This thesis is a proof of concept for the potential of Variational Auto-Encoder (VAE) on representation learning of real-world Knowledge Graphs (KG). Inspired by successful approaches to the generation of molecular graphs, we evaluate the capabilities of our model, the Relational Graph Variational Auto-Encoder (RGVAE). The impact of the modular hyperparameter choices, encoding through graph convolutions, graph matching and latent space prior, is compared. The RGVAE is first evaluated on link prediction. The mean reciprocal rank (MRR) scores on the two datasets FB15K-237 and WN18RR are compared to the embedding-based model DistMult. A variational DistMult and a RGVAE without latent space prior constraint are implemented as control models. The results show that between different settings, the RGVAE with relaxed latent space, scores highest on both datasets, yet does not outperform the DistMult. Further, we investigate the latent space in a twofold experiment: first, linear interpolation between the latent representation of two triples, then the exploration of each latent dimension in a $95\%$ confidence interval. Both interpolations show that the RGVAE learns to reconstruct the adjacency matrix but fails to disentangle. For the last experiment we introduce a new validation method for the FB15K-237 data set. The relation type-constrains of generated triples are filtered and matched with entity types. The observed rate of valid generated triples is insignificantly higher than the random threshold. All generated and valid triples are unseen. A comparison between different latent space priors, using the $\delta$-VAE method, reveals a decoder collapse. Finally we analyze the limiting factors of our approach compared to molecule generation and propose solutions for the decoder collapse and successful representation learning of multi-relational KGs.
In recent years, there has been a resurgence in methods that use distributed (neural) representations to represent and reason about semantic knowledge for robotics applications. However, while robots often observe previously unknown concepts, these representations typically assume that all concepts are known a priori, and incorporating new information requires all concepts to be learned afresh. Our work relaxes this limiting assumption of existing representations and tackles the incremental knowledge graph embedding problem by leveraging the principles of a range of continual learning methods. Through an experimental evaluation with several knowledge graphs and embedding representations, we provide insights about trade-offs for practitioners to match a semantics-driven robotics applications to a suitable continual knowledge graph embedding method.
Entity Resolution (ER) is a constitutional part for integrating different knowledge graphs in order to identify entities referring to the same real-world object. A promising approach is the use of graph embeddings for ER in order to determine the similarity of entities based on the similarity of their graph neighborhood. The similarity computations for such embeddings translates to calculating the distance between them in the embedding space which is comparatively simple. However, previous work has shown that the use of graph embeddings alone is not sufficient to achieve high ER quality. We therefore propose a more comprehensive ER approach for knowledge graphs called EAGER (Embedding-Assisted Knowledge Graph Entity Resolution) to flexibly utilize both the similarity of graph embeddings and attribute values within a supervised machine learning approach. We evaluate our approach on 23 benchmark datasets with differently sized and structured knowledge graphs and use hypothesis tests to ensure statistical significance of our results. Furthermore we compare our approach with state-of-the-art ER solutions, where our approach yields competitive results for table-oriented ER problems and shallow knowledge graphs but much better results for deeper knowledge graphs.
There has been an increasing interest in inferring future links on temporal knowledge graphs (KG). While links on temporal KGs vary continuously over time, the existing approaches model the temporal KGs in discrete state spaces. To this end, we propose a novel continuum model by extending the idea of neural ordinary differential equations (ODEs) to multi-relational graph convolutional networks. The proposed model preserves the continuous nature of dynamic multi-relational graph data and encodes both temporal and structural information into continuous-time dynamic embeddings. In addition, a novel graph transition layer is applied to capture the transitions on the dynamic graph, i.e., edge formation and dissolution. We perform extensive experiments on five benchmark datasets for temporal KG reasoning, showing our model's superior performance on the future link forecasting task.
