Ruifeng Yuan, Chaohao Yuan, David Dai, Yu Rong, Hong Cheng, Hou Pong Chan, Chenghao Xiao. Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2026.

Graph Transformers (GTs) have emerged as a promising graph learning tool, leveraging their all-pair connected property to effectively capture global information. To address the over-smoothing problem in deep GNNs, global attention was initially introduced, eliminating the necessity for using deep GNNs. However, through empirical and theoretical analysis, we verify that the introduced global attention exhibits severe over-smoothing, causing node representations to become indistinguishable due to its inherent low-pass filtering. This effect is even stronger than that observed in GNNs. To mitigate this, we propose PageRank Transformer (ParaFormer), which features a PageRank-enhanced attention module designed to mimic the behavior of deep Transformers. We theoretically and empirically demonstrate that ParaFormer mitigates over-smoothing by functioning as an adaptive-pass filter. Experiments show that ParaFormer achieves consistent performance improvements across both node classification and graph classification tasks on 11 datasets ranging from thousands to millions of nodes, validating its efficacy. The supplementary material, including code and appendix, can be found in https://github.com/chaohaoyuan/ParaFormer.

Guizhen Chen, Weiwen Xu, Hao Zhang, Hou Pong Chan, Chaoqun Liu, Lidong Bing, Deli Zhao, Anh Tuan Luu, Yu Rong. Proceedings of the 63rd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2025.

While understanding the knowledge boundaries of LLMs is crucial to prevent hallucination, research on the knowledge boundaries of LLMs has predominantly focused on English. In this work, we present the first study to analyze how LLMs recognize knowledge boundaries across different languages by probing their internal representations when processing known and unknown questions in multiple languages. Our empirical studies reveal three key findings: 1) LLMs' perceptions of knowledge boundaries are encoded in the middle to middle-upper layers across different languages. 2) Language differences in knowledge boundary perception follow a linear structure, which motivates our proposal of a training-free alignment method that effectively transfers knowledge boundary perception ability across languages, thereby helping reduce hallucination risk in low-resource languages; 3) Fine-tuning on bilingual question pair translation further enhances LLMs' recognition of knowledge boundaries across languages. Given the absence of standard testbeds for cross-lingual knowledge boundary analysis, we construct a multilingual evaluation suite comprising three representative types of knowledge boundary data. Our code and datasets are publicly available at https://github.com/DAMO-NLP-SG/ LLM-Multilingual-Knowledge-Boundaries.

This paper introduces a Dual Evaluation Framework to comprehensively assess the multilingual capabilities of LLMs.By decomposing the evaluation along the dimensions of linguistic medium and cultural context, this framework enables a nuanced analysis of LLMs' ability to process questions within both native and cross-cultural contexts cross-lingually.Extensive evaluations are conducted on a wide range of models, revealing a notable "Cultural-Linguistic Synergy" phenomenon, where models exhibit better performance when questions are culturally aligned with the language.This phenomenon is further explored through interpretability probing, which shows that a higher proportion of specific neurons are activated in a language's cultural context.This activation proportion could serve as a potential indicator for evaluating multilingual performance during model training.Our findings challenge the prevailing notion that LLMs, primarily trained on English data, perform uniformly across languages and highlight the necessity of culturally and linguistically model evaluations.Our code can be found at https://yingjiahao14. github.io/Dual-Evaluation/.

Personality prediction from social media posts is a critical task that implies diverse applications in psychology and sociology. The Myers-Briggs Type Indicator (MBTI), a popular personality inventory, has been traditionally predicted by machine learning (ML) and deep learning (DL) techniques. Recently, the success of Large Language Models (LLMs) has revealed their huge potential in understanding and inferring personality traits from social media content. However, directly exploiting LLMs for MBTI prediction faces two key challenges: the hallucination problem inherent in LLMs and the naturally imbalanced distribution of MBTI types in the population. In this paper, we propose PostToPersonality (P2P), a novel LLM- based framework for MBTI prediction from social media posts of individuals. Specifically, P2P leverages Retrieval-Augmented Generation with in-context learning to mitigate hallucination in LLMs. Furthermore, we fine-tune a pre-trained LLM to improve model specification in MBTI understanding with synthetic minority oversampling, which balances the class imbalance by generating synthetic samples. Experiments conducted on a real-world social media dataset demonstrate that P2P achieves state-of-the-art performance compared with 10 ML/DL baselines.

Yu Sun, Xingyu Qian, Weiwen Xu, Hao Zhang, Chenghao Xiao, Long Li, Deli Zhao, Wenbing Huang, Tingyang Xu, Qifeng Bai, Yu Rong. Proceedings of the 2025 Conference on Empirical Methods in Natural Language Processing. 2025.

Cold-start rating prediction is a fundamental problem in recommender systems that has been extensively studied. Many methods have been proposed that exploit explicit relations among existing data, such as collaborative filtering, social recommendations and heterogeneous information network, to alleviate the data insufficiency issue for cold-start users and items. However, the explicit relations constructed based on data between different entities may be unreliable and irrelevant, which limits the performance ceiling of a specific recommendation task. Motivated by this, in this paper, we propose a flexible framework dubbed heterogeneous interaction rating network (HIRE). HIRE does not solely rely on pre-defined interaction patterns or a manually constructed heterogeneous information network. Instead, we devise a Heterogeneous Interaction Module (HIM) to jointly model heterogeneous interactions and directly infer the important interactions via the observed data. In the experiments, we evaluate our framework under 3 cold-start settings on 3 real-world datasets. The experimental results show that HIRE outperforms other baselines by a large margin. Furthermore, we visualize the inferred interactions of HIRE to reveal the intuition behind our framework.

Establishing the relationship between 3D structures and the energy states of molecular systems has proven to be a promising approach for learning 3D molecular representations. However, existing methods are limited to modeling the molecular energy states from classical mechanics. This limitation results in a significant oversight of quantum mechanical effects, such as quantized (discrete) energy level structures, which offer a more accurate estimation of molecular energy and can be experimentally measured through energy spectra. In this paper, we propose to utilize the energy spectra to enhance the pre-training of 3D molecular representations (MolSpectra), thereby infusing the knowledge of quantum mechanics into the molecular representations. Specifically, we propose SpecFormer, a multi-spectrum encoder for encoding molecular spectra via masked patch reconstruction. By further aligning outputs from the 3D encoder and spectrum encoder using a contrastive objective, we enhance the 3D encoder's understanding of molecules. Evaluations on public benchmarks reveal that our pre-trained representations surpass existing methods in predicting molecular properties and modeling dynamics.

Accurate Subseasonal-to-Seasonal (S2S) climate forecasting is pivotal for decision-making including agriculture planning and disaster preparedness but is known to be challenging due to its chaotic nature. Although recent data-driven models have shown promising results, their performance is limited by inadequate consideration of geometric inductive biases. Usually, they treat the spherical weather data as planar images, resulting in an inaccurate representation of locations and spatial relations. In this work, we propose the geometric-inspired Circular Transformer (CirT) to model the cyclic characteristic of the graticule, consisting of two key designs: (1) Decomposing the weather data by latitude into circular patches that serve as input tokens to the Transformer; (2) Leveraging Fourier transform in self-attention to capture the global information and model the spatial periodicity. Extensive experiments on the Earth Reanalysis 5 (ERA5) reanalysis dataset demonstrate our model yields a significant improvement over the advanced data-driven models, including PanguWeather and GraphCast, as well as skillful ECMWF systems. Additionally, we empirically show the effectiveness of our model designs and high-quality prediction over spatial and temporal dimensions.

Exploring chemical space to find novel molecules that simultaneously satisfy multiple properties is crucial in drug discovery. However, existing methods often struggle with trading off multiple properties due to the conflicting or correlated nature of chemical properties. To tackle this issue, we introduce InversionGNN framework, an effective yet sample-efficient dual-path graph neural network (GNN) for multi-objective drug discovery. In the direct prediction path of InversionGNN, we train the model for multi-property prediction to acquire knowledge of the optimal combination of functional groups. Then the learned chemical knowledge helps the inversion generation path to generate molecules with required properties. In order to decode the complex knowledge of multiple properties in the inversion path, we propose a gradient-based Pareto search method to balance conflicting properties and generate Pareto optimal molecules. Additionally, InversionGNN is able to search the full Pareto front approximately in discrete chemical space. Comprehensive experimental evaluations show that InversionGNN is both effective and sample-efficient in various discrete multi-objective settings including drug discovery.

Molecule-and-text cross-modal representation learning has emerged as a promising direction for enhancing the quality of molecular representation, thereby improving performance in various scientific fields. However, most approaches employ a global alignment approach to learn the knowledge from different modalities that may fail to capture fine-grained information, such as molecule-and-text fragments and stereoisomeric nuances, which is crucial for downstream tasks. Furthermore, it is incapable of modeling such information using a similar global alignment strategy due to the lack of annotations about the fine-grained fragments in the existing dataset. In this paper, we propose Atomas, a hierarchical molecular representation learning framework that jointly learns representations from SMILES strings and text. We design a Hierarchical Adaptive Alignment model to automatically learn the fine-grained fragment correspondence between two modalities and align these representations at three semantic levels. Atomas's end-to-end training framework supports understanding and generating molecules, enabling a wider range of downstream tasks. Atomas achieves superior performance across 12 tasks on 11 datasets, outperforming 11 baseline models thus highlighting the effectiveness and versatility of our method. Scaling experiments further demonstrate Atomas’s robustness and scalability. Moreover, visualization and qualitative analysis, validated by human experts, confirm the chemical relevance of our approach. Codes are released on ~\url{https://github.com/yikunpku/Atomas}.

Circuit discovery has recently attracted attention as a potential research direction to explain the non-trivial behaviors of language models. It aims to find the computational subgraphs, also known as circuits, within the model that are responsible for solving specific tasks. However, most existing studies overlook the holistic nature of these circuits and require designing specific corrupted activations for different tasks, which is inaccurate and inefficient. In this work, we propose an end-to-end approach based on the principle of Information Bottleneck, called IBCircuit, to holistically identify informative circuits. In contrast to traditional causal interventions, IBCircuit is an optimization framework for holistic circuit discovery and can be applied to any given task without tediously corrupted activation design. In both the Indirect Object Identification (IOI) and Greater-Than tasks, IBCircuit identifies more faithful and minimal circuits in terms of critical node components and edge components compared to recent related work.

