GenAI4ELab/papercli-papers huggingface dataset:
PHSIC against Random Consistency and Its Application in Causal Inference
Authors: Jue Li; Yuhua Qian; Jieting Wang; Saixiong Liu
Venue: IJCAI 2024 (main)

Abstract: The Hilbert-Schmidt Independence Criterion (HSIC) based on kernel functions is capable of detecting nonlinear dependencies between variables, making it a common method for association relationship mining. However, in situations with small samples, high dimensions, or noisy data, it may generate spurious associations, causing two unrelated variables to have certain scores. To address this issue, we propose a novel criterion, named as Pure Hilbert-Schmidt Independence Criterion (PHSIC). PHSIC is achieved by subtracting the mean HSIC obtained under random conditions from the original HSIC value. We demonstrate three significant advantages of PHSIC through theoretical and simulation experiments: (1) PHSIC has a baseline of zero, enhancing the interpretability of HSIC. (2) Compared to HSIC, PHSIC exhibits lower bias. (3) PHSIC enables a fairer comparison across different samples and dimensions. To validate the effectiveness of PHSIC, we apply it to multiple causal inference tasks to measure the independence between cause and residual. Experimental results demonstrate that the causal model based on PHSIC performs well compared to other methods in scenarios involving small sample sizes and noisy data, both in real and simulated datasets.
Zero-shot Learning for Preclinical Drug Screening
Authors: Kun Li; Weiwei Liu; Yong Luo; Xiantao Cai; Jia Wu; Wenbin Hu
Venue: IJCAI 2024 (main)

Abstract: Conventional deep learning methods typically employ supervised learning for drug response prediction (DRP). This entails dependence on labeled response data from drugs for model training. However, practical applications in the preclinical drug screening phase demand that DRP models predict responses for novel compounds, often with unknown drug responses. This presents a challenge, rendering supervised deep learning methods unsuitable for such scenarios. In this paper, we propose a zero-shot learning solution for the DRP task in preclinical drug screening. Specifically, we propose a Multi-branch Multi-Source Domain Adaptation Test Enhancement Plug-in, called MSDA. MSDA can be seamlessly integrated with conventional DRP methods, learning invariant features from the prior response data of similar drugs to enhance real-time predictions of unlabeled compounds. The results of experiments on two large drug response datasets showed that MSDA efficiently predicts drug responses for novel compounds, leading to a general performance improvement of 5-10% in the preclinical drug screening phase. The significance of this solution resides in its potential to accelerate the drug discovery process, improve drug candidate assessment, and facilitate the success of drug discovery. The code is available at https://github.com/DrugD/MSDA.
Contrastive Learning Drug Response Models from Natural Language Supervision
Authors: Kun Li; Xiuwen Gong; Jia Wu; Wenbin Hu
Venue: IJCAI 2024 (main)

Abstract: Deep learning-based drug response prediction (DRP) methods can accelerate the drug discovery process and reduce research and development costs. Despite their high accuracy, generating regression-aware representations remains challenging for mainstream approaches. For instance, the representations are often disordered, aggregated, and overlapping, and they fail to characterize distinct samples effectively. This results in poor representation during the DRP task, diminishing generalizability and potentially leading to substantial costs during the drug discovery. In this paper, we propose CLDR, a contrastive learning framework with natural language supervision for the DRP. The CLDR converts regression labels into text, which is merged with the drug response caption as a second sample modality instead of the traditional modes, i.e., graphs and sequences. Simultaneously, a common-sense numerical knowledge graph is introduced to improve the continuous text representation. Our framework is validated using the genomics of drug sensitivity in cancer dataset with average performance increases ranging from 7.8% to 31.4%. Furthermore, experiments demonstrate that the proposed CLDR effectively maps samples with distinct label values into a high-dimensional space. In this space, the sample representations are scattered, significantly alleviating feature overlap. The code is available at: https://github.com/DrugD/CLDR.
LLM-based Multi-Level Knowledge Generation for Few-shot Knowledge Graph Completion
Authors: Qian Li; Zhuo Chen; Cheng Ji; Shiqi Jiang; Jianxin Li
Venue: IJCAI 2024 (main)

