Standardising the representation of biomedical knowledge among all researchers is an insurmountable task, hindering the effectiveness of many computational methods. To facilitate harmonisation and interoperability despite this fundamental challenge, we propose to standardise the framework of knowledge graph creation instead. We implement this standardisation in BioCypher, a FAIR (findable, accessible, interoperable, reusable) framework to transparently build biomedical knowledge graphs while preserving provenances of the source data. Mapping the knowledge onto biomedical ontologies helps to balance the needs for harmonisation, human and machine readability, and ease of use and accessibility to non-specialist researchers. We demonstrate the usefulness of this framework on a variety of use cases, from maintenance of task-specific knowledge stores, to interoperability between biomedical domains, to on-demand building of task-specific knowledge graphs for federated learning. BioCypher (https://biocypher.org) frees up valuable developer time; we encourage further development and usage by the community.
Conversational recommender systems (CRSs) often utilize external knowledge graphs (KGs) to introduce rich semantic information and recommend relevant items through natural language dialogues. However, original KGs employed in existing CRSs are often incomplete and sparse, which limits the reasoning capability in recommendation. Moreover, only few of existing studies exploit the dialogue context to dynamically refine knowledge from KGs for better recommendation. To address the above issues, we propose the Variational Reasoning over Incomplete KGs Conversational Recommender (VRICR). Our key idea is to incorporate the large dialogue corpus naturally accompanied with CRSs to enhance the incomplete KGs; and perform dynamic knowledge reasoning conditioned on the dialogue context. Specifically, we denote the dialogue-specific subgraphs of KGs as latent variables with categorical priors for adaptive knowledge graphs refactor. We propose a variational Bayesian method to approximate posterior distributions over dialogue-specific subgraphs, which not only leverages the dialogue corpus for restructuring missing entity relations but also dynamically selects knowledge based on the dialogue context. Finally, we infuse the dialogue-specific subgraphs to decode the recommendation and responses. We conduct experiments on two benchmark CRSs datasets. Experimental results confirm the effectiveness of our proposed method.
Answering complex logical queries on incomplete knowledge graphs is a challenging task, and has been widely studied. Embedding-based methods require training on complex queries, and cannot generalize well to out-of-distribution query structures. Recent work frames this task as an end-to-end optimization problem, and it only requires a pretrained link predictor. However, due to the exponentially large combinatorial search space, the optimal solution can only be approximated, limiting the final accuracy. In this work, we propose QTO (Query Computation Tree Optimization) that can efficiently find the exact optimal solution. QTO finds the optimal solution by a forward-backward propagation on the tree-like computation graph, i.e., query computation tree. In particular, QTO utilizes the independence encoded in the query computation tree to reduce the search space, where only local computations are involved during the optimization procedure. Experiments on 3 datasets show that QTO obtains state-of-the-art performance on complex query answering, outperforming previous best results by an average of 22%. Moreover, QTO can interpret the intermediate solutions for each of the one-hop atoms in the query with over 90% accuracy. The code of our paper is at https://github.com/bys0318/QTO.
Understanding novel situations in the traffic domain requires an intricate combination of domain-specific and causal commonsense knowledge. Prior work has provided sufficient perception-based modalities for traffic monitoring, in this paper, we focus on a complementary research aspect of Intelligent Transportation: traffic understanding. We scope our study to text-based methods and datasets given the abundant commonsense knowledge that can be extracted using language models from large corpus and knowledge graphs. We adopt three knowledge-driven approaches for zero-shot QA over traffic situations, based on prior natural language inference methods, commonsense models with knowledge graph self-supervision, and dense retriever-based models. We constructed two text-based multiple-choice question answering sets: BDD-QA for evaluating causal reasoning in the traffic domain and HDT-QA for measuring the possession of domain knowledge akin to human driving license tests. Among the methods, Unified-QA reaches the best performance on the BDD-QA dataset with the adaptation of multiple formats of question answers. Language models trained with inference information and commonsense knowledge are also good at predicting the cause and effect in the traffic domain but perform badly at answering human-driving QA sets. For such sets, DPR+Unified-QA performs the best due to its efficient knowledge extraction.
