Borun Shi

Emily Morris, Haotian Shen, Weiling Du et al.

We analyse the geometric instability of embeddings produced by graph neural networks (GNNs). Existing methods are only applicable for small graphs and lack context in the graph domain. We propose a simple, efficient and graph-native Graph Gram Index (GGI) to measure such instability which is invariant to permutation, orthogonal transformation, translation and order of evaluation. This allows us to study the varying instability behaviour of GNN embeddings on large graphs for both node classification and link prediction.

Alfred Clemedtson, Borun Shi

Large language models have shown remarkable language processing and reasoning ability but are prone to hallucinate when asked about private data. Retrieval-augmented generation (RAG) retrieves relevant data that fit into an LLM's context window and prompts the LLM for an answer. GraphRAG extends this approach to structured Knowledge Graphs (KGs) and questions regarding entities multiple hops away. The majority of recent GraphRAG methods either overlook the retrieval step or have ad hoc retrieval processes that are abstract or inefficient. This prevents them from being adopted when the KGs are stored in graph databases supporting graph query languages. In this work, we present GraphRAFT, a retrieve-and-reason framework that finetunes LLMs to generate provably correct Cypher queries to retrieve high-quality subgraph contexts and produce accurate answers. Our method is the first such solution that can be taken off-the-shelf and used on KGs stored in native graph DBs. Benchmarks suggest that our method is sample-efficient and scales with the availability of training data. Our method achieves significantly better results than all state-of-the-art models across all four standard metrics on two challenging Q&As on large text-attributed KGs.

Dmytro Lopushanskyy, Borun Shi

Training graph neural networks on large datasets has long been a challenge. Traditional approaches include efficiently representing the whole graph in-memory, designing parameter efficient and sampling-based models, and graph partitioning in a distributed setup. Separately, graph databases with native graph storage and query engines have been developed, which enable time and resource efficient graph analytics workloads. We show how to directly train a GNN on a graph DB, by retrieving minimal data into memory and sampling using the query engine. Our experiments show resource advantages for single-machine and distributed training. Our approach opens up a new way of scaling GNNs as well as a new application area for graph DBs.

Borun Shi, Ioannis Panagiotas

Large language models (LLMs) have shown remarkable multimodal information processing and reasoning ability. When equipped with tools through function calling and enhanced with retrieval-augmented techniques, compound LLM-based systems can access closed data sources and answer questions about them. However, they still struggle to process and reason over large-scale graph-structure data. We introduce the GDS (Graph Data Science) agent in this technical report. The GDS agent introduces a comprehensive set of graph algorithms as tools, together with preprocessing (retrieval) and postprocessing of algorithm results, in a model context protocol (MCP) server. The server can be used with any modern LLM out-of-the-box. GDS agent allows users to ask any question that implicitly and intrinsically requires graph algorithmic reasoning about their data, and quickly obtain accurate and grounded answers. We introduce new benchmarks that evaluate intermediate tool calls as well as final responses. The results indicate that GDS agent is able to solve a wide spectrum of graph tasks. We also provide detailed case studies for more open-ended tasks and study scenarios where the agent struggles. Finally, we discuss the remaining challenges and the future roadmap.

Ville Bergholm, Josh Izaac, Maria Schuld et al.

PennyLane is a Python 3 software framework for differentiable programming of quantum computers. The library provides a unified architecture for near-term quantum computing devices, supporting both qubit and continuous-variable paradigms. PennyLane's core feature is the ability to compute gradients of variational quantum circuits in a way that is compatible with classical techniques such as backpropagation. PennyLane thus extends the automatic differentiation algorithms common in optimization and machine learning to include quantum and hybrid computations. A plugin system makes the framework compatible with any gate-based quantum simulator or hardware. We provide plugins for hardware providers including the Xanadu Cloud, Amazon Braket, and IBM Quantum, allowing PennyLane optimizations to be run on publicly accessible quantum devices. On the classical front, PennyLane interfaces with accelerated machine learning libraries such as TensorFlow, PyTorch, JAX, and Autograd. PennyLane can be used for the optimization of variational quantum eigensolvers, quantum approximate optimization, quantum machine learning models, and many other applications.