55 accepted papers
Diffusion language models, especially masked discrete diffusion models, have achieved great success recently. While there are some theoretical and primary empirical results showing the advantages of latent reasoning with looped transformers or continuous CoT, continuous diffusion models typically un…
Expressivity has been a major focus in the design of Graph Neural Networks (GNNs), yet a significant gap persists between theoretical universal expressivity and practical performance. While many expressive GNNs are efficient and achieve strong results, they often focus on specific graph properties a…
Long context understanding remains challenging for large language models due to their limited context windows. This paper introduces Long Input Fine-Tuning (LIFT), a novel framework for long-context modeling that can enhance the long-context performance of arbitrary short-context LLMs by dynamically…
Relational Databases (RDBs) are the backbone of modern business, yet they have missed the Foundation Model revolution. Unlike text or images, high-quality RDB data is private and scarce, rendering the standard approach of ``pre-training on the internet'' infeasible. Consequently, existing solutions …
We propose SHINE (Scalable Hyper In-context NEtwork), a scalable hypernetwork that can map diverse meaningful contexts into high-quality LoRA adapters for large language models (LLM). By reusing the frozen LLM's own parameters in an in-context hypernetwork design and introducing architectural innova…
Generative modeling of three-dimensional (3D) molecules is a fundamental yet challenging problem in drug discovery and materials science. Existing approaches typically represent molecules as 3D graphs and co-generate discrete atom types with continuous atomic coordinates, leading to intrinsic learni…
Length generalization—the ability to solve problems longer than those seen during training—remains a critical challenge for large language models (LLMs). Previous work modifies positional encodings (PEs) and data formats to improve length generalization on specific symbolic tasks such as addition an…
Decoder-only models generate tokens autoregressively by caching key/value vectors, but as the cache grows, inference becomes memory-bounded. To address this challenge, we introduce CLOVER (Cross-Layer Orthogonal Vectors) pruning, a novel approach that treats pairs of components of the attention mech…
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…
Recent advances in molecular generative models have demonstrated great promise for accelerating scientific discovery, particularly in drug design. However, these models often struggle to generate high-quality molecules, especially in conditional scenarios where specific molecular properties must be…
We introduce Griffin, the first foundation model attemptation designed specifically for Relational Databases (RDBs). Unlike previous smaller models focused on single RDB tasks, Griffin unifies the data encoder and task decoder to handle diverse tasks. Additionally, we enhance the architecture by inc…
Existing parameter-efficient fine-tuning (PEFT) methods for large language models (LLMs), such as LoRA and PiSSA, constrain model updates to low-rank subspaces, limiting their expressiveness and leading to suboptimal performance on complex tasks. To address this, we introduce **H**igh-rank **D**istr
As Large Language Models (LLMs) are frequently updated, LoRA weights trained on earlier versions quickly become obsolete. The conventional practice of retraining LoRA weights from scratch on the latest model is costly, time-consuming, and environmentally detrimental, particularly as the diversity of…
Large language models (LLMs) are equipped with increasingly extended context windows recently, yet their long context understanding capabilities over long dependency tasks remain fundamentally limited and underexplored. This gap is especially significant in many real-world long-context applications…
Large language models (LLMs) can solve an increasing number of complex reasoning tasks while making surprising mistakes in basic numerical understanding and processing (such as $9.11 > 9.9$). The latter ability is essential for tackling complex arithmetic and mathematical problems and serves as a fo…
Common Neighbors (CNs) and their higher-order variants are important pairwise features widely used in state-of-the-art link prediction methods. However, existing methods often struggle with the repetition across different orders of CNs and fail to fully leverage their potential. We identify that the…
Invariant models, one important class of geometric deep learning models, are capable of generating meaningful geometric representations by leveraging informative geometric features in point clouds. These models are characterized by their simplicity, good experimental results and computational effici…
Current benchmarks for evaluating the reasoning capabilities of Large Language Models (LLMs) face significant limitations: task oversimplification, data contamination, and flawed evaluation items. These deficiencies necessitate more rigorous assessment methods. To address these limitations, we intro…
