Towards Graph Foundation Models: A Transferability Perspective

In recent years, Graph Foundation Models (GFMs) have gained significant attention for their potential to generalize across diverse graph domains and tasks. Some works focus on Domain-Specific GFMs, which are designed to address a variety of tasks within a specific domain, while others aim to create General-Purpose GFMs that extend the capabilities of domain-specific models to multiple domains. Regardless of the type, transferability is crucial for applying GFMs across different domains and tasks. However, achieving strong transferability is a major challenge due to the structural, feature, and distributional variations in graph data. To date, there has been no systematic research examining and analyzing GFMs from the perspective of transferability. To bridge the gap, we present the first comprehensive taxonomy that categorizes and analyzes existing GFMs through the lens of transferability, structuring GFMs around their application scope (domain-specific vs. general-purpose) and their approaches to knowledge acquisition and transfer. We provide a structured perspective on current progress and identify potential pathways for advancing GFM generalization across diverse graph datasets and tasks. We aims to shed light on the current landscape of GFMs and inspire future research directions in GFM development.

Exploring Graph Tasks with Pure LLMs: A Comprehensive Benchmark and Investigation

Graph-structured data has become increasingly prevalent across various domains, raising the demand for effective models to handle graph tasks like node classification and link prediction. Traditional graph learning models like Graph Neural Networks (GNNs) have made significant strides, but their capabilities in handling graph data remain limited in certain contexts. In recent years, large language models (LLMs) have emerged as promising candidates for graph tasks, yet most studies focus primarily on performance benchmarks and fail to address their broader potential, including their ability to handle limited data, their transferability across tasks, and their robustness. In this work, we provide a comprehensive exploration of LLMs applied to graph tasks. We evaluate the performance of pure LLMs, including those without parameter optimization and those fine-tuned with instructions, across various scenarios. Our analysis goes beyond accuracy, assessing LLM ability to perform in few-shot/zero-shot settings, transfer across domains, understand graph structures, and demonstrate robustness in challenging scenarios. We conduct extensive experiments with 16 graph learning models alongside 6 LLMs (e.g., Llama3B, GPT-4o, Qwen-plus), comparing their performance on datasets like Cora, PubMed, ArXiv, and Products. Our findings show that LLMs, particularly those with instruction tuning, outperform traditional models in few-shot settings, exhibit strong domain transferability, and demonstrate excellent generalization and robustness. This work offers valuable insights into the capabilities of LLMs for graph learning, highlighting their advantages and potential for real-world applications, and paving the way for future research in this area. Codes and datasets are released in https://github.com/myflashbarry/LLM-benchmarking.

Unifying and Optimizing Data Values for Selection via Sequential-Decision-Making

Data selection has emerged as a crucial downstream application of data valuation. While existing data valuation methods have shown promise in selection tasks, the theoretical foundations and full potential of using data values for selection remain largely unexplored. In this work, we first demonstrate that data values applied for selection can be naturally reformulated as a sequential-decision-making problem, where the optimal data value can be derived through dynamic programming. We show this framework unifies and reinterprets existing methods like Data Shapley through the lens of approximate dynamic programming, specifically as myopic reward function approximations to this sequential problem. Furthermore, we analyze how sequential data selection optimality is affected when the ground-truth utility function exhibits monotonic submodularity with curvature. To address the computational challenges in obtaining optimal data values, we propose an efficient approximation scheme using learned bipartite graphs as surrogate utility models, ensuring greedy selection is still optimal when the surrogate utility is correctly specified and learned. Extensive experiments demonstrate the effectiveness of our approach across diverse datasets.

Reinforcement Learning for Quantum Circuit Design: Using Matrix Representations

Quantum computing promises advantages over classical computing. The manufacturing of quantum hardware is in the infancy stage, called the Noisy Intermediate-Scale Quantum (NISQ) era. A major challenge is automated quantum circuit design that map a quantum circuit to gates in a universal gate set. In this paper, we present a generic MDP modeling and employ Q-learning and DQN algorithms for quantum circuit design. By leveraging the power of deep reinforcement learning, we aim to provide an automatic and scalable approach over traditional hand-crafted heuristic methods.

Extending Graph Condensation to Multi-Label Datasets: A Benchmark Study

As graph data grows increasingly complicate, training graph neural networks (GNNs) on large-scale datasets presents significant challenges, including computational resource constraints, data redundancy, and transmission inefficiencies. While existing graph condensation techniques have shown promise in addressing these issues, they are predominantly designed for single-label datasets, where each node is associated with a single class label. However, many real-world applications, such as social network analysis and bioinformatics, involve multi-label graph datasets, where one node can have various related labels. To deal with this problem, we extends traditional graph condensation approaches to accommodate multi-label datasets by introducing modifications to synthetic dataset initialization and condensing optimization. Through experiments on eight real-world multi-label graph datasets, we prove the effectiveness of our method. In experiment, the GCond framework, combined with K-Center initialization and binary cross-entropy loss (BCELoss), achieves best performance in general. This benchmark for multi-label graph condensation not only enhances the scalability and efficiency of GNNs for multi-label graph data, but also offering substantial benefits for diverse real-world applications.