Abstract: Knowledge Graphs (KGs) are pivotal in various NLP applications but often grapple with incompleteness, especially due to the long-tail problem where infrequent, unpopular relationships drastically reduce the KG completion performance. In this paper, we focus on Few-shot Knowledge Graph Completion (FKGC), a task addressing these gaps in long-tail scenarios. Amidst the rapid evolution of Large Language Models, we propose a generation-based FKGC paradigm facilitated by LLM distillation. Our MuKDC framework employs multi-level knowledge distillation for few-shot KG completion, generating supplementary knowledge to mitigate data scarcity in few-shot environments. MuKDC comprises two primary components: Multi-level Knowledge Generation, which enriches the KG at various levels, and Consistency Assessment, to ensure the coherence and reliability of the generated knowledge. Most notably, our method achieves SOTA results in both FKGC and multi-modal FKGC benchmarks, significantly advancing KG completion and enhancing the understanding and application of LLMs in structured knowledge generation and assessment.
Rethinking the Effectiveness of Graph Classification Datasets in Benchmarks for Assessing GNNs
Authors: Zhengdao Li; Yong Cao; Kefan Shuai; Yiming Miao; Kai Hwang
Venue: IJCAI 2024 (main)

Abstract: Graph classification benchmarks, vital for assessing and developing graph neural network (GNN) models, have recently been scrutinized, as simple methods like MLPs have demonstrated comparable performance. This leads to an important question: Do these benchmarks effectively distinguish the advancements of GNNs over other methodologies? If so, how do we quantitatively measure this effectiveness? In response, we first propose an empirical protocol based on a fair benchmarking framework to investigate the performance discrepancy between simple methods and GNNs. We further propose a novel metric to quantify the dataset effectiveness by considering both dataset complexity and model performance. To the best of our knowledge, our work is the first to thoroughly study and provide an explicit definition for dataset effectiveness in the graph learning area. Through testing across 16 real-world datasets, we found our metric to align with existing studies and intuitive assumptions. Finally, we explore the causes behind the low effectiveness of certain datasets by investigating the correlation between intrinsic graph properties and class labels, and we developed a novel technique supporting the correlation-controllable synthetic dataset generation. Our findings shed light on the current understanding of benchmark datasets, and our new platform could fuel the future evolution of graph classification benchmarks.
Enhancing Dual-Target Cross-Domain Recommendation with Federated Privacy-Preserving Learning
Authors: Zhenghong Lin; Wei Huang; Hengyu Zhang; Jiayu Xu; Weiming Liu; Xinting Liao; Fan Wang; Shiping Wang; Yanchao Tan
Venue: IJCAI 2024 (main)

Abstract: Recently, dual-target cross-domain recommendation (DTCDR) has been proposed to alleviate the data sparsity problem by sharing the common knowledge across domains simultaneously. However, existing methods often assume that personal data containing abundant identifiable information can be directly accessed, which results in a controversial privacy leakage problem of DTCDR. To this end, we introduce the P2DTR framework, a novel approach in DTCDR while protecting private user information. Specifically, we first design a novel inter-client knowledge extraction mechanism, which exploits the private set intersection algorithm and prototype-based federated learning to enable collaboratively modeling among multiple users and a server. Furthermore, to improve the recommendation performance based on the extracted common knowledge across domains, we proposed an intra-client enhanced recommendation, consisting of a constrained dominant set (CDS) propagation mechanism and dual-recommendation module. Extensive experiments on real-world datasets validate that our proposed P2DTR framework achieves superior utility under a privacy-preserving guarantee on both domains.
Large Language Model Guided Knowledge Distillation for Time Series Anomaly Detection
Authors: Chen Liu; Shibo He; Qihang Zhou; Shizhong Li; Wenchao Meng
Venue: IJCAI 2024 (main)

