Jia Li

Denis Kocetkov, Raymond Li, Loubna Ben Allal et al. · huggingface

Large Language Models (LLMs) play an ever-increasing role in the field of Artificial Intelligence (AI)--not only for natural language processing but also for code understanding and generation. To stimulate open and responsible research on LLMs for code, we introduce The Stack, a 3.1 TB dataset consisting of permissively licensed source code in 30 programming languages. We describe how we collect the full dataset, construct a permissively licensed subset, present a data governance plan, discuss limitations, and show promising results on text2code benchmarks by training 350M-parameter decoders on different Python subsets. We find that (1) near-deduplicating the data significantly boosts performance across all experiments, and (2) it is possible to match previously reported HumanEval and MBPP performance using only permissively licensed data. We make the dataset available at https://hf.co/BigCode, provide a tool called "Am I in The Stack" (https://hf.co/spaces/bigcode/in-the-stack) for developers to search The Stack for copies of their code, and provide a process for code to be removed from the dataset by following the instructions at https://www.bigcode-project.org/docs/about/the-stack/.

Weiqi Zhang, Guanlue Li, Jianheng Tang et al.

Data imputation is a crucial task due to the widespread occurrence of missing data. Many methods adopt a two-step approach: initially crafting a preliminary imputation (the "draft") and then refining it to produce the final missing data imputation result, commonly referred to as "draft-then-refine". In our study, we examine this prevalent strategy through the lens of graph Dirichlet energy. We observe that a basic "draft" imputation tends to decrease the Dirichlet energy. Therefore, a subsequent "refine" step is necessary to restore the overall energy balance. Existing refinement techniques, such as the Graph Convolutional Network (GCN), often result in further energy reduction. To address this, we introduce a new framework, the Graph Laplacian Pyramid Network (GLPN). GLPN incorporates a U-shaped autoencoder and residual networks to capture both global and local details effectively. Through extensive experiments on multiple real-world datasets, GLPN consistently outperforms state-of-the-art methods across three different missing data mechanisms. The code is available at https://github.com/liguanlue/GLPN.

Jia Li, Yongfeng Huang, Heng Chang et al. · tsinghua

Node classification and graph classification are two graph learning problems that predict the class label of a node and the class label of a graph respectively. A node of a graph usually represents a real-world entity, e.g., a user in a social network, or a document in a document citation network. In this work, we consider a more challenging but practically useful setting, in which a node itself is a graph instance. This leads to a hierarchical graph perspective which arises in many domains such as social network, biological network and document collection. We study the node classification problem in the hierarchical graph where a 'node' is a graph instance. As labels are usually limited, we design a novel semi-supervised solution named SEAL-CI. SEAL-CI adopts an iterative framework that takes turns to update two modules, one working at the graph instance level and the other at the hierarchical graph level. To enforce a consistency among different levels of hierarchical graph, we propose the Hierarchical Graph Mutual Information (HGMI) and further present a way to compute HGMI with theoretical guarantee. We demonstrate the effectiveness of this hierarchical graph modeling and the proposed SEAL-CI method on text and social network data.

Yuhan Li, Zhixun Li, Peisong Wang et al.

Graph plays a significant role in representing and analyzing complex relationships in real-world applications such as citation networks, social networks, and biological data. Recently, Large Language Models (LLMs), which have achieved tremendous success in various domains, have also been leveraged in graph-related tasks to surpass traditional Graph Neural Networks (GNNs) based methods and yield state-of-the-art performance. In this survey, we first present a comprehensive review and analysis of existing methods that integrate LLMs with graphs. First of all, we propose a new taxonomy, which organizes existing methods into three categories based on the role (i.e., enhancer, predictor, and alignment component) played by LLMs in graph-related tasks. Then we systematically survey the representative methods along the three categories of the taxonomy. Finally, we discuss the remaining limitations of existing studies and highlight promising avenues for future research. The relevant papers are summarized and will be consistently updated at: https://github.com/yhLeeee/Awesome-LLMs-in-Graph-tasks.

Xiangguo Sun, Hong Cheng, Jia Li et al.