Gradual Fine-Tuning with Graph Routing for Multi-Source Unsupervised Domain Adaptation

Multi-source unsupervised domain adaptation aims to leverage labeled data from multiple source domains for training a machine learning model to generalize well on a target domain without labels. Source domain selection plays a crucial role in determining the model's performance. It relies on the similarities amongst source and target domains. Nonetheless, existing work for source domain selection often involves heavyweight computational procedures, especially when dealing with numerous source domains and the need to identify the best ones from them. In this paper, we introduce a framework for gradual fine tuning (GFT) of machine learning models on multiple source domains. We represent multiple source domains as an undirected weighted graph. We then give a new generalization error bound for GFT along any path within the graph, which is used to determine the optimal path corresponding to the optimal training order. With this formulation, we introduce three lightweight graph-routing strategies which tend to minimize the error bound. Our best strategy improves $2.3\%$ of accuracy over the state-of-the-art on Natural Language Inference (NLI) task and achieves competitive performance on Sentiment Analysis (SA) task, especially a $3.9\%$ improvement on a more diverse subset of data we use for SA.

A Comprehensive Survey of Small Language Models in the Era of Large Language Models: Techniques, Enhancements, Applications, Collaboration with LLMs, and Trustworthiness

Large language models (LLM) have demonstrated emergent abilities in text generation, question answering, and reasoning, facilitating various tasks and domains. Despite their proficiency in various tasks, LLMs like LaPM 540B and Llama-3.1 405B face limitations due to large parameter sizes and computational demands, often requiring cloud API use which raises privacy concerns, limits real-time applications on edge devices, and increases fine-tuning costs. Additionally, LLMs often underperform in specialized domains such as healthcare and law due to insufficient domain-specific knowledge, necessitating specialized models. Therefore, Small Language Models (SLMs) are increasingly favored for their low inference latency, cost-effectiveness, efficient development, and easy customization and adaptability. These models are particularly well-suited for resource-limited environments and domain knowledge acquisition, addressing LLMs' challenges and proving ideal for applications that require localized data handling for privacy, minimal inference latency for efficiency, and domain knowledge acquisition through lightweight fine-tuning. The rising demand for SLMs has spurred extensive research and development. However, a comprehensive survey investigating issues related to the definition, acquisition, application, enhancement, and reliability of SLM remains lacking, prompting us to conduct a detailed survey on these topics. The definition of SLMs varies widely, thus to standardize, we propose defining SLMs by their capability to perform specialized tasks and suitability for resource-constrained settings, setting boundaries based on the minimal size for emergent abilities and the maximum size sustainable under resource constraints. For other aspects, we provide a taxonomy of relevant models/methods and develop general frameworks for each category to enhance and utilize SLMs effectively.

Efficient Pointwise-Pairwise Learning-to-Rank for News Recommendation

News recommendation is a challenging task that involves personalization based on the interaction history and preferences of each user. Recent works have leveraged the power of pretrained language models (PLMs) to directly rank news items by using inference approaches that predominately fall into three categories: pointwise, pairwise, and listwise learning-to-rank. While pointwise methods offer linear inference complexity, they fail to capture crucial comparative information between items that is more effective for ranking tasks. Conversely, pairwise and listwise approaches excel at incorporating these comparisons but suffer from practical limitations: pairwise approaches are either computationally expensive or lack theoretical guarantees, and listwise methods often perform poorly in practice. In this paper, we propose a novel framework for PLM-based news recommendation that integrates both pointwise relevance prediction and pairwise comparisons in a scalable manner. We present a rigorous theoretical analysis of our framework, establishing conditions under which our approach guarantees improved performance. Extensive experiments show that our approach outperforms the state-of-the-art methods on the MIND and Adressa news recommendation datasets.

Do Neural Scaling Laws Exist on Graph Self-Supervised Learning?

Self-supervised learning~(SSL) is essential to obtain foundation models in NLP and CV domains via effectively leveraging knowledge in large-scale unlabeled data. The reason for its success is that a suitable SSL design can help the model to follow the neural scaling law, i.e., the performance consistently improves with increasing model and dataset sizes. However, it remains a mystery whether existing SSL in the graph domain can follow the scaling behavior toward building Graph Foundation Models~(GFMs) with large-scale pre-training. In this study, we examine whether existing graph SSL techniques can follow the neural scaling behavior with the potential to serve as the essential component for GFMs. Our benchmark includes comprehensive SSL technique implementations with analysis conducted on both the conventional SSL setting and many new settings adopted in other domains. Surprisingly, despite the SSL loss continuously decreasing, no existing graph SSL techniques follow the neural scaling behavior on the downstream performance. The model performance only merely fluctuates on different data scales and model scales. Instead of the scales, the key factors influencing the performance are the choices of model architecture and pretext task design. This paper examines existing SSL techniques for the feasibility of Graph SSL techniques in developing GFMs and opens a new direction for graph SSL design with the new evaluation prototype. Our code implementation is available online to ease reproducibility on https://github.com/GraphSSLScaling/GraphSSLScaling.

Structure-based Drug Design Benchmark: Do 3D Methods Really Dominate?

Currently, the field of structure-based drug design is dominated by three main types of algorithms: search-based algorithms, deep generative models, and reinforcement learning. While existing works have typically focused on comparing models within a single algorithmic category, cross-algorithm comparisons remain scarce. In this paper, to fill the gap, we establish a benchmark to evaluate the performance of sixteen models across these different algorithmic foundations by assessing the pharmaceutical properties of the generated molecules and their docking affinities with specified target proteins. We highlight the unique advantages of each algorithmic approach and offer recommendations for the design of future SBDD models. We emphasize that 1D/2D ligand-centric drug design methods can be used in SBDD by treating the docking function as a black-box oracle, which is typically neglected. The empirical results show that 1D/2D methods achieve competitive performance compared with 3D-based methods that use the 3D structure of the target protein explicitly. Also, AutoGrow4, a 2D molecular graph-based genetic algorithm, dominates SBDD in terms of optimization ability. The relevant code is available in https://github.com/zkysfls/2024-sbdd-benchmark.