful designs-can consistently generate outperformance over both contrastive and generative state-of-the-art baselines. This study provides an understanding of graph autoencoders and demonstrates the potential of generative self-supervised pre-training on graphs.

Linking information across sources is fundamental to a variety of analyses in social science, business, and government. While large language models (LLMs) offer enormous promise for improving record linkage in noisy datasets, in many domains approximate string matching packages in popular softwares such as R and Stata remain predominant. These packages have clean, simple interfaces and can be easily extended to a diversity of languages. Our open-source package LinkTransformer aims to extend the familiarity and ease-of-use of popular string matching methods to deep learning. It is a general purpose package for record linkage with transformer LLMs that treats record linkage as a text retrieval problem. At its core is an off-the-shelf toolkit for applying transformer models to record linkage with four lines of code. LinkTransformer contains a rich repository of pre-trained transformer semantic similarity models for multiple languages and supports easy integration of any transformer language model from Hugging Face or OpenAI. It supports standard functionality such as blocking and linking on multiple noisy fields. LinkTransformer APIs also perform other common text data processing tasks, e.g., aggregation, noisy de-duplication, and translation-free cross-lingual linkage. Importantly, LinkTransformer also contains comprehensive tools for efficient model tuning, to facilitate different levels of customization when off-the-shelf models do not provide the required accuracy. Finally, to promote reusability, reproducibility, and extensibility, LinkTransformer makes it easy for users to contribute their custom-trained models to its model hub. By combining transformer language models with intuitive APIs that will be familiar to many users of popular string matching packages, LinkTransformer aims to democratize the benefits of LLMs among those who may be less familiar with deep learning frameworks.

Despite the significant advancements in pre-training methods for point cloud understanding, directly capturing intricate shape information from irregular point clouds without reliance on external data remains a formidable challenge. To address this problem, we propose GPSFormer, an innovative Global Perception and Local Structure Fitting-based Transformer, which learns detailed shape information from point clouds with remarkable precision. The core of GPSFormer is the Global Perception Module (GPM) and the Local Structure Fitting Convolution (LSFConv). Specifically, GPM utilizes Adaptive Deformable Graph Convolution (ADGConv) to identify short-range dependencies among similar features in the feature space and employs Multi-Head Attention (MHA) to learn long-range dependencies across all positions within the feature space, ultimately enabling flexible learning of contextual representations. Inspired by Taylor series, we design LSFConv, which learns both low-order fundamental and high-order refinement information from explicitly encoded local geometric structures. Integrating the GPM and LSFConv as fundamental components, we construct GPSFormer, a cutting-edge Transformer that effectively captures global and local structures of point clouds. Extensive experiments validate GPSFormer's effectiveness in three point cloud tasks: shape classification, part segmentation, and few-shot learning. The code of GPSFormer is available at https://github.com/changshuowang/GPSFormer.

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.

Graph Neural Networks (GNNs) are a powerful tool for machine learning on graphs.GNNs combine node feature information with the graph structure by recursively passing neural messages along edges of the input graph. However, incorporating both graph structure and feature information leads to complex models, and explaining predictions made by GNNs remains unsolved. Here we propose GNNExplainer, the first general, model-agnostic approach for providing interpretable explanations for predictions of any GNN-based model on any graph-based machine learning task. Given an instance, GNNExplainer identifies a compact subgraph structure and a small subset of node features that have a crucial role in GNN's prediction. Further, GNNExplainer can generate consistent and concise explanations for an entire class of instances. We formulate GNNExplainer as an optimization task that maximizes the mutual information between a GNN's prediction and distribution of possible subgraph structures. Experiments on synthetic and real-world graphs show that our approach can identify important graph structures as well as node features, and outperforms baselines by 17.1% on average. GNNExplainer provides a variety of benefits, from the ability to visualize semantically relevant structures to interpretability, to giving insights into errors of faulty GNNs.

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.

Pre-trained models for programming language have achieved dramatic empirical improvements on a variety of code-related tasks such as code search, code completion, code summarization, etc. However, existing pre-trained models regard a code snippet as a sequence of tokens, while ignoring the inherent structure of code, which provides crucial code semantics and would enhance the code understanding process. We present GraphCodeBERT, a pre-trained model for programming language that considers the inherent structure of code. Instead of taking syntactic-level structure of code like abstract syntax tree (AST), we use data flow in the pre-training stage, which is a semantic-level structure of code that encodes the relation of "where-the-value-comes-from" between variables. Such a semantic-level structure is neat and does not bring an unnecessarily deep hierarchy of AST, the property of which makes the model more efficient. We develop GraphCodeBERT based on Transformer. In addition to using the task of masked language modeling, we introduce two structure-aware pre-training tasks. One is to predict code structure edges, and the other is to align representations between source code and code structure. We implement the model in an efficient way with a graph-guided masked attention function to incorporate the code structure. We evaluate our model on four tasks, including code search, clone detection, code translation, and code refinement. Results show that code structure and newly introduced pre-training tasks can improve GraphCodeBERT and achieves state-of-the-art performance on the four downstream tasks. We further show that the model prefers structure-level attentions over token-level attentions in the task of code search.

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.

Tool use has turned large language models (LLMs) into powerful agents that can perform complex multi-step tasks by dynamically utilising external software components. However, these tools must be implemented in advance by human developers, hindering the applicability of LLM agents in domains which demand large numbers of highly specialised tools, like in life sciences and medicine. Motivated by the growing trend of scientific studies accompanied by public code repositories, we propose ToolMaker, a novel agentic framework that autonomously transforms papers with code into LLM-compatible tools. Given a short task description and a repository URL, ToolMaker autonomously installs required dependencies and generates code to perform the task, using a closed-loop self-correction mechanism to iteratively diagnose and rectify errors. To evaluate our approach, we introduce a benchmark comprising 15 diverse and complex computational tasks spanning both medical and non-medical domains with over 100 unit tests to objectively assess tool correctness and robustness. ToolMaker correctly implements 80% of the tasks, substantially outperforming current state-of-the-art software engineering agents. ToolMaker therefore is a step towards fully autonomous agent-based scientific workflows.

To address intricate real-world tasks, there has been a rising interest in tool utilization in applications of large language models (LLMs). To develop LLM-based agents, it usually requires LLMs to understand many tool functions from different tool documentation. But these documentations could be diverse, redundant or incomplete, which immensely affects the capability of LLMs in using tools. To solve this, we introduce EASYTOOL, a framework transforming diverse and lengthy tool documentation into a unified and concise tool instruction for easier tool usage. EasyTool purifies essential information from extensive tool documentation of different sources, and elaborates a unified interface (i.e., tool instruction) to offer standardized tool descriptions and functionalities for LLM-based agents. Extensive experiments on multiple different tasks demonstrate that EasyTool can significantly reduce token consumption and improve the performance of tool utilization in real-world scenarios. Our code will be available at https://github.com/microsoft/JARVIS/ in the future.

Transformers have greatly advanced the state-of-the-art in Natural Language Processing (NLP) in recent years, but present very large computation and storage requirements. We observe that the design process of Transformers (pre-train a foundation model on a large dataset in a self-supervised manner, and subsequently fine-tune it for different downstream tasks) leads to task-specific models that are highly over-parameterized, adversely impacting both accuracy and inference efficiency. We propose AxFormer, a systematic framework that applies accuracy-driven approximations to create optimized transformer models for a given downstream task. AxFormer combines two key optimizations -- accuracy-driven pruning and selective hard attention. Accuracy-driven pruning identifies and removes parts of the fine-tuned transformer that hinder performance on the given downstream task. Sparse hard-attention optimizes attention blocks in selected layers by eliminating irrelevant word aggregations, thereby helping the model focus only on the relevant parts of the input. In effect, AxFormer leads to models that are more accurate, while also being faster and smaller. Our experiments on GLUE and SQUAD tasks show that AxFormer models are up to 4.5% more accurate, while also being up to 2.5X faster and up to 3.2X smaller than conventional fine-tuned models. In addition, we demonstrate that AxFormer can be combined with previous efforts such as distillation or quantization to achieve further efficiency gains.

Transformer model architectures have garnered immense interest lately due to their effectiveness across a range of domains like language, vision and reinforcement learning. In the field of natural language processing for example, Transformers have become an indispensable staple in the modern deep learning stack. Recently, a dizzying number of "X-former" models have been proposed - Reformer, Linformer, Performer, Longformer, to name a few - which improve upon the original Transformer architecture, many of which make improvements around computational and memory efficiency. With the aim of helping the avid researcher navigate this flurry, this paper characterizes a large and thoughtful selection of recent efficiency-flavored "X-former" models, providing an organized and comprehensive overview of existing work and models across multiple domains.

In the realm of generative models for graphs, extensive research has been conducted. However, most existing methods struggle with large graphs due to the complexity of representing the entire joint distribution across all node pairs and capturing both global and local graph structures simultaneously. To overcome these issues, we introduce a method that generates a graph by progressively expanding a single node to a target graph. In each step, nodes and edges are added in a localized manner through denoising diffusion, building first the global structure, and then refining the local details. The local generation avoids modeling the entire joint distribution over all node pairs, achieving substantial computational savings with subquadratic runtime relative to node count while maintaining high expressivity through multiscale generation. Our experiments show that our model achieves state-of-the-art performance on well-established benchmark datasets while successfully scaling to graphs with at least 5000 nodes. Our method is also the first to successfully extrapolate to graphs outside of the training distribution, showcasing a much better generalization capability over existing methods.

Graph Neural Networks (GNNs) are widely deployed in vast fields, but they often struggle to maintain accurate representations as graphs evolve. We theoretically establish a lower bound, proving that under mild conditions, representation distortion inevitably occurs over time. To estimate the temporal distortion without human annotation after deployment, one naive approach is to pre-train a recurrent model (e.g., RNN) before deployment and use this model afterwards, but the estimation is far from satisfactory. In this paper, we analyze the representation distortion from an information theory perspective, and attribute it primarily to inaccurate feature extraction during evolution. Consequently, we introduce Smart, a straightforward and effective baseline enhanced by an adaptive feature extractor through self-supervised graph reconstruction. In synthetic random graphs, we further refine the former lower bound to show the inevitable distortion over time and empirically observe that Smart achieves good estimation performance. Moreover, we observe that Smart consistently shows outstanding generalization estimation on four real-world evolving graphs. The ablation studies underscore the necessity of graph reconstruction. For example, on OGB-arXiv dataset, the estimation metric MAPE deteriorates from 2.19% to 8.00% without reconstruction.