Recently, there has been a rising surge of momentum for deep representation learning in hyperbolic spaces due to theirhigh capacity of modeling data like knowledge graphs or synonym hierarchies, possessing hierarchical structure. We refer to the model as hyperbolic deep neural network in this paper. Such a hyperbolic neural architecture potentially leads to drastically compact model withmuch more physical interpretability than its counterpart in Euclidean space. To stimulate future research, this paper presents acoherent and comprehensive review of the literature around the neural components in the construction of hyperbolic deep neuralnetworks, as well as the generalization of the leading deep approaches to the Hyperbolic space. It also presents current applicationsaround various machine learning tasks on several publicly available datasets, together with insightful observations and identifying openquestions and promising future directions.
Personalized recommendations are popular in these days of Internet driven activities, specifically shopping. Recommendation methods can be grouped into three major categories, content based filtering, collaborative filtering and machine learning enhanced. Information about products and preferences of different users are primarily used to infer preferences for a specific user. Inadequate information can obviously cause these methods to fail or perform poorly. The more information we provide to these methods, the more likely it is that the methods perform better. Knowledge graphs represent the current trend in recording information in the form of relations between entities, and can provide additional (side) information about products and users. Such information can be used to improve nearest neighbour search, clustering users and products, or train the neural network, when one is used. In this work, we present a new generic recommendation systems framework, that integrates knowledge graphs into the recommendation pipeline. We describe its software design and implementation, and then show through experiments, how such a framework can be specialized for a domain, say movie recommendations, and the improvements in recommendation results possible due to side information obtained from knowledge graphs representation of such information. Our framework supports different knowledge graph representation formats, and facilitates format conversion, merging and information extraction needed for training recommendation methods.
Entity alignment (EA) is the task of identifying the entities that refer to the same real-world object but are located in different knowledge graphs (KGs). For entities to be aligned, existing EA solutions treat them separately and generate alignment results as ranked lists of entities on the other side. Nevertheless, this decision-making paradigm fails to take into account the interdependence among entities. Although some recent efforts mitigate this issue by imposing the 1-to-1 constraint on the alignment process, they still cannot adequately model the underlying interdependence and the results tend to be sub-optimal. To fill in this gap, in this work, we delve into the dynamics of the decision-making process, and offer a reinforcement learning (RL) based model to align entities collectively. Under the RL framework, we devise the coherence and exclusiveness constraints to characterize the interdependence and restrict collective alignment. Additionally, to generate more precise inputs to the RL framework, we employ representative features to capture different aspects of the similarity between entities in heterogeneous KGs, which are integrated by an adaptive feature fusion strategy. Our proposal is evaluated on both cross-lingual and mono-lingual EA benchmarks and compared against state-of-the-art solutions. The empirical results verify its effectiveness and superiority.
We present Knowledge Enhanced Multimodal BART (KM-BART), which is a Transformer-based sequence-to-sequence model capable of reasoning about commonsense knowledge from multimodal inputs of images and texts. We adapt the generative BART architecture to a multimodal model with visual and textual inputs. We further develop novel pretraining tasks to improve the model performance on the Visual Commonsense Generation (VCG) task. In particular, our pretraining task of Knowledge-based Commonsense Generation (KCG) boosts model performance on the VCG task by leveraging commonsense knowledge from a large language model pretrained on external commonsense knowledge graphs. To the best of our knowledge, we are the first to propose a dedicated task for improving model performance on the VCG task. Experimental results show that our model reaches state-of-the-art performance on the VCG task by applying these novel pretraining tasks.
Reading and writing research papers is one of the most privileged abilities that a qualified researcher should master. However, it is difficult for new researchers (\eg{students}) to fully {grasp} this ability. It would be fascinating if we could train an intelligent agent to help people read and summarize papers, and perhaps even discover and exploit the potential knowledge clues to write novel papers. Although there have been existing works focusing on summarizing (\emph{i.e.}, reading) the knowledge in a given text or generating (\emph{i.e.}, writing) a text based on the given knowledge, the ability of simultaneously reading and writing is still under development. Typically, this requires an agent to fully understand the knowledge from the given text materials and generate correct and fluent novel paragraphs, which is very challenging in practice. In this paper, we propose a Deep ReAder-Writer (DRAW) network, which consists of a \textit{Reader} that can extract knowledge graphs (KGs) from input paragraphs and discover potential knowledge, a graph-to-text \textit{Writer} that generates a novel paragraph, and a \textit{Reviewer} that reviews the generated paragraph from three different aspects. Extensive experiments show that our DRAW network outperforms considered baselines and several state-of-the-art methods on AGENDA and M-AGENDA datasets. Our code and supplementary are released at https://github.com/menggehe/DRAW.
