CLAug 22, 2023Code
Knowledge Graph Prompting for Multi-Document Question AnsweringYu Wang, Nedim Lipka, Ryan A. Rossi et al.
The `pre-train, prompt, predict' paradigm of large language models (LLMs) has achieved remarkable success in open-domain question answering (OD-QA). However, few works explore this paradigm in the scenario of multi-document question answering (MD-QA), a task demanding a thorough understanding of the logical associations among the contents and structures of different documents. To fill this crucial gap, we propose a Knowledge Graph Prompting (KGP) method to formulate the right context in prompting LLMs for MD-QA, which consists of a graph construction module and a graph traversal module. For graph construction, we create a knowledge graph (KG) over multiple documents with nodes symbolizing passages or document structures (e.g., pages/tables), and edges denoting the semantic/lexical similarity between passages or intra-document structural relations. For graph traversal, we design an LLM-based graph traversal agent that navigates across nodes and gathers supporting passages assisting LLMs in MD-QA. The constructed graph serves as the global ruler that regulates the transitional space among passages and reduces retrieval latency. Concurrently, the graph traversal agent acts as a local navigator that gathers pertinent context to progressively approach the question and guarantee retrieval quality. Extensive experiments underscore the efficacy of KGP for MD-QA, signifying the potential of leveraging graphs in enhancing the prompt design for LLMs. Our code: https://github.com/YuWVandy/KG-LLM-MDQA.
LGJun 9, 2023Code
NeuroGraph: Benchmarks for Graph Machine Learning in Brain ConnectomicsAnwar Said, Roza G. Bayrak, Tyler Derr et al.
Machine learning provides a valuable tool for analyzing high-dimensional functional neuroimaging data, and is proving effective in predicting various neurological conditions, psychiatric disorders, and cognitive patterns. In functional magnetic resonance imaging (MRI) research, interactions between brain regions are commonly modeled using graph-based representations. The potency of graph machine learning methods has been established across myriad domains, marking a transformative step in data interpretation and predictive modeling. Yet, despite their promise, the transposition of these techniques to the neuroimaging domain has been challenging due to the expansive number of potential preprocessing pipelines and the large parameter search space for graph-based dataset construction. In this paper, we introduce NeuroGraph, a collection of graph-based neuroimaging datasets, and demonstrated its utility for predicting multiple categories of behavioral and cognitive traits. We delve deeply into the dataset generation search space by crafting 35 datasets that encompass static and dynamic brain connectivity, running in excess of 15 baseline methods for benchmarking. Additionally, we provide generic frameworks for learning on both static and dynamic graphs. Our extensive experiments lead to several key observations. Notably, using correlation vectors as node features, incorporating larger number of regions of interest, and employing sparser graphs lead to improved performance. To foster further advancements in graph-based data driven neuroimaging analysis, we offer a comprehensive open-source Python package that includes the benchmark datasets, baseline implementations, model training, and standard evaluation.
LGJun 7, 2022Code
Improving Fairness in Graph Neural Networks via Mitigating Sensitive Attribute LeakageYu Wang, Yuying Zhao, Yushun Dong et al.
Graph Neural Networks (GNNs) have shown great power in learning node representations on graphs. However, they may inherit historical prejudices from training data, leading to discriminatory bias in predictions. Although some work has developed fair GNNs, most of them directly borrow fair representation learning techniques from non-graph domains without considering the potential problem of sensitive attribute leakage caused by feature propagation in GNNs. However, we empirically observe that feature propagation could vary the correlation of previously innocuous non-sensitive features to the sensitive ones. This can be viewed as a leakage of sensitive information which could further exacerbate discrimination in predictions. Thus, we design two feature masking strategies according to feature correlations to highlight the importance of considering feature propagation and correlation variation in alleviating discrimination. Motivated by our analysis, we propose Fair View Graph Neural Network (FairVGNN) to generate fair views of features by automatically identifying and masking sensitive-correlated features considering correlation variation after feature propagation. Given the learned fair views, we adaptively clamp weights of the encoder to avoid using sensitive-related features. Experiments on real-world datasets demonstrate that FairVGNN enjoys a better trade-off between model utility and fairness. Our code is publicly available at https://github.com/YuWVandy/FairVGNN.
IRJul 3, 2022Code
Collaboration-Aware Graph Convolutional Network for Recommender SystemsYu Wang, Yuying Zhao, Yi Zhang et al.
Graph Neural Networks (GNNs) have been successfully adopted in recommender systems by virtue of the message-passing that implicitly captures collaborative effect. Nevertheless, most of the existing message-passing mechanisms for recommendation are directly inherited from GNNs without scrutinizing whether the captured collaborative effect would benefit the prediction of user preferences. In this paper, we first analyze how message-passing captures the collaborative effect and propose a recommendation-oriented topological metric, Common Interacted Ratio (CIR), which measures the level of interaction between a specific neighbor of a node with the rest of its neighbors. After demonstrating the benefits of leveraging collaborations from neighbors with higher CIR, we propose a recommendation-tailored GNN, Collaboration-Aware Graph Convolutional Network (CAGCN), that goes beyond 1-Weisfeiler-Lehman(1-WL) test in distinguishing non-bipartite-subgraph-isomorphic graphs. Experiments on six benchmark datasets show that the best CAGCN variant outperforms the most representative GNN-based recommendation model, LightGCN, by nearly 10% in Recall@20 and also achieves around 80% speedup. Our code is publicly available at https://github.com/YuWVandy/CAGCN.
LGJun 24, 2022Code
On Structural Explanation of Bias in Graph Neural NetworksYushun Dong, Song Wang, Yu Wang et al.
Graph Neural Networks (GNNs) have shown satisfying performance in various graph analytical problems. Hence, they have become the \emph{de facto} solution in a variety of decision-making scenarios. However, GNNs could yield biased results against certain demographic subgroups. Some recent works have empirically shown that the biased structure of the input network is a significant source of bias for GNNs. Nevertheless, no studies have systematically scrutinized which part of the input network structure leads to biased predictions for any given node. The low transparency on how the structure of the input network influences the bias in GNN outcome largely limits the safe adoption of GNNs in various decision-critical scenarios. In this paper, we study a novel research problem of structural explanation of bias in GNNs. Specifically, we propose a novel post-hoc explanation framework to identify two edge sets that can maximally account for the exhibited bias and maximally contribute to the fairness level of the GNN prediction for any given node, respectively. Such explanations not only provide a comprehensive understanding of bias/fairness of GNN predictions but also have practical significance in building an effective yet fair GNN model. Extensive experiments on real-world datasets validate the effectiveness of the proposed framework towards delivering effective structural explanations for the bias of GNNs. Open-source code can be found at https://github.com/yushundong/REFEREE.