Abstract: Self-supervised methods have gained prominence in time series anomaly detection due to the scarcity of available annotations. Nevertheless, they typically demand extensive training data to acquire a generalizable representation map, which conflicts with scenarios of a few available samples, thereby limiting their performance. To overcome the limitation, we propose AnomalyLLM, a knowledge distillation-based time series anomaly detection approach where the student network is trained to mimic the features of the large language model (LLM)-based teacher network that is pretrained on large-scale datasets. During the testing phase, anomalies are detected when the discrepancy between the features of the teacher and student networks is large. To circumvent the student network from learning the teacher network’s feature of anomalous samples, we devise two key strategies. 1) Prototypical signals are incorporated into the student network to consolidate the normal feature extraction. 2) We use synthetic anomalies to enlarge the representation gap between the two networks. AnomalyLLM demonstrates state-of-the-art performance on 15 datasets, improving accuracy by at least 14.5% in the UCR dataset.
Gradformer: Graph Transformer with Exponential Decay
Authors: Chuang Liu; Zelin Yao; Yibing Zhan; Xueqi Ma; Shirui Pan; Wenbin Hu
Venue: IJCAI 2024 (main)

Abstract: Graph Transformers (GTs) have demonstrated their advantages across a wide range of tasks. However, the self-attention mechanism in GTs overlooks the graph's inductive biases, particularly biases related to structure, which are crucial for the graph tasks. Although some methods utilize positional encoding and attention bias to model inductive biases, their effectiveness is still suboptimal analytically. Therefore, this paper presents Gradformer, a method innovatively integrating GT with the intrinsic inductive bias by applying an exponential decay mask to the attention matrix. Specifically, the values in the decay mask matrix diminish exponentially, correlating with the decreasing node proximities within the graph structure. This design enables Gradformer to retain its ability to capture information from distant nodes while focusing on the graph's local details. Furthermore, Gradformer introduces a learnable constraint into the decay mask, allowing different attention heads to learn distinct decay masks. Such an design diversifies the attention heads, enabling a more effective assimilation of diverse structural information within the graph. Extensive experiments on various benchmarks demonstrate that Gradformer consistently outperforms the Graph Neural Network and GT baseline models in various graph classification and regression tasks. Additionally, Gradformer has proven to be an effective method for training deep GT models, maintaining or even enhancing accuracy compared to shallow models as the network deepens, in contrast to the significant accuracy drop observed in other GT models. Codes are available at https://github.com/LiuChuang0059/Gradformer.
Where to Mask: Structure-Guided Masking for Graph Masked Autoencoders
Authors: Chuang Liu; Yuyao Wang; Yibing Zhan; Xueqi Ma; Dapeng Tao; Jia Wu; Wenbin Hu
Venue: IJCAI 2024 (main)

Abstract: Graph masked autoencoders (GMAE) have emerged as a significant advancement in self-supervised pre-training for graph-structured data. Previous GMAE models primarily utilize a straightforward random masking strategy for nodes or edges during training. However, this strategy fails to consider the varying significance of different nodes within the graph structure. In this paper, we investigate the potential of leveraging the graph's structural composition as a fundamental and unique prior in the masked pre-training process. To this end, we introduce a novel structure-guided masking strategy (i.e., StructMAE), designed to refine the existing GMAE models. StructMAE involves two steps: 1) Structure-based Scoring: Each node is evaluated and assigned a score reflecting its structural significance. Two distinct types of scoring manners are proposed: predefined and learnable scoring. 2) Structure-guided Masking: With the obtained assessment scores, we develop an easy-to-hard masking strategy that gradually increases the structural awareness of the self-supervised reconstruction task. Specifically, the strategy begins with random masking and progresses to masking structure-informative nodes based on the assessment scores. This design gradually and effectively guides the model in learning graph structural information. Furthermore, extensive experiments consistently demonstrate that our StructMAE method outperforms existing state-of-the-art GMAE models in both unsupervised and transfer learning tasks. Codes are available at https: //github.com/LiuChuang0059/StructMAE.
Encoding Auxiliary Information to Restore Compressed Point Cloud Geometry
Authors: Gexin Liu; Jiahao Zhu; Dandan Ding; Zhan Ma
Venue: IJCAI 2024 (main)