Recently, ''pre-training and fine-tuning'' has been adopted as a standard workflow for many graph tasks since it can take general graph knowledge to relieve the lack of graph annotations from each application. However, graph tasks with node level, edge level, and graph level are far diversified, making the pre-training pretext often incompatible with these multiple tasks. This gap may even cause a ''negative transfer'' to the specific application, leading to poor results. Inspired by the prompt learning in natural language processing (NLP), which has presented significant effectiveness in leveraging prior knowledge for various NLP tasks, we study the prompting topic for graphs with the motivation of filling the gap between pre-trained models and various graph tasks. In this paper, we propose a novel multi-task prompting method for graph models. Specifically, we first unify the format of graph prompts and language prompts with the prompt token, token structure, and inserting pattern. In this way, the prompting idea from NLP can be seamlessly introduced to the graph area. Then, to further narrow the gap between various graph tasks and state-of-the-art pre-training strategies, we further study the task space of various graph applications and reformulate downstream problems to the graph-level task. Afterward, we introduce meta-learning to efficiently learn a better initialization for the multi-task prompt of graphs so that our prompting framework can be more reliable and general for different tasks. We conduct extensive experiments, results from which demonstrate the superiority of our method.

Nuo Chen, Hongguang Li, Junqing He et al.

The conversational machine reading comprehension (CMRC) task aims to answer questions in conversations, which has been a hot research topic in recent years because of its wide applications. However, existing CMRC benchmarks in which each conversation is assigned a static passage are inconsistent with real scenarios. Thus, model's comprehension ability towards real scenarios are hard to evaluate reasonably. To this end, we propose the first Chinese CMRC benchmark Orca and further provide zero-shot/few-shot settings to evaluate model's generalization ability towards diverse domains. We collect 831 hot-topic driven conversations with 4,742 turns in total. Each turn of a conversation is assigned with a response-related passage, aiming to evaluate model's comprehension ability more reasonably. The topics of conversations are collected from social media platform and cover 33 domains, trying to be consistent with real scenarios. Importantly, answers in Orca are all well-annotated natural responses rather than the specific spans or short phrase in previous datasets. Besides, we implement three strong baselines to tackle the challenge in Orca. The results indicate the great challenge of our CMRC benchmark. Our datatset and checkpoints are available at https://github.com/nuochenpku/Orca.

Amit Roy, Juan Shu, Jia Li et al.

Graph Anomaly Detection (GAD) is a technique used to identify abnormal nodes within graphs, finding applications in network security, fraud detection, social media spam detection, and various other domains. A common method for GAD is Graph Auto-Encoders (GAEs), which encode graph data into node representations and identify anomalies by assessing the reconstruction quality of the graphs based on these representations. However, existing GAE models are primarily optimized for direct link reconstruction, resulting in nodes connected in the graph being clustered in the latent space. As a result, they excel at detecting cluster-type structural anomalies but struggle with more complex structural anomalies that do not conform to clusters. To address this limitation, we propose a novel solution called GAD-NR, a new variant of GAE that incorporates neighborhood reconstruction for graph anomaly detection. GAD-NR aims to reconstruct the entire neighborhood of a node, encompassing the local structure, self-attributes, and neighbor attributes, based on the corresponding node representation. By comparing the neighborhood reconstruction loss between anomalous nodes and normal nodes, GAD-NR can effectively detect any anomalies. Extensive experimentation conducted on six real-world datasets validates the effectiveness of GAD-NR, showcasing significant improvements (by up to 30% in AUC) over state-of-the-art competitors. The source code for GAD-NR is openly available. Importantly, the comparative analysis reveals that the existing methods perform well only in detecting one or two types of anomalies out of the three types studied. In contrast, GAD-NR excels at detecting all three types of anomalies across the datasets, demonstrating its comprehensive anomaly detection capabilities.

Heng Chang, Jie Cai, Jia Li · tsinghua

Graph Neural Networks (GNNs) have demonstrated great success in Knowledge Graph Completion (KGC) by modeling how entities and relations interact in recent years. However, most of them are designed to learn from the observed graph structure, which appears to have imbalanced relation distribution during the training stage. Motivated by the causal relationship among the entities on a knowledge graph, we explore this defect through a counterfactual question: "would the relation still exist if the neighborhood of entities became different from observation?". With a carefully designed instantiation of a causal model on the knowledge graph, we generate the counterfactual relations to answer the question by regarding the representations of entity pair given relation as context, structural information of relation-aware neighborhood as treatment, and validity of the composed triplet as the outcome. Furthermore, we incorporate the created counterfactual relations with the GNN-based framework on KGs to augment their learning of entity pair representations from both the observed and counterfactual relations. Experiments on benchmarks show that our proposed method outperforms existing methods on the task of KGC, achieving new state-of-the-art results. Moreover, we demonstrate that the proposed counterfactual relations-based augmentation also enhances the interpretability of the GNN-based framework through the path interpretations of predictions.