Accurately predicting 3D structures and dynamics of physical systems is crucial in scientific applications. Existing approaches that rely on geometric Graph Neural Networks (GNNs) effectively enforce $\mathrm{E}(3)$-equivariance, but they often fail in leveraging extensive broader information. While direct application of Large Language Models (LLMs) can incorporate external knowledge, they lack the capability for spatial reasoning with guaranteed equivariance. In this paper, we propose EquiLLM, a novel framework for representing 3D physical systems that seamlessly integrates $\mathrm{E}(3)$-equivariance with LLM capabilities. Specifically, EquiLLM comprises four key components: geometry-aware prompting, an equivariant encoder, an LLM, and an equivariant adapter. Essentially, the LLM guided by the instructive prompt serves as a sophisticated invariant feature processor, while 3D directional information is exclusively handled by the equivariant encoder and adapter modules. Experimental results demonstrate that EquiLLM delivers significant improvements over previous methods across molecular dynamics simulation, human motion simulation, and antibody design, highlighting its promising generalizability.

Accurate weather forecasting on Subseasonal-to-Seasonal (S2S) timescale is critical to human society such as agriculture planning and extreme weather preparation. Although data-driven models have become alternatives to computationally intensive Numerical Weather Prediction (NWP) systems, existing Transformer-based approaches suffer from biases due to planar projections distorting the spherical geometry and inadequate handling of vector-scalar variable interactions (e.g., wind velocity vs. temperature). To address these limitations, we propose a graph-based Equivariant and Invariant Message Passing (EIMP) framework that directly processes spherical grid data. It maintains SO(3) equivariant embeddings for vector data and SO(3) invariant embeddings for scalar data, which are interacted by a shared invariant message embedding. Guaranteed equivariant and invariant message aggregation functions are proposed to update embeddings under strict symmetry constraints. Extensive experiments on the Earth Reanalysis 5 (ERA5) reanalysis dataset of 41 years demonstrate the proposed model achieves significant improvement over advanced data-driven models and skillful numerical ECMWF systems. Additionally, we empirically show that EIMP demonstrates geometrically superior predictions and conduct ablation studies to validate the efficacy of its design.

Equivariant Graph Neural Networks (GNNs) have demonstrated significant success across various applications. To achieve completeness---that is, the universal approximation property over the space of equivariant functions---the network must effectively capture the intricate multi-body interactions among different nodes. Prior methods attain this via deeper architectures, augmented body orders, or increased degrees of steerable features, often at high computational cost and without polynomial-time solutions. In this work, we present a theoretically grounded framework for constructing complete equivariant GNNs that is both efficient and practical. We prove that a complete equivariant GNN can be achieved through two key components: 1) a complete scalar function, referred to as the canonical form of the geometric graph; and 2) a full-rank steerable basis set. Leveraging this finding, we propose an efficient algorithm for constructing complete equivariant GNNs based on two common models: EGNN and TFN. Empirical results demonstrate that our model demonstrates superior completeness and excellent performance with only a few layers, thereby significantly reducing computational overhead while maintaining strong practical efficacy.

Over time, a growing wave of large language models from various series has been introduced to the community. Researchers are striving to maximize the performance of language models with constrained parameter sizes. However, from a microscopic perspective, there has been limited research on how to better store knowledge in model parameters, particularly within MLPs, to enable more effective utilization of this knowledge by the model. In this work, we analyze twenty publicly available open-source large language models to investigate the relationship between their strong performance and the way knowledge is stored in their corresponding MLP parameters. Our findings reveal that as language models become more advanced and demonstrate stronger knowledge capabilities, their parameters exhibit increased specialization. Specifically, parameters in the MLPs tend to be more focused on encoding similar types of knowledge. We experimentally validate that this specialized distribution of knowledge contributes to improving the efficiency of knowledge utilization in these models. Furthermore, by conducting causal training experiments, we confirm that this specialized knowledge distribution plays a critical role in improving the model's efficiency in leveraging stored knowledge.

Metal-Organic Frameworks (MOFs) have attracted considerable attention due to their unique properties including high surface area and tunable porosity, and promising applications in catalysis, gas storage, and drug delivery. Structure prediction for MOFs is a challenging task, as these frameworks are intrinsically periodic and hierarchically organized, where the entire structure is assembled from building blocks like metal nodes and organic linkers. To address this, we introduce MOF-BFN, a novel generative model for MOF structure prediction based on Bayesian Flow Networks (BFNs). Given the local geometry of building blocks, MOF-BFN jointly predicts the lattice parameters, as well as the positions and orientations of all building blocks within the unit cell. In particular, the positions are modelled in the fractional coordinate system to naturally incorporate the periodicity. Meanwhile, the orientations are modeled as unit quaternions sampled from learned Bingham distributions via the proposed Bingham BFN, enabling effective orientation generation on the 4D unit hypersphere. Experimental results demonstrate that MOF-BFN achieves state-of-the-art performance across multiple tasks, including structure prediction, geometric property evaluation, and de novo generation, offering a promising tool for designing complex MOF materials.

Recent multimodal embedding approaches leveraging multimodal large language models (MLLMs) fine-tuned with contrastive learning (CL) have shown promising results, yet the underlying reasons behind their superiority remain underexplored. This work argues that a crucial advantage of MLLM-based approaches stems from implicit cross-modal alignment achieved during generative pretraining, where the language decoder learns to exploit multimodal signals within a shared representation space for generating unimodal outputs. Through analysis of anisotropy and kernel similarity structure, we empirically confirm that latent alignment emerges within MLLM representations, allowing CL to serve as a lightweight refinement stage. Leveraging this insight, we propose a Language-Centric Omnimodal Embedding framework, termed LCO-Embed. Extensive experiments across diverse backbones and benchmarks demonstrate its effectiveness, achieving state-of-the-art performance across modalities. Furthermore, we identify a Generation-Representation Scaling Law (GRSL), showing that the representational capabilities gained through contrastive refinement scale positively with the MLLM's generative capabilities. This suggests that improving generative abilities evolves as an effective paradigm for enhancing representation quality. We provide a theoretical explanation of GRSL, which formally links the MLLM's generative quality to the upper bound on its representation performance, and validate it on a challenging, low-resource visual-document retrieval task, showing that continual generative pretraining before CL can further enhance the potential of a model's embedding capabilities. Codes, models, and resources are available at https://github.com/LCO-Embedding/LCO-Embedding.

To enhance the generalization ability of graph neural networks (GNNs) in learning and simulation physical dynamics, a series of equivariant GNNs have been developed to incorporate the symmetric inductive bias. However, the existing methods do not take into account the non-stationarity nature of physical dynamics, where the joint distribution changes over time. Moreover, previous approaches for modeling non-stationary time series typically involve normalizing the data, which disrupts the symmetric assumption inherent in physical dynamics. To model the non-stationary physical dynamics while preserving the symmetric inductive bias, we introduce a Non-Stationary Equivariant Graph Neural Network (NS-EGNN) to capture the non-stationarity in physical dynamics while preserving the symmetric property of the model. Specifically, NS-EGNN employs Fourier Transform on segments of physical dynamics to extract time-varying frequency information from the trajectories. It then uses the first and second-order differences to mitigate non-stationarity, followed by pooling for future predictions. Through capturing varying frequency characteristics and alleviate the linear and quadric trend in the raw physical dynamics, NS-EGNN better models the temporal dependencies in the physical dynamics. NS-EGNN has been applied on various types of physical dynamics, including molecular, motion and protein dynamics. In various scenario, NS-EGNN consistently surpasses the performance of existing state-of-the-art algorithms, underscoring its effectiveness. The implementation of NS-EGNN is available at https://github.com/MaojiWEN/NS-EGNN.

In real-world recommendation scenarios, users typically engage with platforms through multiple types of behavioral interactions. Multi-behavior recommendation algorithms aim to leverage various auxiliary user behaviors to enhance prediction for target behaviors of primary interest (e.g., buy), thereby overcoming performance limitations caused by data sparsity in target behavior records. Current state-of-the-art approaches typically employ hierarchical design following either cascading (e.g., view$\rightarrow$cart$\rightarrow$buy) or parallel (unified$\rightarrow$behavior$\rightarrow$specific components) paradigms, to capture behavioral relationships. However, these methods still face two critical challenges: (1) severe distribution disparities across behaviors, and (2) negative transfer effects caused by noise in auxiliary behaviors. In this paper, we propose a novel model-agnostic Hierarchical Graph Information Bottleneck (HGIB) framework for multi-behavior recommendation to effectively address these challenges. Following information bottleneck principles, our framework optimizes the learning of compact yet sufficient representations that preserve essential information for target behavior prediction while eliminating task-irrelevant redundancies. To further mitigate interaction noise, we introduce a Graph Refinement Encoder (GRE) that dynamically prunes redundant edges through learnable edge dropout mechanisms. We conduct comprehensive experiments on three real-world public datasets, which demonstrate the superior effectiveness of our framework. Beyond these widely used datasets in the academic community, we further expand our evaluation on several real industrial scenarios and conduct an online A/B testing, showing again a significant improvement in multi-behavior recommendations. The source code of our proposed HGIB is available at https://github.com/zhy99426/HGIB.

In the digital era, users typically interact with diverse items across multiple domains (e.g., e-commerce, streaming platforms, and social networks), generating intricate heterogeneous interaction graphs. Leveraging multi-domain data can improve recommendation systems by enriching user insights and mitigating data sparsity in individual domains. However, integrating such multi-domain knowledge for cross-domain recommendation remains challenging due to inherent disparities in user behavior and item characteristics and the risk of negative transfer, where irrelevant or conflicting information from the source domains adversely impacts the target domain's performance. To tackle these challenges, we propose HAGO, a novel framework with Heterogeneous Adaptive Graph coOrdinators, which dynamically integrates multi-domain graphs into a cohesive structure. HAGO adaptively adjusts the connections between coordinators and multi-domain graph nodes to enhance beneficial inter-domain interactions while alleviating negative transfer. Furthermore, we introduce a universal multi-domain graph pre-training strategy alongside HAGO to collaboratively learn high-quality node representations across domains. Being compatible with various graph-based models and pre-training techniques, HAGO demonstrates broad applicability and effectiveness. Extensive experiments show that our framework outperforms state-of-the-art methods in cross-domain recommendation scenarios, underscoring its potential for real-world applications. The source code is available at https://github.com/zhy99426/HAGO.

Abstract Geometric graphs are a special kind of graph with geometric features, which are vital to model many scientific problems. Unlike generic graphs, geometric graphs often exhibit physical symmetries of translations, rotations, and reflections, making them ineffectively processed by current Graph Neural Networks (GNNs). To address this issue, researchers proposed a variety of geometric GNNs equipped with invariant/equivariant properties to better characterize the geometry and topology of geometric graphs. Given the current progress in this field, it is imperative to conduct a comprehensive survey of data structures, models, and applications related to geometric GNNs. In this paper, based on the necessary but concise mathematical preliminaries, we formalize geometric graph as the data structure, on top of which we provide a unified view of existing models from the geometric message passing perspective. Additionally, we summarize the applications as well as the related datasets to facilitate later research for methodology development and experimental evaluation. We also discuss the challenges and future potential directions of geometric GNNs at the end of this survey.