Hyper-relational knowledge graphs (HKGs) extend standard knowledge graphs by associating attribute-value qualifiers to triples, which effectively represent additional fine-grained information about its associated triple. Hyper-relational knowledge graph completion (HKGC) aims at inferring unknown triples while considering its qualifiers. Most existing approaches to HKGC exploit a global-level graph structure to encode hyper-relational knowledge into the graph convolution message passing process. However, the addition of multi-hop information might bring noise into the triple prediction process. To address this problem, we propose HyperFormer, a model that considers local-level sequential information, which encodes the content of the entities, relations and qualifiers of a triple. More precisely, HyperFormer is composed of three different modules: an entity neighbor aggregator module allowing to integrate the information of the neighbors of an entity to capture different perspectives of it; a relation qualifier aggregator module to integrate hyper-relational knowledge into the corresponding relation to refine the representation of relational content; a convolution-based bidirectional interaction module based on a convolutional operation, capturing pairwise bidirectional interactions of entity-relation, entity-qualifier, and relation-qualifier. realize the depth perception of the content related to the current statement. Furthermore, we introduce a Mixture-of-Experts strategy into the feed-forward layers of HyperFormer to strengthen its representation capabilities while reducing the amount of model parameters and computation. Extensive experiments on three well-known datasets with four different conditions demonstrate HyperFormer's effectiveness. Datasets and code are available at https://github.com/zhiweihu1103/HKGC-HyperFormer.

Graph Transformers have recently been successful in various graph representation learning tasks, providing a number of advantages over message-passing Graph Neural Networks. Utilizing Graph Transformers for learning the representation of the brain functional connectivity network is also gaining interest. However, studies to date have underlooked the temporal dynamics of functional connectivity, which fluctuates over time. Here, we propose a method for learning the representation of dynamic functional connectivity with Graph Transformers. Specifically, we define the connectome embedding, which holds the position, structure, and time information of the functional connectivity graph, and use Transformers to learn its representation across time. We perform experiments with over 50,000 resting-state fMRI samples obtained from three datasets, which is the largest number of fMRI data used in studies by far. The experimental results show that our proposed method outperforms other competitive baselines in gender classification and age regression tasks based on the functional connectivity extracted from the fMRI data.

Large Generative Models (LGMs) such as GPT, Stable Diffusion, Sora, and Suno are trained on a huge amount of language corpus, images, videos, and audio that are extremely diverse from numerous domains. This training paradigm over diverse well-curated data lies at the heart of generating creative and sensible content. However, all previous graph generative models (e.g., GraphRNN, MDVAE, MoFlow, GDSS, and DiGress) have been trained only on one dataset each time, which cannot replicate the revolutionary success achieved by LGMs in other fields. To remedy this crucial gap, we propose a new class of graph generative model called Large Graph Generative Model (LGGM) that is trained on a large corpus of graphs (over 5000 graphs) from 13 different domains. We empirically demonstrate that the pre-trained LGGM has superior zero-shot generative capability to existing graph generative models. Furthermore, our pre-trained LGGM can be easily fine-tuned with graphs from target domains and demonstrate even better performance than those directly trained from scratch, behaving as a solid starting point for real-world customization. Inspired by Stable Diffusion, we further equip LGGM with the capability to generate graphs given text prompts (Text-to-Graph), such as the description of the network name and domain (i.e., "The power-1138-bus graph represents a network of buses in a power distribution system."), and network statistics (i.e., "The graph has a low average degree, suitable for modeling social media interactions."). This Text-to-Graph capability integrates the extensive world knowledge in the underlying language model, offering users fine-grained control of the generated graphs. We release the code, the model checkpoint, and the datasets at https://lggm-lg.github.io/.

Can we model non-Euclidean graphs as pure language or even Euclidean vectors while retaining their inherent information? The non-Euclidean property have posed a long term challenge in graph modeling. Despite recent GNN and Graphformer efforts encoding graphs as Euclidean vectors, recovering original graph from the vectors remains a challenge. We introduce GraphsGPT, featuring a Graph2Seq encoder that transforms non-Euclidean graphs into learnable graph words in a Euclidean space, along with a GraphGPT decoder that reconstructs the original graph from graph words to ensure information equivalence. We pretrain GraphsGPT on 100M molecules and yield some interesting findings: (1) Pretrained Graph2Seq excels in graph representation learning, achieving state-of-the-art results on 8/9 graph classification and regression tasks. (2) Pretrained GraphGPT serves as a strong graph generator, demonstrated by its ability to perform both unconditional and conditional graph generation. (3) Graph2Seq+GraphGPT enables effective graph mixup in the Euclidean space, overcoming previously known non-Euclidean challenge. (4) Our proposed novel edge-centric GPT pretraining task is effective in graph fields, underscoring its success in both representation and generation.

Recently, large language models (LLMs) have demonstrated superior capabilities in understanding and zero-shot learning on textual data, promising significant advances for many text-related domains. In the graph domain, various real-world scenarios also involve textual data, where tasks and node features can be described by text. These text-attributed graphs (TAGs) have broad applications in social media, recommendation systems, etc. Thus, this paper explores how to utilize LLMs to model TAGs. Previous methods for TAG modeling are based on million-scale LMs. When scaled up to billion-scale LLMs, they face huge challenges in computational costs. Additionally, they also ignore the zero-shot inference capabilities of LLMs. Therefore, we propose GraphAdapter, which uses a graph neural network (GNN) as an efficient adapter in collaboration with LLMs to tackle TAGs. In terms of efficiency, the GNN adapter introduces only a few trainable parameters and can be trained with low computation costs. The entire framework is trained using auto-regression on node text (next token prediction). Once trained, GraphAdapter can be seamlessly fine-tuned with task-specific prompts for various downstream tasks. Through extensive experiments across multiple real-world TAGs, GraphAdapter based on Llama 2 gains an average improvement of approximately 5\% in terms of node classification. Furthermore, GraphAdapter can also adapt to other language models, including RoBERTa, GPT-2. The promising results demonstrate that GNNs can serve as effective adapters for LLMs in TAG modeling.

Large Language Models~(LLMs) have demonstrated capabilities across various applications but face challenges such as hallucination, limited reasoning abilities, and factual inconsistencies, especially when tackling complex, domain-specific tasks like question answering~(QA). While Knowledge Graphs~(KGs) have been shown to help mitigate these issues, research on the integration of LLMs with background KGs remains limited. In particular, user accessibility and the flexibility of the underlying KG have not been thoroughly explored. We introduce AGENTiGraph (Adaptive Generative ENgine for Task-based Interaction and Graphical Representation), a platform for knowledge management through natural language interaction. It integrates knowledge extraction, integration, and real-time visualization. AGENTiGraph employs a multi-agent architecture to dynamically interpret user intents, manage tasks, and integrate new knowledge, ensuring adaptability to evolving user requirements and data contexts. Our approach demonstrates superior performance in knowledge graph interactions, particularly for complex domain-specific tasks. Experimental results on a dataset of 3,500 test cases show AGENTiGraph significantly outperforms state-of-the-art zero-shot baselines, achieving 95.12\% accuracy in task classification and 90.45\% success rate in task execution. User studies corroborate its effectiveness in real-world scenarios. To showcase versatility, we extended AGENTiGraph to legislation and healthcare domains, constructing specialized KGs capable of answering complex queries in legal and medical contexts.

Graphs can model complex relationships between objects, enabling a myriad of Web applications such as online page/article classification and social recommendation. While graph neural networks(GNNs) have emerged as a powerful tool for graph representation learning, in an end-to-end supervised setting, their performance heavily rely on a large amount of task-specific supervision. To reduce labeling requirement, the "pre-train, fine-tune" and "pre-train, prompt" paradigms have become increasingly common. In particular, prompting is a popular alternative to fine-tuning in natural language processing, which is designed to narrow the gap between pre-training and downstream objectives in a task-specific manner. However, existing study of prompting on graphs is still limited, lacking a universal treatment to appeal to different downstream tasks. In this paper, we propose GraphPrompt, a novel pre-training and prompting framework on graphs. GraphPrompt not only unifies pre-training and downstream tasks into a common task template, but also employs a learnable prompt to assist a downstream task in locating the most relevant knowledge from the pre-train model in a task-specific manner. Finally, we conduct extensive experiments on five public datasets to evaluate and analyze GraphPrompt.

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.

The CLEVR dataset has been used extensively in language grounded visual reasoning in Machine Learning (ML) and Natural Language Processing (NLP) domains. We present a graph parser library for CLEVR, that provides functionalities for object-centric attributes and relationships extraction, and construction of structural graph representations for dual modalities. Structural order-invariant representations enable geometric learning and can aid in downstream tasks like language grounding to vision, robotics, compositionality, interpretability, and computational grammar construction. We provide three extensible main components - parser, embedder, and visualizer that can be tailored to suit specific learning setups. We also provide out-of-the-box functionality for seamless integration with popular deep graph neural network (GNN) libraries. Additionally, we discuss downstream usage and applications of the library, and how it accelerates research for the NLP research community.

Augmenting large language models (LLMs) with external tools has emerged as a promising approach to solving complex problems. However, traditional methods, which finetune LLMs with tool demonstration data, can be both costly and restricted to a predefined set of tools. Recent in-context learning paradigm alleviates these issues, but the limited context length only allows for a few shots of demonstrations, leading to suboptimal understandings of the tools. Moreover, when there are numerous tools to choose from, in-context learning could completely fail to work. In this paper, we propose an alternative approach, ToolkenGPT, which combines the benefits of both sides. Our approach represents each tool as a token (toolken) and learns an embedding for it, enabling tool calls in the same way as generating a regular word token. Once a toolken is triggered, the LLM is prompted to complete arguments for the tool to execute. ToolkenGPT offers the flexibility to plug in an arbitrary number of tools by expanding the set of toolkens on the fly. In addition, it improves tool use by allowing extensive demonstration data for learning the toolken embeddings. In diverse domains, including numerical reasoning, knowledge-based question answering, and embodied plan generation, our approach effectively augments LLMs with tools and substantially outperforms various latest baselines. ToolkenGPT demonstrates the promising ability to use relevant tools from a large tool set in complex scenarios.

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.

