Dennis Tsang

Dennis Tsang

Graph Enthusiast

Publications

You can also find my articles on my Google Scholar profile.

Conference Papers

From Automation to Autonomy: A Survey on Large Language Models in Scientific Discovery.

Tianshi Zheng , Zheye Deng, Hong Ting Tsang, Weiqi Wang, Jiaxin Bai, Zihao Wang, Yangqiu Song

Published in EMNLP, 2025

Large Language Models (LLMs) are catalyzing a paradigm shift in scientific discovery, evolving from task-specific automation tools into increasingly autonomous agents and fundamentally redefining research processes and human-AI collaboration. This survey systematically charts this burgeoning field, placing a central focus on the changing roles and escalating capabilities of LLMs in science. Through the lens of the scientific method, we introduce a foundational three-level taxonomy-Tool, Analyst, and Scientist-to delineate their escalating autonomy and evolving responsibilities within the research lifecycle. We further identify pivotal challenges and future research trajectories such as robotic automation, self-improvement, and ethical governance. Overall, this survey provides a conceptual architecture and strategic foresight to navigate and shape the future of AI-driven scientific discovery, fostering both rapid innovation and responsible advancement. Github Repository: https://github.com/HKUST-KnowComp/Awesome-LLM-Scientific-Discovery.

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TERAG: Token-Efficient Graph-Based Retrieval-Augmented Generation

Qiao Xiao, Hong Ting Tsang, Jiaxin Bai

Published in ICMLC, 2025

Graph-based Retrieval-augmented generation (RAG) has become a widely studied approach for improving the reasoning, accuracy, and factuality of Large Language Models. However, many existing graph-based RAG systems overlook the high cost associated with LLM token usage during graph construction, hindering large-scale adoption. To address this, we propose TERAG, a simple yet effective framework designed to build informative graphs at a significantly lower cost. Inspired by HippoRAG, we incorporate Personalized PageRank (PPR) during the retrieval phase, and we achieve at least 80% of the accuracy of widely used graph-based RAG methods while consuming only 3%-11% of the output tokens.

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Journal Papers

Top Ten Challenges Towards Agentic Neural Graph Databases

Jiaxin Bai, Zihao Wang, Yukun Zhou, Hang Yin, Weizhi Fei, Qi Hu, Zheye Deng, Jiayang Cheng, Tianshi Zheng, Hong Ting Tsang, Yisen Gao, Zhongwei Xie, Yufei Li, Lixin Fan, Binhang Yuan, Wei Wang, Lei Chen, Xiaofang Zhou, Yangqiu Song

Published in IEEE Data Engineering Bulletin, 2025

Graph databases (GDBs) like Neo4j and TigerGraph excel at handling interconnected data but lack advanced inference capabilities. Neural Graph Databases (NGDBs) address this by integrating Graph Neural Networks (GNNs) for predictive analysis and reasoning over incomplete or noisy data. However, NGDBs rely on predefined queries and lack autonomy and adaptability. This paper introduces Agentic Neural Graph Databases (Agentic NGDBs), which extend NGDBs with three core functionalities: autonomous query construction, neural query execution, and continuous learning. We identify ten key challenges in realizing Agentic NGDBs: semantic unit representation, abductive reasoning, scalable query execution, and integration with foundation models like large language models (LLMs). By addressing these challenges, Agentic NGDBs can enable intelligent, self-improving systems for modern data-driven applications, paving the way for adaptable and autonomous data management solutions.

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Preprints

AutoGraph-R1: End-to-End Reinforcement Learning for Knowledge Graph Construction

Hong Ting Tsang, Jiaxin Bai, Haoyu Huang, Qiao Xiao, Tianshi Zheng, Baixuan Xu, Shujie Liu, Yangqiu Song