Jiawen Zhang, Shun Zheng, Wei Cao et al.

Irregularly sampled multivariate time series are ubiquitous in various fields, particularly in healthcare, and exhibit two key characteristics: intra-series irregularity and inter-series discrepancy. Intra-series irregularity refers to the fact that time-series signals are often recorded at irregular intervals, while inter-series discrepancy refers to the significant variability in sampling rates among diverse series. However, recent advances in irregular time series have primarily focused on addressing intra-series irregularity, overlooking the issue of inter-series discrepancy. To bridge this gap, we present Warpformer, a novel approach that fully considers these two characteristics. In a nutshell, Warpformer has several crucial designs, including a specific input representation that explicitly characterizes both intra-series irregularity and inter-series discrepancy, a warping module that adaptively unifies irregular time series in a given scale, and a customized attention module for representation learning. Additionally, we stack multiple warping and attention modules to learn at different scales, producing multi-scale representations that balance coarse-grained and fine-grained signals for downstream tasks. We conduct extensive experiments on widely used datasets and a new large-scale benchmark built from clinical databases. The results demonstrate the superiority of Warpformer over existing state-of-the-art approaches.

Jianheng Tang, Weiqi Zhang, Jiajin Li et al.

Graph alignment, which aims at identifying corresponding entities across multiple networks, has been widely applied in various domains. As the graphs to be aligned are usually constructed from different sources, the inconsistency issues of structures and features between two graphs are ubiquitous in real-world applications. Most existing methods follow the ``embed-then-cross-compare'' paradigm, which computes node embeddings in each graph and then processes node correspondences based on cross-graph embedding comparison. However, we find these methods are unstable and sub-optimal when structure or feature inconsistency appears. To this end, we propose SLOTAlign, an unsupervised graph alignment framework that jointly performs Structure Learning and Optimal Transport Alignment. We convert graph alignment to an optimal transport problem between two intra-graph matrices without the requirement of cross-graph comparison. We further incorporate multi-view structure learning to enhance graph representation power and reduce the effect of structure and feature inconsistency inherited across graphs. Moreover, an alternating scheme based algorithm has been developed to address the joint optimization problem in SLOTAlign, and the provable convergence result is also established. Finally, we conduct extensive experiments on six unsupervised graph alignment datasets and the DBP15K knowledge graph (KG) alignment benchmark dataset. The proposed SLOTAlign shows superior performance and strongest robustness over seven unsupervised graph alignment methods and five specialized KG alignment methods.

Ziqi Gao, Yifan Niu, Jiashun Cheng et al.

Graph neural networks (GNNs) are popular weapons for modeling relational data. Existing GNNs are not specified for attribute-incomplete graphs, making missing attribute imputation a burning issue. Until recently, many works notice that GNNs are coupled with spectral concentration, which means the spectrum obtained by GNNs concentrates on a local part in spectral domain, e.g., low-frequency due to oversmoothing issue. As a consequence, GNNs may be seriously flawed for reconstructing graph attributes as graph spectral concentration tends to cause a low imputation precision. In this work, we present a regularized graph autoencoder for graph attribute imputation, named MEGAE, which aims at mitigating spectral concentration problem by maximizing the graph spectral entropy. Notably, we first present the method for estimating graph spectral entropy without the eigen-decomposition of Laplacian matrix and provide the theoretical upper error bound. A maximum entropy regularization then acts in the latent space, which directly increases the graph spectral entropy. Extensive experiments show that MEGAE outperforms all the other state-of-the-art imputation methods on a variety of benchmark datasets.

Jiashun Cheng, Man Li, Jia Li et al.