We introduce a linguistically enhanced combination of pre-training methods for transformers. The pre-training objectives include POS-tagging, synset prediction based on semantic knowledge graphs, and parent prediction based on dependency parse trees. Our approach achieves competitive results on the Natural Language Inference task, compared to the state of the art. Specifically for smaller models, the method results in a significant performance boost, emphasizing the fact that intelligent pre-training can make up for fewer parameters and help building more efficient models. Combining POS-tagging and synset prediction yields the overall best results.
Knowledge graphs contain rich knowledge about various entities and the relational information among them, while temporal knowledge graphs (TKGs) describe and model the interactions of the entities over time. In this context, automatic temporal knowledge graph completion (TKGC) has gained great interest. Recent TKGC methods integrate advanced deep learning techniques, e.g., Transformers, and achieve superior model performance. However, this also introduces a large number of excessive parameters, which brings a heavier burden for parameter optimization. In this paper, we propose a simple but powerful graph encoder for TKGC, called TARGCN. TARGCN is parameter-efficient, and it extensively explores every entity's temporal context for learning contextualized representations. We find that instead of adopting various kinds of complex modules, it is more beneficial to efficiently capture the temporal contexts of entities. We experiment TARGCN on three benchmark datasets. Our model can achieve a more than 46% relative improvement on the GDELT dataset compared with state-of-the-art TKGC models. Meanwhile, it outperforms the strongest baseline on the ICEWS05-15 dataset with around 18% fewer parameters.
Numerous Graph Neural Networks (GNNs) have been developed to tackle the challenge of Knowledge Graph Embedding (KGE). However, many of these approaches overlook the crucial role of relation information and inadequately integrate it with entity information, resulting in diminished expressive power. In this paper, we propose a novel knowledge graph encoder that incorporates tensor decomposition within the aggregation function of Relational Graph Convolutional Network (R-GCN). Our model enhances the representation of neighboring entities by employing projection matrices of a low-rank tensor defined by relation types. This approach facilitates multi-task learning, thereby generating relation-aware representations. Furthermore, we introduce a low-rank estimation technique for the core tensor through CP decomposition, which effectively compresses and regularizes our model. We adopt a training strategy inspired by contrastive learning, which relieves the training limitation of the 1-N method inherent in handling vast graphs. We outperformed all our competitors on two common benchmark datasets, FB15k-237 and WN18RR, while using low-dimensional embeddings for entities and relations.
By focusing the pre-training process on domain-specific corpora, some domain-specific pre-trained language models (PLMs) have achieved state-of-the-art results. However, it is under-investigated to design a unified paradigm to inject domain knowledge in the PLM fine-tuning stage. We propose KnowledgeDA, a unified domain language model development service to enhance the task-specific training procedure with domain knowledge graphs. Given domain-specific task texts input, KnowledgeDA can automatically generate a domain-specific language model following three steps: (i) localize domain knowledge entities in texts via an embedding-similarity approach; (ii) generate augmented samples by retrieving replaceable domain entity pairs from two views of both knowledge graph and training data; (iii) select high-quality augmented samples for fine-tuning via confidence-based assessment. We implement a prototype of KnowledgeDA to learn language models for two domains, healthcare and software development. Experiments on domain-specific text classification and QA tasks verify the effectiveness and generalizability of KnowledgeDA.