Query optimization is a complex planning and decision-making problem within the exponentially growing plan space in database management systems (DBMS). Traditional optimization techniques have been extensively studied over decades, leaving limited room for further improvement along this track. Recent developments of Large Language Models (LLMs) have demonstrated their potential in solving complex planning and decision-making problems, such as arithmetic and programmatic tasks. In this paper, we try to explore the potential of LLMs in handling query optimization and propose a tentative LLM-based query optimizer dubbed LLM-QO, established on PostgreSQL's execution engine. In LLM-QO, we formulate query optimization in an autoregressive fashion which directly generates the execution plan without explicit plan enumeration. To investigate the essential input of LLM-QO, we design a customized data recipe named QInstruct to collect the training data from various optimizers and serialize the database's meta data, queries and corresponding plans into a textual format. Based on QInstruct, we implement a two-stage fine-tuning pipeline, Query Instruction Tuning (QIT) and Query Direct Preference Optimization (QDPO), to empower the capability of general-purpose LLMs in handling query optimization. In our experiments, LLM-QO can generate valid and high-quality plans and consistently outperforms both traditional and learned optimizers on three query workloads. Our findings verify that LLMs can be derived as query optimizers where generalization, efficiency and adaptivity deserve further research efforts.

Hypergraph-based modeling has gained significant attention for capturing complex higher-order interactions among vertices. While random walks serve as fundamental tools for analyzing hypergraphs, existing approaches either fail to fully leverage edge-dependent vertex weights (EDVWs) or lack sufficient expressiveness to model intricate hypergraph structures. To address these limitations, we propose a unified random walk framework that integrates hyperedge degrees and vertex weights, offering a more robust approach to hypergraph modeling. We establish equivalence conditions between hypergraph and graph random walks, leading to a novel unified random-walk-based hypergraph Laplacian that incorporates EDVWs, ensuring expressiveness and desirable spectral properties. Building on this foundation, we introduce the General Hypergraph Spectral Convolution (GHSC) framework, which extends existing Graph Convolutional Neural Networks (GCNNs) for effective hypergraph learning, supporting both edge-independent and edge-dependent vertex weights. Extensive experiments across diverse datasets, including citation networks, visual objects, and protein modeling tasks, demonstrate state-of-the-art performance, with notable improvements in protein structure modeling using EDVW-hypergraphs. This work advances the theoretical understanding of hypergraph random walks and spectral theory while providing a versatile framework for deep hypergraph learning. Code is available at GHSC_H_GNNs.

Recently, generative models based on the diffusion process have emerged as a promising direction for automating the design of molecules. However, directly adding continuous Gaussian noise to discrete graphs leads to the problem that the generated data do not conform to the discrete graph data distribution in the training set. Current graph diffusion models either corrupt discrete data through a transition matrix or relax the discrete data to continuous space for the diffusion process. These approaches make it hard to perform extensible conditional generation, such as adapting to text-based conditions, due to the lack of embedding representations and require significant computation resources due to the diffusion process of the bond type matrix. This paper introduces the Hierarchical Graph Latent Diffusion Model (HGLDM), a novel variant of latent diffusion models that overcomes the problem of applying continuous diffusion models directly to discrete graph data. Meanwhile, based on the latent diffusion framework, HGLDM avoids the issues of computational consumption and lack of embeddings for extensible conditional generation. In addition, by comparing the HGLDM with its variant, the Graph Latent Diffusion Model (GLDM), which only has graph-level embeddings, we validate the advantage of the hierarchical graph structure for capturing the relationship between structure information and molecular properties. We evaluate the performance of our model through various conditional generation tasks, demonstrating its superior performance.

Combinatorial medication recommendation (CMR) is a fundamental task of healthcare, which offers opportunities for clinical physicians to provide more precise prescriptions for patients with intricate health conditions, particularly in the scenarios of long-term medical care. Previous research efforts have sought to extract meaningful information from electronic health records (EHRs) to facilitate combinatorial medication recommendations. Existing learning-based approaches further consider the chemical structures of medications, but ignore the textual medication descriptions in which the functionalities are clearly described. Furthermore, the textual knowledge derived from the EHRs of patients remains largely underutilized. To address these issues, we introduce the Natural Language-Assisted Multi-modal Medication Recommendation (NLA-MMR), a multimodal alignment framework designed to learn knowledge from the patient view and medication view jointly. Specifically, NLA-MMR formulates CMR as an alignment problem from patient and medication modalities. In this vein, we employ pretrained language models (PLMs) to extract in-domain knowledge regarding patients and medications, serving as the foundational representation for both modalities. In the medication modality, we exploit both chemical structures and textual descriptions to create medication representations. In the patient modality, we generate the patient representations based on textual descriptions of diagnosis, procedure, and symptom. Extensive experiments conducted on three publicly accessible datasets demonstrate that NLA-MMR achieves new state-of-the-art performance, with a notable average improvement of 4.72% in Jaccard score.

Graph Neural Networks (GNNs) have been widely adopted for drug discovery with molecular graphs. Nevertheless, current GNNs mainly excel in leveraging short-range interactions (SRI) but struggle to capture long-range interactions (LRI), both of which are crucial for determining molecular properties. To tackle this issue, we propose a method to abstract the collective information of atomic groups into a few $\textit{Neural Atoms}$ by implicitly projecting the atoms of a molecular. Specifically, we explicitly exchange the information among neural atoms and project them back to the atoms’ representations as an enhancement. With this mechanism, neural atoms establish the communication channels among distant nodes, effectively reducing the interaction scope of arbitrary node pairs into a single hop. To provide an inspection of our method from a physical perspective, we reveal its connection to the traditional LRI calculation method, Ewald Summation. The Neural Atom can enhance GNNs to capture LRI by approximating the potential LRI of the molecular. We conduct extensive experiments on four long-range graph benchmarks, covering graph-level and link-level tasks on molecular graphs. We achieve up to a 27.32% and 38.27% improvement in the 2D and 3D scenarios, respectively. Empirically, our method can be equipped with an arbitrary GNN to help capture LRI. Code and datasets are publicly available in https://github.com/tmlr-group/NeuralAtom.

Graph Neural Networks (GNNs) with equivariant properties have emerged as powerful tools for modeling complex dynamics of multi-object physical systems. However, their generalization ability is limited by the inadequate consideration of physical inductive biases: (1) Existing studies overlook the continuity of transitions among system states, opting to employ several discrete transformation layers to learn the direct mapping between two adjacent states; (2) Most models only account for first-order velocity information, despite the fact that many physical systems are governed by second-order motion laws. To incorporate these inductive biases, we propose the Second-order Equivariant Graph Neural Ordinary Differential Equation (SEGNO). Specifically, we show how the second-order continuity can be incorporated into GNNs while maintaining the equivariant property. Furthermore, we offer theoretical insights into SEGNO, highlighting that it can learn a unique trajectory between adjacent states, which is crucial for model generalization. Additionally, we prove that the discrepancy between this learned trajectory of SEGNO and the true trajectory is bounded. Extensive experiments on complex dynamical systems including molecular dynamics and motion capture demonstrate that our model yields a significant improvement over the state-of-the-art baselines.

Incorporating Euclidean symmetries (e.g. rotation equivariance) as inductive biases into graph neural networks has improved their generalization ability and data efficiency in unbounded physical dynamics modeling. However, in various scientific and engineering applications, the symmetries of dynamics are frequently discrete due to the boundary conditions. Thus, existing GNNs either over-look necessary symmetry, resulting in suboptimal representation ability, or impose excessive equivariance, which fails to generalize to unobserved symmetric dynamics. In this work, we propose a general Discrete Equivariant Graph Neural Network (DEGNN) that guarantees equivariance to a given discrete point group. Specifically, we show that such discrete equivariant message passing could be constructed by transforming geometric features into permutation-invariant embeddings. Through relaxing continuous equivariant constraints, DEGNN can employ more geometric feature combinations to approximate unobserved physical object interaction functions. Two implementation approaches of DEGNN are proposed based on ranking or pooling permutation-invariant functions. We apply DEGNN to various physical dynamics, ranging from particle, molecular, crowd to vehicle dynamics. In twenty scenarios, DEGNN significantly outperforms existing state-of-the-art approaches. Moreover, we show that DEGNN is data efficient, learning with less data, and can generalize across scenarios such as unobserved orientation.

The emergence of Graph Convolutional Network (GCN) has greatly boosted the progress of graph learning. However, two disturbing factors, noise and redundancy in graph data, and lack of interpretation for prediction results, impede further development of GCN. One solution is to recognize a predictive yet compressed subgraph to get rid of the noise and redundancy and obtain the interpretable part of the graph. This setting of subgraph is similar to the information bottleneck (IB) principle, which is less studied on graph-structured data and GCN. Inspired by the IB principle, we propose a novel subgraph information bottleneck (SIB) framework to recognize such subgraphs, named IB-subgraph. However, the intractability of mutual information and the discrete nature of graph data makes the objective of SIB notoriously hard to optimize. To this end, we introduce a bilevel optimization scheme coupled with a mutual information estimator for irregular graphs. Moreover, we propose a continuous relaxation for subgraph selection with a connectivity loss for stabilization. We further theoretically prove the error bound of our estimation scheme for mutual information and the noise-invariant nature of IB-subgraph. Extensive experiments on graph learning and large-scale point cloud tasks demonstrate the superior property of IB-subgraph.

Attributed community search (ACS) aims to identify subgraphs satisfying both structure cohesiveness and attribute homogeneity in attributed graphs, for a given query that contains query nodes and query attributes. Previously, algorithmic approaches deal with ACS in a two-stage paradigm, which suffer from structural inflexibility and attribute irrelevance. To overcome this problem, recently, learning-based approaches have been proposed to learn both structures and attributes simultaneously as a one-stage paradigm. However, these approaches train a transductive model which assumes the graph to infer unseen queries is as same as the graph used for training. That limits the generalization and adaptation of these approaches to different heterogeneous graphs. In this paper, we propose a new framework, Inductive Attributed Community Search, IACS , by inductive learning, which can be used to infer new queries for different communities/graphs. Specifically, IACS employs an encoder-decoder neural architecture to handle an ACS task at a time, where a task consists of a graph with only a few queries and corresponding ground-truth. We design a three-phase workflow, "training-adaptation-inference", which learns a shared model to absorb and induce prior effective common knowledge about ACS across different tasks. And the shared model can swiftly adapt to a new task with small number of ground-truth. We conduct substantial experiments in 7 real-world datasets to verify the effectiveness of IACS for CS/ACS. Our approach IACS achieves 28.97% and 25.60% improvements in F1-score on average in CS and ACS, respectively.

