Mufei Li

Mufei Li, Eleonora Kreačić, Vamsi K. Potluru et al. · gatech

Large-scale graphs with node attributes are increasingly common in various real-world applications. Creating synthetic, attribute-rich graphs that mirror real-world examples is crucial, especially for sharing graph data for analysis and developing learning models when original data is restricted to be shared. Traditional graph generation methods are limited in their capacity to handle these complex structures. Recent advances in diffusion models have shown potential in generating graph structures without attributes and smaller molecular graphs. However, these models face challenges in generating large attributed graphs due to the complex attribute-structure correlations and the large size of these graphs. This paper introduces a novel diffusion model, GraphMaker, specifically designed for generating large attributed graphs. We explore various combinations of node attribute and graph structure generation processes, finding that an asynchronous approach more effectively captures the intricate attribute-structure correlations. We also address scalability issues through edge mini-batching generation. To demonstrate the practicality of our approach in graph data dissemination, we introduce a new evaluation pipeline. The evaluation demonstrates that synthetic graphs generated by GraphMaker can be used to develop competitive graph machine learning models for the tasks defined over the original graphs without actually accessing these graphs, while many leading graph generation methods fall short in this evaluation.

Deyu Zou, Yongqiang Chen, Fan Feng et al. · gatech

Reinforcement learning (RL) with outcome-based rewards has achieved significant success in training large language model (LLM) agents for complex reasoning tasks. However, in active reasoning where agents need to strategically ask questions to acquire task-relevant information, we find that LLM agents trained with RL often suffer from information self-locking: the agent ceases to ask informative questions and struggles to internalize already-obtained information. To understand the phenomenon, we decompose active reasoning into two core capabilities: Action Selection (AS), which determines the observation stream through queries, and Belief Tracking (BT), which updates the agent's belief based on collected evidence. We show that deficient AS and BT capabilities will limit the information exploration during RL training. Furthermore, insufficient exploration in turn hinders the improvement of AS and BT, creating a feedback loop that locks the agent in a low-information regime. To resolve the issue, we propose a simple yet effective approach that reallocates the learning signal by injecting easy- to-obtain directional critiques to help the agent escape self-locking. Extensive experiments with 7 datasets show that our approach significantly mitigates the information self-locking, bringing up to 60% improvements.

Siqi Miao, Ziyang Chen, Yuhong Luo et al.

While Large Language Model (LLM) multi-agent systems (MAS) offer a transformative approach to simulating human behavior in complex systems, it remains largely unexplored whether these simulations can replicate realistic structural and temporal dynamics from a dynamic network perspective. Our evaluation indicates that existing frameworks excel at generating plausible micro-level interactions but fail to capture the emergent, macroscopic topologies necessary for domains that rely on realistic network dynamics, such as modeling information propagation and cybersecurity threats. To bridge this gap, we introduce two easily integrable extensions to simulation frameworks to ensure they preserve macroscopic network fidelity: 1) augmenting LLM agents with data-driven event triggers to organically sustain long-horizon interactions, and 2) integrating Hawkes processes to accurately model temporal activation dynamics. Our approach allows LLM MAS to capture both plausible micro-level patterns and macroscopic topologies. We further demonstrate the utility of this framework in synthesizing realistic phishing campaigns within evolving communication networks. The study reveals how threats exploit structural vulnerabilities, highlighting the potential of our framework for developing next-generation defenses. Our code is available at https://github.com/Graph-COM/NSL.

