Towards Stable, Globally Expressive Graph Representations with Laplacian Eigenvectors

Graph neural networks (GNNs) have achieved remarkable success in a variety of machine learning tasks over graph data. Existing GNNs usually rely on message passing, i.e., computing node representations by gathering information from the neighborhood, to build their underlying computational graphs. They are known fairly limited in expressive power, and often fail to capture global characteristics of graphs. To overcome the issue, a popular solution is to use Laplacian eigenvectors as additional node features, as they contain global positional information of nodes, and can serve as extra node identifiers aiding GNNs to separate structurally similar nodes. For such an approach, properly handling the orthogonal group symmetry among eigenvectors with equal eigenvalue is crucial for its stability and generalizability. However, using a naive orthogonal group invariant encoder for each separate eigenspace may not keep the full expressivity in the Laplacian eigenvectors. Moreover, computing such invariants inevitably entails a hard split of Laplacian eigenvalues according to their numerical identity, which suffers from great instability when the graph structure is perturbed. In this paper, we propose a novel method exploiting Laplacian eigenvectors to generate stable and globally expressive graph representations. The main difference from previous works is that (i) our method utilizes learnable orthogonal group invariant representations for each Laplacian eigenspace, based upon powerful orthogonal group equivariant neural network layers already well studied in the literature, and that (ii) our method deals with numerically close eigenvalues in a smooth fashion, ensuring its better robustness against perturbations. Experiments on various graph learning benchmarks witness the competitive performance of our method, especially its great potential to learn global properties of graphs.

Mars: Situated Inductive Reasoning in an Open-World Environment

Large Language Models (LLMs) trained on massive corpora have shown remarkable success in knowledge-intensive tasks. Yet, most of them rely on pre-stored knowledge. Inducing new general knowledge from a specific environment and performing reasoning with the acquired knowledge -- \textit{situated inductive reasoning}, is crucial and challenging for machine intelligence. In this paper, we design Mars, an interactive environment devised for situated inductive reasoning. It introduces counter-commonsense game mechanisms by modifying terrain, survival setting and task dependency while adhering to certain principles. In Mars, agents need to actively interact with their surroundings, derive useful rules and perform decision-making tasks in specific contexts. We conduct experiments on various RL-based and LLM-based methods, finding that they all struggle on this challenging situated inductive reasoning benchmark. Furthermore, we explore \textit{Induction from Reflection}, where we instruct agents to perform inductive reasoning from history trajectory. The superior performance underscores the importance of inductive reasoning in Mars. Through Mars, we aim to galvanize advancements in situated inductive reasoning and set the stage for developing the next generation of AI systems that can reason in an adaptive and context-sensitive way.

Fine-Grained Expressive Power of Weisfeiler-Leman: A Homomorphism Counting Perspective

The ability of graph neural networks (GNNs) to count homomorphisms has recently been proposed as a practical and fine-grained measure of their expressive power. Although several existing works have investigated the homomorphism counting power of certain GNN families, a simple and unified framework for analyzing the problem is absent. In this paper, we first propose \emph{generalized folklore Weisfeiler-Leman (GFWL)} algorithms as a flexible design basis for expressive GNNs, and then provide a theoretical framework to algorithmically determine the homomorphism counting power of an arbitrary class of GNN within the GFWL design space. As the considered design space is large enough to accommodate almost all known powerful GNNs, our result greatly extends all existing works, and may find its application in the automation of GNN model design.