Large-scale pre-trained language models have demonstrated strong knowledge representation ability. However, recent studies suggest that even though these giant models contains rich simple commonsense knowledge (e.g., bird can fly and fish can swim.), they often struggle with the complex commonsense knowledge that involves multiple eventualities (verb-centric phrases, e.g., identifying the relationship between ``Jim yells at Bob'' and ``Bob is upset'').To address this problem, in this paper, we propose to help pre-trained language models better incorporate complex commonsense knowledge. Different from existing fine-tuning approaches, we do not focus on a specific task and propose a general language model named CoCoLM. Through the careful training over a large-scale eventuality knowledge graphs ASER, we successfully teach pre-trained language models (i.e., BERT and RoBERTa) rich complex commonsense knowledge among eventualities. Experiments on multiple downstream commonsense tasks that requires the correct understanding of eventualities demonstrate the effectiveness of CoCoLM.
Modeling time-evolving knowledge graphs (KGs) has recently gained increasing interest. Here, graph representation learning has become the dominant paradigm for link prediction on temporal KGs. However, the embedding-based approaches largely operate in a black-box fashion, lacking the ability to interpret their predictions. This paper provides a link forecasting framework that reasons over query-relevant subgraphs of temporal KGs and jointly models the structural dependencies and the temporal dynamics. Especially, we propose a temporal relational attention mechanism and a novel reverse representation update scheme to guide the extraction of an enclosing subgraph around the query. The subgraph is expanded by an iterative sampling of temporal neighbors and by attention propagation. Our approach provides human-understandable evidence explaining the forecast. We evaluate our model on four benchmark temporal knowledge graphs for the link forecasting task. While being more explainable, our model obtains a relative improvement of up to 20% on Hits@1 compared to the previous best KG forecasting method. We also conduct a survey with 53 respondents, and the results show that the evidence extracted by the model for link forecasting is aligned with human understanding.
Knowledge Graphs (KGs) are ubiquitous structures for information storagein several real-world applications such as web search, e-commerce, social networks, and biology. Querying KGs remains a foundational and challenging problem due to their size and complexity. Promising approaches to tackle this problem include embedding the KG units (e.g., entities and relations) in a Euclidean space such that the query embedding contains the information relevant to its results. These approaches, however, fail to capture the hierarchical nature and semantic information of the entities present in the graph. Additionally, most of these approaches only utilize multi-hop queries (that can be modeled by simple translation operations) to learn embeddings and ignore more complex operations such as intersection and union of simpler queries. To tackle such complex operations, in this paper, we formulate KG representation learning as a self-supervised logical query reasoning problem that utilizes translation, intersection and union queries over KGs. We propose Hyperboloid Embeddings (HypE), a novel self-supervised dynamic reasoning framework, that utilizes positive first-order existential queries on a KG to learn representations of its entities and relations as hyperboloids in a Poincar\'e ball. HypE models the positive first-order queries as geometrical translation, intersection, and union. For the problem of KG reasoning in real-world datasets, the proposed HypE model significantly outperforms the state-of-the art results. We also apply HypE to an anomaly detection task on a popular e-commerce website product taxonomy as well as hierarchically organized web articles and demonstrate significant performance improvements compared to existing baseline methods. Finally, we also visualize the learned HypE embeddings in a Poincar\'e ball to clearly interpret and comprehend the representation space.