Abstract: The standardized Geometry-based Point Cloud Compression (G-PCC) suffers from limited coding performance and low-quality reconstruction. To address this, we propose AuxGR, a performance-complexity tradeoff solution for point cloud geometry restoration: leveraging auxiliary bitstream to enhance the quality of G-PCC compressed point cloud geometry. This auxiliary bitstream efficiently encapsulates spatio-temporal information. For static coding, we perform paired information embedding (PIE) on the G-PCC decoded frame by employing target convolutions from its original counterpart, producing an auxiliary bitstream containing abundant original information. For dynamic coding, in addition to PIE, we propose temporal information embedding (TIE) to capture motion information between the previously restored and the current G-PCC decoded frames. TIE applies target kNN attention between them, which ensures the temporal neighborhood construction for each point and implicitly represents motions. Due to the similarity across temporal frames, only the residuals between TIE and PIE outputs are compressed as auxiliary bitstream. Experimental results demonstrate that AuxGR notably outperforms existing methods in both static and dynamic coding scenarios. Moreover, our framework enables the flexible incorporation of auxiliary information under computation constraints, which is attractive to real applications.
Fast and Continual Knowledge Graph Embedding via Incremental LoRA
Authors: Jiajun Liu; Wenjun Ke; Peng Wang; Jiahao Wang; Jinhua Gao; Ziyu Shang; Guozheng Li; Zijie Xu; Ke Ji; Yining Li
Venue: IJCAI 2024 (main)

Abstract: Continual Knowledge Graph Embedding (CKGE) aims to efficiently learn new knowledge and simultaneously preserve old knowledge. Dominant approaches primarily focus on alleviating catastrophic forgetting of old knowledge but neglect efficient learning for the emergence of new knowledge. However, in real-world scenarios, knowledge graphs (KGs) are continuously growing, which brings a significant challenge to fine-tuning KGE models efficiently. To address this issue, we propose a fast CKGE framework (FastKGE), incorporating an incremental low-rank adapter (IncLoRA) mechanism to efficiently acquire new knowledge while preserving old knowledge. Specifically, to mitigate catastrophic forgetting, FastKGE isolates and allocates new knowledge to specific layers based on the fine-grained influence between old and new KGs. Subsequently, to accelerate fine-tuning, FastKGE devises an efficient IncLoRA mechanism, which embeds the specific layers into incremental low-rank adapters with fewer training parameters. Moreover, IncLoRA introduces adaptive rank allocation, which makes the LoRA aware of the importance of entities and adjusts its rank scale adaptively. We conduct experiments on four public datasets and two new datasets with a larger initial scale. Experimental results demonstrate that FastKGE can reduce training time by 34%-49% while still achieving competitive link prediction performance against state-of-the-art models on four public datasets (average MRR score of 21.0% vs. 21.1%). Meanwhile, on two newly constructed datasets, FastKGE saves 51%-68% training time and improves link prediction performance by 1.5%.
KDDC: Knowledge-Driven Disentangled Causal Metric Learning for Pre-Travel Out-of-Town Recommendation
Authors: Yinghui Liu; Guojiang Shen; Chengyong Cui; Zhenzhen Zhao; Xiao Han; Jiaxin Du; Xiangyu Zhao; Xiangjie Kong
Venue: IJCAI 2024 (main)

Abstract: Pre-travel recommendation is developed to provide a variety of out-of-town Point-of-Interests (POIs) for users planning to travel away from their hometowns but have not yet decided on their destination. Existing out-of-town recommender systems work on constructing users' latent preferences and inferring travel intentions from their check-in sequences. However, there are still two challenges that hamper the performance of these approaches: i) Users' interactive data (including hometown and out-of-town check-ins) tend to be rare, and while candidate POIs that come from different regions contain various semantic information; ii) The causes for user check-in include not only interest but also conformity, which are easily entangled and overlooked. To fill these gaps, we propose a Knowledge-Driven Disentangled Causal metric learning framework (KDDC) that mitigates interaction data sparsity by enhancing POI semantic representation and considers the distributions of two causes (i.e., conformity and interest) for pre-travel recommendation. Specifically, we pretrain a constructed POI attribute knowledge graph through a segmented interaction method and POI semantic information is aggregated via relational heterogeneity. In addition, we devise a disentangled causal metric learning to model and infer userrelated representations. Extensive experiments on two real-world nationwide datasets display the consistent superiority of our KDDC over state-of-theart baselines.
Full Bayesian Significance Testing for Neural Networks in Traffic Forecasting
Authors: Zehua Liu; Jingyuan Wang; Zimeng Li; Yue He
Venue: IJCAI 2024 (main)