Geometric Representation Condition Improves Equivariant Molecule Generation

Recent advancements in molecular generative models have demonstrated substantial potential in accelerating scientific discovery, particularly in drug design. However, these models often face challenges in generating high-quality molecules, especially in conditional scenarios where specific molecular properties must be satisfied. In this work, we introduce GeoRCG, a general framework to enhance the performance of molecular generative models by integrating geometric representation conditions. We decompose the molecule generation process into two stages: first, generating an informative geometric representation; second, generating a molecule conditioned on the representation. Compared to directly generating a molecule, the relatively easy-to-generate representation in the first-stage guides the second-stage generation to reach a high-quality molecule in a more goal-oriented and much faster way. Leveraging EDM as the base generator, we observe significant quality improvements in unconditional molecule generation on the widely-used QM9 and GEOM-DRUG datasets. More notably, in the challenging conditional molecular generation task, our framework achieves an average 31\% performance improvement over state-of-the-art approaches, highlighting the superiority of conditioning on semantically rich geometric representations over conditioning on individual property values as in previous approaches. Furthermore, we show that, with such representation guidance, the number of diffusion steps can be reduced to as small as 100 while maintaining superior generation quality than that achieved with 1,000 steps, thereby significantly accelerating the generation process.

On Lexical Invariance on Multisets and Graphs

In this draft, we study a novel problem, called lexical invariance, using the medium of multisets and graphs. Traditionally in the NLP domain, lexical invariance indicates that the semantic meaning of a sentence should remain unchanged regardless of the specific lexical or word-based representation of the input. For example, ``The movie was extremely entertaining'' would have the same meaning as ``The film was very enjoyable''. In this paper, we study a more challenging setting, where the output of a function is invariant to any injective transformation applied to the input lexical space. For example, multiset {1,2,3,2} is equivalent to multiset {a,b,c,b} if we specify an injective transformation that maps 1 to a, 2 to b and 3 to c. We study the sufficient and necessary conditions for a most expressive lexical invariant (and permutation invariant) function on multisets and graphs, and proves that for multisets, the function must have a form that only takes the multiset of counts of the unique elements in the original multiset as input. For example, a most expressive lexical invariant function on {a,b,c,b} must have a form that only operates on {1,1,2} (meaning that there are 1, 1, 2 unique elements corresponding to a,c,b). For graphs, we prove that a most expressive lexical invariant and permutation invariant function must have a form that only takes the adjacency matrix and a difference matrix as input, where the (i,j)th element of the difference matrix is 1 if node i and node j have the same feature and 0 otherwise. We perform synthetic experiments on TU datasets to verify our theorems.

GOFA: A Generative One-For-All Model for Joint Graph Language Modeling

Foundation models, such as Large Language Models (LLMs) or Large Vision Models (LVMs), have emerged as one of the most powerful tools in the respective fields. However, unlike text and image data, graph data do not have a definitive structure, posing great challenges to developing a Graph Foundation Model (GFM). For example, current attempts at designing general graph models either transform graph data into a language format for LLM-based prediction or still train a GNN model with LLM as an assistant. The former can handle unlimited tasks, while the latter captures graph structure much better -- yet, no existing work can achieve both simultaneously. In this paper, we identify three key desirable properties of a GFM: self-supervised pretraining, fluidity in tasks, and graph awareness. To account for these properties, we extend the conventional language modeling to the graph domain and propose a novel generative graph language model GOFA to solve the problem. The model interleaves randomly initialized GNN layers into a frozen pre-trained LLM so that the semantic and structural modeling abilities are organically combined. GOFA is pre-trained on newly proposed graph-level next-word prediction, question-answering, and structural tasks to obtain the above GFM properties. The pre-trained model is further fine-tuned on downstream tasks to obtain task-solving ability. The fine-tuned model is evaluated on various downstream tasks, demonstrating a strong ability to solve structural and contextual problems in zero-shot scenarios. The code is available at https://github.com/JiaruiFeng/GOFA.