It has been discovered that graph convolutional networks (GCNs) encounter a remarkable drop in performance when multiple layers are piled up. The main factor that accounts for why deep GCNs fail lies in oversmoothing, which isolates the network output from the input with the increase of network depth, weakening expressivity and trainability. In this article, we start by investigating refined measures upon DropEdge-an existing simple yet effective technique to relieve oversmoothing. We term our method as DropEdge++ for its two structure-aware samplers in contrast to DropEdge: layer-dependent (LD) sampler and feature-dependent (FD) sampler. Regarding the LD sampler, we interestingly find that increasingly sampling edges from the bottom layer yields superior performance than the decreasing counterpart as well as DropEdge. We theoretically reveal this phenomenon with mean-edge-number (MEN), a metric closely related to oversmoothing. For the FD sampler, we associate the edge sampling probability with the feature similarity of node pairs and prove that it further correlates the convergence subspace of the output layer with the input features. Extensive experiments on several node classification benchmarks, including both full- and semi-supervised tasks, illustrate the efficacy of DropEdge++ and its compatibility with a variety of backbones by achieving generally better performance over DropEdge and the no-drop version.

AI-aided drug discovery (AIDD) is gaining popularity due to its potential to make the search for new pharmaceuticals faster, less expensive, and more effective. Despite its extensive use in numerous fields (e.g., ADMET prediction, virtual screening), little research has been conducted on the out-of-distribution (OOD) learning problem with noise. We present DrugOOD, a systematic OOD dataset curator and benchmark for AIDD. Particularly, we focus on the drug-target binding affinity prediction problem, which involves both macromolecule (protein target) and small-molecule (drug compound). DrugOOD offers an automated dataset curator with user-friendly customization scripts, rich domain annotations aligned with biochemistry knowledge, realistic noise level annotations, and rigorous benchmarking of SOTA OOD algorithms, as opposed to only providing fixed datasets. Since the molecular data is often modeled as irregular graphs using graph neural network (GNN) backbones, DrugOOD also serves as a valuable testbed for graph OOD learning problems. Extensive empirical studies have revealed a significant performance gap between in-distribution and out-of-distribution experiments, emphasizing the need for the development of more effective schemes that permit OOD generalization under noise for AIDD.

Pretraining molecular representation models without labels is fundamental to various applications. Conventional methods mainly process 2D molecular graphs and focus solely on 2D tasks, making their pretrained models incapable of characterizing 3D geometry and thus defective for downstream 3D tasks. In this work, we tackle 3D molecular pretraining in a complete and novel sense. In particular, we first propose to adopt an equivariant energy-based model as the backbone for pretraining, which enjoys the merits of fulfilling the symmetry of 3D space. Then we develop a node-level pretraining loss for force prediction, where we further exploit the Riemann-Gaussian distribution to ensure the loss to be E(3)-invariant, enabling more robustness. Moreover, a graph-level noise scale prediction task is also leveraged to further promote the eventual performance. We evaluate our model pretrained from a large-scale 3D dataset GEOM-QM9 on two challenging 3D benchmarks: MD17 and QM9. Experimental results demonstrate the efficacy of our method against current state-of-the-art pretraining approaches, and verify the validity of our design for each proposed component. Code is available at https://github.com/jiaor17/3D-EMGP.

Non-Pharmaceutical Interventions (NPIs), such as social gathering restrictions, have shown effectiveness to slow the transmission of COVID-19 by reducing the contact of people. To support policy-makers, multiple studies have first modelled human mobility via macro indicators (e.g., average daily travel distance) and then study the effectiveness of NPIs. In this work, we focus on mobility modelling and, from a micro perspective, aim to predict locations that will be visited by COVID-19 cases. Since NPIs generally cause economic and societal loss, such a prediction benefits governments when they design and evaluate them. However, in real-world situations, strict privacy data protection regulations result in severe data sparsity problems (i.e., limited case and location information). To address these challenges and jointly model variables including a geometric graph, a set of diffusions and a set of locations, we propose a model named Deep Graph Diffusion Infomax (DGDI). We show the maximization of DGDI can be bounded by two tractable components: a univariate Mutual Information (MI) between geometric graph and diffusion representation, and a univariate MI between diffusion representation and location representation. To facilitate the research of COVID-19 prediction, we present two benchmarks that contain geometric graphs and location histories of COVID-19 cases. Extensive experiments on the two benchmarks show that DGDI significantly outperforms other competing methods.

Proteins govern a wide range of biological systems. Evaluating the changes in protein properties upon protein mutation is a fundamental application of protein design, where modeling the 3D protein structure is a principal task for AI-driven computational approaches. Existing deep learning (DL) approaches represent the protein structure as a 3D geometric graph and simplify the graph modeling to different degrees, thereby failing to capture the low-level atom patterns and high-level amino acid patterns simultaneously. In addition, limited training samples with ground truth labels and protein structures further restrict the effectiveness of DL approaches. In this paper, we propose a new graph learning framework, Hierarchical Graph Invariant Network (HGIN), a fine-grained and data-efficient graph neural encoder for encoding protein structures and predicting the mutation effect on protein properties. For fine-grained modeling, HGIN hierarchically models the low-level interactions of atoms and the high-level interactions of amino acid residues by Graph Neural Networks. For data efficiency, HGIN preserves the invariant encoding for atom permutation and coordinate transformation, which is an intrinsic inductive bias of property prediction that bypasses data augmentations. We integrate HGIN into a Siamese network to predict the quantitative effect on protein properties upon mutations. Our approach outperforms 9 state-of-the-art approaches on 3 protein datasets. More inspiringly, when predicting the neutralizing ability of human antibodies against COVID-19 mutant viruses, HGIN achieves an absolute improvement of 0.23 regarding the Spearman coefficient.

Many patients with chronic diseases resort to multiple medications to relieve various symptoms, which raises concerns about the safety of multiple medication use, as severe drug-drug antagonism can lead to serious adverse effects or even death. This paper presents a Decision Support System, called DSSDDI, based on drug-drug interactions to support doctors prescribing decisions. DSSDDI contains three modules, Drug-Drug Interaction (DDI) module, Medical Decision (MD) module and Medical Support (MS) module. The DDI module learns safer and more effective drug representations from the drug-drug interactions. To capture the potential causal relationship between DDI and medication use, the MD module considers the representations of patients and drugs as context, DDI and patients’ similarity as treatment, and medication use as outcome to construct counterfactual links for the representation learning. Furthermore, the MS module provides drug candidates to doctors with explanations. Experiments on the chronic data collected from the Hong Kong Chronic Disease Study Project and a public diagnostic data MIMIC-III demonstrate that DSSDDI can be a reliable reference for doctors in terms of safety and efficiency of clinical diagnosis, with significant improvements compared to baseline methods. Source code of the proposed DSSDDI is publicly available at https://github.com/TianBian95/DSSDDI.

Recent awareness of privacy protection and compliance requirement resulted in a controversial view of recommendation system due to personal data usage. Therefore, privacy-protected recommendation emerges as a novel research direction. In this paper, we first formulate this problem as a vertical federated learning problem, i.e., features are vertically distributed over different departments. We study a contextual bandit learning problem for recommendation in the vertical federated setting. To this end, we carefully design a customized encryption scheme named orthogonal matrix-based mask mechanism (O3M). O3M mechanism, a tailored component for contextual bandits by carefully exploiting their shared structure, can ensure privacy protection while avoiding expensive conventional cryptographic techniques. We further apply the mechanism to two commonly-used bandit algorithms, LinUCB and LinTS, and instantiate two practical protocols for online recommendation. The proposed protocols can perfectly recover the service quality of centralized bandit algorithms while achieving a satisfactory runtime efficiency, which is theoretically proved and analysed in this paper. By conducting extensive experiments on both synthetic and real-world datasets, we show the superiority of the proposed method in terms of privacy protection and recommendation performance.

Pseudo labeling (PL) is a wide-applied strategy to enlarge the labeled dataset by self-annotating the potential samples during the training process. Several works have shown that it can improve the graph learning model performance in general. However, we notice that the incorrect labels can be fatal to the graph training process. Inappropriate PL may result in the performance degrading, especially on graph data where the noise can propagate. Surprisingly, the corresponding error is seldom theoretically analyzed in the literature. In this paper, we aim to give deep insights of PL on graph learning models. We first present the error analysis of PL strategy by showing that the error is bounded by the confidence of PL threshold and consistency of multi-view prediction. Then, we theoretically illustrate the effect of PL on convergence property. Based on the analysis, we propose a cautious pseudo labeling methodology in which we pseudo label the samples with highest confidence and multi-view consistency. Finally, extensive experiments demonstrate that the proposed strategy improves graph learning process and outperforms other PL strategies on link prediction and node classification tasks.

Learning to represent and simulate the dynamics of physical systems is a crucial yet challenging task. Existing equivariant Graph Neural Network (GNN) based methods have encapsulated the symmetry of physics, \emph{e.g.}, translations, rotations, etc, leading to better generalization ability. Nevertheless, their frame-to-frame formulation of the task overlooks the non-Markov property mainly incurred by unobserved dynamics in the environment. In this paper, we reformulate dynamics simulation as a spatio-temporal prediction task, by employing the trajectory in the past period to recover the Non-Markovian interactions. We propose Equivariant Spatio-Temporal Attentive Graph Networks (ESTAG), an equivariant version of spatio-temporal GNNs, to fulfil our purpose. At its core, we design a novel Equivariant Discrete Fourier Transform (EDFT) to extract periodic patterns from the history frames, and then construct an Equivariant Spatial Module (ESM) to accomplish spatial message passing, and an Equivariant Temporal Module (ETM) with the forward attention and equivariant pooling mechanisms to aggregate temporal message. We evaluate our model on three real datasets corresponding to the molecular-, protein- and macro-level. Experimental results verify the effectiveness of ESTAG compared to typical spatio-temporal GNNs and equivariant GNNs.

Technological advances have now made it possible to simultaneously profile the changes of epigenomic, transcriptomic and proteomic at the single cell level, allowing a more unified view of cellular phenotypes and heterogeneities. However, current computational tools for single-cell multi-omics data integration are mainly tailored for bi-modality data, so new tools are urgently needed to integrate tri-modality data with complex associations. To this end, we develop scMHNN to integrate single-cell multi-omics data based on hypergraph neural network. After modeling the complex data associations among various modalities, scMHNN performs message passing process on the multi-omics hypergraph, which can capture the high-order data relationships and integrate the multiple heterogeneous features. Followingly, scMHNN learns discriminative cell representation via a dual-contrastive loss in self-supervised manner. Based on the pretrained hypergraph encoder, we further introduce the pre-training and fine-tuning paradigm, which allows more accurate cell-type annotation with only a small number of labeled cells as reference. Benchmarking results on real and simulated single-cell tri-modality datasets indicate that scMHNN outperforms other competing methods on both cell clustering and cell-type annotation tasks. In addition, we also demonstrate scMHNN facilitates various downstream tasks, such as cell marker detection and enrichment analysis.