LGDec 7, 2022Code
Fairness and Explainability: Bridging the Gap Towards Fair Model ExplanationsYuying Zhao, Yu Wang, Tyler Derr
While machine learning models have achieved unprecedented success in real-world applications, they might make biased/unfair decisions for specific demographic groups and hence result in discriminative outcomes. Although research efforts have been devoted to measuring and mitigating bias, they mainly study bias from the result-oriented perspective while neglecting the bias encoded in the decision-making procedure. This results in their inability to capture procedure-oriented bias, which therefore limits the ability to have a fully debiasing method. Fortunately, with the rapid development of explainable machine learning, explanations for predictions are now available to gain insights into the procedure. In this work, we bridge the gap between fairness and explainability by presenting a novel perspective of procedure-oriented fairness based on explanations. We identify the procedure-based bias by measuring the gap of explanation quality between different groups with Ratio-based and Value-based Explanation Fairness. The new metrics further motivate us to design an optimization objective to mitigate the procedure-based bias where we observe that it will also mitigate bias from the prediction. Based on our designed optimization objective, we propose a Comprehensive Fairness Algorithm (CFA), which simultaneously fulfills multiple objectives - improving traditional fairness, satisfying explanation fairness, and maintaining the utility performance. Extensive experiments on real-world datasets demonstrate the effectiveness of our proposed CFA and highlight the importance of considering fairness from the explainability perspective. Our code is publicly available at https://github.com/YuyingZhao/FairExplanations-CFA .
LGOct 6, 2023Code
A Topological Perspective on Demystifying GNN-Based Link Prediction PerformanceYu Wang, Tong Zhao, Yuying Zhao et al.
Graph Neural Networks (GNNs) have shown great promise in learning node embeddings for link prediction (LP). While numerous studies aim to improve the overall LP performance of GNNs, none have explored its varying performance across different nodes and its underlying reasons. To this end, we aim to demystify which nodes will perform better from the perspective of their local topology. Despite the widespread belief that low-degree nodes exhibit poorer LP performance, our empirical findings provide nuances to this viewpoint and prompt us to propose a better metric, Topological Concentration (TC), based on the intersection of the local subgraph of each node with the ones of its neighbors. We empirically demonstrate that TC has a higher correlation with LP performance than other node-level topological metrics like degree and subgraph density, offering a better way to identify low-performing nodes than using cold-start. With TC, we discover a novel topological distribution shift issue in which newly joined neighbors of a node tend to become less interactive with that node's existing neighbors, compromising the generalizability of node embeddings for LP at testing time. To make the computation of TC scalable, We further propose Approximated Topological Concentration (ATC) and theoretically/empirically justify its efficacy in approximating TC and reducing the computation complexity. Given the positive correlation between node TC and its LP performance, we explore the potential of boosting LP performance via enhancing TC by re-weighting edges in the message-passing and discuss its effectiveness with limitations. Our code is publicly available at https://github.com/YuWVandy/Topo_LP_GNN.
92.1CLApr 27
A Survey on LLM-based Conversational User SimulationBo Ni, Leyao Wang, Yu Wang et al.
User simulation has long played a vital role in computer science due to its potential to support a wide range of applications. Language, as the primary medium of human communication, forms the foundation of social interaction and behavior. Consequently, simulating conversational behavior has become a key area of study. Recent advancements in large language models (LLMs) have significantly catalyzed progress in this domain by enabling high-fidelity generation of synthetic user conversation. In this paper, we survey recent advancements in LLM-based conversational user simulation. We introduce a novel taxonomy covering user granularity and simulation objectives. Additionally, we systematically analyze core techniques and evaluation methodologies. We aim to keep the research community informed of the latest advancements in conversational user simulation and to further facilitate future research by identifying open challenges and organizing existing work under a unified framework.
LGAug 31, 2023
A Survey on Privacy in Graph Neural Networks: Attacks, Preservation, and ApplicationsYi Zhang, Yuying Zhao, Zhaoqing Li et al.
Graph Neural Networks (GNNs) have gained significant attention owing to their ability to handle graph-structured data and the improvement in practical applications. However, many of these models prioritize high utility performance, such as accuracy, with a lack of privacy consideration, which is a major concern in modern society where privacy attacks are rampant. To address this issue, researchers have started to develop privacy-preserving GNNs. Despite this progress, there is a lack of a comprehensive overview of the attacks and the techniques for preserving privacy in the graph domain. In this survey, we aim to address this gap by summarizing the attacks on graph data according to the targeted information, categorizing the privacy preservation techniques in GNNs, and reviewing the datasets and applications that could be used for analyzing/solving privacy issues in GNNs. We also outline potential directions for future research in order to build better privacy-preserving GNNs.
LGAug 23, 2023
A Survey of Graph UnlearningAnwar Said, Ngoc N. Tran, Yuying Zhao et al.
Graph unlearning emerges as a crucial advancement in the pursuit of responsible AI, providing the means to remove sensitive data traces from trained models, thereby upholding the \textit{right to be forgotten}. It is evident that graph machine learning exhibits sensitivity to data privacy and adversarial attacks, necessitating the application of graph unlearning techniques to address these concerns effectively. In this comprehensive survey paper, we present the first systematic review of graph unlearning approaches, encompassing a diverse array of methodologies and offering a detailed taxonomy and up-to-date literature overview to facilitate the understanding of researchers new to this field. To ensure clarity, we provide lucid explanations of the fundamental concepts and evaluation measures used in graph unlearning, catering to a broader audience with varying levels of expertise. Delving into potential applications, we explore the versatility of graph unlearning across various domains, including but not limited to social networks, adversarial settings, recommender systems, and resource-constrained environments like the Internet of Things, illustrating its potential impact in safeguarding data privacy and enhancing AI systems' robustness. Finally, we shed light on promising research directions, encouraging further progress and innovation within the domain of graph unlearning. By laying a solid foundation and fostering continued progress, this survey seeks to inspire researchers to further advance the field of graph unlearning, thereby instilling confidence in the ethical growth of AI systems and reinforcing the responsible application of machine learning techniques in various domains.
SIOct 10, 2023
Enhanced Graph Neural Networks with Ego-Centric Spectral Subgraph Embeddings AugmentationAnwar Said, Mudassir Shabbir, Tyler Derr et al.
Graph Neural Networks (GNNs) have shown remarkable merit in performing various learning-based tasks in complex networks. The superior performance of GNNs often correlates with the availability and quality of node-level features in the input networks. However, for many network applications, such node-level information may be missing or unreliable, thereby limiting the applicability and efficacy of GNNs. To address this limitation, we present a novel approach denoted as Ego-centric Spectral subGraph Embedding Augmentation (ESGEA), which aims to enhance and design node features, particularly in scenarios where information is lacking. Our method leverages the topological structure of the local subgraph to create topology-aware node features. The subgraph features are generated using an efficient spectral graph embedding technique, and they serve as node features that capture the local topological organization of the network. The explicit node features, if present, are then enhanced with the subgraph embeddings in order to improve the overall performance. ESGEA is compatible with any GNN-based architecture and is effective even in the absence of node features. We evaluate the proposed method in a social network graph classification task where node attributes are unavailable, as well as in a node classification task where node features are corrupted or even absent. The evaluation results on seven datasets and eight baseline models indicate up to a 10% improvement in AUC and a 7% improvement in accuracy for graph and node classification tasks, respectively.
LGNov 25, 2023Code
Robust Graph Neural Networks via Unbiased AggregationZhichao Hou, Ruiqi Feng, Tyler Derr et al.
The adversarial robustness of Graph Neural Networks (GNNs) has been questioned due to the false sense of security uncovered by strong adaptive attacks despite the existence of numerous defenses. In this work, we delve into the robustness analysis of representative robust GNNs and provide a unified robust estimation point of view to understand their robustness and limitations. Our novel analysis of estimation bias motivates the design of a robust and unbiased graph signal estimator. We then develop an efficient Quasi-Newton Iterative Reweighted Least Squares algorithm to solve the estimation problem, which is unfolded as robust unbiased aggregation layers in GNNs with theoretical guarantees. Our comprehensive experiments confirm the strong robustness of our proposed model under various scenarios, and the ablation study provides a deep understanding of its advantages. Our code is available at https://github.com/chris-hzc/RUNG.