Modern large-language models often face communication bottlenecks on current hardware rather than computational limitations. *Multi-head latent attention (MLA)* addresses this by compressing the key-value cache using low-rank matrices, while the Absorb operation prevents the KV cache from reverting…
Given a relational database (RDB), how can we predict missing column values in some target table of interest? Although RDBs store vast amounts of rich, informative data spread across interconnected tables, the progress of predictive machine learning models as applied to such tasks arguably falls we…
Research on the theoretical expressiveness of Graph Neural Networks (GNNs) has developed rapidly, and many methods have been proposed to enhance the expressiveness. However, most methods do not have a uniform expressiveness measure except for a few that strictly follow the $k$-dimensional Weisfeiler…
Despite the impressive performance in a variety of complex tasks, modern large language models (LLMs) still have trouble dealing with some math problems that are simple and intuitive for humans, such as addition. While we can easily learn basic *rules* of addition and apply them to new problems of a…
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…
Large language models (LLMs) are typically limited to processing texts within context window size, which has spurred significant research efforts into enhancing LLMs’ long-context understanding as well as developing high-quality benchmarks to evaluate the ability. However, prior datasets suffer from…
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—situated inductive reaso…
In this work, we propose a novel link prediction model and further boost it by studying graph incompleteness. First, We introduce MPNN-then-SF, an innovative architecture leveraging structural feature (SF) to guide MPNN's representation pooling, with its implementation, namely Neural Common Neighbor…
Designing effective positional encodings for graphs is key to building powerful graph transformers and enhancing message-passing graph neural networks. Although widespread, using Laplacian eigenvectors as positional encodings faces two fundamental challenges: (1) *Non-uniqueness*: there are many dif…
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 u…
To parameter-efficiently fine-tune (PEFT) large language models (LLMs), the low-rank adaptation (LoRA) method approximates the model changes $\Delta W \in \mathbb{R}^{m \times n}$ through the product of two matrices $A \in \mathbb{R}^{m \times r}$ and $B \in \mathbb{R}^{r \times n}$, where $r \ll \m…
The expressivity of Graph Neural Networks (GNNs) has been studied broadly in recent years to reveal the design principles for more powerful GNNs. Graph canonization is known as a typical approach to distinguish non-isomorphic graphs, yet rarely adopted when developing expressive GNNs. This paper pro…
Knowledge graph reasoning is an important problem for knowledge graphs. In this paper, we propose a novel and principled framework called RulE (stands for Rule Embedding) to effectively leverage logical rules to enhance KG reasoning. Unlike knowledge graph embedding methods, RulE learns rule embeddi…
In this paper, we propose the first framework that enables solving graph learning tasks of all levels (node, edge and graph) and all types (generation, regression and classification) using one formulation. We first formulate prediction tasks including regression and classification into a generic (co…
GNN-to-MLP distillation aims to utilize knowledge distillation (KD) to learn computationally-efficient multi-layer perceptron (student MLP) on graph data by mimicking the output representations of teacher GNN. Existing methods mainly make the MLP to mimic the GNN predictions over a few class labels.…
Message Passing Neural Networks (MPNNs) are a widely used class of Graph Neural Networks (GNNs). The limited representational power of MPNNs inspires the study of provably powerful GNN architectures. However, knowing one model is more powerful than another gives little insight about what functions t…
The electronic design automation of analog circuits has been a longstanding challenge in the integrated circuit field due to the huge design space and complex design trade-offs among circuit specifications. In the past decades, intensive research efforts have only been paid to automate the transisto…
The ability of graph neural networks (GNNs) to count certain graph substructures, especially cycles, is important for the success of GNNs on a wide range of tasks. It has been recently used as a popular metric for evaluating the expressive power of GNNs. Many of the proposed GNN models with provable…
Message passing neural networks (MPNNs) have emerged as the most popular framework of graph neural networks (GNNs) in recent years. However, their expressive power is limited by the 1-dimensional Weisfeiler-Lehman (1-WL) test. Some works are inspired by $k$-WL/FWL (Folklore WL) and design the corres…
Node-level random walk has been widely used to improve Graph Neural Networks. However, there is limited attention to random walk on edge and, more generally, on $k$-simplices. This paper systematically analyzes how random walk on different orders of simplicial complexes (SC) facilitates GNNs in thei…