Abstract Deep Learning (DL) has been widely used in many applications, and its success is achieved with large training data. A key issue is how to provide a DL solution when there is no large training data to learn initially. In this paper, we explore a meta-learning approach for a specific problem, subgraph isomorphism counting, which is a fundamental problem in graph analysis to count the number of a given pattern graph, p , in a data graph, g , that matches p . There are various data graphs and pattern graphs. A subgraph isomorphism counting query is specified by a pair, ( g , p ). This problem is NP-hard and needs large training data to learn by DL in nature. We design a Gaussian Process (GP) model which combines Graph Neural Network with Bayesian nonparametric, and we train the GP by a meta-learning algorithm on a small set of training data. By meta-learning, we can obtain a generalized meta-model to better encode the information of data and pattern graphs and capture the prior of small tasks. With the meta-model learned, we handle a collection of pairs ( g , p ), as a task, where some pairs may be associated with the ground-truth, and some pairs are the queries to answer. There are two cases. One is there are some with ground-truth (few-shot), and one is there is none with ground-truth (zero-shot). We provide our solutions for both. In particular, for zero-shot, we propose a new data-driven approach to predict the count values. Note that zero-shot learning for our regression tasks is difficult, and there is no hands-on solution in the literature. We conducted extensive experimental studies to confirm that our approach is robust to model degeneration on small training data, and our meta-model can fast adapt to new queries by few-shot and zero-shot learning.

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.

Graph edit distance (GED) computation is a fundamental NP-hard problem in graph theory. Given a graph pair ( G 1 , G 2 ), GED is defined as the minimum number of primitive operations converting G 1 to G 2 . Early studies focus on search-based inexact algorithms such as A*-beam search, and greedy algorithms using bipartite matching due to its NP-hardness. They can obtain a sub-optimal solution by constructing an edit path (the sequence of operations that converts G 1 to G 2 ). Recent studies convert the GED between a given graph pair ( G 1 , G 2 ) into a similarity score in the range (0, 1) by a well designed function. Then machine learning models (mostly based on graph neural networks) are applied to predict the similarity score. They achieve a much higher numerical precision than the sub-optimal solutions found by classical algorithms. However, a major limitation is that these machine learning models cannot generate an edit path. They treat the GED computation as a pure regression task to bypass its intrinsic complexity, but ignore the essential task of converting G 1 to G 2 . This severely limits the interpretability and usability of the solution. In this paper, we propose a novel deep learning framework that solves the GED problem in a two-step manner: 1) The proposed graph neural network GEDGNN is in charge of predicting the GED value and a matching matrix; and 2) A post-processing algorithm based on k -best matching is used to derive k possible node matchings from the matching matrix generated by GEDGNN. The best matching will finally lead to a high-quality edit path. Extensive experiments are conducted on three real graph data sets and synthetic power-law graphs to demonstrate the effectiveness of our framework. Compared to the best result of existing GNN-based models, the mean absolute error (MAE) on GED value prediction decreases by 4.9% ~ 74.3%. Compared to the state-of-the-art searching algorithm Noah, the MAE on GED value based on edit path reduces by 53.6% ~ 88.1%.

With the success of the graph embedding model in both academic and industry areas, the robustness of graph embedding against adversarial attack inevitably becomes a crucial problem in graph learning. Existing works usually perform the attack in a white-box fashion: they need to access the predictions/labels to construct their adversarial loss. However, the inaccessibility of predictions/labels makes the white-box attack impractical for a real graph learning system. This paper promotes current frameworks in a more general and flexible sense -- we consider the ability of various types of graph embedding models to remain resilient against black-box driven attacks. We investigate the theoretical connection between graph signal processing and graph embedding models, and formulate the graph embedding model as a general graph signal process with a corresponding graph filter. Therefore, we design a generalized adversarial attack framework: GF-Attack. Without accessing any labels and model predictions, GF-Attack can perform the attack directly on the graph filter in a black-box fashion. We further prove that GF-Attack can perform an effective attack without assumption on the number of layers/window-size of graph embedding models. To validate the generalization of GF-Attack, we construct GF-Attack on five popular graph embedding models. Extensive experiments validate the effectiveness of GF-Attack on several benchmark datasets.

Finding critical users in social networks is an important issue. The criticalness of a user can be measured by the number of followers who will leave the community together when the user leaves. By taking a social community as a k-core, the problem of finding critical users is to find a set of nodes, U, of size b in a k-core that maximizes the number of nodes to be deleted from the k-core when all nodes in U are deleted. This problem is NP-hard. The state-of-the-art greedy algorithm is with no guarantee on the set of nodes U found. In this paper, we propose a neural network model, called Self-attentive Core Graph Convolution Network (SCGCN), to capture the hidden structure of the criticalness among node combinations that break the engagement of a specific social community. Supervised by sampling node combinations, SCGCN has the ability to inference the criticalness of unseen combinations of nodes. To further reduce the sampling and inference space, we propose a deterministic strategy to prune unpromising nodes on the graph. Our experiments conducted on many real-world graphs show that SCGCN significantly improves the quality of the solution compared with the state-of-the-art greedy algorithm.

Inferring gene regulatory networks based on single-cell transcriptomes is critical for systematically understanding cell-specific regulatory networks and discovering drug targets in tumor cells. Here we show that existing methods mainly perform co-expression analysis and apply the image-based model to deal with the non-euclidean scRNA-seq data, which may not reasonably handle the dropout problem and not fully take advantage of the validated gene regulatory topology. We propose a graph-based end-to-end deep learning model for GRN inference (GRNInfer) with the help of known regulatory relations through transductive learning. The robustness and superiority of the model are demonstrated by comparative experiments.

Finding critical users whose existence keeps a social community cohesive is an important problem in social networks. Considering a k-core community, finding critical users is to find a set of nodes U, with a given size b, in the community that maximizes the number of nodes to be deleted when nodes$U$are deleted. The problem is NP-complete. The state-of-the-art algorithm is a greedy algorithm without a performance guaran-tee. To improve the performance, we propose a novel learning-based heuristic. A neural network model, Self-attentive Core Graph Convolution Network, SCGCN is learned for inference the criticalness of unseen node combinations. Furthermore, to reduce the inference space, we propose a deterministic strategy to prune unpromising nodes. Our experiments show that SCGCN signifi-cantly improves the quality of the solutions compared with the state-of-the-art algorithms.

Transferability estimation has been an essential tool in selecting a pre-trained model and the layers in it for transfer learning, to transfer, so as to maximize the performance on a target task and prevent negative transfer. Existing estimation algorithms either require intensive training on target tasks or have difficulties in evaluating the transferability between layers. To this end, we propose a simple, efficient, and effective transferability measure named TransRate. Through a single pass over examples of a target task, TransRate measures the transferability as the mutual information between features of target examples extracted by a pre-trained model and their labels. We overcome the challenge of efficient mutual information estimation by resorting to coding rate that serves as an effective alternative to entropy. From the perspective of feature representation, the resulting TransRate evaluates both completeness (whether features contain sufficient information of a target task) and compactness (whether features of each class are compact enough for good generalization) of pre-trained features. Theoretically, we have analyzed the close connection of TransRate to the performance after transfer learning. Despite its extraordinary simplicity in 10 lines of codes, TransRate performs remarkably well in extensive evaluations on 35 pre-trained models and 16 downstream tasks.

Graph Neural Networks (GNNs) have achieved remarkable performance on graph-based tasks. The key idea for GNNs is to obtain informative representation through aggregating information from local neighborhoods. However, it remains an open question whether the neighborhood information is adequately aggregated for learning representations of nodes with few neighbors. To address this, we propose a simple and efficient data augmentation strategy, local augmentation, to learn the distribution of the node representations of the neighbors conditioned on the central node’s representation and enhance GNN’s expressive power with generated features. Local augmentation is a general framework that can be applied to any GNN model in a plug-and-play manner. It samples feature vectors associated with each node from the learned conditional distribution as additional input for the backbone model at each training iteration. Extensive experiments and analyses show that local augmentation consistently yields performance improvement when applied to various GNN architectures across a diverse set of benchmarks. For example, experiments show that plugging in local augmentation to GCN and GAT improves by an average of 3.4% and 1.6% in terms of test accuracy on Cora, Citeseer, and Pubmed. Besides, our experimental results on large graphs (OGB) show that our model consistently improves performance over backbones. Code is available at https://github.com/SongtaoLiu0823/LAGNN.

Recently, the pretrain-finetuning paradigm has attracted tons of attention in graph learning community due to its power of alleviating the lack of labels problem in many real-world applications. Current studies use existing techniques, such as weight constraint, representation constraint, which are derived from images or text data, to transfer the invariant knowledge from the pre-train stage to fine-tuning stage. However, these methods failed to preserve invariances from graph structure and Graph Neural Network (GNN) style models. In this paper, we present a novel optimal transport-based fine-tuning framework called GTOT-Tuning, namely, Graph Topology induced Optimal Transport fine-Tuning, for GNN style backbones. GTOT-Tuning is required to utilize the property of graph data to enhance the preservation of representation produced by fine-tuned networks. Toward this goal, we formulate graph local knowledge transfer as an Optimal Transport (OT) problem with a structural prior and construct the GTOT regularizer to constrain the fine-tuned model behaviors. By using the adjacency relationship amongst nodes, the GTOT regularizer achieves node-level optimal transport procedures and reduces redundant transport procedures, resulting in efficient knowledge transfer from the pre-trained models. We evaluate GTOT-Tuning on eight downstream tasks with various GNN backbones and demonstrate that it achieves state-of-the-art fine-tuning performance for GNNs.

Equivariant Graph neural Networks (EGNs) are powerful in characterizing the dynamics of multi-body physical systems. Existing EGNs conduct flat message passing, which, yet, is unable to capture the spatial/dynamical hierarchy for complex systems particularly, limiting substructure discovery and global information fusion. In this paper, we propose Equivariant Hierarchy-based Graph Networks (EGHNs) which consist of the three key components: generalized Equivariant Matrix Message Passing (EMMP) , E-Pool and E-UnPool. In particular, EMMP is able to improve the expressivity of conventional equivariant message passing, E-Pool assigns the quantities of the low-level nodes into high-level clusters, while E-UnPool leverages the high-level information to update the dynamics of the low-level nodes. As their names imply, both E-Pool and E-UnPool are guaranteed to be equivariant to meet physic symmetry. Considerable experimental evaluations verify the effectiveness of our EGHN on several applications including multi-object dynamics simulation, motion capture, and protein dynamics modeling.

