ICLR 2023 Papers

Recent studies have shown that structural perturbations are significantly effective in degrading the accuracy of Graph Neural Networks (GNNs) in the semi-supervised node classification (SSNC) task. However, why the gradient-based methods are so destructive is rarely explored. In this work, we discover an interesting phenomenon: the adversarial edges are not uniformly distributed on the graph. Nearly all perturbations are generated around the training nodes in poisoning attack. Combined with this phenomenon, we provide an explanation for the effectiveness of the gradient-based attack method from a data distribution perspective and revisit both poisoning attack and evasion attack in SSNC. From this new perspective, we empirically and theoretically discuss some other attack tendencies. Based on the analysis, we provide nine practical tips on both attack and defense and meanwhile leverage them to improve existing attack and defense methods. Moreover, we design a fast attack method and a self-training defense method, which outperform the state-of-the-art methods and can effectively scale to large graphs like ogbn-arxiv. We conduct extensive experiments on four benchmark datasets to verify our claims.

Learning to optimize is a rapidly growing area that aims to solve optimization problems or improve existing optimization algorithms using machine learning (ML). In particular, the graph neural network (GNN) is considered a suitable ML model for optimization problems whose variables and constraints are permutation--invariant, for example, the linear program (LP). While the literature has reported encouraging numerical results, this paper establishes the theoretical foundation of applying GNNs to solving LPs. Given any size limit of LPs, we construct a GNN that maps different LPs to different outputs. We show that properly built GNNs can reliably predict feasibility, boundedness, and an optimal solution for each LP in a broad class. Our proofs are based upon the recently--discovered connections between the Weisfeiler--Lehman isomorphism test and the GNN. To validate our results, we train a simple GNN and present its accuracy in mapping LPs to their feasibilities and solutions.

Transformers flexibly operate over sets of real-valued vectors representing task-specific entities and their attributes, where each vector might encode one word-piece token and its position in a sequence, or some piece of information that carries no position at all. As set processors, transformers are at a disadvantage in reasoning over more general graph-structured data where nodes represent entities and edges represent relations between entities. To address this shortcoming, we generalize transformer attention to consider and update edge vectors in each transformer layer. We evaluate this relational transformer on a diverse array of graph-structured tasks, including the large and challenging CLRS Algorithmic Reasoning Benchmark. There, it dramatically outperforms state-of-the-art graph neural networks expressly designed to reason over graph-structured data. Our analysis demonstrates that these gains are attributable to relational attention's inherent ability to leverage the greater expressivity of graphs over sets.

Fully-parametric language models generally require a huge number of model parameters to store the necessary knowledge for solving multiple natural language tasks in zero/few-shot settings. In addition, it is hard to adapt to the evolving world knowledge without the costly model re-training. In this paper, we develop a novel semi-parametric language model architecture, Knowledge-in-Context (KiC), which empowers a parametric text-to-text language model with a knowledge-rich external memory. Specifically, the external memory contains six different types of knowledge: entity, dictionary, commonsense, event, script, and causality knowledge. For each input instance, the KiC model adaptively selects a knowledge type and retrieves the most helpful pieces of knowledge. The input instance along with its knowledge augmentation is fed into a text-to-text model (e.g., T5) to generate the output answer, where both the input and the output are in natural language forms after prompting. Interestingly, we find that KiC can be identified as a special mixture-of-experts (MoE) model, where the knowledge selector plays the role of a router that is used to determine the sequence-to-expert assignment in MoE. This key observation inspires us to develop a novel algorithm for training KiC with an instance-adaptive knowledge selector. As a knowledge-rich semi-parametric language model, KiC only needs a much smaller parametric part to achieve superior zero-shot performance on unseen tasks. By evaluating on 40+ different tasks, we show that KiC-Large with 770M parameters easily outperforms large language models that are 4-39x larger. In addition, KiC also exhibits emergent abilities at a much smaller model scale compared to the fully-parametric models.

Compared with static knowledge graphs, temporal knowledge graphs (tKG), which can capture the evolution and change of information over time, are more realistic and general. However, due to the complexity that the notion of time introduces to the learning of the rules, an accurate graph reasoning, e.g., predicting new links between entities, is still a difficult problem. In this paper, we propose TILP, a differentiable framework for temporal logical rules learning. By designing a constrained random walk mechanism and the introduction of temporal operators, we ensure the efficiency of our model. We present temporal features modeling in tKG, e.g., recurrence, temporal order, interval between pair of relations, and duration, and incorporate it into our learning process. We compare TILP with state-of-the-art methods on two benchmark datasets. We show that our proposed framework can improve upon the performance of baseline methods while providing interpretable results. In particular, we consider various scenarios in which training samples are limited, data is biased, and the time range between training and inference are different. In all these cases, TILP works much better than the state-of-the-art methods.