Given a graph with textual attributes, we enable users to `chat with their graph': that is, to ask questions about the graph using a conversational interface. In response to a user's questions, our method provides textual replies and highlights the relevant parts of the graph. While existing works integrate large language models (LLMs) and graph neural networks (GNNs) in various ways, they mostly focus on either conventional graph tasks (such as node, edge, and graph classification), or on answering simple graph queries on small or synthetic graphs. In contrast, we develop a flexible question-answering framework targeting real-world textual graphs, applicable to multiple applications including scene graph understanding, common sense reasoning, and knowledge graph reasoning. Toward this goal, we first develop a Graph Question Answering (GraphQA) benchmark with data collected from different tasks. Then, we propose our G-Retriever method, introducing the first retrieval-augmented generation (RAG) approach for general textual graphs, which can be fine-tuned to enhance graph understanding via soft prompting. To resist hallucination and to allow for textual graphs that greatly exceed the LLM's context window size, G-Retriever performs RAG over a graph by formulating this task as a Prize-Collecting Steiner Tree optimization problem. Empirical evaluations show that our method outperforms baselines on textual graph tasks from multiple domains, scales well with larger graph sizes, and mitigates hallucination.~Our codes and datasets are available at: \url{https://github.com/XiaoxinHe/G-Retriever}

Controllable 3D scene generation has extensive applications in virtual reality and interior design, where the generated scenes should exhibit high levels of realism and controllability in terms of geometry. Scene graphs provide a suitable data representation that facilitates these applications. However, current graph-based methods for scene generation are constrained to text-based inputs and exhibit insufficient adaptability to flexible user inputs, hindering the ability to precisely control object geometry. To address this issue, we propose MMGDreamer, a dual-branch diffusion model for scene generation that incorporates a novel Mixed-Modality Graph, visual enhancement module, and relation predictor. The mixed-modality graph allows object nodes to integrate textual and visual modalities, with optional relationships between nodes. It enhances adaptability to flexible user inputs and enables meticulous control over the geometry of objects in the generated scenes. The visual enhancement module enriches the visual fidelity of text-only nodes by constructing visual representations using text embeddings. Furthermore, our relation predictor leverages node representations to infer absent relationships between nodes, resulting in more coherent scene layouts. Extensive experimental results demonstrate that MMGDreamer exhibits superior control of object geometry, achieving state-of-the-art scene generation performance. Project page: https://yangzhifeio.github.io/project/MMGDreamer.

Large language models (LLMs) have garnered significant attention due to their impressive natural language processing (NLP) capabilities. Recently, many studies have focused on the tool utilization ability of LLMs. They primarily investigated how LLMs effectively collaborate with given specific tools. However, in scenarios where LLMs serve as intelligent agents, as seen in applications like AutoGPT and MetaGPT, LLMs are expected to engage in intricate decision-making processes that involve deciding whether to employ a tool and selecting the most suitable tool(s) from a collection of available tools to fulfill user requests. Therefore, in this paper, we introduce MetaTool, a benchmark designed to evaluate whether LLMs have tool usage awareness and can correctly choose tools. Specifically, we create a dataset called ToolE within the benchmark. This dataset contains various types of user queries in the form of prompts that trigger LLMs to use tools, including both single-tool and multi-tool scenarios. Subsequently, we set the tasks for both tool usage awareness and tool selection. We define four subtasks from different perspectives in tool selection, including tool selection with similar choices, tool selection in specific scenarios, tool selection with possible reliability issues, and multi-tool selection. We conduct experiments involving nine popular LLMs and find that the majority of them still struggle to effectively select tools, highlighting the existing gaps between LLMs and genuine intelligent agents. However, through the error analysis, we found there is still significant room for improvement. Finally, we conclude with insights for tool developers that follow ChatGPT to provide detailed descriptions that can enhance the tool selection performance of LLMs.

Tool learning enables Large Language Models (LLMs) to interact with external environments by invoking tools, serving as an effective strategy to mitigate the limitations inherent in their pre-training data. In this process, tool documentation plays a crucial role by providing usage instructions for LLMs, thereby facilitating effective tool utilization. This paper concentrates on the critical challenge of bridging the comprehension gap between LLMs and external tools due to the inadequacies and inaccuracies inherent in existing human-centric tool documentation. We propose a novel framework, DRAFT, aimed at Dynamically Refining tool documentation through the Analysis of Feedback and Trails emanating from LLMs' interactions with external tools. This methodology pivots on an innovative trial-and-error approach, consisting of three distinct learning phases: experience gathering, learning from experience, and documentation rewriting, to iteratively enhance the tool documentation. This process is further optimized by implementing a diversity-promoting exploration strategy to ensure explorative diversity and a tool-adaptive termination mechanism to prevent overfitting while enhancing efficiency. Extensive experiments on multiple datasets demonstrate that DRAFT's iterative, feedback-based refinement significantly ameliorates documentation quality, fostering a deeper comprehension and more effective utilization of tools by LLMs. Notably, our analysis reveals that the tool documentation refined via our approach demonstrates robust cross-model generalization capabilities.

This paper introduces WeatherFormer, a transformer encoder-based model designed to learn robust weather features from minimal observations. It addresses the challenge of modeling complex weather dynamics from small datasets, a bottleneck for many prediction tasks in agriculture, epidemiology, and climate science. WeatherFormer was pretrained on a large pretraining dataset comprised of 39 years of satellite measurements across the Americas. With a novel pretraining task and fine-tuning, WeatherFormer achieves state-of-the-art performance in county-level soybean yield prediction and influenza forecasting. Technical innovations include a unique spatiotemporal encoding that captures geographical, annual, and seasonal variations, adapting the transformer architecture to continuous weather data, and a pretraining strategy to learn representations that are robust to missing weather features. This paper for the first time demonstrates the effectiveness of pretraining large transformer encoder models for weather-dependent applications across multiple domains.

Tool learning aims to enhance and expand large language models' (LLMs) capabilities with external tools, which has gained significant attention recently. Current methods have shown that LLMs can effectively handle a certain amount of tools through in-context learning or fine-tuning. However, in real-world scenarios, the number of tools is typically extensive and irregularly updated, emphasizing the necessity for a dedicated tool retrieval component. Tool retrieval is nontrivial due to the following challenges: 1) complex user instructions and tool descriptions; 2) misalignment between tool retrieval and tool usage models. To address the above issues, we propose to enhance tool retrieval with iterative feedback from the large language model. Specifically, we prompt the tool usage model, i.e., the LLM, to provide feedback for the tool retriever model in multi-round, which could progressively improve the tool retriever's understanding of instructions and tools and reduce the gap between the two standalone components. We build a unified and comprehensive benchmark to evaluate tool retrieval models. The extensive experiments indicate that our proposed approach achieves advanced performance in both in-domain evaluation and out-of-domain evaluation.

Rationale discovery is defined as finding a subset of the input data that maximally supports the prediction of downstream tasks. In graph machine learning context, graph rationale is defined to locate the critical subgraph in the given graph topology, which fundamentally determines the prediction results. In contrast to the rationale subgraph, the remaining subgraph is named the environment subgraph. Graph rationalization can enhance the model performance as the mapping between the graph rationale and prediction label is viewed as invariant, by assumption. To ensure the discriminative power of the extracted rationale subgraphs, a key technique named "intervention" is applied. The core idea of intervention is that given any changing environment subgraphs, the semantics from the rationale subgraph is invariant, which guarantees the correct prediction result. However, most, if not all, of the existing rationalization works on graph data develop their intervention strategies on the graph level, which is coarse-grained. In this paper, we propose well-tailored intervention strategies on graph data. Our idea is driven by the development of Transformer models, whose self-attention module provides rich interactions between input nodes. Based on the self-attention module, our proposed invariant graph Transformer (IGT) can achieve fine-grained, more specifically, node-level and virtual node-level intervention. Our comprehensive experiments involve 7 real-world datasets, and the proposed IGT shows significant performance advantages compared to 13 baseline methods.

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.

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/

Classification tasks in NLP are typically addressed by selecting a pre-trained language model (PLM) from a model hub, and fine-tuning it for the task at hand. However, given the very large number of PLMs that are currently available, a practical challenge is to determine which of them will perform best for a specific downstream task. With this paper, we introduce TransformerRanker, a lightweight library that efficiently ranks PLMs for classification tasks without the need for computationally costly fine-tuning. Our library implements current approaches for transferability estimation (LogME, H-Score, kNN), in combination with layer aggregation options, which we empirically showed to yield state-of-the-art rankings of PLMs (Garbas et al., 2024). We designed the interface to be lightweight and easy to use, allowing users to directly connect to the HuggingFace Transformers and Dataset libraries. Users need only select a downstream classification task and a list of PLMs to create a ranking of likely best-suited PLMs for their task. We make TransformerRanker available as a pip-installable open-source library https://github.com/flairNLP/transformer-ranker.

Humans possess an extraordinary ability to create and utilize tools, allowing them to overcome physical limitations and explore new frontiers. With the advent of foundation models, AI systems have the potential to be equally adept in tool use as humans. This paradigm, i.e., tool learning with foundation models, combines the strengths of specialized tools and foundation models to achieve enhanced accuracy, efficiency, and automation in problem-solving. Despite its immense potential, there is still a lack of a comprehensive understanding of key challenges, opportunities, and future endeavors in this field. To this end, we present a systematic investigation of tool learning in this paper. We first introduce the background of tool learning, including its cognitive origins, the paradigm shift of foundation models, and the complementary roles of tools and models. Then we recapitulate existing tool learning research into tool-augmented and tool-oriented learning. We formulate a general tool learning framework: starting from understanding the user instruction, models should learn to decompose a complex task into several subtasks, dynamically adjust their plan through reasoning, and effectively conquer each sub-task by selecting appropriate tools. We also discuss how to train models for improved tool-use capabilities and facilitate the generalization in tool learning. Considering the lack of a systematic tool learning evaluation in prior works, we experiment with 17 representative tools and show the potential of current foundation models in skillfully utilizing tools. Finally, we discuss several open problems that require further investigation for tool learning. Overall, we hope this paper could inspire future research in integrating tools with foundation models.

Deep generative models (DGMs) have been widely developed for graph data. However, much less investigation has been carried out on understanding the latent space of such pretrained graph DGMs. These understandings possess the potential to provide constructive guidelines for crucial tasks, such as graph controllable generation. Thus in this work, we are interested in studying this problem and propose GraphCG, a method for the unsupervised discovery of steerable factors in the latent space of pretrained graph DGMs. We first examine the representation space of three pretrained graph DGMs with six disentanglement metrics, and we observe that the pretrained representation space is entangled. Motivated by this observation, GraphCG learns the steerable factors via maximizing the mutual information between semantic-rich directions, where the controlled graph moving along the same direction will share the same steerable factors. We quantitatively verify that GraphCG outperforms four competitive baselines on two graph DGMs pretrained on two molecule datasets. Additionally, we qualitatively illustrate seven steerable factors learned by GraphCG on five pretrained DGMs over five graph datasets, including two for molecules and three for point clouds.