Click-Through Rate (CTR) prediction, which aims to estimate the probability that a user will click an item, is an essential component of online advertising. Existing methods mainly attempt to mine user interests from users' historical behaviours, which contain users' directly interacted items. Although these methods have made great progress, they are often limited by the recommender system's direct exposure and inactive interactions, and thus fail to mine all potential user interests. To tackle these problems, we propose Neighbor-Interaction based CTR prediction (NI-CTR), which considers this task under a Heterogeneous Information Network (HIN) setting. In short, Neighbor-Interaction based CTR prediction involves the local neighborhood of the target user-item pair in the HIN to predict their linkage. In order to guide the representation learning of the local neighbourhood, we further consider different kinds of interactions among the local neighborhood nodes from both explicit and implicit perspective, and propose a novel Graph-Masked Transformer (GMT) to effectively incorporates these kinds of interactions to produce highly representative embeddings for the target user-item pair. Moreover, in order to improve model robustness against neighbour sampling, we enforce a consistency regularization loss over the neighbourhood embedding. We conduct extensive experiments on two real-world datasets with millions of instances and the experimental results show that our proposed method outperforms state-of-the-art CTR models significantly. Meanwhile, the comprehensive ablation studies verify the effectiveness of every component of our model. Furthermore, we have deployed this framework on the WeChat Official Account Platform with billions of users. The online A/B tests demonstrate an average CTR improvement of 21.9% against all online baselines.

Fake News detection has attracted much attention in recent years. Social context based detection methods attempt to model the spreading patterns of fake news by utilizing the collective wisdom from users on social media. This task is challenging for three reasons: (1) There are multiple types of entities and relations in social context, requiring methods to effectively model the heterogeneity. (2) The emergence of news in novel topics in social media causes distribution shifts, which can significantly degrade the performance of fake news detectors. (3) Existing fake news datasets usually lack of great scale, topic diversity and user social relations, impeding the development of this field. To solve these problems, we formulate social context based fake news detection as a heterogeneous graph classification problem, and propose a fake news detection model named Post-User Interaction Network (PSIN), which adopts a divide-and-conquer strategy to model the post-post, user-user and post-user interactions in social context effectively while maintaining their intrinsic characteristics. Moreover,we adopt an adversarial topic discriminator for topic-agnostic feature learning, in order to improve the generalizability of our method for new-emerging topics. Furthermore, we curate a new dataset for fake news detection, which contains over 27,155 news from 5 topics, 5 million posts, 2 million users and their induced social graph with 0.2 billion edges. It has been published on https://github.com/qwerfdsaplking/MC-Fake. Extensive experiments illustrate that our method outperforms SOTA baselines in both in-topic and out-of-topic settings.

MOTIVATION: The crux of molecular property prediction is to generate meaningful representations of the molecules. One promising route is to exploit the molecular graph structure through graph neural networks (GNNs). Both atoms and bonds significantly affect the chemical properties of a molecule, so an expressive model ought to exploit both node (atom) and edge (bond) information simultaneously. Inspired by this observation, we explore the multi-view modeling with GNN (MVGNN) to form a novel paralleled framework, which considers both atoms and bonds equally important when learning molecular representations. In specific, one view is atom-central and the other view is bond-central, then the two views are circulated via specifically designed components to enable more accurate predictions. To further enhance the expressive power of MVGNN, we propose a cross-dependent message-passing scheme to enhance information communication of different views. The overall framework is termed as CD-MVGNN. RESULTS: We theoretically justify the expressiveness of the proposed model in terms of distinguishing non-isomorphism graphs. Extensive experiments demonstrate that CD-MVGNN achieves remarkably superior performance over the state-of-the-art models on various challenging benchmarks. Meanwhile, visualization results of the node importance are consistent with prior knowledge, which confirms the interpretability power of CD-MVGNN. AVAILABILITY AND IMPLEMENTATION: The code and data underlying this work are available in GitHub at https://github.com/uta-smile/CD-MVGNN. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Temporal action localization, which requires a machine to recognize the location as well as the category of action instances in videos, has long been researched in computer vision. The main challenge of temporal action localization lies in that videos are usually long and untrimmed with diverse action contents involved. Existing state-of-the-art action localization methods divide each video into multiple action units (i.e., proposals in two-stage methods and segments in one-stage methods) and then perform action recognition/regression on each of them individually, without explicitly exploiting their relations during learning. In this paper, we claim that the relations between action units play an important role in action localization, and a more powerful action detector should not only capture the local content of each action unit but also allow a wider field of view on the context related to it. To this end, we propose a general graph convolutional module (GCM) that can be easily plugged into existing action localization methods, including two-stage and one-stage paradigms. To be specific, we first construct a graph, where each action unit is represented as a node and their relations between two action units as an edge. Here, we use two types of relations, one for capturing the temporal connections between different action units, and the other one for characterizing their semantic relationship. Particularly for the temporal connections in two-stage methods, we further explore two different kinds of edges, one connecting the overlapping action units and the other one connecting surrounding but disjointed units. Upon the graph we built, we then apply graph convolutional networks (GCNs) to model the relations among different action units, which is able to learn more informative representations to enhance action localization. Experimental results show that our GCM consistently improves the performance of existing action localization methods, including two-stage methods (e.g., CBR [15] and R-C3D [47]) and one-stage methods (e.g., D-SSAD [22]), verifying the generality and effectiveness of our GCM. Moreover, with the aid of GCM, our approach significantly outperforms the state-of-the-art on THUMOS14 (50.9 percent versus 42.8 percent). Augmentation experiments on ActivityNet also verify the efficacy of modeling the relationships between action units. The source code and the pre-trained models are available at https://github.com/Alvin-Zeng/GCM.

Given one or more query vertices, Community Search (CS) aims to find densely intra-connected and loosely inter-connected structures containing query vertices. Attributed Community Search (ACS), a related problem, is more challenging since it finds communities with both cohesive structures and homogeneous vertex attributes. However, most methods for the CS task rely on inflexible pre-defined structures and studies for ACS treat each attribute independently. Moreover, the most popular ACS strategies decompose ACS into two separate sub-problems, i.e., the CS task and subsequent attribute filtering task. However, in real-world graphs, the community structure and the vertex attributes are closely correlated to each other. This correlation is vital for the ACS problem. In this vein, we argue that the separation strategy cannot fully capture the correlation between structure and attributes simultaneously and it would compromise the final performance. In this paper, we propose Graph Neural Network (GNN) models for both CS and ACS problems, i.e., Query Driven-GNN (QD-GNN) and Attributed Query Driven-GNN (AQD-GNN). In QD-GNN, we combine the local query-dependent structure and global graph embedding. In order to extend QD-GNN to handle attributes, we model vertex attributes as a bipartite graph and capture the relation between attributes by constructing GNNs on this bipartite graph. With a Feature Fusion operator, AQD-GNN processes the structure and attribute simultaneously and predicts communities according to each attributed query. Experiments on real-world graphs with ground-truth communities demonstrate that the proposed models outperform existing CS and ACS algorithms in terms of both efficiency and effectiveness. More recently, an interactive setting for CS is proposed that allows users to adjust the predicted communities. We further verify our approaches under the interactive setting and extend to the attributed context. Our method achieves 2.37% and 6.29% improvements in F1-score than the state-of-the-art model without attributes and with attributes respectively.

Graph Neural Networks (GNNs) draw their strength from explicitly modeling the topological information of structured data. However, existing GNNs suffer from limited capability in capturing the hierarchical graph representation which plays an important role in graph classification. In this paper, we innovatively propose hierarchical graph capsule network (HGCN) that can jointly learn node embeddings and extract graph hierarchies. Specifically, disentangled graph capsules are established by identifying heterogeneous factors underlying each node, such that their instantiation parameters represent different properties of the same entity. To learn the hierarchical representation, HGCN characterizes the part-whole relationship between lower-level capsules (part) and higher-level capsules (whole) by explicitly considering the structure information among the parts. Experimental studies demonstrate the effectiveness of HGCN and the contribution of each component. Code: https://github.com/uta-smile/HGCN

Molecular property prediction is one fundamental yet challenging task for drug discovery. Many studies have addressed this problem by designing deep learning algorithms, e.g., sequence-based models and graph-based models. However, the underlying data distribution is rarely explored. We discover that there exist easy samples and hard samples in the molecule datasets, and the overall distribution is usually imbalanced. Current research mainly treats them equally during the model training, while we believe that they shall not share the same weights since neural networks training is dominated by the majority class. Therefore, we propose to utilize a self-attention mechanism to generate a learnable weight for each data sample according to the associated gradient norm. The learned attention value is then embedded into the prediction models to construct an attentive loss for the network updating and back-propagation. It is empirically demonstrated that our proposed method can consistently boost the prediction performance for both classification and regression tasks.

Variants of Graph Neural Networks (GNNs) for representation learning have been proposed recently and achieved fruitful results in various fields. Among them, Graph Attention Network (GAT) first employs a self-attention strategy to learn attention weights for each edge in the spatial domain. However, learning the attentions over edges can only focus on the local information of graphs and greatly increases the computational costs. In this paper, we first introduce the attention mechanism in the spectral domain of graphs and present Spectral Graph Attention Network (SpGAT) that learns representations for different frequency components regarding weighted filters and graph wavelets bases. In this way, SpGAT can better capture global patterns of graphs in an efficient manner with much fewer learned parameters than that of GAT. Further, to reduce the computational cost of SpGAT brought by the eigen-decomposition, we propose a fast approximation variant SpGAT-Cheby. We thoroughly evaluate the performance of SpGAT and SpGAT-Cheby in semi-supervised node classification tasks and verify the effectiveness of the learned attentions in the spectral domain.

Nowadays, it is common for a person to possess different identities on multiple social platforms. Social network alignment aims to match the identities that from different networks. Recently, unsupervised network alignment methods have received significant attention since no identity anchor is required. However, to capture the relevance between identities, the existing unsupervised methods generally rely heavily on user profiles, which is unobtainable and unreliable in real-world scenarios. In this paper, we propose an unsupervised alignment framework named Large-Scale Network Alignment (LSNA) to integrate the network information and reduce the requirement on user profile. The embedding module of LSNA, named Cross Network Embedding Model (CNEM), aims to integrate the topology information and the network correlation to simultaneously guide the embedding process. Moreover, in order to adapt LSNA to large-scale networks, we propose a network disassembling strategy to divide the costly large-scale network alignment problem into multiple executable sub-problems. The proposed method is evaluated over multiple real-world social network datasets, and the results demonstrate that the proposed method outperforms the state-of-the-art methods.

Recent studies imply that deep neural networks are vulnerable to adversarial examples, i.e., inputs with a slight but intentional perturbation are incorrectly classified by the network. Such vulnerability makes it risky for some security-related applications (e.g., semantic segmentation in autonomous cars) and triggers tremendous concerns on the model reliability. For the first time, we comprehensively evaluate the robustness of existing UDA methods and propose a robust UDA approach. It is rooted in two observations: i) the robustness of UDA methods in semantic segmentation remains unexplored, which poses a security concern in this field; and ii) although commonly used self-supervision (e.g., rotation and jigsaw) benefits model robustness in classification and recognition tasks, they fail to provide the critical supervision signals that are essential in semantic segmentation. These observations motivate us to propose adversarial self-supervision UDA (or ASSUDA) that maximizes the agreement between clean images and their adversarial examples by a contrastive loss in the output space. Extensive empirical studies on commonly used benchmarks demonstrate that ASSUDA is resistant to adversarial attacks.