Foundations and Frontiers of Graph Learning Theory

Recent advancements in graph learning have revolutionized the way to understand and analyze data with complex structures. Notably, Graph Neural Networks (GNNs), i.e. neural network architectures designed for learning graph representations, have become a popular paradigm. With these models being usually characterized by intuition-driven design or highly intricate components, placing them within the theoretical analysis framework to distill the core concepts, helps understand the key principles that drive the functionality better and guide further development. Given this surge in interest, this article provides a comprehensive summary of the theoretical foundations and breakthroughs concerning the approximation and learning behaviors intrinsic to prevalent graph learning models. Encompassing discussions on fundamental aspects such as expressiveness power, generalization, optimization, and unique phenomena such as over-smoothing and over-squashing, this piece delves into the theoretical foundations and frontier driving the evolution of graph learning. In addition, this article also presents several challenges and further initiates discussions on possible solutions.

TAGLAS: An atlas of text-attributed graph datasets in the era of large graph and language models

In this report, we present TAGLAS, an atlas of text-attributed graph (TAG) datasets and benchmarks. TAGs are graphs with node and edge features represented in text, which have recently gained wide applicability in training graph-language or graph foundation models. In TAGLAS, we collect and integrate more than 23 TAG datasets with domains ranging from citation graphs to molecule graphs and tasks from node classification to graph question-answering. Unlike previous graph datasets and benchmarks, all datasets in TAGLAS have a unified node and edge text feature format, which allows a graph model to be simultaneously trained and evaluated on multiple datasets from various domains. Further, we provide a standardized, efficient, and simplified way to load all datasets and tasks. We also provide useful utils like text-to-embedding conversion, and graph-to-text conversion, which can facilitate different evaluation scenarios. Finally, we also provide standard and easy-to-use evaluation utils. The project is open-sourced at https://github.com/JiaruiFeng/TAGLAS and is still under construction. Please expect more datasets/features in the future.

Efficient Neural Common Neighbor for Temporal Graph Link Prediction

Temporal graphs are ubiquitous in real-world scenarios, such as social network, trade and transportation. Predicting dynamic links between nodes in a temporal graph is of vital importance. Traditional methods usually leverage the temporal neighborhood of interaction history to generate node embeddings first and then aggregate the source and target node embeddings to predict the link. However, such methods focus on learning individual node representations, but overlook the pairwise representation learning nature of link prediction and fail to capture the important pairwise features of links such as common neighbors (CN). Motivated by the success of Neural Common Neighbor (NCN) for static graph link prediction, we propose TNCN, a temporal version of NCN for link prediction in temporal graphs. TNCN dynamically updates a temporal neighbor dictionary for each node, and utilizes multi-hop common neighbors between the source and target node to learn a more effective pairwise representation. We validate our model on five large-scale real-world datasets from the Temporal Graph Benchmark (TGB), and find that it achieves new state-of-the-art performance on three of them. Additionally, TNCN demonstrates excellent scalability on large datasets, outperforming popular GNN baselines by up to 6.4 times in speed. Our code is available at https: //github.com/GraphPKU/TNCN.

Graph as Point Set

Graph is a fundamental data structure to model interconnections between entities. Set, on the contrary, stores independent elements. To learn graph representations, current Graph Neural Networks (GNNs) primarily use message passing to encode the interconnections. In contrast, this paper introduces a novel graph-to-set conversion method that bijectively transforms interconnected nodes into a set of independent points and then uses a set encoder to learn the graph representation. This conversion method holds dual significance. Firstly, it enables using set encoders to learn from graphs, thereby significantly expanding the design space of GNNs. Secondly, for Transformer, a specific set encoder, we provide a novel and principled approach to inject graph information losslessly, different from all the heuristic structural/positional encoding methods adopted in previous graph transformers. To demonstrate the effectiveness of our approach, we introduce Point Set Transformer (PST), a transformer architecture that accepts a point set converted from a graph as input. Theoretically, PST exhibits superior expressivity for both short-range substructure counting and long-range shortest path distance tasks compared to existing GNNs. Extensive experiments further validate PST's outstanding real-world performance. Besides Transformer, we also devise a Deepset-based set encoder, which achieves performance comparable to representative GNNs, affirming the versatility of our graph-to-set method.