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

Graph generation is integral to various engineering and scientific disciplines. Nevertheless, existing methodologies tend to overlook the generation of edge attributes. However, we identify critical applications where edge attributes are essential, making prior methods potentially unsuitable in such contexts. Moreover, while trivial adaptations are available, empirical investigations reveal their limited efficacy as they do not properly model the interplay among graph components. To address this, we propose a joint score-based model of nodes and edges for graph generation that considers all graph components. Our approach offers two key novelties: (i) node and edge attributes are combined in an attention module that generates samples based on the two ingredients; and (ii) node, edge and adjacency information are mutually dependent during the graph diffusion process. We evaluate our method on challenging benchmarks involving real-world and synthetic datasets in which edge features are crucial. Additionally, we introduce a new synthetic dataset that incorporates edge values. Furthermore, we propose a novel application that greatly benefits from the method due to its nature: the generation of traffic scenes represented as graphs. Our method outperforms other graph generation methods, demonstrating a significant advantage in edge-related measures.

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.

Automatically generating source code from natural language descriptions has been a growing field of research in recent years. However, current large-scale code generation models often encounter difficulties when selecting appropriate APIs for specific contexts. These models may generate APIs that do not meet requirements or refer to non-existent APIs in third-party libraries, especially for lesser-known or private libraries. Inspired by the process of human developers using tools to search APIs, we propose ToolCoder, a novel approach that integrates API search tools with existing models to assist in code generation and API selection. To teach our model to use tools, we introduce an automated data annotation method using ChatGPT to add tool usage information into the source code data and fine-tune code generation models. During inference, we integrate API search tools into the generation process so that our model can automatically use the search tool to get suggestions when selecting an API. Our experimental results demonstrate that ToolCoder exhibits excellent performance and generalization across five public and private library code generation benchmarks, with at least 6.21\% improvement on average pass@1 metrics and 9.64\% improvement on average pass@10 metrics compared to state-of-the-art methods. Furthermore, we show that our relatively small ToolCoder model is comparable to one of the current best models, GPT-3.5, highlighting the potential of incorporating programming tools into the code generation process.

Conditional graphic layout generation, which automatically maps user constraints to high-quality layouts, has attracted widespread attention today. Although recent works have achieved promising performance, the lack of versatility and data efficiency hinders their practical applications. In this work, we propose LayoutPrompter, which leverages large language models (LLMs) to address the above problems through in-context learning. LayoutPrompter is made up of three key components, namely input-output serialization, dynamic exemplar selection and layout ranking. Specifically, the input-output serialization component meticulously designs the input and output formats for each layout generation task. Dynamic exemplar selection is responsible for selecting the most helpful prompting exemplars for a given input. And a layout ranker is used to pick the highest quality layout from multiple outputs of LLMs. We conduct experiments on all existing layout generation tasks using four public datasets. Despite the simplicity of our approach, experimental results show that LayoutPrompter can compete with or even outperform state-of-the-art approaches on these tasks without any model training or fine-tuning. This demonstrates the effectiveness of this versatile and training-free approach. In addition, the ablation studies show that LayoutPrompter is significantly superior to the training-based baseline in a low-data regime, further indicating the data efficiency of LayoutPrompter. Our project is available at https://github.com/microsoft/LayoutGeneration/tree/main/LayoutPrompter.

GraphRAG addresses significant challenges in Retrieval-Augmented Generation (RAG) by leveraging graphs with embedded knowledge to enhance the reasoning capabilities of Large Language Models (LLMs). Despite its promising potential, the GraphRAG community currently lacks a unified framework for fine-grained decomposition of the graph-based knowledge retrieval process. Furthermore, there is no systematic categorization or evaluation of existing solutions within the retrieval process. In this paper, we present LEGO-GraphRAG, a modular framework that decomposes the retrieval process of GraphRAG into three interconnected modules: subgraph-extraction, path-filtering, and path-refinement. We systematically summarize and classify the algorithms and neural network (NN) models relevant to each module, providing a clearer understanding of the design space for GraphRAG instances. Additionally, we identify key design factors, such as Graph Coupling and Computational Cost, that influence the effectiveness of GraphRAG implementations. Through extensive empirical studies, we construct high-quality GraphRAG instances using a representative selection of solutions and analyze their impact on retrieval and reasoning performance. Our findings offer critical insights into optimizing GraphRAG instance design, ultimately contributing to the advancement of more accurate and contextually relevant LLM applications.

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

Diffusion-based generative graph models have been proven effective in generating high-quality small graphs. However, they need to be more scalable for generating large graphs containing thousands of nodes desiring graph statistics. In this work, we propose EDGE, a new diffusion-based generative graph model that addresses generative tasks with large graphs. To improve computation efficiency, we encourage graph sparsity by using a discrete diffusion process that randomly removes edges at each time step and finally obtains an empty graph. EDGE only focuses on a portion of nodes in the graph at each denoising step. It makes much fewer edge predictions than previous diffusion-based models. Moreover, EDGE admits explicitly modeling the node degrees of the graphs, further improving the model performance. The empirical study shows that EDGE is much more efficient than competing methods and can generate large graphs with thousands of nodes. It also outperforms baseline models in generation quality: graphs generated by our approach have more similar graph statistics to those of the training graphs.

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.

Large Language Models (LLMs) have demonstrated significant progress in utilizing external APIs as tools for various tasks. However, their tool-using ability is limited by the availability of suitable APIs and the instability of implicit reasoning, particularly when simultaneously engaging in reasoning about plans and actual calculations. To address these limitations, we propose CREATOR, a novel framework that empowers LLMs to create their own tools through documentation and code realization. CREATOR disentangles the LLM's ability into two distinct phases: abstract tool creation and concrete decision execution, which results in improved LLM performance. We evaluate CREATOR on two established benchmarks: MATH, which consists of challenging math competition problems, and TabMWP, which includes diverse tabular contents for problem-solving. Remarkably, CREATOR significantly outperforms existing chain-of-thought (CoT), program-of-thought (PoT), and tool-using baselines on these two benchmarks. Additionally, we present a new dataset, Creation Challenge, comprising 2K diverse questions, to highlight the necessity and benefits of LLMs' tool creation ability in effectively addressing these problems. Furthermore, our research reveals that leveraging LLMs as tool creators facilitates knowledge transfer, and LLMs exhibit varying levels of tool creation abilities, enabling them to flexibly tackle diverse situations. Our study represents a promising avenue for maximizing the potential of LLMs and advancing toward truly intelligent and adaptable AI systems.

To create rich visualizations, data analysts often need to iterate back and forth among data processing and chart specification to achieve their goals. To achieve this, analysts need not only proficiency in data transformation and visualization tools but also efforts to manage the branching history consisting of many different versions of data and charts. Recent LLM-powered AI systems have greatly improved visualization authoring experiences, for example by mitigating manual data transformation barriers via LLMs' code generation ability. However, these systems do not work well for iterative visualization authoring, because they often require analysts to provide, in a single turn, a text-only prompt that fully describes the complex visualization task to be performed, which is unrealistic to both users and models in many cases. In this paper, we present Data Formulator 2, an LLM-powered visualization system to address these challenges. With Data Formulator 2, users describe their visualization intent with blended UI and natural language inputs, and data transformation are delegated to AI. To support iteration, Data Formulator 2 lets users navigate their iteration history and reuse previous designs towards new ones so that they don't need to start from scratch every time. In a user study with eight participants, we observed that Data Formulator 2 allows participants to develop their own iteration strategies to complete challenging data exploration sessions.

Foundation models have emerged as critical components in a variety of artificial intelligence applications, and showcase significant success in natural language processing and several other domains. Meanwhile, the field of graph machine learning is witnessing a paradigm transition from shallow methods to more sophisticated deep learning approaches. The capabilities of foundation models to generalize and adapt motivate graph machine learning researchers to discuss the potential of developing a new graph learning paradigm. This paradigm envisions models that are pre-trained on extensive graph data and can be adapted for various graph tasks. Despite this burgeoning interest, there is a noticeable lack of clear definitions and systematic analyses pertaining to this new domain. To this end, this article introduces the concept of Graph Foundation Models (GFMs), and offers an exhaustive explanation of their key characteristics and underlying technologies. We proceed to classify the existing work related to GFMs into three distinct categories, based on their dependence on graph neural networks and large language models. In addition to providing a thorough review of the current state of GFMs, this article also outlooks potential avenues for future research in this rapidly evolving domain.

Recently, the incredible progress of large language models (LLMs) has ignited the spark of task automation, which decomposes the complex tasks described by user instructions into sub-tasks, and invokes external tools to execute them, and plays a central role in autonomous agents. However, there lacks a systematic and standardized benchmark to foster the development of LLMs in task automation. To this end, we introduce TaskBench to evaluate the capability of LLMs in task automation. Specifically, task automation can be formulated into three critical stages: task decomposition, tool invocation, and parameter prediction to fulfill user intent. This complexity makes data collection and evaluation more challenging compared to common NLP tasks. To generate high-quality evaluation datasets, we introduce the concept of Tool Graph to represent the decomposed tasks in user intent, and adopt a back-instruct method to simulate user instruction and annotations. Furthermore, we propose TaskEval to evaluate the capability of LLMs from different aspects, including task decomposition, tool invocation, and parameter prediction. Experimental results demonstrate that TaskBench can effectively reflects the capability of LLMs in task automation. Benefiting from the mixture of automated data construction and human verification, TaskBench achieves a high consistency compared to the human evaluation, which can be utilized as a comprehensive and faithful benchmark for LLM-based autonomous agents.

Complex Logical Query Answering (CLQA) over incomplete knowledge graphs is a challenging task. Recently, Query Embedding (QE) methods are proposed to solve CLQA by performing multi-hop logical reasoning. However, most of them only consider historical query context information while ignoring future information, which leads to their failure to capture the complex dependencies behind the elements of a query. In recent years, the transformer architecture has shown a strong ability to model long-range dependencies between words. The bidirectional attention mechanism proposed by the transformer can solve the limitation of these QE methods regarding query context. Still, as a sequence model, it is difficult for the transformer to model complex logical queries with branch structure computation graphs directly. To this end, we propose a neural one-point embedding method called Pathformer based on the tree-like computation graph, i.e., query computation tree. Specifically, Pathformer decomposes the query computation tree into path query sequences by branches and then uses the transformer encoder to recursively encode these path query sequences to obtain the final query embedding. This allows Pathformer to fully utilize future context information to explicitly model the complex interactions between various parts of the path query. Experimental results show that Pathformer outperforms existing competitive neural QE methods, and we found that Pathformer has the potential to be applied to non-one-point embedding space.