In adversarial training (AT), the main focus has been the objective and optimizer while the model has been less studied, so that the models being used are still those classic ones in standard training (ST). Classic network architectures (NAs) are generally worse than searched NA in ST, which should be the same in AT. In this paper, we argue that NA and AT cannot be handled independently, since given a dataset, the optimal NA in ST would be no longer optimal in AT. That being said, AT is time-consuming itself; if we directly search NAs in AT over large search spaces, the computation will be practically infeasible. Thus, we propose diverse-structured network (DS-Net), to significantly reduce the size of the search space: instead of low-level operations, we only consider predefined atomic blocks, where an atomic block is a time-tested building block like the residual block. There are only a few atomic blocks and thus we can weight all atomic blocks rather than find the best one in a searched block of DS-Net, which is an essential tradeoff between exploring diverse structures and exploiting the best structures. Empirical results demonstrate the advantages of DS-Net, i.e., weighting the atomic blocks.

Recently, the teacher-student knowledge distillation framework has demonstrated its potential in training Graph Neural Networks (GNNs). However, due to the difficulty of training over-parameterized GNN models, one may not easily obtain a satisfactory teacher model for distillation. Furthermore, the inefficient training process of teacher-student knowledge distillation also impedes its applications in GNN models. In this paper, we propose the first teacher-free knowledge distillation method for GNNs, termed GNN Self-Distillation (GNN-SD), that serves as a drop-in replacement of the standard training process. The method is built upon the proposed neighborhood discrepancy rate (NDR), which quantifies the non-smoothness of the embedded graph in an efficient way. Based on this metric, we propose the adaptive discrepancy retaining (ADR) regularizer to empower the transferability of knowledge that maintains high neighborhood discrepancy across GNN layers. We also summarize a generic GNN-SD framework that could be exploited to induce other distillation strategies. Experiments further prove the effectiveness and generalization of our approach, as it brings: 1) state-of-the-art GNN distillation performance with less training cost, 2) consistent and considerable performance enhancement for various popular backbones.

It is widely recognized that for the traveling salesman problem (TSP), there exists no universal best solver for all problem instances. This observation has greatly facilitated the research on Algorithm Selection (AS), which seeks to identify the solver best suited for each TSP instance. Such segregation usually relies on a prior representation step, in which problem instances are first represented by carefully established problem features. However, the creation of good features is non-trivial, typically requiring considerable domain knowledge and human effort. To alleviate this issue, this paper proposes a deep learning framework, named CTAS, for TSP solver selection. Specifically, CTAS exploits deep convolutional neural networks (CNN) to automatically extract informative features from TSP instances and utilizes data augmentation to handle the scarcity of labeled instances. Extensive experiments are conducted on a challenging TSP benchmark with 6,000 instances, which is the largest benchmark ever considered in this area. CTAS achieves over 2 × speedup of the average running time, compared with the single best solver. More importantly, CTAS is the first feature-free approach that notably outperforms classical AS models, showing huge potential of applying deep learning to AS tasks.

Graph Convolutional Networks (GCNs) are promising deep learning approaches in learning representations for graph-structured data. Despite the proliferation of such methods, it is well known that they are vulnerable to carefully crafted adversarial attacks on the graph structure. In this paper, we first conduct an adversarial vulnerability analysis based on matrix perturbation theory. We prove that the low- frequency components of the symmetric normalized Laplacian, which is usually used as the convolutional filter in GCNs, could be more robust against structural perturbations when their eigenvalues fall into a certain robust interval. Our results indicate that not all low-frequency components are robust to adversarial attacks and provide a deeper understanding of the relationship between graph spectrum and robustness of GCNs. Motivated by the theory, we present GCN-LFR, a general robust co-training paradigm for GCN-based models, that encourages transferring the robustness of low-frequency components with an auxiliary neural network. To this end, GCN-LFR could enhance the robustness of various kinds of GCN-based models against poisoning structural attacks in a plug-and-play manner. Extensive experiments across five benchmark datasets and five GCN-based models also confirm that GCN-LFR is resistant to the adversarial attacks without compromising on performance in the benign situation.

Subgraph counting, as a fundamental problem in network analysis, is to count the number of subgraphs in a data graph that match a given query graph by either homomorphism or subgraph isomorphism. The importance of subgraph counting derives from the fact that it provides insights of a large graph, in particular a labeled graph, when a collection of query graphs with different sizes and labels are issued. The problem of counting is challenging. On one hand, exact counting by enumerating subgraphs is NP-hard. % On the other hand, approximate counting by subgraph isomorphism can only support 3/5-node query graphs over unlabeled graphs. % Another way for subgraph counting is to specify it as an \SQL query and estimate the cardinality of the query in \rdbm. Existing approaches for cardinality estimation can only support subgraph counting by homomorphism up to some extent, as it is difficult to deal with sampling failure when a query graph becomes large. A question that arises is if subgraph counting can be supported by machine learning (ML) and deep learning (DL). The existing DL approach for subgraph isomorphism can only support small data graphs. The ML/DL approaches proposed in \rdbm context for approximate query processing and cardinality estimation cannot be used, as subgraph counting is to do complex self-joins over one relation, whereas existing approaches focus on multiple relations. In this paper, we propose an Active Learned Sketch for Subgraph Counting (\ALSS) with two main components: a sketch learned (ŁSS) and an active learner (\AL). The sketch is learned by a neural network regression model, and the active learner is to perform model updates based on new arrival test query graphs. % We conduct extensive experimental studies to confirm the effectiveness and efficiency of \ALSS using large real labeled graphs. Moreover, we show that \ALSS can assist query optimizers to find a better query plan for complex multi-way self-joins.

Social media has been developing rapidly in public due to its nature of spreading new information, which leads to rumors being circulated. Meanwhile, detecting rumors from such massive information in social media is becoming an arduous challenge. Therefore, some deep learning methods are applied to discover rumors through the way they spread, such as Recursive Neural Network (RvNN) and so on. However, these deep learning methods only take into account the patterns of deep propagation but ignore the structures of wide dispersion in rumor detection. Actually, propagation and dispersion are two crucial characteristics of rumors. In this paper, we propose a novel bi-directional graph model, named Bi-Directional Graph Convolutional Networks (Bi-GCN), to explore both characteristics by operating on both top-down and bottom-up propagation of rumors. It leverages a GCN with a top-down directed graph of rumor spreading to learn the patterns of rumor propagation; and a GCN with an opposite directed graph of rumor diffusion to capture the structures of rumor dispersion. Moreover, the information from source post is involved in each layer of GCN to enhance the influences from the roots of rumors. Encouraging empirical results on several benchmarks confirm the superiority of the proposed method over the state-of-the-art approaches.

With the great success of graph embedding model on both academic and industry area, the robustness of graph embedding against adversarial attack inevitably becomes a central problem in graph learning domain. Regardless of the fruitful progress, most of the current works perform the attack in a white-box fashion: they need to access the model predictions and labels to construct their adversarial loss. However, the inaccessibility of model predictions in real systems makes the white-box attack impractical to real graph learning system. This paper promotes current frameworks in a more general and flexible sense – we demand to attack various kinds of graph embedding model with black-box driven. To this end, we begin by investigating the theoretical connections between graph signal processing and graph embedding models in a principled way and formulate the graph embedding model as a general graph signal process with corresponding graph filter. As such, a generalized adversarial attacker: GF-Attack is constructed by the graph filter and feature matrix. Instead of accessing any knowledge of the target classifiers used in graph embedding, GF-Attack performs the attack only on the graph filter in a black-box attack fashion. To validate the generalization of GF-Attack, we construct the attacker on four popular graph embedding models. Extensive experimental results validate the effectiveness of our attacker on several benchmark datasets. Particularly by using our attack, even small graph perturbations like one-edge flip is able to consistently make a strong attack in performance to different graph embedding models.

Many real data come in the form of non-grid objects, i.e. graphs, from social networks to molecules. Adaptation of deep learning from grid-alike data (e.g. images) to graphs has recently received unprecedented attention from both machine learning and data mining communities, leading to a new cross-domain field---Deep Graph Learning (DGL). Instead of painstaking feature engineering, DGL aims to learn informative representations of graphs in an end-to-end manner. It has exhibited remarkable success in various tasks, such as node/graph classification, link prediction, etc.

Graph Neural Networks (GNN) and Variational Autoencoders (VAEs) have been widely used in modeling and generating graphs with latent factors. However there is no clear explanation of what these latent factors are and why they perform well. In this work, we present Dirichlet Graph Variational Autoencoder (DGVAE) with graph cluster memberships as latent factors. Our study connects VAEs based graph generation and balanced graph cut, and provides a new way to understand and improve the internal mechanism of VAEs based graph generation. Specifically, we first interpret the reconstruction term of DGVAE as balanced graph cut in a principled way. Furthermore, motivated by the low pass characteristics in balanced graph cut, we propose a new variant of GNN named Heatts to encode the input graph into cluster memberships. Heatts utilizes the Taylor series for fast computation of Heat kernels and has better low pass characteristics than Graph Convolutional Networks (GCN). Through experiments on graph generation and graph clustering, we demonstrate the effectiveness of our proposed framework.

How to obtain informative representations of molecules is a crucial prerequisite in AI-driven drug design and discovery. Recent researches abstract molecules as graphs and employ Graph Neural Networks (GNNs) for molecular representation learning. Nevertheless, two issues impede the usage of GNNs in real scenarios: (1) insufficient labeled molecules for supervised training; (2) poor generalization capability to new-synthesized molecules. To address them both, we propose a novel framework, GROVER, which stands for Graph Representation frOm self-superVised mEssage passing tRansformer. With carefully designed self-supervised tasks in node-, edge- and graph-level, GROVER can learn rich structural and semantic information of molecules from enormous unlabelled molecular data. Rather, to encode such complex information, GROVER integrates Message Passing Networks into the Transformer-style architecture to deliver a class of more expressive encoders of molecules. The flexibility of GROVER allows it to be trained efficiently on large-scale molecular dataset without requiring any supervision, thus being immunized to the two issues mentioned above. We pre-train GROVER with 100 million parameters on 10 million unlabelled molecules---the biggest GNN and the largest training dataset in molecular representation learning. We then leverage the pre-trained GROVER for molecular property prediction followed by task-specific fine-tuning, where we observe a huge improvement (more than 6% on average) from current state-of-the-art methods on 11 challenging benchmarks. The insights we gained are that well-designed self-supervision losses and largely-expressive pre-trained models enjoy the significant potential on performance boosting.