Xinjie Shen, Mufei Li, Pan Li · gatech

The deployment of Large Language Models (LLMs) in embodied agents creates an urgent need to measure their privacy awareness in the physical world. Existing evaluation methods, however, are confined to natural language based scenarios. To bridge this gap, we introduce EAPrivacy, a comprehensive evaluation benchmark designed to quantify the physical-world privacy awareness of LLM-powered agents. EAPrivacy utilizes procedurally generated scenarios across four tiers to test an agent's ability to handle sensitive objects, adapt to changing environments, balance task execution with privacy constraints, and resolve conflicts with social norms. Our measurements reveal a critical deficit in current models. The top-performing model, Gemini 2.5 Pro, achieved only 59\% accuracy in scenarios involving changing physical environments. Furthermore, when a task was accompanied by a privacy request, models prioritized completion over the constraint in up to 86\% of cases. In high-stakes situations pitting privacy against critical social norms, leading models like GPT-4o and Claude-3.5-haiku disregarded the social norm over 15\% of the time. These findings, demonstrated by our benchmark, underscore a fundamental misalignment in LLMs regarding physically grounded privacy and establish the need for more robust, physically-aware alignment. Codes and datasets will be available at https://github.com/Graph-COM/EAPrivacy.

Mufei Li, Jinjing Zhou, Jiajing Hu et al.

Graph neural networks (GNNs) constitute a class of deep learning methods for graph data. They have wide applications in chemistry and biology, such as molecular property prediction, reaction prediction and drug-target interaction prediction. Despite the interest, GNN-based modeling is challenging as it requires graph data pre-processing and modeling in addition to programming and deep learning. Here we present DGL-LifeSci, an open-source package for deep learning on graphs in life science. DGL-LifeSci is a python toolkit based on RDKit, PyTorch and Deep Graph Library (DGL). DGL-LifeSci allows GNN-based modeling on custom datasets for molecular property prediction, reaction prediction and molecule generation. With its command-line interfaces, users can perform modeling without any background in programming and deep learning. We test the command-line interfaces using standard benchmarks MoleculeNet, USPTO, and ZINC. Compared with previous implementations, DGL-LifeSci achieves a speed up by up to 6x. For modeling flexibility, DGL-LifeSci provides well-optimized modules for various stages of the modeling pipeline. In addition, DGL-LifeSci provides pre-trained models for reproducing the test experiment results and applying models without training. The code is distributed under an Apache-2.0 License and is freely accessible at https://github.com/awslabs/dgl-lifesci.

Mufei Li, Siqi Miao, Pan Li · gatech

Large Language Models (LLMs) demonstrate strong reasoning abilities but face limitations such as hallucinations and outdated knowledge. Knowledge Graph (KG)-based Retrieval-Augmented Generation (RAG) addresses these issues by grounding LLM outputs in structured external knowledge from KGs. However, current KG-based RAG frameworks still struggle to optimize the trade-off between retrieval effectiveness and efficiency in identifying a suitable amount of relevant graph information for the LLM to digest. We introduce SubgraphRAG, extending the KG-based RAG framework that retrieves subgraphs and leverages LLMs for reasoning and answer prediction. Our approach innovatively integrates a lightweight multilayer perceptron with a parallel triple-scoring mechanism for efficient and flexible subgraph retrieval while encoding directional structural distances to enhance retrieval effectiveness. The size of retrieved subgraphs can be flexibly adjusted to match the query's need and the downstream LLM's capabilities. This design strikes a balance between model complexity and reasoning power, enabling scalable and generalizable retrieval processes. Notably, based on our retrieved subgraphs, smaller LLMs like Llama3.1-8B-Instruct deliver competitive results with explainable reasoning, while larger models like GPT-4o achieve state-of-the-art accuracy compared with previous baselines -- all without fine-tuning. Extensive evaluations on the WebQSP and CWQ benchmarks highlight SubgraphRAG's strengths in efficiency, accuracy, and reliability by reducing hallucinations and improving response grounding.