LGAug 2, 2024
A Survey of MambaHaohao Qu, Liangbo Ning, Rui An et al.
As one of the most representative DL techniques, Transformer architecture has empowered numerous advanced models, especially the large language models (LLMs) that comprise billions of parameters, becoming a cornerstone in deep learning. Despite the impressive achievements, Transformers still face inherent limitations, particularly the time-consuming inference resulting from the quadratic computation complexity of attention calculation. Recently, a novel architecture named Mamba, drawing inspiration from classical state space models (SSMs), has emerged as a promising alternative for building foundation models, delivering comparable modeling abilities to Transformers while preserving near-linear scalability concerning sequence length. This has sparked an increasing number of studies actively exploring Mamba's potential to achieve impressive performance across diverse domains. Given such rapid evolution, there is a critical need for a systematic review that consolidates existing Mamba-empowered models, offering a comprehensive understanding of this emerging model architecture. In this survey, we therefore conduct an in-depth investigation of recent Mamba-associated studies, covering three main aspects: the advancements of Mamba-based models, the techniques of adapting Mamba to diverse data, and the applications where Mamba can excel. Specifically, we first review the foundational knowledge of various representative deep learning models and the details of Mamba-1&2 as preliminaries. Then, to showcase the significance of Mamba for AI, we comprehensively review the related studies focusing on Mamba models' architecture design, data adaptability, and applications. Finally, we present a discussion of current limitations and explore various promising research directions to provide deeper insights for future investigations.
83.6LGMar 17
A Survey of MambaHaohao Qu, Liangbo Ning, Rui An et al.
As one of the most representative DL techniques, Transformer architecture has empowered numerous advanced models, especially the large language models (LLMs) that comprise billions of parameters, becoming a cornerstone in deep learning. Despite the impressive achievements, Transformers still face inherent limitations, particularly the time-consuming inference resulting from the quadratic computation complexity of attention calculation. Recently, a novel architecture named Mamba, drawing inspiration from classical state space models (SSMs), has emerged as a promising alternative for building foundation models, delivering comparable modeling abilities to Transformers while preserving near-linear scalability concerning sequence length. This has sparked an increasing number of studies actively exploring Mamba's potential to achieve impressive performance across diverse domains. Given such rapid evolution, there is a critical need for a systematic review that consolidates existing Mamba-empowered models, offering a comprehensive understanding of this emerging model architecture. In this survey, we therefore conduct an in-depth investigation of recent Mamba-associated studies, covering three main aspects: the advancements of Mamba-based models, the techniques of adapting Mamba to diverse data, and the applications where Mamba can excel. Specifically, we first review the foundational knowledge of various representative deep learning models and the details of Mamba-1&2 as preliminaries. Then, to showcase the significance of Mamba for AI, we comprehensively review the related studies focusing on Mamba models' architecture design, data adaptability, and applications. Finally, we present a discussion of current limitations and explore various promising research directions to provide deeper insights for future investigations.
83.3AIApr 27
Sparse Personalized Text Generation with Multi-Trajectory ReasoningBo Ni, Haowei Fu, Qinwen Ge et al.
As Large Language Models (LLMs) advance, personalization has become a key mechanism for tailoring outputs to individual user needs. However, most existing methods rely heavily on dense interaction histories, making them ineffective in cold-start scenarios where such data is sparse or unavailable. While external signals (e.g., content of similar users) can offer a potential remedy, leveraging them effectively remains challenging: raw context is often noisy, and existing methods struggle to reason over heterogeneous data sources. To address these issues, we introduce PAT (Personalization with Aligned Trajectories), a reasoning framework for cold-start LLM personalization. PAT first retrieves information along two complementary trajectories: writing-style cues from stylistically similar users and topic-specific context from preference-aligned users. It then employs a reinforcement learning-based, iterative dual-reasoning mechanism that enables the LLM to jointly refine and integrate these signals. Experimental results across real-world personalization benchmarks show that PAT consistently improves generation quality and alignment under sparse-data conditions, establishing a strong solution to the cold-start personalization problem.
62.7CLMay 11Code
ReAD: Reinforcement-Guided Capability Distillation for Large Language ModelsXueqi Cheng, Xugui Zhou, Tyler Derr et al.
Capability distillation applies knowledge distillation to selected model capabilities, aiming to compress a large language model (LLM) into a smaller one while preserving the abilities needed for a downstream task. However, most existing methods treat capabilities as independent training targets and overlook how improving one capability can reshape the student's broader capability profile, especially when multiple abilities jointly determine task success. We study capability distillation under a fixed token budget and identify two consistent patterns: distillation induces systematic, budget-dependent cross-capability transfer, and additional budget often brings limited task-relevant gains while sometimes degrading other useful abilities. Building on these insights, we propose ReAD, a Reinforcement-guided cApability Distillation framework that explicitly accounts for capability interdependence. ReAD first infers task-essential capabilities, then generates capability-targeted supervision on the fly, and finally uses an uncertainty-aware contextual bandit to adaptively allocate the distillation budget based on expected utility gains. Extensive experiments show that ReAD improves downstream utility under the same token budget while reducing harmful spillover and wasted distillation effort compared to strong baselines. Our code is publicly available at https://github.com/LabRAI/ReAD.
79.2CLMay 11Code
SOMA: Efficient Multi-turn LLM Serving via Small Language ModelXueqi Cheng, Qiong Wu, Zhengyi Zhou et al.
Large Language Models (LLMs) are increasingly deployed in multi-turn dialogue settings where preserving conversational context across turns is essential. A standard serving practice concatenates the full dialogue history at every turn, which reliably maintains coherence but incurs substantial cost in latency, memory, and API expenditure, especially when queries are routed to large proprietary models. Existing approaches often struggle to balance the trade-off between response quality and efficiency. We propose a framework that exploits the early turns of a session to estimate a local response manifold and then adapt a smaller surrogate model to this local region for the remainder of the conversation. Concretely, we learn soft prompts that maximize semantic divergence between the large and surrogate small language models' responses to surface least-aligned local directions, stabilize training with anti-degeneration control, and distill the mined cases into localized LoRA fine-tuning so the surrogate runs without prompts at inference. A simple gate enables a one-time switch with rollback on drift. We further provide a theoretical analysis for key components in SOMA. Extensive experiments show the effectiveness of SOMA. The source code is provided at: https://github.com/LabRAI/SOMA.
45.6CLApr 21
Assessing Capabilities of Large Language Models in Social Media Analytics: A Multi-task QuestRamtin Davoudi, Kartik Thakkar, Nazanin Donyapour et al.
In this study, we present the first comprehensive evaluation of modern LLMs - including GPT-4, GPT-4o, GPT-3.5-Turbo, Gemini 1.5 Pro, DeepSeek-V3, Llama 3.2, and BERT - across three core social media analytics tasks on a Twitter (X) dataset: (I) Social Media Authorship Verification, (II) Social Media Post Generation, and (III) User Attribute Inference. For the authorship verification, we introduce a systematic sampling framework over diverse user and post selection strategies and evaluate generalization on newly collected tweets from January 2024 onward to mitigate "seen-data" bias. For post generation, we assess the ability of LLMs to produce authentic, user-like content using comprehensive evaluation metrics. Bridging Tasks I and II, we conduct a user study to measure real users' perceptions of LLM-generated posts conditioned on their own writing. For attribute inference, we annotate occupations and interests using two standardized taxonomies (IAB Tech Lab 2023 and 2018 U.S. SOC) and benchmark LLMs against existing baselines. Overall, our unified evaluation provides new insights and establishes reproducible benchmarks for LLM-driven social media analytics. The code and data are provided in the supplementary material and will also be made publicly available upon publication.