Relational pooling is a framework for building more expressive and permutation-invariant graph neural networks. However, there is limited understanding of the exact enhancement in the expressivity of RP and its connection with the Weisfeiler-Lehman hierarchy. Starting from RP, we propose to explicit…
Graph Neural Networks (GNNs) are often used for tasks involving the 3D geometry of a given graph, such as molecular dynamics simulation. While incorporating Euclidean distance into Message Passing Neural Networks (referred to as Vanilla DisGNN) is a straightforward way to learn the geometry, it has…
While Graph Neural Networks (GNNs) recently became powerful tools in graph learning tasks, considerable efforts have been spent on improving GNNs' structural encoding ability. A particular line of work proposed subgraph GNNs that use subgraph information to improve GNNs' expressivity and achieved gr…
Deep learning has achieved tremendous success in designing novel chemical compounds with desirable pharmaceutical properties. In this work, we focus on a new type of drug design problem — generating a small “linker” to physically attach two independent molecules with their distinct functions. The ma…
Graph neural networks (GNN) have shown great advantages in many graph-based learning tasks but often fail to predict accurately for a task-based on sets of nodes such as link/motif prediction and so on. Many works have recently proposed to address this problem by using random node features or node…
Despite the remarkable achievements of Graph Neural Networks (GNNs) on graph representation learning, few works have tried to use them to predict properties of subgraphs in the whole graph. The existing state-of-the-art method SubGNN introduces an overly complicated subgraph-level GNN model which sy…
Graph Neural Networks (GNNs) have recently been applied to graph learning tasks and achieved state-of-the-art (SOTA) results. However, many competitive methods run GNNs multiple times with subgraph extraction and customized labeling to capture information that is hard for normal GNNs to learn. Such…
The most popular design paradigm for Graph Neural Networks (GNNs) is 1-hop message passing---aggregating information from 1-hop neighbors repeatedly. However, the expressive power of 1-hop message passing is bounded by the Weisfeiler-Lehman (1-WL) test. Recently, researchers extended 1-hop message p…
Spectral Graph Neural Network is a kind of Graph Neural Network (GNN) based on graph signal filters. Some models able to learn arbitrary spectral filters have emerged recently. However, few works analyze the expressive power of spectral GNNs. This paper studies spectral GNNs’ expressive power theore…
Optimization of directed acyclic graph (DAG) structures has many applications, such as neural architecture search (NAS) and probabilistic graphical model learning. Encoding DAGs into real vectors is a dominant component in most neural-network-based DAG optimization frameworks. Currently, most popula…
Most knowledge graphs (KGs) are incomplete, which motivates one important research topic on automatically complementing knowledge graphs. However, evaluation of knowledge graph completion (KGC) models often ignores the incompleteness---facts in the test set are ranked against all unknown triplets wh…
State-of-the-art Graph Neural Networks (GNNs) have limited scalability with respect to the graph and model sizes. On large graphs, increasing the model depth often means exponential expansion of the scope (i.e., receptive field). Beyond just a few layers, two fundamental challenges emerge: 1. degra…
In this paper, we provide a theory of using graph neural networks (GNNs) for multi-node representation learning (where we are interested in learning a representation for a set of more than one node, such as link). We know that GNN is designed to learn single-node representations. When we want to lea…
Graph neural network (GNN)'s success in graph classification is closely related to the Weisfeiler-Lehman (1-WL) algorithm. By iteratively aggregating neighboring node features to a center node, both 1-WL and GNN obtain a node representation that encodes a rooted subtree around the center node. These…
We propose an inductive matrix completion model without using side information. By factorizing the (rating) matrix into the product of low-dimensional latent embeddings of rows (users) and columns (items), a majority of existing matrix completion methods are transductive, since the learned embedding…
Graph structured data are abundant in the real world. Among different graph types, directed acyclic graphs (DAGs) are of particular interest to machine learning researchers, as many machine learning models are realized as computations on DAGs, including neural networks and Bayesian networks. In this…
Link prediction is a key problem for network-structured data. Link prediction heuristics use some score functions, such as common neighbors and Katz index, to measure the likelihood of links. They have obtained wide practical uses due to their simplicity, interpretability, and for some of them, scal…