Graph self-supervised learning (SSL) has been vastly employed to learn representations from unlabeled graphs. Existing methods can be roughly divided into predictive learning and contrastive learning, where the latter one attracts more research attention with better empirical performance. We argue that, however, predictive models weaponed with powerful decoder could achieve comparable or even better representation power than contrastive models. In this work, we propose a Wiener Graph Deconvolutional Network (WGDN), an augmentation-adaptive decoder empowered by graph wiener filter to perform information reconstruction. Theoretical analysis proves the superior reconstruction ability of graph wiener filter. Extensive experimental results on various datasets demonstrate the effectiveness of our approach.

Weiqi Zhang, Jianfeng Zhang, Jia Li et al.

In this work, we focus on robust time series representation learning. Our assumption is that real-world time series is noisy and complementary information from different views of the same time series plays an important role while analyzing noisy input. Based on this, we create two views for the input time series through two different encoders. We conduct co-training based contrastive learning iteratively to learn the encoders. Our experiments demonstrate that this co-training approach leads to a significant improvement in performance. Especially, by leveraging the complementary information from different views, our proposed TS-CoT method can mitigate the impact of data noise and corruption. Empirical evaluations on four time series benchmarks in unsupervised and semi-supervised settings reveal that TS-CoT outperforms existing methods. Furthermore, the representations learned by TS-CoT can transfer well to downstream tasks through fine-tuning.

Bo Guo, Sijia Wen, Yifan Zhao et al. · pku

Recent advances in surface reconstruction for 3D Gaussian Splatting (3DGS) have enabled remarkable geometric accuracy. However, their performance degrades in photometrically ambiguous regions such as reflective and textureless surfaces, where unreliable cues disrupt photometric consistency and hinder accurate geometry estimation. Reflected light is often partially polarized in a manner that reveals surface orientation, making polarization an optic complement to photometric cues in resolving such ambiguities. Therefore, we propose PolarGS, an optics-aware extension of RGB-based 3DGS that leverages polarization as an optical prior to resolve photometric ambiguities and enhance reconstruction accuracy. Specifically, we introduce two complementary modules: a polarization-guided photometric correction strategy, which ensures photometric consistency by identifying reflective regions via the Degree of Linear Polarization (DoLP) and refining reflective Gaussians with Color Refinement Maps; and a polarization-enhanced Gaussian densification mechanism for textureless area geometry recovery, which integrates both Angle and Degree of Linear Polarization (A/DoLP) into a PatchMatch-based depth completion process. This enables the back-projection and fusion of new Gaussians, leading to more complete reconstruction. PolarGS is framework-agnostic and achieves superior geometric accuracy compared to state-of-the-art methods.

Yu Zhang, Jia Li, Jie Ding et al.

Learning and analysis of network robustness, including controllability robustness and connectivity robustness, is critical for various networked systems against attacks. Traditionally, network robustness is determined by attack simulations, which is very time-consuming and even incapable for large-scale networks. Network Robustness Learning, which is dedicated to learning network robustness with high precision and high speed, provides a powerful tool to analyze network robustness by replacing simulations. In this paper, a novel versatile and unified robustness learning approach via graph transformer (NRL-GT) is proposed, which accomplishes the task of controllability robustness learning and connectivity robustness learning from multiple aspects including robustness curve learning, overall robustness learning, and synthetic network classification. Numerous experiments show that: 1) NRL-GT is a unified learning framework for controllability robustness and connectivity robustness, demonstrating a strong generalization ability to ensure high precision when training and test sets are distributed differently; 2) Compared to the cutting-edge methods, NRL-GT can simultaneously perform network robustness learning from multiple aspects and obtains superior results in less time. NRL-GT is also able to deal with complex networks of different size with low learning error and high efficiency; 3) It is worth mentioning that the backbone of NRL-GT can serve as a transferable feature learning module for complex networks of different size and different downstream tasks.

Jiexia Ye, Yongzi Yu, Weiqi Zhang et al.