LGAug 17, 2025Code
Defining and Benchmarking a Data-Centric Design Space for Brain Graph ConstructionQinwen Ge, Roza G. Bayrak, Anwar Said et al.
The construction of brain graphs from functional Magnetic Resonance Imaging (fMRI) data plays a crucial role in enabling graph machine learning for neuroimaging. However, current practices often rely on rigid pipelines that overlook critical data-centric choices in how brain graphs are constructed. In this work, we adopt a Data-Centric AI perspective and systematically define and benchmark a data-centric design space for brain graph construction, constrasting with primarily model-centric prior work. We organize this design space into three stages: temporal signal processing, topology extraction, and graph featurization. Our contributions lie less in novel components and more in evaluating how combinations of existing and modified techniques influence downstream performance. Specifically, we study high-amplitude BOLD signal filtering, sparsification and unification strategies for connectivity, alternative correlation metrics, and multi-view node and edge features, such as incorporating lagged dynamics. Experiments on the HCP1200 and ABIDE datasets show that thoughtful data-centric configurations consistently improve classification accuracy over standard pipelines. These findings highlight the critical role of upstream data decisions and underscore the importance of systematically exploring the data-centric design space for graph-based neuroimaging. Our code is available at https://github.com/GeQinwen/DataCentricBrainGraphs.
LGDec 1, 2021Code
Imbalanced Graph Classification via Graph-of-Graph Neural NetworksYu Wang, Yuying Zhao, Neil Shah et al.
Graph Neural Networks (GNNs) have achieved unprecedented success in identifying categorical labels of graphs. However, most existing graph classification problems with GNNs follow the protocol of balanced data splitting, which misaligns with many real-world scenarios in which some classes have much fewer labels than others. Directly training GNNs under this imbalanced scenario may lead to uninformative representations of graphs in minority classes, and compromise the overall classification performance, which signifies the importance of developing effective GNNs towards handling imbalanced graph classification. Existing methods are either tailored for non-graph structured data or designed specifically for imbalanced node classification while few focus on imbalanced graph classification. To this end, we introduce a novel framework, Graph-of-Graph Neural Networks (G$^2$GNN), which alleviates the graph imbalance issue by deriving extra supervision globally from neighboring graphs and locally from stochastic augmentations of graphs. Globally, we construct a graph of graphs (GoG) based on kernel similarity and perform GoG propagation to aggregate neighboring graph representations. Locally, we employ topological augmentation via masking node features or dropping edges with self-consistency regularization to generate stochastic augmentations of each graph that improve the model generalibility. Extensive graph classification experiments conducted on seven benchmark datasets demonstrate our proposed G$^2$GNN outperforms numerous baselines by roughly 5\% in both F1-macro and F1-micro scores. The implementation of G$^2$GNN is available at https://github.com/YuWVandy/G2GNN}{https://github.com/YuWVandy/G2GNN
LGOct 22, 2021Code
Distance-wise Prototypical Graph Neural Network in Node Imbalance ClassificationYu Wang, Charu Aggarwal, Tyler Derr
Recent years have witnessed the significant success of applying graph neural networks (GNNs) in learning effective node representations for classification. However, current GNNs are mostly built under the balanced data-splitting, which is inconsistent with many real-world networks where the number of training nodes can be extremely imbalanced among the classes. Thus, directly utilizing current GNNs on imbalanced data would generate coarse representations of nodes in minority classes and ultimately compromise the classification performance. This therefore portends the importance of developing effective GNNs for handling imbalanced graph data. In this work, we propose a novel Distance-wise Prototypical Graph Neural Network (DPGNN), which proposes a class prototype-driven training to balance the training loss between majority and minority classes and then leverages distance metric learning to differentiate the contributions of different dimensions of representations and fully encode the relative position of each node to each class prototype. Moreover, we design a new imbalanced label propagation mechanism to derive extra supervision from unlabeled nodes and employ self-supervised learning to smooth representations of adjacent nodes while separating inter-class prototypes. Comprehensive node classification experiments and parameter analysis on multiple networks are conducted and the proposed DPGNN almost always significantly outperforms all other baselines, which demonstrates its effectiveness in imbalanced node classification. The implementation of DPGNN is available at \url{https://github.com/YuWVandy/DPGNN}.
LGAug 25, 2021Code
Tree Decomposed Graph Neural NetworkYu Wang, Tyler Derr
Graph Neural Networks (GNNs) have achieved significant success in learning better representations by performing feature propagation and transformation iteratively to leverage neighborhood information. Nevertheless, iterative propagation restricts the information of higher-layer neighborhoods to be transported through and fused with the lower-layer neighborhoods', which unavoidably results in feature smoothing between neighborhoods in different layers and can thus compromise the performance, especially on heterophily networks. Furthermore, most deep GNNs only recognize the importance of higher-layer neighborhoods while yet to fully explore the importance of multi-hop dependency within the context of different layer neighborhoods in learning better representations. In this work, we first theoretically analyze the feature smoothing between neighborhoods in different layers and empirically demonstrate the variance of the homophily level across neighborhoods at different layers. Motivated by these analyses, we further propose a tree decomposition method to disentangle neighborhoods in different layers to alleviate feature smoothing among these layers. Moreover, we characterize the multi-hop dependency via graph diffusion within our tree decomposition formulation to construct Tree Decomposed Graph Neural Network (TDGNN), which can flexibly incorporate information from large receptive fields and aggregate this information utilizing the multi-hop dependency. Comprehensive experiments demonstrate the superior performance of TDGNN on both homophily and heterophily networks under a variety of node classification settings. Extensive parameter analysis highlights the ability of TDGNN to prevent over-smoothing and incorporate features from shallow layers with deeper multi-hop dependencies, which provides new insights towards deeper graph neural networks. Code of TDGNN: http://github.com/YuWVandy/TDGNN
CVAug 6, 2021Code
Interpretable Visual Understanding with Cognitive Attention NetworkXuejiao Tang, Wenbin Zhang, Yi Yu et al.
While image understanding on recognition-level has achieved remarkable advancements, reliable visual scene understanding requires comprehensive image understanding on recognition-level but also cognition-level, which calls for exploiting the multi-source information as well as learning different levels of understanding and extensive commonsense knowledge. In this paper, we propose a novel Cognitive Attention Network (CAN) for visual commonsense reasoning to achieve interpretable visual understanding. Specifically, we first introduce an image-text fusion module to fuse information from images and text collectively. Second, a novel inference module is designed to encode commonsense among image, query and response. Extensive experiments on large-scale Visual Commonsense Reasoning (VCR) benchmark dataset demonstrate the effectiveness of our approach. The implementation is publicly available at https://github.com/tanjatang/CAN
LGNov 19, 2020Code
Node Similarity Preserving Graph Convolutional NetworksWei Jin, Tyler Derr, Yiqi Wang et al.