Graph generation with Machine Learning is an open problem with applications in various research fields. In this work, we propose to cast the generative process of a graph into a sequential one, relying on a node ordering procedure. We use this sequential process to design a novel generative model composed of two recurrent neural networks that learn to predict the edges of graphs: the first network generates one endpoint of each edge, while the second network generates the other endpoint conditioned on the state of the first. We test our approach extensively on five different datasets, comparing with two well-known baselines coming from graph literature, and two recurrent approaches, one of which holds state of the art performances. Evaluation is conducted considering quantitative and qualitative characteristics of the generated samples. Results show that our approach is able to yield novel, and unique graphs originating from very different distributions, while retaining structural properties very similar to those in the training sample. Under the proposed evaluation framework, our approach is able to reach performances comparable to the current state of the art on the graph generation task.

Graph transformers (GTs) have emerged as a promising architecture that is theoretically more expressive than message-passing graph neural networks (GNNs). However, typical GT models have at least quadratic complexity and thus cannot scale to large graphs. While there are several linear GTs recently proposed, they still lag behind GNN counterparts on several popular graph datasets, which poses a critical concern on their practical expressivity. To balance the trade-off between expressivity and scalability of GTs, we propose Polynormer, a polynomial-expressive GT model with linear complexity. Polynormer is built upon a novel base model that learns a high-degree polynomial on input features. To enable the base model permutation equivariant, we integrate it with graph topology and node features separately, resulting in local and global equivariant attention models. Consequently, Polynormer adopts a linear local-to-global attention scheme to learn high-degree equivariant polynomials whose coefficients are controlled by attention scores. Polynormer has been evaluated on 13 homophilic and heterophilic datasets, including large graphs with millions of nodes. Our extensive experiment results show that Polynormer outperforms state-of-the-art GNN and GT baselines on most datasets, even without the use of nonlinear activation functions.

Tool learning enables large language models (LLMs) to interact with external tools and APIs, greatly expanding the application scope of LLMs. However, due to the dynamic nature of external environments, these tools and APIs may become outdated over time, preventing LLMs from correctly invoking tools. Existing research primarily focuses on static environments and overlooks this issue, limiting the adaptability of LLMs in real-world applications. In this paper, we propose ToolEVO, a novel framework designed to enhance the adaptive and reflective capabilities of LLMs against tool variability. By leveraging Monte Carlo Tree Search, ToolEVO facilitates active exploration and interaction of LLMs within dynamic environments, allowing for autonomous self-reflection and self-updating of tool usage based on environmental feedback. Additionally, we introduce ToolQA-D, a benchmark specifically designed to evaluate the impact of tool variability. Extensive experiments demonstrate the effectiveness and stability of our approach, highlighting the importance of adaptability to tool variability for effective tool learning.

Recent research has demonstrated that Large Language Models (LLMs) can enhance their capabilities by utilizing external tools. However, three pivotal questions remain unanswered: (1) How effective are current LLMs in utilizing tools? (2) How can we enhance LLMs' ability to utilize tools? (3) What obstacles need to be overcome to leverage tools? To address these questions, we introduce API-Bank, a groundbreaking benchmark, specifically designed for tool-augmented LLMs. For the first question, we develop a runnable evaluation system consisting of 73 API tools. We annotate 314 tool-use dialogues with 753 API calls to assess the existing LLMs' capabilities in planning, retrieving, and calling APIs. For the second question, we construct a comprehensive training set containing 1,888 tool-use dialogues from 2,138 APIs spanning 1,000 distinct domains. Using this dataset, we train Lynx, a tool-augmented LLM initialized from Alpaca. Experimental results demonstrate that GPT-3.5 exhibits improved tool utilization compared to GPT-3, while GPT-4 excels in planning. However, there is still significant potential for further improvement. Moreover, Lynx surpasses Alpaca's tool utilization performance by more than 26 pts and approaches the effectiveness of GPT-3.5. Through error analysis, we highlight the key challenges for future research in this field to answer the third question.

In this paper, we approach an overlooked yet critical task Graph2Image: generating images from multimodal attributed graphs (MMAGs). This task poses significant challenges due to the explosion in graph size, dependencies among graph entities, and the need for controllability in graph conditions. To address these challenges, we propose a graph context-conditioned diffusion model called InstructG2I. InstructG2I first exploits the graph structure and multimodal information to conduct informative neighbor sampling by combining personalized page rank and re-ranking based on vision-language features. Then, a Graph-QFormer encoder adaptively encodes the graph nodes into an auxiliary set of graph prompts to guide the denoising process of diffusion. Finally, we propose graph classifier-free guidance, enabling controllable generation by varying the strength of graph guidance and multiple connected edges to a node. Extensive experiments conducted on three datasets from different domains demonstrate the effectiveness and controllability of our approach. The code is available at https://github.com/PeterGriffinJin/InstructG2I.

Advances in Visually Rich Document Understanding (VrDU) have enabled information extraction and question answering over documents with complex layouts. Two tropes of architectures have emerged -- transformer-based models inspired by LLMs, and Graph Neural Networks. In this paper, we introduce DocGraphLM, a novel framework that combines pre-trained language models with graph semantics. To achieve this, we propose 1) a joint encoder architecture to represent documents, and 2) a novel link prediction approach to reconstruct document graphs. DocGraphLM predicts both directions and distances between nodes using a convergent joint loss function that prioritizes neighborhood restoration and downweighs distant node detection. Our experiments on three SotA datasets show consistent improvement on IE and QA tasks with the adoption of graph features. Moreover, we report that adopting the graph features accelerates convergence in the learning process during training, despite being solely constructed through link prediction.

Charts are a powerful tool for visually conveying complex data, but their comprehension poses a challenge due to the diverse chart types and intricate components. Existing chart comprehension methods suffer from either heuristic rules or an over-reliance on OCR systems, resulting in suboptimal performance. To address these issues, we present ChartReader, a unified framework that seamlessly integrates chart derendering and comprehension tasks. Our approach includes a transformer-based chart component detection module and an extended pre-trained vision-language model for chart-to-X tasks. By learning the rules of charts automatically from annotated datasets, our approach eliminates the need for manual rule-making, reducing effort and enhancing accuracy.~We also introduce a data variable replacement technique and extend the input and position embeddings of the pre-trained model for cross-task training. We evaluate ChartReader on Chart-to-Table, ChartQA, and Chart-to-Text tasks, demonstrating its superiority over existing methods. Our proposed framework can significantly reduce the manual effort involved in chart analysis, providing a step towards a universal chart understanding model. Moreover, our approach offers opportunities for plug-and-play integration with mainstream LLMs such as T5 and TaPas, extending their capability to chart comprehension tasks. The code is available at https://github.com/zhiqic/ChartReader.

Recent advances in Graph Neural Networks (GNNs) and Graph Transformers (GTs) have been driven by innovations in architectures and Positional Encodings (PEs), which are critical for augmenting node features and capturing graph topology. PEs are essential for GTs, where topological information would otherwise be lost without message-passing. However, PEs are often tested alongside novel architectures, making it difficult to isolate their effect on established models. To address this, we present a comprehensive benchmark of PEs in a unified framework that includes both message-passing GNNs and GTs. We also establish theoretical connections between MPNNs and GTs and introduce a sparsified GRIT attention mechanism to examine the influence of global connectivity. Our findings demonstrate that previously untested combinations of GNN architectures and PEs can outperform existing methods and offer a more comprehensive picture of the state-of-the-art. To support future research and experimentation in our framework, we make the code publicly available.

We present SkexGen, a novel autoregressive generative model for computer-aided design (CAD) construction sequences containing sketch-and-extrude modeling operations. Our model utilizes distinct Transformer architectures to encode topological, geometric, and extrusion variations of construction sequences into disentangled codebooks. Autoregressive Transformer decoders generate CAD construction sequences sharing certain properties specified by the codebook vectors. Extensive experiments demonstrate that our disentangled codebook representation generates diverse and high-quality CAD models, enhances user control, and enables efficient exploration of the design space. The code is available at https://samxuxiang.github.io/skexgen.

Which transformer scaling regimes are able to perfectly solve different classes of algorithmic problems? While tremendous empirical advances have been attained by transformer-based neural networks, a theoretical understanding of their algorithmic reasoning capabilities in realistic parameter regimes is lacking. We investigate this question in terms of the network's depth, width, and number of extra tokens for algorithm execution. Our novel representational hierarchy separates 9 algorithmic reasoning problems into classes solvable by transformers in different realistic parameter scaling regimes. We prove that logarithmic depth is necessary and sufficient for tasks like graph connectivity, while single-layer transformers with small embedding dimensions can solve contextual retrieval tasks. We also support our theoretical analysis with ample empirical evidence using the GraphQA benchmark. These results show that transformers excel at many graph reasoning tasks, even outperforming specialized graph neural networks.

Utilizing pre-trained language models has achieved great success for neural document ranking. Limited by the computational and memory requirements, long document modeling becomes a critical issue. Recent works propose to modify the full attention matrix in Transformer by designing sparse attention patterns. However, most of them only focus on local connections of terms within a fixed-size window. How to build suitable remote connections between terms to better model document representation remains underexplored. In this paper, we propose the model Socialformer, which introduces the characteristics of social networks into designing sparse attention patterns for long document modeling in document ranking. Specifically, we consider several attention patterns to construct a graph like social networks. Endowed with the characteristic of social networks, most pairs of nodes in such a graph can reach with a short path while ensuring the sparsity. To facilitate efficient calculation, we segment the graph into multiple subgraphs to simulate friend circles in social scenarios. Experimental results confirm the effectiveness of our model on long document modeling.

We address 2D floorplan reconstruction from 3D scans. Existing approaches typically employ heuristically designed multi-stage pipelines. Instead, we formulate floorplan reconstruction as a single-stage structured prediction task: find a variable-size set of polygons, which in turn are variable-length sequences of ordered vertices. To solve it we develop a novel Transformer architecture that generates polygons of multiple rooms in parallel, in a holistic manner without hand-crafted intermediate stages. The model features two-level queries for polygons and corners, and includes polygon matching to make the network end-to-end trainable. Our method achieves a new state-of-the-art for two challenging datasets, Structured3D and SceneCAD, along with significantly faster inference than previous methods. Moreover, it can readily be extended to predict additional information, i.e., semantic room types and architectural elements like doors and windows. Our code and models are available at: https://github.com/ywyue/RoomFormer.

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.