Time series data are ubiquitous across diverse real-world applications, making time series analysis critically important. Traditional approaches are largely task-specific, offering limited functionality and poor transferability. In recent years, foundation models have revolutionized NLP and CV with their remarkable cross-task transferability, zero-/few-shot learning capabilities, and multimodal integration capacity. This success has motivated increasing efforts to explore foundation models for addressing time series modeling challenges. Although some tutorials and surveys were published in the early stages of this field, the rapid pace of recent developments necessitates a more comprehensive and in-depth synthesis to cover the latest advances. Our survey aims to fill this gap by introducing a modality-aware, challenge-oriented perspective, which reveals how foundation models pre-trained on different modalities face distinct hurdles when adapted to time series tasks. Building on this perspective, we propose a taxonomy of existing works organized by pre-training modality (time series, language, and vision), analyze modality-specific challenges and categorize corresponding solutions, discussing their advantages and limitations. Beyond this, we review real-world applications to illustrate domain-specific advancements, provide open-source codes, and conclude with potential future research directions in this rapidly evolving field.

Ruifeng Tan, Weixiang Hong, Jiayue Tang et al.

Battery Life Prediction (BLP), which relies on time series data produced by battery degradation tests, is crucial for battery utilization, optimization, and production. Despite impressive advancements, this research area faces three key challenges. Firstly, the limited size of existing datasets impedes insights into modern battery life data. Secondly, most datasets are restricted to small-capacity lithium-ion batteries tested under a narrow range of diversity in labs, raising concerns about the generalizability of findings. Thirdly, inconsistent and limited benchmarks across studies obscure the effectiveness of baselines and leave it unclear if models popular in other time series fields are effective for BLP. To address these challenges, we propose BatteryLife, a comprehensive dataset and benchmark for BLP. BatteryLife integrates 16 datasets, offering a 2.5 times sample size compared to the previous largest dataset, and provides the most diverse battery life resource with batteries from 8 formats, 59 chemical systems, 9 operating temperatures, and 421 charge/discharge protocols, including both laboratory and industrial tests. Notably, BatteryLife is the first to release battery life datasets of zinc-ion batteries, sodium-ion batteries, and industry-tested large-capacity lithium-ion batteries. With the comprehensive dataset, we revisit the effectiveness of baselines popular in this and other time series fields. Furthermore, we propose CyclePatch, a plug-in technique that can be employed in various neural networks. Extensive benchmarking of 18 methods reveals that models popular in other time series fields can be unsuitable for BLP, and CyclePatch consistently improves model performance establishing state-of-the-art benchmarks. Moreover, BatteryLife evaluates model performance across aging conditions and domains. BatteryLife is available at https://github.com/Ruifeng-Tan/BatteryLife.

Chenyi Zi, Haihong Zhao, Xiangguo Sun et al.

Artificial general intelligence on graphs has shown significant advancements across various applications, yet the traditional 'Pre-train & Fine-tune' paradigm faces inefficiencies and negative transfer issues, particularly in complex and few-shot settings. Graph prompt learning emerges as a promising alternative, leveraging lightweight prompts to manipulate data and fill the task gap by reformulating downstream tasks to the pretext. However, several critical challenges still remain: how to unify diverse graph prompt models, how to evaluate the quality of graph prompts, and to improve their usability for practical comparisons and selection. In response to these challenges, we introduce the first comprehensive benchmark for graph prompt learning. Our benchmark integrates SIX pre-training methods and FIVE state-of-the-art graph prompt techniques, evaluated across FIFTEEN diverse datasets to assess performance, flexibility, and efficiency. We also present 'ProG', an easy-to-use open-source library that streamlines the execution of various graph prompt models, facilitating objective evaluations. Additionally, we propose a unified framework that categorizes existing graph prompt methods into two main approaches: prompts as graphs and prompts as tokens. This framework enhances the applicability and comparison of graph prompt techniques. The code is available at: https://github.com/sheldonresearch/ProG.

Haihong Zhao, Aochuan Chen, Xiangguo Sun et al.

Large Language Models (LLMs) have revolutionized the fields of computer vision (CV) and natural language processing (NLP). One of the most notable advancements of LLMs is that a single model is trained on vast and diverse datasets spanning multiple domains -- a paradigm we term `All in One'. This methodology empowers LLMs with super generalization capabilities, facilitating an encompassing comprehension of varied data distributions. Leveraging these capabilities, a single LLM demonstrates remarkable versatility across a variety of domains -- a paradigm we term `One for All'. However, applying this idea to the graph field remains a formidable challenge, with cross-domain pretraining often resulting in negative transfer. This issue is particularly important in few-shot learning scenarios, where the paucity of training data necessitates the incorporation of external knowledge sources. In response to this challenge, we propose a novel approach called Graph COordinators for PrEtraining (GCOPE), that harnesses the underlying commonalities across diverse graph datasets to enhance few-shot learning. Our novel methodology involves a unification framework that amalgamates disparate graph datasets during the pretraining phase to distill and transfer meaningful knowledge to target tasks. Extensive experiments across multiple graph datasets demonstrate the superior efficacy of our approach. By successfully leveraging the synergistic potential of multiple graph datasets for pretraining, our work stands as a pioneering contribution to the realm of graph foundational model.