Submitted to Arxiv, 2025

Building effective knowledge graphs (KGs) for Retrieval-Augmented Generation (RAG) is pivotal for advancing question answering (QA) systems. However, its effectiveness is hindered by a fundamental disconnect: the knowledge graph (KG) construction process is decoupled from its downstream application, yielding suboptimal graph structures. To bridge this gap, we introduce AutoGraph-R1, the first framework to directly optimize KG construction for task performance using Reinforcement Learning (RL). AutoGraph-R1 trains an LLM constructor by framing graph generation as a policy learning problem, where the reward is derived from the graph’s functional utility in a RAG pipeline. We design two novel, task-aware reward functions, one for graphs as knowledge carriers and another as knowledge indices. Across multiple QA benchmarks, AutoGraph-R1 consistently enables graph RAG methods to achieve significant performance gains over using task-agnostic baseline graphs. Our work shows it is possible to close the loop between construction and application, shifting the paradigm from building intrinsically ‘‘good’’ graphs to building demonstrably ‘‘useful’’ ones.

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NewtonBench: Benchmarking Generalizable Scientific Law Discovery in LLM Agents

Tianshi Zheng, Kelvin Kiu-Wai Tam, Newt Hue-Nam K. Nguyen, Baixuan Xu, Zhaowei Wang, Jiayang Cheng, Hong Ting Tsang, Weiqi Wang, Jiaxin Bai, Tianqing Fang, Yangqiu Song, Ginny Y. Wong, Simon See

Submitted to Arxiv, 2025

Large language models are emerging as powerful tools for scientific law discovery, a foundational challenge in AI-driven science. However, existing benchmarks for this task suffer from a fundamental methodological trilemma, forcing a trade-off between scientific relevance, scalability, and resistance to memorization. Furthermore, they oversimplify discovery as static function fitting, failing to capture the authentic scientific process of uncovering embedded laws through the interactive exploration of complex model systems. To address these critical gaps, we introduce NewtonBench, a benchmark comprising 324 scientific law discovery tasks across 12 physics domains. Our design mitigates the evaluation trilemma by using metaphysical shifts - systematic alterations of canonical laws - to generate a vast suite of problems that are scalable, scientifically relevant, and memorization-resistant. Moreover, we elevate the evaluation from static function fitting to interactive model discovery, requiring agents to experimentally probe simulated complex systems to uncover hidden principles. Our extensive experiment reveals a clear but fragile capability for discovery in frontier LLMs: this ability degrades precipitously with increasing system complexity and exhibits extreme sensitivity to observational noise. Notably, we uncover a paradoxical effect of tool assistance: providing a code interpreter can hinder more capable models by inducing a premature shift from exploration to exploitation, causing them to satisfice on suboptimal solutions. These results demonstrate that robust, generalizable discovery in complex, interactive environments remains the core challenge. By providing a scalable, robust, and scientifically authentic testbed, NewtonBench offers a crucial tool for measuring true progress and guiding the development of next-generation AI agents capable of genuine scientific discovery.

[Paper]  [Code]

The Cognitive Bandwidth Bottleneck: Shifting Long-Horizon Agent from Planning with Actions to Planning with Schemas

Baixuan Xu, Tianshi Zheng, Zhaowei Wang, Hong Ting Tsang, Weiqi Wang, Tianqing Fang, Yangqiu Song

Submitted to Arxiv, 2025

Enabling LLMs to effectively operate long-horizon task which requires long-term planning and multiple interactions is essential for open-world autonomy. Conventional methods adopt planning with actions where a executable action list would be provided as reference. However, this action representation choice would be impractical when the environment action space is combinatorial exploded (e.g., open-ended real world). This naturally leads to a question: As environmental action space scales, what is the optimal action representation for long-horizon agents? In this paper, we systematically study the effectiveness of two different action representations. The first one is conventional planning with actions (PwA) which is predominantly adopted for its effectiveness on existing benchmarks. The other one is planning with schemas (PwS) which instantiate an action schema into action lists (e.g., “move [OBJ] to [OBJ]” -> “move apple to desk”) to ensure concise action space and reliable scalability. This alternative is motivated by its alignment with human cognition and its compliance with environment-imposed action format restriction. We propose cognitive bandwidth perspective as a conceptual framework to qualitatively understand the differences between these two action representations and empirically observe a representation-choice inflection point between ALFWorld (~35 actions) and SciWorld (~500 actions), which serve as evidence of the need for scalable representations. We further conduct controlled experiments to study how the location of this inflection point interacts with different model capacities: stronger planning proficiency shifts the inflection rightward, whereas better schema instantiation shifts it leftward. Finally, noting the suboptimal performance of PwS agents, we provide an actionable guide for building more capable PwS agents for better scalable autonomy.