Graph Neural Networks (GNNs) have achieved tremendous success in various real-world applications due to their strong ability in graph representation learning. GNNs explore the graph structure and node features by aggregating and transforming information within node neighborhoods. However, through theoretical and empirical analysis, we reveal that the aggregation process of GNNs tends to destroy node similarity in the original feature space. There are many scenarios where node similarity plays a crucial role. Thus, it has motivated the proposed framework SimP-GCN that can effectively and efficiently preserve node similarity while exploiting graph structure. Specifically, to balance information from graph structure and node features, we propose a feature similarity preserving aggregation which adaptively integrates graph structure and node features. Furthermore, we employ self-supervised learning to explicitly capture the complex feature similarity and dissimilarity relations between nodes. We validate the effectiveness of SimP-GCN on seven benchmark datasets including three assortative and four disassorative graphs. The results demonstrate that SimP-GCN outperforms representative baselines. Further probe shows various advantages of the proposed framework. The implementation of SimP-GCN is available at \url{https://github.com/ChandlerBang/SimP-GCN}.
LGJun 17, 2020Code
Self-supervised Learning on Graphs: Deep Insights and New DirectionWei Jin, Tyler Derr, Haochen Liu et al.
The success of deep learning notoriously requires larger amounts of costly annotated data. This has led to the development of self-supervised learning (SSL) that aims to alleviate this limitation by creating domain specific pretext tasks on unlabeled data. Simultaneously, there are increasing interests in generalizing deep learning to the graph domain in the form of graph neural networks (GNNs). GNNs can naturally utilize unlabeled nodes through the simple neighborhood aggregation that is unable to thoroughly make use of unlabeled nodes. Thus, we seek to harness SSL for GNNs to fully exploit the unlabeled data. Different from data instances in the image and text domains, nodes in graphs present unique structure information and they are inherently linked indicating not independent and identically distributed (or i.i.d.). Such complexity is a double-edged sword for SSL on graphs. On the one hand, it determines that it is challenging to adopt solutions from the image and text domains to graphs and dedicated efforts are desired. On the other hand, it provides rich information that enables us to build SSL from a variety of perspectives. Thus, in this paper, we first deepen our understandings on when, why, and which strategies of SSL work with GNNs by empirically studying numerous basic SSL pretext tasks on graphs. Inspired by deep insights from the empirical studies, we propose a new direction SelfTask to build advanced pretext tasks that are able to achieve state-of-the-art performance on various real-world datasets. The specific experimental settings to reproduce our results can be found in \url{https://github.com/ChandlerBang/SelfTask-GNN}.
LGDec 24, 2019Code
Characterizing the Decision Boundary of Deep Neural NetworksHamid Karimi, Tyler Derr, Jiliang Tang
Deep neural networks and in particular, deep neural classifiers have become an integral part of many modern applications. Despite their practical success, we still have limited knowledge of how they work and the demand for such an understanding is evergrowing. In this regard, one crucial aspect of deep neural network classifiers that can help us deepen our knowledge about their decision-making behavior is to investigate their decision boundaries. Nevertheless, this is contingent upon having access to samples populating the areas near the decision boundary. To achieve this, we propose a novel approach we call Deep Decision boundary Instance Generation (DeepDIG). DeepDIG utilizes a method based on adversarial example generation as an effective way of generating samples near the decision boundary of any deep neural network model. Then, we introduce a set of important principled characteristics that take advantage of the generated instances near the decision boundary to provide multifaceted understandings of deep neural networks. We have performed extensive experiments on multiple representative datasets across various deep neural network models and characterized their decision boundaries. The code is publicly available at https://github.com/hamidkarimi/DeepDIG/.
CLOct 29, 2024
Personalization of Large Language Models: A SurveyZhehao Zhang, Ryan A. Rossi, Branislav Kveton et al.
Personalization of Large Language Models (LLMs) has recently become increasingly important with a wide range of applications. Despite the importance and recent progress, most existing works on personalized LLMs have focused either entirely on (a) personalized text generation or (b) leveraging LLMs for personalization-related downstream applications, such as recommendation systems. In this work, we bridge the gap between these two separate main directions for the first time by introducing a taxonomy for personalized LLM usage and summarizing the key differences and challenges. We provide a formalization of the foundations of personalized LLMs that consolidates and expands notions of personalization of LLMs, defining and discussing novel facets of personalization, usage, and desiderata of personalized LLMs. We then unify the literature across these diverse fields and usage scenarios by proposing systematic taxonomies for the granularity of personalization, personalization techniques, datasets, evaluation methods, and applications of personalized LLMs. Finally, we highlight challenges and important open problems that remain to be addressed. By unifying and surveying recent research using the proposed taxonomies, we aim to provide a clear guide to the existing literature and different facets of personalization in LLMs, empowering both researchers and practitioners.
CVMar 9
Graph2Video: Leveraging Video Models to Model Dynamic Graph EvolutionHua Liu, Yanbin Wei, Fei Xing et al.
Dynamic graphs are common in real-world systems such as social media, recommender systems, and traffic networks. Existing dynamic graph models for link prediction often fall short in capturing the complexity of temporal evolution. They tend to overlook fine-grained variations in temporal interaction order, struggle with dependencies that span long time horizons, and offer limited capability to model pair-specific relational dynamics. To address these challenges, we propose \textbf{Graph2Video}, a video-inspired framework that views the temporal neighborhood of a target link as a sequence of "graph frames". By stacking temporally ordered subgraph frames into a "graph video", Graph2Video leverages the inductive biases of video foundation models to capture both fine-grained local variations and long-range temporal dynamics. It generates a link-level embedding that serves as a lightweight and plug-and-play link-centric memory unit. This embedding integrates seamlessly into existing dynamic graph encoders, effectively addressing the limitations of prior approaches. Extensive experiments on benchmark datasets show that Graph2Video outperforms state-of-the-art baselines on the link prediction task in most cases. The results highlight the potential of borrowing spatio-temporal modeling techniques from computer vision as a promising and effective approach for advancing dynamic graph learning.
CLFeb 8, 2025
Towards Trustworthy Retrieval Augmented Generation for Large Language Models: A SurveyBo Ni, Zheyuan Liu, Leyao Wang et al.
Retrieval-Augmented Generation (RAG) is an advanced technique designed to address the challenges of Artificial Intelligence-Generated Content (AIGC). By integrating context retrieval into content generation, RAG provides reliable and up-to-date external knowledge, reduces hallucinations, and ensures relevant context across a wide range of tasks. However, despite RAG's success and potential, recent studies have shown that the RAG paradigm also introduces new risks, including robustness issues, privacy concerns, adversarial attacks, and accountability issues. Addressing these risks is critical for future applications of RAG systems, as they directly impact their trustworthiness. Although various methods have been developed to improve the trustworthiness of RAG methods, there is a lack of a unified perspective and framework for research in this topic. Thus, in this paper, we aim to address this gap by providing a comprehensive roadmap for developing trustworthy RAG systems. We place our discussion around five key perspectives: reliability, privacy, safety, fairness, explainability, and accountability. For each perspective, we present a general framework and taxonomy, offering a structured approach to understanding the current challenges, evaluating existing solutions, and identifying promising future research directions. To encourage broader adoption and innovation, we also highlight the downstream applications where trustworthy RAG systems have a significant impact.