Mufei Li, Viraj Shitole, Eli Chien et al. · gatech

Directed acyclic graphs (DAGs) serve as crucial data representations in domains such as hardware synthesis and compiler/program optimization for computing systems. DAG generative models facilitate the creation of synthetic DAGs, which can be used for benchmarking computing systems while preserving intellectual property. However, generating realistic DAGs is challenging due to their inherent directional and logical dependencies. This paper introduces LayerDAG, an autoregressive diffusion model, to address these challenges. LayerDAG decouples the strong node dependencies into manageable units that can be processed sequentially. By interpreting the partial order of nodes as a sequence of bipartite graphs, LayerDAG leverages autoregressive generation to model directional dependencies and employs diffusion models to capture logical dependencies within each bipartite graph. Comparative analyses demonstrate that LayerDAG outperforms existing DAG generative models in both expressiveness and generalization, particularly for generating large-scale DAGs with up to 400 nodes-a critical scenario for system benchmarking. Extensive experiments on both synthetic and real-world flow graphs from various computing platforms show that LayerDAG generates valid DAGs with superior statistical properties and benchmarking performance. The synthetic DAGs generated by LayerDAG enhance the training of ML-based surrogate models, resulting in improved accuracy in predicting performance metrics of real-world DAGs across diverse computing platforms.

Rongzhe Wei, Mufei Li, Mohsen Ghassemi et al. · gatech

Large Language Models (LLMs) embed sensitive, human-generated data, prompting the need for unlearning methods. Although certified unlearning offers strong privacy guarantees, its restrictive assumptions make it unsuitable for LLMs, giving rise to various heuristic approaches typically assessed through empirical evaluations. These standard evaluations randomly select data for removal, apply unlearning techniques, and use membership inference attacks (MIAs) to compare unlearned models against models retrained without the removed data. However, to ensure robust privacy protections for every data point, it is essential to account for scenarios in which certain data subsets face elevated risks. Prior research suggests that outliers, particularly including data tied to minority groups, often exhibit higher memorization propensity which indicates they may be more difficult to unlearn. Building on these insights, we introduce a complementary, minority-aware evaluation framework to highlight blind spots in existing frameworks. We substantiate our findings with carefully designed experiments, using canaries with personally identifiable information (PII) to represent these minority subsets and demonstrate that they suffer at least 20% higher privacy leakage across various unlearning methods, MIAs, datasets, and LLM scales. Our proposed minority-aware evaluation framework marks an essential step toward more equitable and comprehensive assessments of LLM unlearning efficacy.

Tengfei Ma, Xiang song, Wen Tao et al. · gatech

Knowledge graph completion (KGC) aims to alleviate the inherent incompleteness of knowledge graphs (KGs), which is a critical task for various applications, such as recommendations on the web. Although knowledge graph embedding (KGE) models have demonstrated superior predictive performance on KGC tasks, these models infer missing links in a black-box manner that lacks transparency and accountability, preventing researchers from developing accountable models. Existing KGE-based explanation methods focus on exploring key paths or isolated edges as explanations, which is information-less to reason target prediction. Additionally, the missing ground truth leads to these explanation methods being ineffective in quantitatively evaluating explored explanations. To overcome these limitations, we propose KGExplainer, a model-agnostic method that identifies connected subgraph explanations and distills an evaluator to assess them quantitatively. KGExplainer employs a perturbation-based greedy search algorithm to find key connected subgraphs as explanations within the local structure of target predictions. To evaluate the quality of the explored explanations, KGExplainer distills an evaluator from the target KGE model. By forwarding the explanations to the evaluator, our method can examine the fidelity of them. Extensive experiments on benchmark datasets demonstrate that KGExplainer yields promising improvement and achieves an optimal ratio of 83.3% in human evaluation.