Abstract: Due to the complex and dynamic traffic contexts, the interpretability and uncertainty of traffic forecasting have gained increasing attention. Significance testing is a powerful tool in statistics used to determine whether a hypothesis is valid, facilitating the identification of pivotal features that predominantly contribute to the true relationship. However, existing works mainly regard traffic forecasting as a deterministic problem, making it challenging to perform effective significance testing. To fill this gap, we propose to conduct Full Bayesian Significance Testing for Neural Networks in Traffic Forecasting, namely ST-nFBST. A Bayesian neural network is utilized to capture the complicated traffic relationships through an optimization function resolved in the context of aleatoric uncertainty and epistemic uncertainty. Thereupon, ST-nFBST can achieve the significance testing by means of a delicate grad-based evidence value, further capturing the inherent traffic schema for better spatiotemporal modeling. Extensive experiments are conducted on METR-LA and PEMS-BAY to verify the advantages of our method in terms of uncertainty analysis and significance testing, helping the interpretability and promotion of traffic forecasting.
Graph Contrastive Learning with Reinforcement Augmentation
Authors: Ziyang Liu; Chaokun Wang; Cheng Wu
Venue: IJCAI 2024 (main)

Abstract: Graph contrastive learning (GCL), designing contrastive objectives to learn embeddings from augmented graphs, has become a prevailing method for extracting embeddings from graphs in an unsupervised manner. As an important procedure in GCL, graph data augmentation (GDA) directly affects the model performance on downstream tasks. Currently, the GCL methods typically treat GDA as independent events, neglecting its continuity. In this paper, we regard the GDA in GCL as a Markov decision process and propose a novel graph reinforcement augmentation framework for GCL. Based on this framework, we design a Graph Advantage Actor-Critic (GA2C) model. We conduct extensive experiments to evaluate GA2C on unsupervised learning, transfer learning, and semi-supervised learning. The experimental results demonstrate the performance superiority of GA2C over the state-of-the-art GCL models. Furthermore, we verify that GA2C is more efficient than the other GCL methods with learnable GDA and provide two examples of chemical molecular graphs from ZINC-2M to demonstrate that GA2C generates meaningful augmented views, where the edge weights reflect the importance of chemical bonds in the molecule.
Heterogeneous Graph Transformer with Poly-Tokenization
Authors: Zhiyuan Lu; Yuan Fang; Cheng Yang; Chuan Shi
Venue: IJCAI 2024 (main)

Abstract: Graph neural networks have shown widespread success for learning on graphs, but they still face fundamental drawbacks, such as limited expressive power, over-smoothing, and over-squashing. Meanwhile, the transformer architecture offers a potential solution to these issues. However, existing graph transformers primarily cater to homogeneous graphs and are unable to model the intricate semantics of heterogeneous graphs. Moreover, unlike small molecular graphs where the entire graph can be considered as the receptive field in graph transformers, real-world heterogeneous graphs comprise a significantly larger number of nodes and cannot be entirely treated as such. Consequently, existing graph transformers struggle to capture the long-range dependencies in these complex heterogeneous graphs. To address these two limitations, we present Poly-tokenized Heterogeneous Graph Transformer (PHGT), a novel transformer-based heterogeneous graph model. In addition to traditional node tokens, PHGT introduces a novel poly-token design with two more token types: semantic tokens and global tokens. Semantic tokens encapsulate high-order heterogeneous semantic relationships, while global tokens capture semantic-aware long-range interactions. We validate the effectiveness of PHGT through extensive experiments on standardized heterogeneous graph benchmarks, demonstrating significant improvements over state-of-the-art heterogeneous graph representation learning models.