Heng Chang, Jiangnan Ye, Alejo Lopez Avila et al.

Graph Neural Networks (GNNs) have achieved great success in Knowledge Graph Completion (KGC) by modelling how entities and relations interact in recent years. However, the explanation of the predicted facts has not caught the necessary attention. Proper explanations for the results of GNN-based KGC models increase model transparency and help researchers develop more reliable models. Existing practices for explaining KGC tasks rely on instance/subgraph-based approaches, while in some scenarios, paths can provide more user-friendly and interpretable explanations. Nonetheless, the methods for generating path-based explanations for KGs have not been well-explored. To address this gap, we propose Power-Link, the first path-based KGC explainer that explores GNN-based models. We design a novel simplified graph-powering technique, which enables the generation of path-based explanations with a fully parallelisable and memory-efficient training scheme. We further introduce three new metrics for quantitative evaluation of the explanations, together with a qualitative human evaluation. Extensive experiments demonstrate that Power-Link outperforms the SOTA baselines in interpretability, efficiency, and scalability.

Miao Peng, Nuo Chen, Zongrui Suo et al.

Despite significant advancements in Large Language Models (LLMs), developing advanced reasoning capabilities in LLMs remains a key challenge. Process Reward Models (PRMs) have demonstrated exceptional promise in enhancing reasoning by providing step-wise feedback, particularly in the context of mathematical reasoning. However, their application to broader reasoning domains remains understudied, largely due to the high costs associated with manually creating step-level supervision. In this work, we explore the potential of PRMs in graph reasoning problems - a domain that demands sophisticated multi-step reasoning and offers opportunities for automated step-level data generation using established graph algorithms. We introduce GraphSILO, the largest dataset for graph reasoning problems with fine-grained step-wise labels, built using automated Task-oriented Trajectories and Monte Carlo Tree Search (MCTS) to generate detailed reasoning steps with step-wise labels. Building upon this dataset, we train GraphPRM, the first PRM designed for graph reasoning problems, and evaluate its effectiveness in two key settings: inference-time scaling and reinforcement learning via Direct Preference Optimization (DPO). Experimental results show that GraphPRM significantly improves LLM performance across 13 graph reasoning tasks, delivering a 9% gain for Qwen2.5-7B and demonstrating transferability to new graph reasoning datasets and new reasoning domains like mathematical problem-solving. Notably, GraphPRM enhances LLM performance on GSM8K and Math500, underscoring the cross-domain applicability of graph-based reasoning rewards. Our findings highlight the potential of PRMs in advancing reasoning across diverse domains, paving the way for more versatile and effective LLMs.

Botao Wang, Jia Li, Heng Chang et al.

In this work, we discover that causal inference provides a promising approach to capture heterophilic message-passing in Graph Neural Network (GNN). By leveraging cause-effect analysis, we can discern heterophilic edges based on asymmetric node dependency. The learned causal structure offers more accurate relationships among nodes. To reduce the computational complexity, we introduce intervention-based causal inference in graph learning. We first simplify causal analysis on graphs by formulating it as a structural learning model and define the optimization problem within the Bayesian scheme. We then present an analysis of decomposing the optimization target into a consistency penalty and a structure modification based on cause-effect relations. We then estimate this target by conditional entropy and present insights into how conditional entropy quantifies the heterophily. Accordingly, we propose CausalMP, a causal message-passing discovery network for heterophilic graph learning, that iteratively learns the explicit causal structure of input graphs. We conduct extensive experiments in both heterophilic and homophilic graph settings. The result demonstrates that the our model achieves superior link prediction performance. Training on causal structure can also enhance node representation in classification task across different base models.