Deyu Zou, Yongqiang Chen, Mufei Li et al. · gatech

Graph-based retrieval-augmented generation (RAG) enables large language models (LLMs) to ground responses with structured external knowledge from up-to-date knowledge graphs (KGs) and reduce hallucinations. However, LLMs often rely on a weak retriever in graph-based RAG: I) Due to the lack of ground truth, the retriever is often trained on weak supervision, which often introduces spurious signals to the LLMs. II) Due to the abstraction of graph data, the retrieved knowledge is often presented in unorganized forms. To mitigate the issue, we present Refined Graph-based RAG (ReG) to align weak retrievers to LLMs for graph-based RAG. Specifically, ReG incorporates LLM feedback to get rid of spurious signals and improve the quality of the supervision. Meanwhile, ReG introduces a structure-aware reorganization module to refactor the retrieval results into logically coherent evidence chains. Experiments on prominent benchmarks demonstrate that ReG significantly and consistently brings improvements across different LLM backbones by up to 10%. The improved supervision quality enables ReG to match the state-of-the-art performance with 5% training data and to transfer to out-of-distribution KGs. Notably, when adopted to reasoning-based LLMs, ReG reduces the reasoning token cost by up to 30% and improves the performance by up to 4%.

Haoyu Wang, Peihao Wang, Mufei Li et al. · gatech

Modern large language models (LLMs) are inherently auto-regressive, requiring input to be serialized into flat sequences regardless of their structural dependencies. This serialization hinders the model's ability to leverage structural inductive biases, especially in tasks such as retrieval-augmented generation (RAG) and reasoning on data with native graph structures, where inter-segment dependencies are crucial. We introduce Graph-KV with the potential to overcome this limitation. Graph-KV leverages the KV-cache of text segments as condensed representations and governs their interaction through structural inductive biases. In this framework, 'target' segments selectively attend only to the KV-caches of their designated 'source' segments, rather than all preceding segments in a serialized sequence. This approach induces a graph-structured block mask, sparsifying attention and enabling a message-passing-like step within the LLM. Furthermore, strategically allocated positional encodings for source and target segments reduce positional bias and context window consumption. We evaluate Graph-KV across three scenarios: (1) seven RAG benchmarks spanning direct inference, multi-hop reasoning, and long-document understanding; (2) Arxiv-QA, a novel academic paper QA task with full-text scientific papers structured as citation ego-graphs; and (3) paper topic classification within a citation network. By effectively reducing positional bias and harnessing structural inductive biases, Graph-KV substantially outperforms baselines, including standard costly sequential encoding, across various settings. Code and the Graph-KV data are publicly available.

Deyu Zou, Yongqiang Chen, Jianxiang Wang et al. · gatech

Active reasoning requires large language models (LLMs) to interact with external sources and strategically gather information to solve problems. Central to this process is belief tracking: maintaining a coherent understanding of the problem state and the missing information toward the solution. However, due to limited reasoning capabilities, LLM-based agents often suffer from belief deviation: they struggle to correctly model beliefs, lose track of problem states, and fall into uninformative or repetitive actions. Once this happens, errors compound and reinforcement learning (RL) training fails to properly credit the crucial exploratory steps. To address this issue, we propose to track the deviation of model beliefs and develop $\mathbf{T^3}$, a simple yet effective method that detects excessive belief deviation and truncates trajectories during training to remove uninformative tails. By preserving credit for informative prefixes, $\mathbf{T^3}$ systematically improves policy optimization. Across 5 challenging tasks, $\mathbf{T^3}$ consistently enhances training stability, token efficiency, and final performance, achieving up to 30% gains while cutting rollout tokens by roughly 25%. These results highlight belief control as a key principle for developing robust and generalizable LLM-based active reasoners.

Shikun Liu, Haoyu Wang, Mufei Li et al. · gatech

Text embeddings from Large Language Models (LLMs) have become foundational for numerous applications. However, these models typically operate on raw text, overlooking the rich structural information, such as hyperlinks or citations, that provides crucial context in many real-world datasets. This paper introduces and systematically evaluates a new paradigm for generating structure-aware text embeddings by integrating these structural relations directly into the LLM's internal encoding process, rather than relying on traditional post-hoc aggregation. We investigate two primary in-process methods: sequential concatenation and parallel caching. Through extensive zero-shot experiments across retrieval, clustering, classification, and recommendation tasks, we demonstrate that our structure-aware approaches consistently outperform both text-only and post-hoc baselines. Our analysis reveals critical trade-offs: sequential concatenation excels with noisy, moderate-length contexts, while parallel caching scales more effectively to long, high-signal contexts but is more susceptible to distractors. To address the challenge of noisy structural data, we also introduce and validate two effective techniques: Context Distillation and Semantic Balancing. This work provides the first comprehensive analysis of in-process structure-aware encoding, offering a blueprint for building more powerful and contextually aware embedding models.