In this paper, we present the findings of our Project ALPINE which stands for ``Autoregressive Learning for Planning In NEtworks." Project ALPINE initiates a theoretical investigation into the development of planning capabilities in Transformer-based language models through their autoregressive learning mechanisms, aiming to identify any potential limitations in their planning abilities. We abstract planning as a network path-finding task where the objective is to generate a valid path from a specified source node to a designated target node. In terms of expressiveness, we show that the Transformer is capable of executing path-finding by embedding the adjacency and reachability matrices within its weights. Our theoretical analysis of the gradient-based learning dynamic of the Transformer reveals that the Transformer is capable of learning both the adjacency matrix and a limited form of the reachability matrix. These theoretical insights are then validated through experiments, which demonstrate that the Transformer indeed learns the adjacency matrix and an incomplete reachability matrix, which aligns with the predictions made in our theoretical analysis. Additionally, when applying our methodology to a real-world planning benchmark, called Blocksworld, our observations remain consistent. Our theoretical and empirical analyses further unveil a potential limitation of Transformer in path-finding: it cannot identify reachability relationships through transitivity, and thus would fail when path concatenation is needed to generate a path. In summary, our findings shed new light on how the internal mechanisms of autoregressive learning enable planning in networks. This study may contribute to our understanding of the general planning capabilities in other related domains.

The robustness of a model for real-world deployment is decided by how well it performs on unseen data and distinguishes between in-domain and out-of-domain samples. Visual document classifiers have shown impressive performance on in-distribution test sets. However, they tend to have a hard time correctly classifying and differentiating out-of-distribution examples. Image-based classifiers lack the text component, whereas multi-modality transformer-based models face the token serialization problem in visual documents due to their diverse layouts. They also require a lot of computing power during inference, making them impractical for many real-world applications. We propose, GVdoc, a graph-based document classification model that addresses both of these challenges. Our approach generates a document graph based on its layout, and then trains a graph neural network to learn node and graph embeddings. Through experiments, we show that our model, even with fewer parameters, outperforms state-of-the-art models on out-of-distribution data while retaining comparable performance on the in-distribution test set.

Graph Neural Networks (GNNs) have shown promising potential in graph representation learning. The majority of GNNs define a local message-passing mechanism, propagating information over the graph by stacking multiple layers. These methods, however, are known to suffer from two major limitations: over-squashing and poor capturing of long-range dependencies. Recently, Graph Transformers (GTs) emerged as a powerful alternative to Message-Passing Neural Networks (MPNNs). GTs, however, have quadratic computational cost, lack inductive biases on graph structures, and rely on complex Positional/Structural Encodings (SE/PE). In this paper, we show that while Transformers, complex message-passing, and SE/PE are sufficient for good performance in practice, neither is necessary. Motivated by the recent success of State Space Models (SSMs), such as Mamba, we present Graph Mamba Networks (GMNs), a general framework for a new class of GNNs based on selective SSMs. We discuss and categorize the new challenges when adopting SSMs to graph-structured data, and present four required and one optional steps to design GMNs, where we choose (1) Neighborhood Tokenization, (2) Token Ordering, (3) Architecture of Bidirectional Selective SSM Encoder, (4) Local Encoding, and dispensable (5) PE and SE. We further provide theoretical justification for the power of GMNs. Experiments demonstrate that despite much less computational cost, GMNs attain an outstanding performance in long-range, small-scale, large-scale, and heterophilic benchmark datasets.

Graph-to-text generation has benefited from pre-trained language models (PLMs) in achieving better performance than structured graph encoders. However, they fail to fully utilize the structure information of the input graph. In this paper, we aim to further improve the performance of the pre-trained language model by proposing a structured graph-to-text model with a two-step fine-tuning mechanism which first fine-tunes the model on Wikipedia before adapting to the graph-to-text generation. In addition to using the traditional token and position embeddings to encode the knowledge graph (KG), we propose a novel tree-level embedding method to capture the inter-dependency structures of the input graph. This new approach has significantly improved the performance of all text generation metrics for the English WebNLG 2017 dataset.

Recent advancements in tool-equipped Agents (LLMs) have enabled complex tasks like secure database interactions and multi-agent code development. However, scaling tool capacity beyond agent reasoning or model limits remains a challenge. In this paper, we address these challenges by introducing Toolshed Knowledge Bases, a tool knowledge base (vector database) designed to store enhanced tool representations and optimize tool selection for large-scale tool-equipped Agents. Additionally, we propose Advanced RAG-Tool Fusion, a novel ensemble of tool-applied advanced retrieval-augmented generation (RAG) techniques across the pre-retrieval, intra-retrieval, and post-retrieval phases, without requiring model fine-tuning. During pre-retrieval, tool documents are enhanced with key information and stored in the Toolshed Knowledge Base. Intra-retrieval focuses on query planning and transformation to increase retrieval accuracy. Post-retrieval refines the retrieved tool documents and enables self-reflection. Furthermore, by varying both the total number of tools (tool-M) an Agent has access to and the tool selection threshold (top-k), we address trade-offs between retrieval accuracy, agent performance, and token cost. Our approach achieves 46%, 56%, and 47% absolute improvements on the ToolE single-tool, ToolE multi-tool and Seal-Tools benchmark datasets, respectively (Recall@5).

All tables can be represented as grids. Based on this observation, we propose GridFormer, a novel approach for interpreting unconstrained table structures by predicting the vertex and edge of a grid. First, we propose a flexible table representation in the form of an MXN grid. In this representation, the vertexes and edges of the grid store the localization and adjacency information of the table. Then, we introduce a DETR-style table structure recognizer to efficiently predict this multi-objective information of the grid in a single shot. Specifically, given a set of learned row and column queries, the recognizer directly outputs the vertexes and edges information of the corresponding rows and columns. Extensive experiments on five challenging benchmarks which include wired, wireless, multi-merge-cell, oriented, and distorted tables demonstrate the competitive performance of our model over other methods.

Learning effective representations of source code is critical for any Machine Learning for Software Engineering (ML4SE) system. Inspired by natural language processing, large language models (LLMs) like Codex and CodeGen treat code as generic sequences of text and are trained on huge corpora of code data, achieving state of the art performance on several software engineering (SE) tasks. However, valid source code, unlike natural language, follows a strict structure and pattern governed by the underlying grammar of the programming language. Current LLMs do not exploit this property of the source code as they treat code like a sequence of tokens and overlook key structural and semantic properties of code that can be extracted from code-views like the Control Flow Graph (CFG), Data Flow Graph (DFG), Abstract Syntax Tree (AST), etc. Unfortunately, the process of generating and integrating code-views for every programming language is cumbersome and time consuming. To overcome this barrier, we propose our tool COMEX - a framework that allows researchers and developers to create and combine multiple code-views which can be used by machine learning (ML) models for various SE tasks. Some salient features of our tool are: (i) it works directly on source code (which need not be compilable), (ii) it currently supports Java and C#, (iii) it can analyze both method-level snippets and program-level snippets by using both intra-procedural and inter-procedural analysis, and (iv) it is easily extendable to other languages as it is built on tree-sitter - a widely used incremental parser that supports over 40 languages. We believe this easy-to-use code-view generation and customization tool will give impetus to research in source code representation learning methods and ML4SE. Tool: https://pypi.org/project/comex - GitHub: https://github.com/IBM/tree-sitter-codeviews - Demo: https://youtu.be/GER6U87FVbU

Given the ubiquity of charts as a data analysis, visualization, and decision-making tool across industries and sciences, there has been a growing interest in developing pre-trained foundation models as well as general purpose instruction-tuned models for chart understanding and reasoning. However, existing methods suffer crucial drawbacks across two critical axes affecting the performance of chart representation models: they are trained on data generated from underlying data tables of the charts, ignoring the visual trends and patterns in chart images, and use weakly aligned vision-language backbone models for domain-specific training, limiting their generalizability when encountering charts in the wild. We address these important drawbacks and introduce ChartGemma, a novel chart understanding and reasoning model developed over PaliGemma. Rather than relying on underlying data tables, ChartGemma is trained on instruction-tuning data generated directly from chart images, thus capturing both high-level trends and low-level visual information from a diverse set of charts. Our simple approach achieves state-of-the-art results across 5 benchmarks spanning chart summarization, question answering, and fact-checking, and our elaborate qualitative studies on real-world charts show that ChartGemma generates more realistic and factually correct summaries compared to its contemporaries. We release the code, model checkpoints, dataset, and demos at https://github.com/vis-nlp/ChartGemma.

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.

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.

Graph generative models become increasingly effective for data distribution approximation and data augmentation. While they have aroused public concerns about their malicious misuses or misinformation broadcasts, just as what Deepfake visual and auditory media has been delivering to society. Hence it is essential to regulate the prevalence of generated graphs. To tackle this problem, we pioneer the formulation of the generated graph detection problem to distinguish generated graphs from real ones. We propose the first framework to systematically investigate a set of sophisticated models and their performance in four classification scenarios. Each scenario switches between seen and unseen datasets/generators during testing to get closer to real-world settings and progressively challenge the classifiers. Extensive experiments evidence that all the models are qualified for generated graph detection, with specific models having advantages in specific scenarios. Resulting from the validated generality and oblivion of the classifiers to unseen datasets/generators, we draw a safe conclusion that our solution can sustain for a decent while to curb generated graph misuses.

While the recent advances in deep neural networks (DNN) bring remarkable success, the computational cost also increases considerably. In this paper, we introduce Greenformer, a toolkit to accelerate the computation of neural networks through matrix factorization while maintaining performance. Greenformer can be easily applied with a single line of code to any DNN model. Our experimental results show that Greenformer is effective for a wide range of scenarios. We provide the showcase of Greenformer at https://samuelcahyawijaya.github.io/greenformer-demo/.

Spreadsheets are a vital tool for end-user data management. Using large language models for formula authoring assistance in these environments can be difficult, as these models are expensive to train and challenging to deploy due to their size (up to billions of parameters). We present FLAME, a transformer-based model trained exclusively on Excel formulas that leverages domain insights to achieve competitive performance while being substantially smaller (60M parameters) and training on two orders of magnitude less data. We curate a training dataset using sketch deduplication, introduce an Excel-specific formula tokenizer, and use domain-specific versions of masked span prediction and noisy auto-encoding as pre-training objectives. We evaluate FLAME on formula repair, formula completion, and similarity-based formula retrieval. FLAME can outperform much larger models, such as the Davinci (175B) and Cushman (12B) variants of Codex and CodeT5 (220M), in 10 of 14 evaluation settings for the repair and completion tasks. For formula retrieval, FLAME outperforms CodeT5, CodeBERT, and GraphCodeBERT.