Multi-hop Question Answering over Knowledge Graph~(KGQA) aims to find the answer entities that are multiple hops away from the topic entities mentioned in a natural language question on a large-scale Knowledge Graph (KG). To cope with the vast search space, existing work usually adopts a two-stage approach: it first retrieves a relatively small subgraph related to the question and then performs the reasoning on the subgraph to find the answer entities accurately. Although these two stages are highly related, previous work employs very different technical solutions for developing the retrieval and reasoning models, neglecting their relatedness in task essence. In this paper, we propose UniKGQA, a novel approach for multi-hop KGQA task, by unifying retrieval and reasoning in both model architecture and parameter learning. For model architecture, UniKGQA consists of a semantic matching module based on a pre-trained language model~(PLM) for question-relation semantic matching, and a matching information propagation module to propagate the matching information along the directed edges on KGs. For parameter learning, we design a shared pre-training task based on question-relation matching for both retrieval and reasoning models, and then propose retrieval- and reasoning-oriented fine-tuning strategies. Compared with previous studies, our approach is more unified, tightly relating the retrieval and reasoning stages. Extensive experiments on three benchmark datasets have demonstrated the effectiveness of our method on the multi-hop KGQA task. Our codes and data are publicly available at~\url{https://github.com/RUCAIBox/UniKGQA}.

This paper investigates a missing feature imputation problem for graph learning tasks. Several methods have previously addressed learning tasks on graphs with missing features. However, in cases of high rates of missing features, they were unable to avoid significant performance degradation. To overcome this limitation, we introduce a novel concept of channel-wise confidence in a node feature, which is assigned to each imputed channel feature of a node for reflecting the certainty of the imputation. We then design pseudo-confidence using the channel-wise shortest path distance between a missing-feature node and its nearest known-feature node to replace unavailable true confidence in an actual learning process. Based on the pseudo-confidence, we propose a novel feature imputation scheme that performs channel-wise inter-node diffusion and node-wise inter-channel propagation. The scheme can endure even at an exceedingly high missing rate (e.g., 99.5\%) and it achieves state-of-the-art accuracy for both semi-supervised node classification and link prediction on various datasets containing a high rate of missing features. Codes are available at https://github.com/daehoum1/pcfi.

Question answering over knowledge bases (KBs) aims to answer natural language questions with factual information such as entities and relations in KBs. Previous methods either generate logical forms that can be executed over KBs to obtain final answers or predict answers directly. Empirical results show that the former often produces more accurate answers, but it suffers from non-execution issues due to potential syntactic and semantic errors in the generated logical forms. In this work, we propose a novel framework DecAF that jointly generates both logical forms and direct answers, and then combines the merits of them to get the final answers. Moreover, different from most of the previous methods, DecAF is based on simple free-text retrieval without relying on any entity linking tools --- this simplification eases its adaptation to different datasets. DecAF achieves new state-of-the-art accuracy on WebQSP, FreebaseQA, and GrailQA benchmarks, while getting competitive results on the ComplexWebQuestions benchmark.

Graph unlearning, which involves deleting graph elements such as nodes, node labels, and relationships from a trained graph neural network (GNN) model, is crucial for real-world applications where data elements may become irrelevant, inaccurate, or privacy-sensitive. However, existing methods for graph unlearning either deteriorate model weights shared across all nodes or fail to effectively delete edges due to their strong dependence on local graph neighborhoods. To address these limitations, we introduce GNNDelete, a novel model-agnostic layer-wise operator that optimizes two critical properties, namely, Deleted Edge Consistency and Neighborhood Influence, for graph unlearning. Deleted Edge Consistency ensures that the influence of deleted elements is removed from both model weights and neighboring representations, while Neighborhood Influence guarantees that the remaining model knowledge is preserved after deletion. GNNDelete updates representations to delete nodes and edges from the model while retaining the rest of the learned knowledge. We conduct experiments on seven real-world graphs, showing that GNNDelete outperforms existing approaches by up to 38.8% (AUC) on edge, node, and node feature deletion tasks, and 32.2% on distinguishing deleted edges from non-deleted ones. Additionally, GNNDelete is efficient, taking 12.3x less time and 9.3x less space than retraining GNN from scratch on WordNet18.

Existing Graph Neural Networks (GNNs) compute the message exchange between nodes by either aggregating uniformly (convolving) the features of all the neighbor- ing nodes, or by applying a non-uniform score (attending) to the features. Recent works have shown the strengths and weaknesses of the resulting GNN architectures, respectively, GCNs and GATs. In this work, we aim at exploiting the strengths of both approaches to their full extent. To this end, we first introduce the graph convolutional attention layer (CAT), which relies on convolutions to compute the attention scores. Unfortunately, as in the case of GCNs and GATs, we show that there exists no clear winner between the three—neither theoretically nor in practice—as their performance directly depends on the nature of the data (i.e., of the graph and features). This result brings us to the main contribution of our work, the learnable graph convolutional attention network (L-CAT): a GNN architecture that automatically interpolates between GCN, GAT and CAT in each layer, by adding only two scalar parameters. Our results demonstrate that L-CAT is able to efficiently combine different GNN layers along the network, outperforming competing methods in a wide range of datasets, and resulting in a more robust model that reduces the need of cross-validating.