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AtlasKV: Augmenting LLMs with Billion-Scale Knowledge Graphs in 20GB VRAM

Haoyu Huang, Hong Ting Tsang, Jiaxin Bai, Xi Peng, Gong Zhang, Yangqiu Song

Submitted to Arxiv, 2025

Retrieval-augmented generation (RAG) has shown some success in augmenting large language models (LLMs) with external knowledge. However, as a non-parametric knowledge integration paradigm for LLMs, RAG methods heavily rely on external retrieval modules and the retrieved textual context prior. Especially for very large scale knowledge augmentation, they would introduce substantial inference latency due to expensive searches and much longer relevant context. In this paper, we propose a parametric knowledge integration method, called AtlasKV, a scalable, effective, and general way to augment LLMs with billion-scale knowledge graphs (KGs) (e.g. 1B triples) using very little GPU memory cost (e.g. less than 20GB VRAM). In AtlasKV, we introduce KG2KV and HiKVP to integrate KG triples into LLMs at scale with sub-linear time and memory complexity. It maintains strong knowledge grounding and generalization performance using the LLMs’ inherent attention mechanism, and requires no external retrievers, long context priors, or retraining when adapting to new knowledge.

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AutoSchemaKG: Autonomous Knowledge Graph Construction through Dynamic Schema Induction from Web-Scale Corpora

Jiaxin Bai, Wei Fan, Qi Hu, Qing Zong, Chunyang Li, Hong Ting Tsang, Hongyu Luo, Yauwai Yim, Haoyu Huang, Xiao Zhou, Feng Qin, Tianshi Zheng, Xi Peng, Xin Yao, Huiwen Yang, Leijie Wu, Yi Ji, Gong Zhang, Renhai Chen, Yangqiu Song

Submitted to Arxiv, 2025

We present AutoSchemaKG, a framework for fully autonomous knowledge graph construction that eliminates the need for predefined schemas. Our system leverages large language models to simultaneously extract knowledge triples and induce comprehensive schemas directly from text, modeling both entities and events while employing conceptualization to organize instances into semantic categories. Processing over 50 million documents, we construct ATLAS (Automated Triple Linking And Schema induction), a family of knowledge graphs with 900+ million nodes and 5.9 billion edges. This approach outperforms state-of-the-art baselines on multi-hop QA tasks and enhances LLM factuality. Notably, our schema induction achieves 92% semantic alignment with human-crafted schemas with zero manual intervention, demonstrating that billion-scale knowledge graphs with dynamically induced schemas can effectively complement parametric knowledge in large language models.

[Paper]  [Code]

Transformers for Complex Query Answering over Knowledge Hypergraphs

Hong Ting Tsang, Zihao Wang, Yangqiu Song

Submitted to Arxiv, 2025

Complex Query Answering (CQA) has been extensively studied in recent years. In order to model data that is closer to real-world distribution, knowledge graphs with different modalities have been introduced. Triple KGs, as the classic KGs composed of entities and relations of arity 2, have limited representation of real-world facts. Real-world data is more sophisticated. While hyper-relational graphs have been introduced, there are limitations in representing relationships of varying arity that contain entities with equal contributions. To address this gap, we sampled new CQA datasets: JF17k-HCQA and M-FB15k-HCQA. Each dataset contains various query types that include logical operations such as projection, negation, conjunction, and disjunction. In order to answer knowledge hypergraph (KHG) existential first-order queries, we propose a two-stage transformer model, the Logical Knowledge Hypergraph Transformer (LKHGT), which consists of a Projection Encoder for atomic projection and a Logical Encoder for complex logical operations. Both encoders are equipped with Type Aware Bias (TAB) for capturing token interactions. Experimental results on CQA datasets show that LKHGT is a state-of-the-art CQA method over KHG and is able to generalize to out-of-distribution query types.

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