AIOct 11, 2024
Towards Trustworthy Knowledge Graph Reasoning: An Uncertainty Aware PerspectiveBo Ni, Yu Wang, Lu Cheng et al.
Recently, Knowledge Graphs (KGs) have been successfully coupled with Large Language Models (LLMs) to mitigate their hallucinations and enhance their reasoning capability, such as in KG-based retrieval-augmented frameworks. However, current KG-LLM frameworks lack rigorous uncertainty estimation, limiting their reliable deployment in high-stakes applications. Directly incorporating uncertainty quantification into KG-LLM frameworks presents challenges due to their complex architectures and the intricate interactions between the knowledge graph and language model components. To address this gap, we propose a new trustworthy KG-LLM framework, Uncertainty Aware Knowledge-Graph Reasoning (UAG), which incorporates uncertainty quantification into the KG-LLM framework. We design an uncertainty-aware multi-step reasoning framework that leverages conformal prediction to provide a theoretical guarantee on the prediction set. To manage the error rate of the multi-step process, we additionally introduce an error rate control module to adjust the error rate within the individual components. Extensive experiments show that our proposed UAG can achieve any pre-defined coverage rate while reducing the prediction set/interval size by 40% on average over the baselines.
LGNov 14, 2024
WelQrate: Defining the Gold Standard in Small Molecule Drug Discovery BenchmarkingYunchao Liu, Ha Dong, Xin Wang et al.
While deep learning has revolutionized computer-aided drug discovery, the AI community has predominantly focused on model innovation and placed less emphasis on establishing best benchmarking practices. We posit that without a sound model evaluation framework, the AI community's efforts cannot reach their full potential, thereby slowing the progress and transfer of innovation into real-world drug discovery. Thus, in this paper, we seek to establish a new gold standard for small molecule drug discovery benchmarking, WelQrate. Specifically, our contributions are threefold: WelQrate Dataset Collection - we introduce a meticulously curated collection of 9 datasets spanning 5 therapeutic target classes. Our hierarchical curation pipelines, designed by drug discovery experts, go beyond the primary high-throughput screen by leveraging additional confirmatory and counter screens along with rigorous domain-driven preprocessing, such as Pan-Assay Interference Compounds (PAINS) filtering, to ensure the high-quality data in the datasets; WelQrate Evaluation Framework - we propose a standardized model evaluation framework considering high-quality datasets, featurization, 3D conformation generation, evaluation metrics, and data splits, which provides a reliable benchmarking for drug discovery experts conducting real-world virtual screening; Benchmarking - we evaluate model performance through various research questions using the WelQrate dataset collection, exploring the effects of different models, dataset quality, featurization methods, and data splitting strategies on the results. In summary, we recommend adopting our proposed WelQrate as the gold standard in small molecule drug discovery benchmarking. The WelQrate dataset collection, along with the curation codes, and experimental scripts are all publicly available at WelQrate.org.
LGOct 18, 2025
Scaffold-Aware Generative Augmentation and Reranking for Enhanced Virtual ScreeningXin Wang, Yu Wang, Yunchao Liu et al.
Ligand-based virtual screening (VS) is an essential step in drug discovery that evaluates large chemical libraries to identify compounds that potentially bind to a therapeutic target. However, VS faces three major challenges: class imbalance due to the low active rate, structural imbalance among active molecules where certain scaffolds dominate, and the need to identify structurally diverse active compounds for novel drug development. We introduce ScaffAug, a scaffold-aware VS framework that addresses these challenges through three modules. The augmentation module first generates synthetic data conditioned on scaffolds of actual hits using generative AI, specifically a graph diffusion model. This helps mitigate the class imbalance and furthermore the structural imbalance, due to our proposed scaffold-aware sampling algorithm, designed to produce more samples for active molecules with underrepresented scaffolds. A model-agnostic self-training module is then used to safely integrate the generated synthetic data from our augmentation module with the original labeled data. Lastly, we introduce a reranking module that improves VS by enhancing scaffold diversity in the top recommended set of molecules, while still maintaining and even enhancing the overall general performance of identifying novel, active compounds. We conduct comprehensive computational experiments across five target classes, comparing ScaffAug against existing baseline methods by reporting the performance of multiple evaluation metrics and performing ablation studies on ScaffAug. Overall, this work introduces novel perspectives on effectively enhancing VS by leveraging generative augmentations, reranking, and general scaffold-awareness.
CVAug 17, 2025
Inverse-LLaVA: Eliminating Alignment Pre-training Through Text-to-Vision MappingXuhui Zhan, Tyler Derr
Traditional multimodal learning approaches require expensive alignment pre-training to bridge vision and language modalities, typically projecting visual features into discrete text token spaces. We challenge both fundamental assumptions underlying this paradigm by proposing Inverse-LLaVA, a novel approach that eliminates alignment pre-training entirely while inverting the conventional mapping direction. Rather than projecting visual features to text space, our method maps text embeddings into continuous visual representation space and performs fusion within transformer intermediate layers. Through selective additive components in attention mechanisms, we enable dynamic integration of visual and textual representations without requiring massive image-text alignment datasets. Comprehensive experiments across nine multimodal benchmarks demonstrate nuanced performance trade-offs: Inverse-LLaVA achieves notable improvements on reasoning-intensive and cognitive tasks (MM-VET: +0.2%, VizWiz: +1.8%, ScienceQA: +0.2%, cognitive reasoning: +27.2%), while showing expected decreases in perception tasks requiring memorized visual-text associations (celebrity recognition: -49.5%, OCR: -21.3%). These results provide the first empirical evidence that alignment pre-training is not necessary for effective multimodal learning, particularly for complex reasoning tasks. Our work establishes the feasibility of a new paradigm that reduces computational requirements by 45%, challenges conventional wisdom about modality fusion, and opens new research directions for efficient multimodal architectures that preserve modality-specific characteristics. Our project website with code and additional resources is available at https://inverse-llava.github.io.
CRAug 8, 2025
Mitigating Distribution Shift in Graph-Based Android Malware Classification via Function Metadata and LLM EmbeddingsNgoc N. Tran, Anwar Said, Waseem Abbas et al.
Graph-based malware classifiers can achieve over 94% accuracy on standard Android datasets, yet we find they suffer accuracy drops of up to 45% when evaluated on previously unseen malware variants from the same family - a scenario where strong generalization would typically be expected. This highlights a key limitation in existing approaches: both the model architectures and their structure-only representations often fail to capture deeper semantic patterns. In this work, we propose a robust semantic enrichment framework that enhances function call graphs with contextual features, including function-level metadata and, when available, code embeddings derived from large language models. The framework is designed to operate under real-world constraints where feature availability is inconsistent, and supports flexible integration of semantic signals. To evaluate generalization under realistic domain and temporal shifts, we introduce two new benchmarks: MalNet-Tiny-Common and MalNet-Tiny-Distinct, constructed using malware family partitioning to simulate cross-family generalization and evolving threat behavior. Experiments across multiple graph neural network backbones show that our method improves classification performance by up to 8% under distribution shift and consistently enhances robustness when integrated with adaptation-based methods. These results offer a practical path toward building resilient malware detection systems in evolving threat environments.
IRAug 2, 2025
Towards Bridging Review Sparsity in Recommendation with Textual Edge Graph RepresentationLeyao Wang, Xutao Mao, Xuhui Zhan et al.