Sources of commonsense knowledge support applications in natural language understanding, computer vision, and knowledge graphs. Given their complementarity, their integration is desired. Yet, their different foci, modeling approaches, and sparse overlap make integration difficult. In this paper, we consolidate commonsense knowledge by following five principles, which we apply to combine seven key sources into a first integrated CommonSense Knowledge Graph (CSKG). We analyze CSKG and its various text and graph embeddings, showing that CSKG is well-connected and that its embeddings provide a useful entry point to the graph. We demonstrate how CSKG can provide evidence for generalizable downstream reasoning and for pre-training of language models. CSKG and all its embeddings are made publicly available to support further research on commonsense knowledge integration and reasoning.
We propose a generalization of transformer neural network architecture for arbitrary graphs. The original transformer was designed for Natural Language Processing (NLP), which operates on fully connected graphs representing all connections between the words in a sequence. Such architecture does not leverage the graph connectivity inductive bias, and can perform poorly when the graph topology is important and has not been encoded into the node features. We introduce a graph transformer with four new properties compared to the standard model. First, the attention mechanism is a function of the neighborhood connectivity for each node in the graph. Second, the positional encoding is represented by the Laplacian eigenvectors, which naturally generalize the sinusoidal positional encodings often used in NLP. Third, the layer normalization is replaced by a batch normalization layer, which provides faster training and better generalization performance. Finally, the architecture is extended to edge feature representation, which can be critical to tasks s.a. chemistry (bond type) or link prediction (entity relationship in knowledge graphs). Numerical experiments on a graph benchmark demonstrate the performance of the proposed graph transformer architecture. This work closes the gap between the original transformer, which was designed for the limited case of line graphs, and graph neural networks, that can work with arbitrary graphs. As our architecture is simple and generic, we believe it can be used as a black box for future applications that wish to consider transformer and graphs.
Accurately predicting the binding affinity between drugs and proteins is an essential step for computational drug discovery. Since graph neural networks (GNNs) have demonstrated remarkable success in various graph-related tasks, GNNs have been considered as a promising tool to improve the binding affinity prediction in recent years. However, most of the existing GNN architectures can only encode the topological graph structure of drugs and proteins without considering the relative spatial information among their atoms. Whereas, different from other graph datasets such as social networks and commonsense knowledge graphs, the relative spatial position and chemical bonds among atoms have significant impacts on the binding affinity. To this end, in this paper, we propose a diStance-aware Molecule graph Attention Network (S-MAN) tailored to drug-target binding affinity prediction. As a dedicated solution, we first propose a position encoding mechanism to integrate the topological structure and spatial position information into the constructed pocket-ligand graph. Moreover, we propose a novel edge-node hierarchical attentive aggregation structure which has edge-level aggregation and node-level aggregation. The hierarchical attentive aggregation can capture spatial dependencies among atoms, as well as fuse the position-enhanced information with the capability of discriminating multiple spatial relations among atoms. Finally, we conduct extensive experiments on two standard datasets to demonstrate the effectiveness of S-MAN.
Relation prediction for knowledge graphs aims at predicting missing relationships between entities. Despite the importance of inductive relation prediction, most previous works are limited to a transductive setting and cannot process previously unseen entities. The recent proposed subgraph-based relation reasoning models provided alternatives to predict links from the subgraph structure surrounding a candidate triplet inductively. However, we observe that these methods often neglect the directed nature of the extracted subgraph and weaken the role of relation information in the subgraph modeling. As a result, they fail to effectively handle the asymmetric/anti-symmetric triplets and produce insufficient embeddings for the target triplets. To this end, we introduce a \textbf{C}\textbf{o}mmunicative \textbf{M}essage \textbf{P}assing neural network for \textbf{I}nductive re\textbf{L}ation r\textbf{E}asoning, \textbf{CoMPILE}, that reasons over local directed subgraph structures and has a vigorous inductive bias to process entity-independent semantic relations. In contrast to existing models, CoMPILE strengthens the message interactions between edges and entitles through a communicative kernel and enables a sufficient flow of relation information. Moreover, we demonstrate that CoMPILE can naturally handle asymmetric/anti-symmetric relations without the need for explosively increasing the number of model parameters by extracting the directed enclosing subgraphs. Extensive experiments show substantial performance gains in comparison to state-of-the-art methods on commonly used benchmark datasets with variant inductive settings.