When manipulating three-dimensional data, it is possible to ensure that rotational and translational symmetries are respected by applying so-called SE(3)-equivariant models. Protein structure prediction is a prominent example of a task which displays these symmetries. Recent work in this area has successfully made use of an SE(3)-equivariant model, applying an iterative SE(3)-equivariant attention mechanism. Motivated by this application, we implement an iterative version of the SE(3)-Transformer, an SE(3)-equivariant attention-based model for graph data. We address the additional complications which arise when applying the SE(3)-Transformer in an iterative fashion, compare the iterative and single-pass versions on a toy problem, and consider why an iterative model may be beneficial in some problem settings. We make the code for our implementation available to the community.

Information flows by routes inside the network via mechanisms implemented in the model. These routes can be represented as graphs where nodes correspond to token representations and edges to operations inside the network. We automatically build these graphs in a top-down manner, for each prediction leaving only the most important nodes and edges. In contrast to the existing workflows relying on activation patching, we do this through attribution: this allows us to efficiently uncover existing circuits with just a single forward pass. Additionally, the applicability of our method is far beyond patching: we do not need a human to carefully design prediction templates, and we can extract information flow routes for any prediction (not just the ones among the allowed templates). As a result, we can talk about model behavior in general, for specific types of predictions, or different domains. We experiment with Llama 2 and show that the role of some attention heads is overall important, e.g. previous token heads and subword merging heads. Next, we find similarities in Llama 2 behavior when handling tokens of the same part of speech. Finally, we show that some model components can be specialized on domains such as coding or multilingual texts.

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

Graph Neural Networks (GNNs) have shown great potential in the field of graph representation learning. Standard GNNs define a local message-passing mechanism which propagates information over the whole graph domain by stacking multiple layers. This paradigm suffers from two major limitations, over-squashing and poor long-range dependencies, that can be solved using global attention but significantly increases the computational cost to quadratic complexity. In this work, we propose an alternative approach to overcome these structural limitations by leveraging the ViT/MLP-Mixer architectures introduced in computer vision. We introduce a new class of GNNs, called Graph ViT/MLP-Mixer, that holds three key properties. First, they capture long-range dependency and mitigate the issue of over-squashing as demonstrated on Long Range Graph Benchmark and TreeNeighbourMatch datasets. Second, they offer better speed and memory efficiency with a complexity linear to the number of nodes and edges, surpassing the related Graph Transformer and expressive GNN models. Third, they show high expressivity in terms of graph isomorphism as they can distinguish at least 3-WL non-isomorphic graphs. We test our architecture on 4 simulated datasets and 7 real-world benchmarks, and show highly competitive results on all of them. The source code is available for reproducibility at: https://github.com/XiaoxinHe/Graph-ViT-MLPMixer.

Recent improvements in KG-to-text generation are due to additional auxiliary pre-training tasks designed to give the fine-tune task a boost in performance. These tasks require extensive computational resources while only suggesting marginal improvements. Here, we demonstrate that by fusing graph-aware elements into existing pre-trained language models, we are able to outperform state-of-the-art models and close the gap imposed by additional pre-training tasks. We do so by proposing a mask structure to capture neighborhood information and a novel type encoder that adds a bias to the graph-attention weights depending on the connection type. Experiments on two KG-to-text benchmark datasets show our models are competitive while involving fewer parameters and no additional pre-training tasks. By formulating the problem as a framework, we can interchange the various proposed components and begin interpreting KG-to-text generative models based on the topological and type information found in a graph.

Geometric Deep Learning has recently attracted significant interest in a wide range of machine learning fields, including document analysis. The application of Graph Neural Networks (GNNs) has become crucial in various document-related tasks since they can unravel important structural patterns, fundamental in key information extraction processes. Previous works in the literature propose task-driven models and do not take into account the full power of graphs. We propose Doc2Graph, a task-agnostic document understanding framework based on a GNN model, to solve different tasks given different types of documents. We evaluated our approach on two challenging datasets for key information extraction in form understanding, invoice layout analysis and table detection. Our code is freely accessible on https://github.com/andreagemelli/doc2graph.

Recent prevailing works on graph machine learning typically follow a similar methodology that involves designing advanced variants of graph neural networks (GNNs) to maintain the superior performance of GNNs on different graphs. In this paper, we aim to streamline the GNN design process and leverage the advantages of Large Language Models (LLMs) to improve the performance of GNNs on downstream tasks. We formulate a new paradigm, coined "LLMs-as-Consultants," which integrates LLMs with GNNs in an interactive manner. A framework named LOGIN (LLM Consulted GNN training) is instantiated, empowering the interactive utilization of LLMs within the GNN training process. First, we attentively craft concise prompts for spotted nodes, carrying comprehensive semantic and topological information, and serving as input to LLMs. Second, we refine GNNs by devising a complementary coping mechanism that utilizes the responses from LLMs, depending on their correctness. We empirically evaluate the effectiveness of LOGIN on node classification tasks across both homophilic and heterophilic graphs. The results illustrate that even basic GNN architectures, when employed within the proposed LLMs-as-Consultants paradigm, can achieve comparable performance to advanced GNNs with intricate designs. Our codes are available at https://github.com/QiaoYRan/LOGIN.

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.

Recently, Retrieval-Augmented Generation (RAG) has achieved remarkable success in addressing the challenges of Large Language Models (LLMs) without necessitating retraining. By referencing an external knowledge base, RAG refines LLM outputs, effectively mitigating issues such as ``hallucination'', lack of domain-specific knowledge, and outdated information. However, the complex structure of relationships among different entities in databases presents challenges for RAG systems. In response, GraphRAG leverages structural information across entities to enable more precise and comprehensive retrieval, capturing relational knowledge and facilitating more accurate, context-aware responses. Given the novelty and potential of GraphRAG, a systematic review of current technologies is imperative. This paper provides the first comprehensive overview of GraphRAG methodologies. We formalize the GraphRAG workflow, encompassing Graph-Based Indexing, Graph-Guided Retrieval, and Graph-Enhanced Generation. We then outline the core technologies and training methods at each stage. Additionally, we examine downstream tasks, application domains, evaluation methodologies, and industrial use cases of GraphRAG. Finally, we explore future research directions to inspire further inquiries and advance progress in the field.

Pre-trained sequence-to-sequence language models have led to widespread success in many natural language generation tasks. However, there has been relatively less work on analyzing their ability to generate structured outputs such as graphs. Unlike natural language, graphs have distinct structural and semantic properties in the context of a downstream NLP task, e.g., generating a graph that is connected and acyclic can be attributed to its structural constraints, while the semantics of a graph can refer to how meaningfully an edge represents the relation between two node concepts. In this work, we study pre-trained language models that generate explanation graphs in an end-to-end manner and analyze their ability to learn the structural constraints and semantics of such graphs. We first show that with limited supervision, pre-trained language models often generate graphs that either violate these constraints or are semantically incoherent. Since curating large amount of human-annotated graphs is expensive and tedious, we propose simple yet effective ways of graph perturbations via node and edge edit operations that lead to structurally and semantically positive and negative graphs. Next, we leverage these graphs in different contrastive learning models with Max-Margin and InfoNCE losses. Our methods lead to significant improvements in both structural and semantic accuracy of explanation graphs and also generalize to other similar graph generation tasks. Lastly, we show that human errors are the best negatives for contrastive learning and also that automatically generating more such human-like negative graphs can lead to further improvements. Our code and models are publicly available at https://github.com/swarnaHub/ExplagraphGen

Most real-world graphs exhibit a hierarchical structure, which is often overlooked by existing graph generation methods. To address this limitation, we propose a novel graph generative network that captures the hierarchical nature of graphs and successively generates the graph sub-structures in a coarse-to-fine fashion. At each level of hierarchy, this model generates communities in parallel, followed by the prediction of cross-edges between communities using separate neural networks. This modular approach enables scalable graph generation for large and complex graphs. Moreover, we model the output distribution of edges in the hierarchical graph with a multinomial distribution and derive a recursive factorization for this distribution. This enables us to generate community graphs with integer-valued edge weights in an autoregressive manner. Empirical studies demonstrate the effectiveness and scalability of our proposed generative model, achieving state-of-the-art performance in terms of graph quality across various benchmark datasets. The code is available at https://github.com/Karami-m/HiGen_main.

We design a new technique for the distributional semantic modeling with a neural network-based approach to learn distributed term representations (or term embeddings) - term vector space models as a result, inspired by the recent ontology-related approach (using different types of contextual knowledge such as syntactic knowledge, terminological knowledge, semantic knowledge, etc.) to the identification of terms (term extraction) and relations between them (relation extraction) called semantic pre-processing technology - SPT. Our method relies on automatic term extraction from the natural language texts and subsequent formation of the problem-oriented or application-oriented (also deeply annotated) text corpora where the fundamental entity is the term (includes non-compositional and compositional terms). This gives us an opportunity to changeover from distributed word representations (or word embeddings) to distributed term representations (or term embeddings). This transition will allow to generate more accurate semantic maps of different subject domains (also, of relations between input terms - it is useful to explore clusters and oppositions, or to test your hypotheses about them). The semantic map can be represented as a graph using Vec2graph - a Python library for visualizing word embeddings (term embeddings in our case) as dynamic and interactive graphs. The Vec2graph library coupled with term embeddings will not only improve accuracy in solving standard NLP tasks, but also update the conventional concept of automated ontology development. The main practical result of our work is the development kit (set of toolkits represented as web service APIs and web application), which provides all necessary routines for the basic linguistic pre-processing and the semantic pre-processing of the natural language texts in Ukrainian for future training of term vector space models.

Advancements in generative models have sparked significant interest in generating images while adhering to specific structural guidelines. Scene graph to image generation is one such task of generating images which are consistent with the given scene graph. However, the complexity of visual scenes poses a challenge in accurately aligning objects based on specified relations within the scene graph. Existing methods approach this task by first predicting a scene layout and generating images from these layouts using adversarial training. In this work, we introduce a novel approach to generate images from scene graphs which eliminates the need of predicting intermediate layouts. We leverage pre-trained text-to-image diffusion models and CLIP guidance to translate graph knowledge into images. Towards this, we first pre-train our graph encoder to align graph features with CLIP features of corresponding images using a GAN based training. Further, we fuse the graph features with CLIP embedding of object labels present in the given scene graph to create a graph consistent CLIP guided conditioning signal. In the conditioning input, object embeddings provide coarse structure of the image and graph features provide structural alignment based on relationships among objects. Finally, we fine tune a pre-trained diffusion model with the graph consistent conditioning signal with reconstruction and CLIP alignment loss. Elaborate experiments reveal that our method outperforms existing methods on standard benchmarks of COCO-stuff and Visual Genome dataset.