Textual reviews enrich recommender systems with fine-grained preference signals and enhanced explainability. However, in real-world scenarios, users rarely leave reviews, resulting in severe sparsity that undermines the effectiveness of existing models. A natural solution is to impute or generate missing reviews to enrich the data. However, conventional imputation techniques -- such as matrix completion and LLM-based augmentation -- either lose contextualized semantics by embedding texts into vectors, or overlook structural dependencies among user-item interactions. To address these shortcomings, we propose TWISTER (ToWards Imputation on Sparsity with Textual Edge Graph Representation), a unified framework that imputes missing reviews by jointly modeling semantic and structural signals. Specifically, we represent user-item interactions as a Textual-Edge Graph (TEG), treating reviews as edge attributes. To capture relational context, we construct line-graph views and employ a large language model as a graph-aware aggregator. For each interaction lacking a textual review, our model aggregates the neighborhood's natural-language representations to generate a coherent and personalized review. Experiments on the Amazon and Goodreads datasets show that TWISTER consistently outperforms traditional numeric, graph-based, and LLM baselines, delivering higher-quality imputed reviews and, more importantly, enhanced recommendation performance. In summary, TWISTER generates reviews that are more helpful, authentic, and specific, while smoothing structural signals for improved recommendations.
AIOct 22, 2024
SaVe-TAG: Semantic-aware Vicinal Risk Minimization for Long-Tailed Text-Attributed GraphsLeyao Wang, Yu Wang, Bo Ni et al.
Real-world graph data often follows long-tailed distributions, making it difficult for Graph Neural Networks (GNNs) to generalize well across both head and tail classes. Recent advances in Vicinal Risk Minimization (VRM) have shown promise in mitigating class imbalance with numeric interpolation; however, existing approaches largely rely on embedding-space arithmetic, which fails to capture the rich semantics inherent in text-attributed graphs. In this work, we propose our method, SaVe-TAG (Semantic-aware Vicinal Risk Minimization for Long-Tailed Text-Attributed Graphs), a novel VRM framework that leverages Large Language Models (LLMs) to perform text-level interpolation, generating on-manifold, boundary-enriching synthetic samples for minority classes. To mitigate the risk of noisy generation, we introduce a confidence-based edge assignment mechanism that uses graph topology as a natural filter to ensure structural consistency. We provide theoretical justification for our method and conduct extensive experiments on benchmark datasets, showing that our approach consistently outperforms both numeric interpolation and prior long-tailed node classification baselines. Our results highlight the importance of integrating semantic and structural signals for balanced and effective learning on text-attributed graphs.
LGJun 21, 2024
FT-AED: Benchmark Dataset for Early Freeway Traffic Anomalous Event DetectionAustin Coursey, Junyi Ji, Marcos Quinones-Grueiro et al.
Early and accurate detection of anomalous events on the freeway, such as accidents, can improve emergency response and clearance. However, existing delays and errors in event identification and reporting make it a difficult problem to solve. Current large-scale freeway traffic datasets are not designed for anomaly detection and ignore these challenges. In this paper, we introduce the first large-scale lane-level freeway traffic dataset for anomaly detection. Our dataset consists of a month of weekday radar detection sensor data collected in 4 lanes along an 18-mile stretch of Interstate 24 heading toward Nashville, TN, comprising over 3.7 million sensor measurements. We also collect official crash reports from the Nashville Traffic Management Center and manually label all other potential anomalies in the dataset. To show the potential for our dataset to be used in future machine learning and traffic research, we benchmark numerous deep learning anomaly detection models on our dataset. We find that unsupervised graph neural network autoencoders are a promising solution for this problem and that ignoring spatial relationships leads to decreased performance. We demonstrate that our methods can reduce reporting delays by over 10 minutes on average while detecting 75% of crashes. Our dataset and all preprocessing code needed to get started are publicly released at https://vu.edu/ft-aed/ to facilitate future research.
LGJun 17, 2024
Edge Classification on Graphs: New Directions in Topological ImbalanceXueqi Cheng, Yu Wang, Yunchao Liu et al.
Recent years have witnessed the remarkable success of applying Graph machine learning (GML) to node/graph classification and link prediction. However, edge classification task that enjoys numerous real-world applications such as social network analysis and cybersecurity, has not seen significant advancement. To address this gap, our study pioneers a comprehensive approach to edge classification. We identify a novel `Topological Imbalance Issue', which arises from the skewed distribution of edges across different classes, affecting the local subgraph of each edge and harming the performance of edge classifications. Inspired by the recent studies in node classification that the performance discrepancy exists with varying local structural patterns, we aim to investigate if the performance discrepancy in topological imbalanced edge classification can also be mitigated by characterizing the local class distribution variance. To overcome this challenge, we introduce Topological Entropy (TE), a novel topological-based metric that measures the topological imbalance for each edge. Our empirical studies confirm that TE effectively measures local class distribution variance, and indicate that prioritizing edges with high TE values can help address the issue of topological imbalance. Based on this, we develop two strategies - Topological Reweighting and TE Wedge-based Mixup - to focus training on (synthetic) edges based on their TEs. While topological reweighting directly manipulates training edge weights according to TE, our wedge-based mixup interpolates synthetic edges between high TE wedges. Ultimately, we integrate these strategies into a novel topological imbalance strategy for edge classification: TopoEdge. Through extensive experiments, we demonstrate the efficacy of our proposed strategies on newly curated datasets and thus establish a new benchmark for (imbalanced) edge classification.
LGJun 7, 2024
Large Generative Graph ModelsYu Wang, Ryan A. Rossi, Namyong Park et al.
Large Generative Models (LGMs) such as GPT, Stable Diffusion, Sora, and Suno are trained on a huge amount of language corpus, images, videos, and audio that are extremely diverse from numerous domains. This training paradigm over diverse well-curated data lies at the heart of generating creative and sensible content. However, all previous graph generative models (e.g., GraphRNN, MDVAE, MoFlow, GDSS, and DiGress) have been trained only on one dataset each time, which cannot replicate the revolutionary success achieved by LGMs in other fields. To remedy this crucial gap, we propose a new class of graph generative model called Large Graph Generative Model (LGGM) that is trained on a large corpus of graphs (over 5000 graphs) from 13 different domains. We empirically demonstrate that the pre-trained LGGM has superior zero-shot generative capability to existing graph generative models. Furthermore, our pre-trained LGGM can be easily fine-tuned with graphs from target domains and demonstrate even better performance than those directly trained from scratch, behaving as a solid starting point for real-world customization. Inspired by Stable Diffusion, we further equip LGGM with the capability to generate graphs given text prompts (Text-to-Graph), such as the description of the network name and domain (i.e., "The power-1138-bus graph represents a network of buses in a power distribution system."), and network statistics (i.e., "The graph has a low average degree, suitable for modeling social media interactions."). This Text-to-Graph capability integrates the extensive world knowledge in the underlying language model, offering users fine-grained control of the generated graphs. We release the code, the model checkpoint, and the datasets at https://lggm-lg.github.io/.
LGFeb 10, 2022
ChemicalX: A Deep Learning Library for Drug Pair ScoringBenedek Rozemberczki, Charles Tapley Hoyt, Anna Gogleva et al.