Mufei Li, Dongqi Fu, Limei Wang et al. · gatech

Modern long-context large language models (LLMs) perform well on synthetic "needle-in-a-haystack" (NIAH) benchmarks, but such tests overlook how noisy contexts arise from biased retrieval and agentic workflows. We argue that haystack engineering is necessary to construct noisy long contexts that faithfully capture key real-world factors -- distraction from heterogeneous biased retrievers and cascading errors in agentic workflows -- to test models' long-context robustness. We instantiate it through HaystackCraft, a new NIAH benchmark built on the full English Wikipedia hyperlink network with multi-hop questions. HaystackCraft evaluates how heterogeneous retrieval strategies (e.g., sparse, dense, hybrid, and graph-based) affect distractor composition, haystack ordering, and downstream LLM performance. HaystackCraft further extends NIAH to dynamic, LLM-dependent settings that simulate agentic operations, where models refine queries, reflect on their past reasonings, and decide when to stop. Experiments with 15 long-context models show that (1) while stronger dense retrievers can introduce more challenging distractors, graph-based reranking simultaneously improves retrieval effectiveness and mitigates more harmful distractors; (2) in agentic tests, even advanced models like Gemini 2.5 Pro and GPT-5 suffer cascading failures from self-generated distractors or struggle to perform early stops. These results highlight persistent challenges in agentic long-context reasoning and establish HaystackCraft as a valuable testbed for future progress.

Fabio Broccatelli, Richard Trager, Michael Reutlinger et al.

In this work, we benchmark a variety of single- and multi-task graph neural network (GNN) models against lower-bar and higher-bar traditional machine learning approaches employing human engineered molecular features. We consider four GNN variants -- Graph Convolutional Network (GCN), Graph Attention Network (GAT), Message Passing Neural Network (MPNN), and Attentive Fingerprint (AttentiveFP). So far deep learning models have been primarily benchmarked using lower-bar traditional models solely based on fingerprints, while more realistic benchmarks employing fingerprints, whole-molecule descriptors and predictions from other related endpoints (e.g., LogD7.4) appear to be scarce for industrial ADME datasets. In addition to time-split test sets based on Genentech data, this study benefits from the availability of measurements from an external chemical space (Roche data). We identify GAT as a promising approach to implementing deep learning models. While all GNN models significantly outperform lower-bar benchmark traditional models solely based on fingerprints, only GATs seem to offer a small but consistent improvement over higher-bar benchmark traditional models. Finally, the accuracy of in vitro assays from different laboratories predicting the same experimental endpoints appears to be comparable with the accuracy of GAT single-task models, suggesting that most of the observed error from the models is a function of the experimental error propagation.

Minjie Wang, Da Zheng, Zihao Ye et al.

Advancing research in the emerging field of deep graph learning requires new tools to support tensor computation over graphs. In this paper, we present the design principles and implementation of Deep Graph Library (DGL). DGL distills the computational patterns of GNNs into a few generalized sparse tensor operations suitable for extensive parallelization. By advocating graph as the central programming abstraction, DGL can perform optimizations transparently. By cautiously adopting a framework-neutral design, DGL allows users to easily port and leverage the existing components across multiple deep learning frameworks. Our evaluation shows that DGL significantly outperforms other popular GNN-oriented frameworks in both speed and memory consumption over a variety of benchmarks and has little overhead for small scale workloads.