Large knowledge graphs often grow to store temporal facts that model the dynamic relations or interactions of entities along the timeline. Since such temporal knowledge graphs often suffer from incompleteness, it is important to develop time-aware representation learning models that help to infer the missing temporal facts. While the temporal facts are typically evolving, it is observed that many facts often show a repeated pattern along the timeline, such as economic crises and diplomatic activities. This observation indicates that a model could potentially learn much from the known facts appeared in history. To this end, we propose a new representation learning model for temporal knowledge graphs, namely CyGNet, based on a novel timeaware copy-generation mechanism. CyGNet is not only able to predict future facts from the whole entity vocabulary, but also capable of identifying facts with repetition and accordingly predicting such future facts with reference to the known facts in the past. We evaluate the proposed method on the knowledge graph completion task using five benchmark datasets. Extensive experiments demonstrate the effectiveness of CyGNet for predicting future facts with repetition as well as de novo fact prediction.
Cycle-consistent training is widely used for jointly learning a forward and inverse mapping between two domains of interest without the cumbersome requirement of collecting matched pairs within each domain. In this regard, the implicit assumption is that there exists (at least approximately) a ground-truth bijection such that a given input from either domain can be accurately reconstructed from successive application of the respective mappings. But in many applications no such bijection can be expected to exist and large reconstruction errors can compromise the success of cycle-consistent training. As one important instance of this limitation, we consider practically-relevant situations where there exists a many-to-one or surjective mapping between domains. To address this regime, we develop a conditional variational autoencoder (CVAE) approach that can be viewed as converting surjective mappings to implicit bijections whereby reconstruction errors in both directions can be minimized, and as a natural byproduct, realistic output diversity can be obtained in the one-to-many direction. As theoretical motivation, we analyze a simplified scenario whereby minima of the proposed CVAE-based energy function align with the recovery of ground-truth surjective mappings. On the empirical side, we consider a synthetic image dataset with known ground-truth, as well as a real-world application involving natural language generation from knowledge graphs and vice versa, a prototypical surjective case. For the latter, our CVAE pipeline can capture such many-to-one mappings during cycle training while promoting textural diversity for graph-to-text tasks. Our code is available at github.com/QipengGuo/CycleGT *A condensed version of this paper has been accepted to AISTATS 2021. This version contains additional content and updates.
Neural embedding-based machine learning models have shown promise for predicting novel links in biomedical knowledge graphs. Unfortunately, their practical utility is diminished by their lack of interpretability. Recently, the fully interpretable, rule-based algorithm AnyBURL yielded highly competitive results on many general-purpose link prediction benchmarks. However, its applicability to large-scale prediction tasks on complex biomedical knowledge bases is limited by long inference times and difficulties with aggregating predictions made by multiple rules. We improve upon AnyBURL by introducing the SAFRAN rule application framework which aggregates rules through a scalable clustering algorithm. SAFRAN yields new state-of-the-art results for fully interpretable link prediction on the established general-purpose benchmark FB15K-237 and the large-scale biomedical benchmark OpenBioLink. Furthermore, it exceeds the results of multiple established embedding-based algorithms on FB15K-237 and narrows the gap between rule-based and embedding-based algorithms on OpenBioLink. We also show that SAFRAN increases inference speeds by up to two orders of magnitude.
Commonsense question answering (QA) requires a model to grasp commonsense and factual knowledge to answer questions about world events. Many prior methods couple language modeling with knowledge graphs (KG). However, although a KG contains rich structural information, it lacks the context to provide a more precise understanding of the concepts. This creates a gap when fusing knowledge graphs into language modeling, especially when there is insufficient labeled data. Thus, we propose to employ external entity descriptions to provide contextual information for knowledge understanding. We retrieve descriptions of related concepts from Wiktionary and feed them as additional input to pre-trained language models. The resulting model achieves state-of-the-art result in the CommonsenseQA dataset and the best result among non-generative models in OpenBookQA.