In this paper, we introduce ChemicalX, a PyTorch-based deep learning library designed for providing a range of state of the art models to solve the drug pair scoring task. The primary objective of the library is to make deep drug pair scoring models accessible to machine learning researchers and practitioners in a streamlined framework.The design of ChemicalX reuses existing high level model training utilities, geometric deep learning, and deep chemistry layers from the PyTorch ecosystem. Our system provides neural network layers, custom pair scoring architectures, data loaders, and batch iterators for end users. We showcase these features with example code snippets and case studies to highlight the characteristics of ChemicalX. A range of experiments on real world drug-drug interaction, polypharmacy side effect, and combination synergy prediction tasks demonstrate that the models available in ChemicalX are effective at solving the pair scoring task. Finally, we show that ChemicalX could be used to train and score machine learning models on large drug pair datasets with hundreds of thousands of compounds on commodity hardware.
LGMay 10, 2021
Graph Feature Gating NetworksWei Jin, Xiaorui Liu, Yao Ma et al.
Graph neural networks (GNNs) have received tremendous attention due to their power in learning effective representations for graphs. Most GNNs follow a message-passing scheme where the node representations are updated by aggregating and transforming the information from the neighborhood. Meanwhile, they adopt the same strategy in aggregating the information from different feature dimensions. However, suggested by social dimension theory and spectral embedding, there are potential benefits to treat the dimensions differently during the aggregation process. In this work, we investigate to enable heterogeneous contributions of feature dimensions in GNNs. In particular, we propose a general graph feature gating network (GFGN) based on the graph signal denoising problem and then correspondingly introduce three graph filters under GFGN to allow different levels of contributions from feature dimensions. Extensive experiments on various real-world datasets demonstrate the effectiveness and robustness of the proposed frameworks.
CLMay 27, 2020
Chat as Expected: Learning to Manipulate Black-box Neural Dialogue ModelsHaochen Liu, Zhiwei Wang, Tyler Derr et al.
Recently, neural network based dialogue systems have become ubiquitous in our increasingly digitalized society. However, due to their inherent opaqueness, some recently raised concerns about using neural models are starting to be taken seriously. In fact, intentional or unintentional behaviors could lead to a dialogue system to generate inappropriate responses. Thus, in this paper, we investigate whether we can learn to craft input sentences that result in a black-box neural dialogue model being manipulated into having its outputs contain target words or match target sentences. We propose a reinforcement learning based model that can generate such desired inputs automatically. Extensive experiments on a popular well-trained state-of-the-art neural dialogue model show that our method can successfully seek out desired inputs that lead to the target outputs in a considerable portion of cases. Consequently, our work reveals the potential of neural dialogue models to be manipulated, which inspires and opens the door towards developing strategies to defend them.
IRMay 17, 2020
Attacking Black-box Recommendations via Copying Cross-domain User ProfilesWenqi Fan, Tyler Derr, Xiangyu Zhao et al.
Recently, recommender systems that aim to suggest personalized lists of items for users to interact with online have drawn a lot of attention. In fact, many of these state-of-the-art techniques have been deep learning based. Recent studies have shown that these deep learning models (in particular for recommendation systems) are vulnerable to attacks, such as data poisoning, which generates users to promote a selected set of items. However, more recently, defense strategies have been developed to detect these generated users with fake profiles. Thus, advanced injection attacks of creating more `realistic' user profiles to promote a set of items is still a key challenge in the domain of deep learning based recommender systems. In this work, we present our framework CopyAttack, which is a reinforcement learning based black-box attack method that harnesses real users from a source domain by copying their profiles into the target domain with the goal of promoting a subset of items. CopyAttack is constructed to both efficiently and effectively learn policy gradient networks that first select, and then further refine/craft, user profiles from the source domain to ultimately copy into the target domain. CopyAttack's goal is to maximize the hit ratio of the targeted items in the Top-$k$ recommendation list of the users in the target domain. We have conducted experiments on two real-world datasets and have empirically verified the effectiveness of our proposed framework and furthermore performed a thorough model analysis.
CLSep 13, 2019
Say What I Want: Towards the Dark Side of Neural Dialogue ModelsHaochen Liu, Tyler Derr, Zitao Liu et al.
Neural dialogue models have been widely adopted in various chatbot applications because of their good performance in simulating and generalizing human conversations. However, there exists a dark side of these models -- due to the vulnerability of neural networks, a neural dialogue model can be manipulated by users to say what they want, which brings in concerns about the security of practical chatbot services. In this work, we investigate whether we can craft inputs that lead a well-trained black-box neural dialogue model to generate targeted outputs. We formulate this as a reinforcement learning (RL) problem and train a Reverse Dialogue Generator which efficiently finds such inputs for targeted outputs. Experiments conducted on a representative neural dialogue model show that our proposed model is able to discover such desired inputs in a considerable portion of cases. Overall, our work reveals this weakness of neural dialogue models and may prompt further researches of developing corresponding solutions to avoid it.
LGJun 10, 2019
Attacking Graph Convolutional Networks via RewiringYao Ma, Suhang Wang, Tyler Derr et al.
Graph Neural Networks (GNNs) have boosted the performance of many graph related tasks such as node classification and graph classification. Recent researches show that graph neural networks are vulnerable to adversarial attacks, which deliberately add carefully created unnoticeable perturbation to the graph structure. The perturbation is usually created by adding/deleting a few edges, which might be noticeable even when the number of edges modified is small. In this paper, we propose a graph rewiring operation which affects the graph in a less noticeable way compared to adding/deleting edges. We then use reinforcement learning to learn the attack strategy based on the proposed rewiring operation. Experiments on real world graphs demonstrate the effectiveness of the proposed framework. To understand the proposed framework, we further analyze how its generated perturbation to the graph structure affects the output of the target model.
IRMay 30, 2019
Deep Adversarial Social RecommendationWenqi Fan, Tyler Derr, Yao Ma et al.
Recent years have witnessed rapid developments on social recommendation techniques for improving the performance of recommender systems due to the growing influence of social networks to our daily life. The majority of existing social recommendation methods unify user representation for the user-item interactions (item domain) and user-user connections (social domain). However, it may restrain user representation learning in each respective domain, since users behave and interact differently in the two domains, which makes their representations to be heterogeneous. In addition, most of traditional recommender systems can not efficiently optimize these objectives, since they utilize negative sampling technique which is unable to provide enough informative guidance towards the training during the optimization process. In this paper, to address the aforementioned challenges, we propose a novel deep adversarial social recommendation framework DASO. It adopts a bidirectional mapping method to transfer users' information between social domain and item domain using adversarial learning. Comprehensive experiments on two real-world datasets show the effectiveness of the proposed framework.
SIFeb 27, 2019
Deep Adversarial Network AlignmentTyler Derr, Hamid Karimi, Xiaorui Liu et al.
Network alignment, in general, seeks to discover the hidden underlying correspondence between nodes across two (or more) networks when given their network structure. However, most existing network alignment methods have added assumptions of additional constraints to guide the alignment, such as having a set of seed node-node correspondences across the networks or the existence of side-information. Instead, we seek to develop a general network alignment algorithm that makes no additional assumptions. Recently, network embedding has proven effective in many network analysis tasks, but embeddings of different networks are not aligned. Thus, we present our Deep Adversarial Network Alignment (DANA) framework that first uses deep adversarial learning to discover complex mappings for aligning the embedding distributions of the two networks. Then, using our learned mapping functions, DANA performs an efficient nearest neighbor node alignment. We perform experiments on real world datasets to show the effectiveness of our framework for first aligning the graph embedding distributions and then discovering node alignments that outperform existing methods.