Xiangguo Sun, Hong Cheng, Jia Li et al.

This paper is an extended abstract of our original work published in KDD23, where we won the best research paper award (Xiangguo Sun, Hong Cheng, Jia Li, Bo Liu, and Jihong Guan. All in one: Multi-task prompting for graph neural networks. KDD 23) The paper introduces a novel approach to bridging the gap between pre-trained graph models and the diverse tasks they're applied to, inspired by the success of prompt learning in NLP. Recognizing the challenge of aligning pre-trained models with varied graph tasks (node level, edge level, and graph level), which can lead to negative transfer and poor performance, we propose a multi-task prompting method for graphs. This method involves unifying graph and language prompt formats, enabling NLP's prompting strategies to be adapted for graph tasks. By analyzing the task space of graph applications, we reformulate problems to fit graph-level tasks and apply meta-learning to improve prompt initialization for multiple tasks. Experiments show our method's effectiveness in enhancing model performance across different graph tasks. Beyond the original work, in this extended abstract, we further discuss the graph prompt from a bigger picture and provide some of the latest work toward this area.

Guanlue Li, Chenran Jiang, Ziqi Gao et al.

Effective generation of molecular structures, or new chemical entities, that bind to target proteins is crucial for lead identification and optimization in drug discovery. Despite advancements in atom- and motif-wise deep learning models for 3D molecular generation, current methods often struggle with validity and reliability. To address these issues, we develop the Atom-Motif Consistency Diffusion Model (AMDiff), utilizing a joint-training paradigm for multi-view learning. This model features a hierarchical diffusion architecture that integrates both atom- and motif-level views of molecules, allowing for comprehensive exploration of complementary information. By leveraging classifier-free guidance and incorporating binding site features as conditional inputs, AMDiff ensures robust molecule generation across diverse targets. Compared to existing approaches, AMDiff exhibits superior validity and novelty in generating molecules tailored to fit various protein pockets. Case studies targeting protein kinases, including Anaplastic Lymphoma Kinase (ALK) and Cyclin-dependent kinase 4 (CDK4), demonstrate the model's capability in structure-based de novo drug design. Overall, AMDiff bridges the gap between atom-view and motif-view drug discovery and speeds up the process of target-aware molecular generation.

Junhao He, Jiaxu Wang, Jia Li et al.

Reconstructing Dynamic 3D Gaussian Splatting (3DGS) from low-framerate RGB videos is challenging. This is because large inter-frame motions will increase the uncertainty of the solution space. For example, one pixel in the first frame might have more choices to reach the corresponding pixel in the second frame. Event cameras can asynchronously capture rapid visual changes and are robust to motion blur, but they do not provide color information. Intuitively, the event stream can provide deterministic constraints for the inter-frame large motion by the event trajectories. Hence, combining low-temporal-resolution images with high-framerate event streams can address this challenge. However, it is challenging to jointly optimize Dynamic 3DGS using both RGB and event modalities due to the significant discrepancy between these two data modalities. This paper introduces a novel framework that jointly optimizes dynamic 3DGS from the two modalities. The key idea is to adopt event motion priors to guide the optimization of the deformation fields. First, we extract the motion priors encoded in event streams by using the proposed LoCM unsupervised fine-tuning framework to adapt an event flow estimator to a certain unseen scene. Then, we present the geometry-aware data association method to build the event-Gaussian motion correspondence, which is the primary foundation of the pipeline, accompanied by two useful strategies, namely motion decomposition and inter-frame pseudo-label. Extensive experiments show that our method outperforms existing image and event-based approaches across synthetic and real scenes and prove that our method can effectively optimize dynamic 3DGS with the help of event data.

Aochuan Chen, Yifan Niu, Ziqi Gao et al.