Protein representation learning has primarily benefited from the remarkable development of language models (LMs). Accordingly, pre-trained protein models also suffer from a problem in LMs: a lack of factual knowledge. The recent solution models the relationships between protein and associated knowledge terms as the knowledge encoding objective. However, it fails to explore the relationships at a more granular level, i.e., the token level. To mitigate this, we propose Knowledge-exploited Auto-encoder for Protein (KeAP), which performs token-level knowledge graph exploration for protein representation learning. In practice, non-masked amino acids iteratively query the associated knowledge tokens to extract and integrate helpful information for restoring masked amino acids via attention. We show that KeAP can consistently outperform the previous counterpart on 9 representative downstream applications, sometimes surpassing it by large margins. These results suggest that KeAP provides an alternative yet effective way to perform knowledge enhanced protein representation learning.

We formally study how \emph{ensemble} of deep learning models can improve test accuracy, and how the superior performance of ensemble can be distilled into a single model using \emph{knowledge distillation}. We consider the challenging case where the ensemble is simply an average of the outputs of a few independently trained neural networks with the \emph{same} architecture, trained using the \emph{same} algorithm on the \emph{same} data set, and they only differ by the random seeds used in the initialization. We show that ensemble/knowledge distillation in \emph{deep learning} works very differently from traditional learning theory (such as boosting or NTKs). We develop a theory showing that when data has a structure we refer to as ``multi-view'', then ensemble of independently trained neural networks can provably improve test accuracy, and such superior test accuracy can also be provably distilled into a single model. Our result sheds light on how ensemble works in deep learning in a way that is completely different from traditional theorems, and how the ``dark knowledge'' is hidden in the outputs of the ensemble and can be used in distillation.

Existing federated learning paradigms usually extensively exchange distributed models, rather than original data, at a central solver to achieve a more powerful model. However, this would incur severe communication burden between a server and multiple clients especially when data distributions are heterogeneous. As a result, current federated learning methods often require plenty of communication rounds in training. Unlike existing paradigms, we introduce an alternative perspective to significantly decrease the federate learning communication cost without leaking original data. In this work, we first present a meta knowledge representation method that extracts meta knowledge from distributed clients. The extracted meta knowledge encodes essential information that can be used to improve the current model. As the training progresses, the contributions of the same training samples to a federated model should also vary. Thus, we introduce a dynamic weight assignment mechanism that enables informative samples to contribute adaptively to the current model update. Then, informative meta knowledge from all active clients is sent to the server for model update. Training model on the combined meta knowledge that is regarded as a condense form of original data can significantly mitigate the heterogeneity issues. Moreover, to further ameliorate data heterogeneity, we also exchange meta knowledge among clients as conditional initialisation for meta knowledge extraction. Extensive experiments demonstrate the effectiveness and efficiency of our proposed method. Remarkably, our method outperforms the state-of-the-art by a large margin (from $74.07\%$ to $92.95\%$) on MNIST with a restricted communication budget (\textit{i.e.}, 10 rounds).

Complex Query Answering (CQA) over Knowledge Graphs (KGs) has attracted a lot of attention to potentially support many applications. Given that KGs are usually incomplete, neural models are proposed to answer the logical queries by parameterizing set operators with complex neural networks. However, such methods usually train neural set operators with a large number of entity and relation embeddings from the zero, where whether and how the embeddings or the neural set operators contribute to the performance remains not clear. In this paper, we propose a simple framework for complex query answering that decomposes the KG embeddings from neural set operators. We propose to represent the complex queries into the query graph. On top of the query graph, we propose the Logical Message Passing Neural Network (LMPNN) that connects the local one-hop inferences on atomic formulas to the global logical reasoning for complex query answering. We leverage existing effective KG embeddings to conduct one-hop inferences on atomic formulas, the results of which are regarded as the messages passed in LMPNN. The reasoning process over the overall logical formulas is turned into the forward pass of LMPNN that incrementally aggregates local information to finally predict the answers' embeddings. The complex logical inference across different types of queries will then be learned from training examples based on the LMPNN architecture. Theoretically, our query-graph represenation is more general than the prevailing operator-tree formulation, so our approach applies to a broader range of complex KG queries. Empirically, our approach yields the new state-of-the-art neural CQA model. Our research bridges the gap between complex KG query answering tasks and the long-standing achievements of knowledge graph representation learning. Our implementation can be found at https://github.com/HKUST-KnowComp/LMPNN.