Despite the advancements of open-source large language models (LLMs) and their variants, e.g., LLaMA and Vicuna, they remain significantly limited in performing higher-level tasks, such as following human instructions to use external tools (APIs). This is because current instruction tuning largely focuses on basic language tasks instead of the tool-use domain. This is in contrast to state-of-the-art (SOTA) LLMs, e.g., ChatGPT, which have demonstrated excellent tool-use capabilities but are unfortunately closed source. To facilitate tool-use capabilities within open-source LLMs, we introduce ToolLLM, a general tool-use framework of data construction, model training and evaluation. We first present ToolBench, an instruction-tuning dataset for tool use, which is created automatically using ChatGPT. Specifically, we collect 16,464 real-world RESTful APIs spanning 49 categories from RapidAPI Hub, then prompt ChatGPT to generate diverse human instructions involving these APIs, covering both single-tool and multi-tool scenarios. Finally, we use ChatGPT to search for a valid solution path (chain of API calls) for each instruction. To make the searching process more efficient, we develop a novel depth-first search-based decision tree (DFSDT), enabling LLMs to evaluate multiple reasoning traces and expand the search space. We show that DFSDT significantly enhances the planning and reasoning capabilities of LLMs. For efficient tool-use assessment, we develop an automatic evaluator: ToolEval. We fine-tune LLaMA on ToolBench and obtain ToolLLaMA. Our ToolEval reveals that ToolLLaMA demonstrates a remarkable ability to execute complex instructions and generalize to unseen APIs, and exhibits comparable performance to ChatGPT. To make the pipeline more practical, we devise a neural API retriever to recommend appropriate APIs for each instruction, negating the need for manual API selection.

While multi-modal models have successfully integrated information from image, video, and audio modalities, integrating graph modality into large language models (LLMs) remains unexplored. This discrepancy largely stems from the inherent divergence between structured graph data and unstructured text data. Incorporating graph knowledge provides a reliable source of information, enabling potential solutions to address issues in text generation, e.g., hallucination, and lack of domain knowledge. To evaluate the integration of graph knowledge into language models, a dedicated dataset is needed. However, there is currently no benchmark dataset specifically designed for multimodal graph-language models. To address this gap, we propose GraphextQA, a question answering dataset with paired subgraphs, retrieved from Wikidata, to facilitate the evaluation and future development of graph-language models. Additionally, we introduce a baseline model called CrossGNN, which conditions answer generation on the paired graphs by cross-attending question-aware graph features at decoding. The proposed dataset is designed to evaluate graph-language models' ability to understand graphs and make use of it for answer generation. We perform experiments with language-only models and the proposed graph-language model to validate the usefulness of the paired graphs and to demonstrate the difficulty of the task.

Recent studies on software tool manipulation with large language models (LLMs) mostly rely on closed model APIs. The industrial adoption of these models is substantially constrained due to the security and robustness risks in exposing information to closed LLM API services. In this paper, we ask can we enhance open-source LLMs to be competitive to leading closed LLM APIs in tool manipulation, with practical amount of human supervision. By analyzing common tool manipulation failures, we first demonstrate that open-source LLMs may require training with usage examples, in-context demonstration and generation style regulation to resolve failures. These insights motivate us to revisit classical methods in LLM literature, and demonstrate that we can adapt them as model alignment with programmatic data generation, system prompts and in-context demonstration retrievers to enhance open-source LLMs for tool manipulation. To evaluate these techniques, we create the ToolBench, a tool manipulation benchmark consisting of diverse software tools for real-world tasks. We demonstrate that our techniques can boost leading open-source LLMs by up to 90% success rate, showing capabilities competitive to OpenAI GPT-4 in 4 out of 8 ToolBench tasks. We show that such enhancement typically requires about one developer day to curate data for each tool, rendering a recipe with practical amount of human supervision.

Effective evaluation of multi-hop tool use is critical for analyzing the understanding, reasoning, and function-calling capabilities of large language models (LLMs). However, progress has been hindered by a lack of reliable evaluation datasets. To address this, we present ToolHop, a dataset comprising 995 user queries and 3,912 associated tools, specifically designed for rigorous evaluation of multi-hop tool use. ToolHop ensures diverse queries, meaningful interdependencies, locally executable tools, detailed feedback, and verifiable answers through a novel query-driven data construction approach that includes tool creation, document refinement, and code generation. We evaluate 14 LLMs across five model families (i.e., LLaMA3.1, Qwen2.5, Gemini1.5, Claude3.5, and GPT), uncovering significant challenges in handling multi-hop tool-use scenarios. The leading model, GPT-4o, achieves an accuracy of 49.04%, underscoring substantial room for improvement. Further analysis reveals variations in tool-use strategies for various families, offering actionable insights to guide the development of more effective approaches. Code and data can be found in https://huggingface.co/bytedance-research/ToolHop.

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.

Recent advances in interpretability suggest we can project weights and hidden states of transformer-based language models (LMs) to their vocabulary, a transformation that makes them human interpretable and enables us to assign semantics to what was seen only as numerical vectors. In this paper, we interpret LM attention heads and memory values, the vectors the models dynamically create and recall while processing a given input. By analyzing the tokens they represent through this projection, we identify patterns in the information flow inside the attention mechanism. Based on these discoveries, we create a tool to visualize a forward pass of Generative Pre-trained Transformers (GPTs) as an interactive flow graph, with nodes representing neurons or hidden states and edges representing the interactions between them. Our visualization simplifies huge amounts of data into easy-to-read plots that reflect why models output their results. We demonstrate the utility of our modeling by identifying the effect LM components have on the intermediate processing in the model before outputting a prediction. For instance, we discover that layer norms are used as semantic filters and find neurons that act as regularization vectors.

Program synthesis strives to generate a computer program as a solution to a given problem specification, expressed with input-output examples or natural language descriptions. The prevalence of large language models advances the state-of-the-art for program synthesis, though limited training resources and data impede open access to such models. To democratize this, we train and release a family of large language models up to 16.1B parameters, called CODEGEN, on natural language and programming language data, and open source the training library JAXFORMER. We show the utility of the trained model by demonstrating that it is competitive with the previous state-of-the-art on zero-shot Python code generation on HumanEval. We further investigate the multi-step paradigm for program synthesis, where a single program is factorized into multiple prompts specifying subproblems. To this end, we construct an open benchmark, Multi-Turn Programming Benchmark (MTPB), consisting of 115 diverse problem sets that are factorized into multi-turn prompts. Our analysis on MTPB shows that the same intent provided to CODEGEN in multi-turn fashion significantly improves program synthesis over that provided as a single turn. We make the training library JAXFORMER and model checkpoints available as open source contribution: https://github.com/salesforce/CodeGen.

The exploitation of syntactic graphs (SyGs) as a word's context has been shown to be beneficial for distributional semantic models (DSMs), both at the level of individual word representations and in deriving phrasal representations via composition. However, notwithstanding the potential performance benefit, the syntactically-aware DSMs proposed to date have huge numbers of parameters (compared to conventional DSMs) and suffer from data sparsity. Furthermore, the encoding of the SyG links (i.e., the syntactic relations) has been largely limited to linear maps. The knowledge graphs' literature, on the other hand, has proposed light-weight models employing different geometric transformations (GTs) to encode edges in a knowledge graph (KG). Our work explores the possibility of adopting this family of models to encode SyGs. Furthermore, we investigate which GT better encodes syntactic relations, so that these representations can be used to enhance phrase-level composition via syntactic contextualisation.

Transformer-based architectures achieved breakthrough performance in natural language processing and computer vision, yet they remain inferior to simpler linear baselines in multivariate long-term forecasting. To better understand this phenomenon, we start by studying a toy linear forecasting problem for which we show that transformers are incapable of converging to their true solution despite their high expressive power. We further identify the attention of transformers as being responsible for this low generalization capacity. Building upon this insight, we propose a shallow lightweight transformer model that successfully escapes bad local minima when optimized with sharpness-aware optimization. We empirically demonstrate that this result extends to all commonly used real-world multivariate time series datasets. In particular, SAMformer surpasses current state-of-the-art methods and is on par with the biggest foundation model MOIRAI while having significantly fewer parameters. The code is available at https://github.com/romilbert/samformer.

Besides natural language processing, transformers exhibit extraordinary performance in solving broader applications, including scientific computing and computer vision. Previous works try to explain this from the expressive power and capability perspectives that standard transformers are capable of performing some algorithms. To empower transformers with algorithmic capabilities and motivated by the recently proposed looped transformer (Yang et al., 2024; Giannou et al., 2023), we design a novel transformer block, dubbed Algorithm Transformer (abbreviated as AlgoFormer). Compared with the standard transformer and vanilla looped transformer, the proposed AlgoFormer can achieve significantly higher expressiveness in algorithm representation when using the same number of parameters. In particular, inspired by the structure of human-designed learning algorithms, our transformer block consists of a pre-transformer that is responsible for task pre-processing, a looped transformer for iterative optimization algorithms, and a post-transformer for producing the desired results after post-processing. We provide theoretical evidence of the expressive power of the AlgoFormer in solving some challenging problems, mirroring human-designed algorithms. Furthermore, some theoretical and empirical results are presented to show that the designed transformer has the potential to be smarter than human-designed algorithms. Experimental results demonstrate the empirical superiority of the proposed transformer in that it outperforms the standard transformer and vanilla looped transformer in some challenging tasks.

Modern sequence models (e.g., Transformers, linear RNNs, etc.) emerged as dominant backbones of recent deep learning frameworks, mainly due to their efficiency, representational power, and/or ability to capture long-range dependencies. Adopting these sequence models for graph-structured data has recently gained popularity as the alternative to Message Passing Neural Networks (MPNNs). There is, however, a lack of a common foundation about what constitutes a good graph sequence model, and a mathematical description of the benefits and deficiencies in adopting different sequence models for learning on graphs. To this end, we first present Graph Sequence Model (GSM), a unifying framework for adopting sequence models for graphs, consisting of three main steps: (1) Tokenization, which translates the graph into a set of sequences; (2) Local Encoding, which encodes local neighborhoods around each node; and (3) Global Encoding, which employs a scalable sequence model to capture long-range dependencies within the sequences. This framework allows us to understand, evaluate, and compare the power of different sequence model backbones in graph tasks. Our theoretical evaluations of the representation power of Transformers and modern recurrent models through the lens of global and local graph tasks show that there are both negative and positive sides for both types of models. Building on this observation, we present GSM++, a fast hybrid model that uses the Hierarchical Affinity Clustering (HAC) algorithm to tokenize the graph into hierarchical sequences, and then employs a hybrid architecture of Transformer to encode these sequences. Our theoretical and experimental results support the design of GSM++, showing that GSM++ outperforms baselines in most benchmark evaluations.