The LifeTime Value (LTV) prediction, which endeavors to forecast the cumulative purchase contribution of a user to a particular item, remains a vital challenge that advertisers are keen to resolve. A precise LTV prediction system enhances the alignment of user interests with meticulously designed advertisements, thereby generating substantial profits for advertisers. Nonetheless, this issue is complicated by the paucity of data typically observed in real-world advertising scenarios. The purchase rate among registered users is often as critically low as 0.1%, resulting in a dataset where the majority of users make only several purchases. Consequently, there is insufficient supervisory signal for effectively training the LTV prediction model. An additional challenge emerges from the interdependencies among tasks with high correlation. It is a common practice to estimate a user's contribution to a game over a specified temporal interval. Varying the lengths of these intervals corresponds to distinct predictive tasks, which are highly correlated. For instance, predictions over a 7-day period are heavily reliant on forecasts made over a 3-day period, where exceptional cases can adversely affect the accuracy of both tasks. In order to comprehensively address the aforementioned challenges, we introduce an innovative framework denoted as Graph-Represented Pareto-Optimal LifeTime Value prediction (GRePO-LTV). Graph representation learning is initially employed to address the issue of data scarcity. Subsequently, Pareto-Optimization is utilized to manage the interdependence of prediction tasks.

Jiexia Ye, Weiqi Zhang, Ziyue Li et al.

Accurate medical time series (MedTS) classification is essential for effective clinical diagnosis, yet remains challenging due to complex multi-channel temporal dependencies, information redundancy, and label scarcity. While transformer-based models have shown promise in time series analysis, most are designed for forecasting tasks and fail to fully exploit the unique characteristics of MedTS. In this paper, we introduce MedSpaformer, a transformer-based framework tailored for MedTS classification. It incorporates a sparse token-based dual-attention mechanism that enables global context modeling and token sparsification, allowing dynamic feature refinement by focusing on informative tokens while reducing redundancy. This mechanism is integrated into a multi-granularity cross-channel encoding scheme to capture intra- and inter-granularity temporal dependencies and inter-channel correlations, enabling progressive refinement of task-relevant patterns in medical signals. The sparsification design allows our model to flexibly accommodate inputs with variable lengths and channel dimensions. We also introduce an adaptive label encoder to extract label semantics and address cross-dataset label space misalignment. Together, these components enhance the model's transferability across heterogeneous medical datasets, which helps alleviate the challenge of label scarcity. Our model outperforms 13 baselines across 7 medical datasets under supervised learning. It also excels in few-shot learning and demonstrates zero-shot capability in both in-domain and cross-domain diagnostics. These results highlight MedSpaformer's robustness and its potential as a unified solution for MedTS classification across diverse settings.

Zhengwei Tao, Zhi Jin, Xiaoying Bai et al.

Events serve as fundamental units of occurrence within various contexts. The processing of event semantics in textual information forms the basis of numerous natural language processing (NLP) applications. Recent studies have begun leveraging large language models (LLMs) to address event semantic processing. However, the extent that LLMs can effectively tackle these challenges remains uncertain. Furthermore, the lack of a comprehensive evaluation framework for event semantic processing poses a significant challenge in evaluating these capabilities. In this paper, we propose an overarching framework for event semantic processing, encompassing understanding, reasoning, and prediction, along with their fine-grained aspects. To comprehensively evaluate the event semantic processing abilities of models, we introduce a novel benchmark called EVEVAL. We collect 8 datasets that cover all aspects of event semantic processing. Extensive experiments are conducted on EVEVAL, leading to several noteworthy findings based on the obtained results.

Jia Li, Jiajin Li, Yang Liu et al.

In this paper, we consider an inverse problem in graph learning domain -- ``given the graph representations smoothed by Graph Convolutional Network (GCN), how can we reconstruct the input graph signal?" We propose Graph Deconvolutional Network (GDN) and motivate the design of GDN via a combination of inverse filters in spectral domain and de-noising layers in wavelet domain, as the inverse operation results in a high frequency amplifier and may amplify the noise. We demonstrate the effectiveness of the proposed method on several tasks including graph feature imputation and graph structure generation.

Jia Li, Haoyu Yang, Xiaowei Jia et al.

Electronic Health Records (EHR) data analysis plays a crucial role in healthcare system quality. Because of its highly complex underlying causality and limited observable nature, causal inference on EHR is quite challenging. Deep Learning (DL) achieved great success among the advanced machine learning methodologies. Nevertheless, it is still obstructed by the inappropriately assumed causal conditions. This work proposed a novel method to quantify clinically well-defined causal effects as a generalized estimation vector that is simply utilizable for causal models. We incorporated it into DL models to achieve better predictive performance and result interpretation. Furthermore, we also proved the existence of causal information blink spots that regular DL models cannot reach.