Temporal networks model a variety of important phenomena involving timed interactions between entities. Existing methods for machine learning on temporal networks generally exhibit at least one of two limitations. First, many methods assume time to be discretized, so if the time data is continuous, the user must determine the discretization and discard precise time information. Second, edge representations can only be calculated indirectly from the nodes, which may be suboptimal for tasks like edge classification. We present a simple method that avoids both shortcomings: construct the line graph of the network, which includes a node for each interaction, and weigh the edges of this graph based on the difference in time between interactions. From this derived graph, edge representations for the original network can be computed with efficient classical methods. The simplicity of this approach facilitates explicit theoretical analysis: we can constructively show the effectiveness of our method's representations for a natural synthetic model of temporal networks. Empirical results on real-world networks demonstrate our method's efficacy and efficiency on both link classification and prediction.

We introduce SignNet and BasisNet---new neural architectures that are invariant to two key symmetries displayed by eigenvectors: (i) sign flips, since if v is an eigenvector then so is -v; and (ii) more general basis symmetries, which occur in higher dimensional eigenspaces with infinitely many choices of basis eigenvectors. We prove that under certain conditions our networks are universal, i.e., they can approximate any continuous function of eigenvectors with the desired invariances. When used with Laplacian eigenvectors, our networks are provably more expressive than existing spectral methods on graphs; for instance, they subsume all spectral graph convolutions, certain spectral graph invariants, and previously proposed graph positional encodings as special cases. Experiments show that our networks significantly outperform existing baselines on molecular graph regression, learning expressive graph representations, and learning neural fields on triangle meshes. Our code is available at https://github.com/cptq/SignNet-BasisNet.

Analogical reasoning is fundamental to human cognition and holds an important place in various fields. However, previous studies mainly focus on single-modal analogical reasoning and ignore taking advantage of structure knowledge. Notably, the research in cognitive psychology has demonstrated that information from multimodal sources always brings more powerful cognitive transfer than single modality sources. To this end, we introduce the new task of multimodal analogical reasoning over knowledge graphs, which requires multimodal reasoning ability with the help of background knowledge. Specifically, we construct a Multimodal Analogical Reasoning dataSet (MARS) and a multimodal knowledge graph MarKG. We evaluate with multimodal knowledge graph embedding and pre-trained Transformer baselines, illustrating the potential challenges of the proposed task. We further propose a novel model-agnostic Multimodal analogical reasoning framework with Transformer (MarT) motivated by the structure mapping theory, which can obtain better performance. We hope our work can deliver benefits and inspire future research. Code and datasets are available in https://github.com/zjunlp/MKG_Analogy.

Graph neural networks (GNNs) for temporal graphs have recently attracted increasing attentions, where a common assumption is that the class set for nodes is closed. However, in real-world scenarios, it often faces the open set problem with the dynamically increased class set as the time passes by. This will bring two big challenges to the existing dynamic GNN methods: (i) How to dynamically propagate appropriate information in an open temporal graph, where new class nodes are often linked to old class nodes. This case will lead to a sharp contradiction. This is because typical GNNs are prone to make the embeddings of connected nodes become similar, while we expect the embeddings of these two interactive nodes to be distinguishable since they belong to different classes. (ii) How to avoid catastrophic knowledge forgetting over old classes when learning new classes occurred in temporal graphs. In this paper, we propose a general and principled learning approach for open temporal graphs, called OTGNet, with the goal of addressing the above two challenges. We assume the knowledge of a node can be disentangled into class-relevant and class-agnostic one, and thus explore a new message passing mechanism by extending the information bottleneck principle to only propagate class-agnostic knowledge between nodes of different classes, avoiding aggregating conflictive information. Moreover, we devise a strategy to select both important and diverse triad sub-graph structures for effective class-incremental learning. Extensive experiments on three real-world datasets of different domains demonstrate the superiority of our method, compared to the baselines.

We propose a novel knowledge distillation (KD) method to selectively instill teacher knowledge into a student model motivated by situations where the student's capacity is significantly smaller than that of the teachers. In vanilla KD, the teacher primarily sets a predictive target for the student to follow, and we posit that this target is overly optimistic due to the student's lack of capacity. We develop a novel scaffolding scheme where the teacher, in addition to setting a predictive target, also scaffolds the student's prediction by censoring hard-to-learn examples. Scaffolding utilizes the same information as the teacher's soft-max predictions as inputs, and in this sense, our proposal can be viewed as a natural variant of vanilla KD. We show on synthetic examples that censoring hard-examples leads to smoothening the student's loss landscape so that the student encounters fewer local minima. As a result, it has good generalization properties. Against vanilla KD, we achieve improved performance and are comparable to more intrusive techniques that leverage feature matching on benchmark datasets.