Deep multimodal fusion by using multiple sources of data for classification or regression has exhibited a clear advantage over the unimodal counterpart on various applications. Yet, current methods including aggregation-based and alignment-based fusion are still inadequate in balancing the trade-off between inter-modal fusion and intra-modal processing, incurring a bottleneck of performance improvement. To this end, this paper proposes Channel-Exchanging-Network (CEN), a parameter-free multimodal fusion framework that dynamically exchanges channels between sub-networks of different modalities. Specifically, the channel exchanging process is self-guided by individual channel importance that is measured by the magnitude of Batch-Normalization (BN) scaling factor during training. The validity of such exchanging process is also guaranteed by sharing convolutional filters yet keeping separate BN layers across modalities, which, as an add-on benefit, allows our multimodal architecture to be almost as compact as a unimodal network. Extensive experiments on semantic segmentation via RGB-D data and image translation through multi-domain input verify the effectiveness of our CEN compared to current state-of-the-art methods. Detailed ablation studies have also been carried out, which provably affirm the advantage of each component we propose. Our code is available at https://github.com/yikaiw/CEN.

It has been demonstrated that adversarial graphs, i.e., graphs with imperceptible perturbations added, can cause deep graph models to fail on node/graph classification tasks. In this paper, we extend adversarial graphs to the problem of community detection which is much more difficult. We focus on black-box attack and aim to hide targeted individuals from the detection of deep graph community detection models, which has many applications in real-world scenarios, for example, protecting personal privacy in social networks and understanding camouflage patterns in transaction networks. We propose an iterative learning framework that takes turns to update two modules: one working as the constrained graph generator and the other as the surrogate community detection model. We also find that the adversarial graphs generated by our method can be transferred to other learning based community detection models.

The richness in the content of various information networks such as social networks and communication networks provides the unprecedented potential for learning high-quality expressive representations without external supervision. This paper investigates how to preserve and extract the abundant information from graph-structured data into embedding space in an unsupervised manner. To this end, we propose a novel concept, Graphical Mutual Information (GMI), to measure the correlation between input graphs and high-level hidden representations. GMI generalizes the idea of conventional mutual information computations from vector space to the graph domain where measuring mutual information from two aspects of node features and topological structure is indispensable. GMI exhibits several benefits: First, it is invariant to the isomorphic transformation of input graphs—an inevitable constraint in many existing graph representation learning algorithms; Besides, it can be efficiently estimated and maximized by current mutual information estimation methods such as MINE; Finally, our theoretical analysis confirms its correctness and rationality. With the aid of GMI, we develop an unsupervised learning model trained by maximizing GMI between the input and output of a graph neural encoder. Considerable experiments on transductive as well as inductive node classification and link prediction demonstrate that our method outperforms state-of-the-art unsupervised counterparts, and even sometimes exceeds the performance of supervised ones.

Unsupervised domain adaptation (UDA) transfers knowledge from a label-rich source domain to a fully-unlabeled target domain. To tackle this task, recent approaches resort to discriminative domain transfer in virtue of pseudo-labels to enforce the class-level distribution alignment across the source and target domains. These methods, however, are vulnerable to the error accumulation and thus incapable of preserving cross-domain category consistency, as the pseudo-labeling accuracy is not guaranteed explicitly. In this paper, we propose the Progressive Feature Alignment Network (PFAN) to align the discriminative features across domains progressively and effectively, via exploiting the intra-class variation in the target domain. To be specific, we first develop an Easy-to-Hard Transfer Strategy (EHTS) and an Adaptive Prototype Alignment (APA) step to train our model iteratively and alternatively. Moreover, upon observing that a good domain adaptation usually requires a non-saturated source classifier, we consider a simple yet efficient way to retard the convergence speed of the source classification loss by further involving a temperature variate into the soft-max function. The extensive experimental results reveal that the proposed PFAN exceeds the state-of-the-art performance on three UDA datasets.

Most state-of-the-art action localization systems process each action proposal individually, without explicitly exploiting their relations during learning. However, the relations between proposals actually play an important role in action localization, since a meaningful action always consists of multiple proposals in a video. In this paper, we propose to exploit the proposal-proposal relations using GraphConvolutional Networks (GCNs). First, we construct an action proposal graph, where each proposal is represented as a node and their relations between two proposals as an edge. Here, we use two types of relations, one for capturing the context information for each proposal and the other one for characterizing the correlations between distinct actions. Then we apply the GCNs over the graph to model the relations among different proposals and learn powerful representations for the action classification and localization. Experimental results show that our approach significantly outperforms the state-of-the-art on THUMOS14(49.1% versus 42.8%). Moreover, augmentation experiments on ActivityNet also verify the efficacy of modeling action proposal relationships.

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 protein in a protein-protein interaction 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. For example, in a social network, a group of people with shared interests forms a user group, whereas a number of user groups are interconnected via interactions or common members. We study the node classification problem in the hierarchical graph where a “node” is a graph instance, e.g., a user group in the above example. As labels are usually limited in real-world data, we design two novel semi-supervised solutions named SEmi-supervised grAph cLassification via Cautious/Active Iteration (or SEAL-C/AI in short). SEAL-C/AI adopt an iterative framework that takes turns to build or update two classifiers, one working at the graph instance level and the other at the hierarchical graph level. To simplify the representation of the hierarchical graph, we propose a novel supervised, self-attentive graph embedding method called SAGE, which embeds graph instances of arbitrary size into fixed-length vectors. Through experiments on synthetic data and Tencent QQ group data, we demonstrate that SEAL-C/AI not only outperform competing methods by a significant margin in terms of accuracy/Macro-F1, but also generate meaningful interpretations of the learned representations.

With the increase of elderly population, Alzheimer's Disease (AD), as the most common cause of dementia among the elderly, is affecting more and more senior people. It is crucial for a patient to receive accurate and timely diagnosis of AD. Current diagnosis relies on doctors' experience and clinical test, which, unfortunately, may not be performed until noticeable AD symptoms are developed. In this work, we present our novel solution named time-aware TICC and CNN (TATC), for predicting AD from actigraphy data. TATC is a multivariate time series classification method using a neural attention-based deep learning approach. It not only performs accurate prediction of AD risk, but also generates meaningful interpretation of daily behavior pattern of subjects. TATC provides an automatic, low-cost solution for continuously monitoring the change of physical activity of subjects in daily living environment. We believe the future deployment of TATC can benefit both doctors and patients in early detection of potential AD risk.

Graph Convolutional Networks (GCNs) have become a crucial tool on learning representations of graph vertices. The main challenge of adapting GCNs on large-scale graphs is the scalability issue that it incurs heavy cost both in computation and memory due to the uncontrollable neighborhood expansion across layers. In this paper, we accelerate the training of GCNs through developing an adaptive layer-wise sampling method. By constructing the network layer by layer in a top-down passway, we sample the lower layer conditioned on the top one, where the sampled neighborhoods are shared by different parent nodes and the over expansion is avoided owing to the fixed-size sampling. More importantly, the proposed sampler is adaptive and applicable for explicit variance reduction, which in turn enhances the training of our method. Furthermore, we propose a novel and economical approach to promote the message passing over distant nodes by applying skip connections. Intensive experiments on several benchmarks verify the effectiveness of our method regarding the classification accuracy while enjoying faster convergence speed.

In recent years, modeling the relation between two graphs has received unprecedented attention from researchers due to its wide applications in many areas, such as social analysis and bioinformatics. The nature of relations between two graphs can be divided into two categories: the vertex relation and the link relation. Many studies focus on modeling the vertex relation between graphs and try to find the vertex correspondence between two graphs. However, the link relation between graphs has not been fully studied. Specifically, we model the cross-graph link relation as cross-graph dependence, which reflects the dependence of a vertex in one graph on a vertex in the other graph. A generic problem, called Graph Dependence Minimization (GDM), is defined as: given two graphs with cross-graph dependence, how to select a subset of vertexes from one graph and copy them to the other, so as to minimize the cross-graph dependence. Many real applications can benefit from the solution to GDM. Examples include reducing the cross-language links in online encyclopedias, optimizing the cross-platform communication cost between different cloud services, and so on. This problem is trivial if we can select as many vertexes as we want to copy. But what if we can only choose a limited number of vertexes to copy so as to make the two graphs as independent as possible? We formulate GDM with a budget constraint into a combinatorial optimization problem, which is proven to be NP-hard. We propose two algorithms to solve GDM. Firstly, we prove the submodularity of the objective function of GDM and adopt the size-constrained submodular minimization (SSM) algorithm to solve it. Since the SSM-based algorithm cannot scale to large graphs, we design a heuristic algorithm with a provable approximation guarantee. We prove that the error achieved by the heuristic algorithm is bounded by an additive factor which is proportional to the square of the given budget. Extensive experiments on both synthetic and real-world graphs show that the proposed algorithms consistently outperform the well-studied graph centrality measure based solutions. Furthermore, we conduct a case study on the Wikipedia graphs with millions of vertexes and links to demonstrate the potential of GDM to solve real-world problems.

Information diffusion through various types of networks, such as social networks and media networks, is a very common phenomenon on the Internet nowadays. In many scenarios, we can track only the time when the information reaches a node. However, the source infecting this node is usually unobserved. Inferring the underlying diffusion network based on cascade data (observed sequence of infected nodes with timestamp) without additional information is an essential and challenging task in information diffusion. Many studies have focused on constructing complex models to infer the underlying diffusion network in a parametric way. However, the diffusion process in the real world is very complex and hard to be captured by a parametric model. Even worse, inferring the parameters of a complex model is impractical under a large data volume.

In nowadays social networks, a huge volume of content containing rich information, such as reviews, ratings, microblogs, etc., is being generated, consumed and diffused by users all the time. Given the temporal information, we can obtain the event cascade which indicates the time sequence of the arrival of information to users. Many models have been proposed to explain how information diffuses. However, most existing models cannot give a clear explanation why every specific event happens in the event cascade. Such explanation is essential for us to have a deeper understanding of information diffusion as well as a better prediction of future event cascade.

Recommendation systems have been widely used in E-commerce sites, social networks, etc. One of the core tasks in recommendation systems is to predict the users' ratings on items. Although many models and algorithms have been proposed, how to make accurate prediction for new users with extremely few rating records still remains a big challenge, which is called the cold start problem. Many existing methods utilize additional information, such as social graphs, to cope with the cold start problem. However, the side information may not always be available. In contrast to such methods, we propose a more general solution to address the cold start problem based on the observed user rating records only. Specifically we define a random walk on a bipartite graph of users and items to simulate the preference propagation among users, in order to alleviate the data sparsity problem for cold start users. Then we propose a Monte Carlo algorithm to estimate the similarity between different users. This algorithm takes a precomputation approach, and thus can efficiently compute the user similarity given any new user for rating prediction. In addition, our algorithm can easily handle dynamic updates and can be parallelized naturally, which are crucial for large recommendation systems. Theoretical analysis is presented to demonstrate the efficiency and effectiveness of our algorithm, and extensive experiments also confirm our theoretical findings.