Curated knowledge graphs encode domain expertise and improve the performance of recommendation, segmentation, ad targeting, and other machine learning systems in several domains. As new concepts emerge in a domain, knowledge graphs must be expanded to preserve machine learning performance. Manually expanding knowledge graphs, however, is infeasible at scale. In this work, we propose a method for knowledge graph expansion with humans-in-the-loop. Concretely, given a knowledge graph, our method predicts the "parents" of new concepts to be added to this graph for further verification by human experts. We show that our method is both accurate and provably "human-friendly". Specifically, we prove that our method predicts parents that are "near" concepts' true parents in the knowledge graph, even when the predictions are incorrect. We then show, with a controlled experiment, that satisfying this property increases both the speed and the accuracy of the human-algorithm collaboration. We further evaluate our method on a knowledge graph from Pinterest and show that it outperforms competing methods on both accuracy and human-friendliness. Upon deployment in production at Pinterest, our method reduced the time needed for knowledge graph expansion by ~400% (compared to manual expansion), and contributed to a subsequent increase in ad revenue of 20%.
Knowledge graph reasoning (KGR), aiming to deduce new facts from existing facts based on mined logic rules underlying knowledge graphs (KGs), has become a fast-growing research direction. It has been proven to significantly benefit the usage of KGs in many AI applications, such as question answering, recommendation systems, and etc. According to the graph types, existing KGR models can be roughly divided into three categories, i.e., static models, temporal models, and multi-modal models. Early works in this domain mainly focus on static KGR, and recent works try to leverage the temporal and multi-modal information, which are more practical and closer to real-world. However, no survey papers and open-source repositories comprehensively summarize and discuss models in this important direction. To fill the gap, we conduct a first survey for knowledge graph reasoning tracing from static to temporal and then to multi-modal KGs. Concretely, the models are reviewed based on bi-level taxonomy, i.e., top-level (graph types) and base-level (techniques and scenarios). Besides, the performances, as well as datasets, are summarized and presented. Moreover, we point out the challenges and potential opportunities to enlighten the readers. The corresponding open-source repository is shared on GitHub https://github.com/LIANGKE23/Awesome-Knowledge-Graph-Reasoning.
Recently, neural language representation models pre-trained on large corpus can capture rich co-occurrence information and be fine-tuned in downstream tasks to improve the performance. As a result, they have achieved state-of-the-art results in a large range of language tasks. However, there exists other valuable semantic information such as similar, opposite, or other possible meanings in external knowledge graphs (KGs). We argue that entities in KGs could be used to enhance the correct semantic meaning of language sentences. In this paper, we propose a new method CKG: Dynamic Representation Based on \textbf{C}ontext and \textbf{K}nowledge \textbf{G}raph. On the one side, CKG can extract rich semantic information of large corpus. On the other side, it can make full use of inside information such as co-occurrence in large corpus and outside information such as similar entities in KGs. We conduct extensive experiments on a wide range of tasks, including QQP, MRPC, SST-5, SQuAD, CoNLL 2003, and SNLI. The experiment results show that CKG achieves SOTA 89.2 on SQuAD compared with SAN (84.4), ELMo (85.8), and BERT$_{Base}$ (88.5).
There has been an explosion of interest in designing various Knowledge Graph Neural Networks (KGNNs), which achieve state-of-the-art performance and provide great explainability for recommendation. The promising performance is mainly resulting from their capability of capturing high-order proximity messages over the knowledge graphs. However, training KGNNs at scale is challenging due to the high memory usage. In the forward pass, the automatic differentiation engines (\textsl{e.g.}, TensorFlow/PyTorch) generally need to cache all intermediate activation maps in order to compute gradients in the backward pass, which leads to a large GPU memory footprint. Existing work solves this problem by utilizing multi-GPU distributed frameworks. Nonetheless, this poses a practical challenge when seeking to deploy KGNNs in memory-constrained environments, especially for industry-scale graphs. Here we present TinyKG, a memory-efficient GPU-based training framework for KGNNs for the tasks of recommendation. Specifically, TinyKG uses exact activations in the forward pass while storing a quantized version of activations in the GPU buffers. During the backward pass, these low-precision activations are dequantized back to full-precision tensors, in order to compute gradients. To reduce the quantization errors, TinyKG applies a simple yet effective quantization algorithm to compress the activations, which ensures unbiasedness with low variance. As such, the training memory footprint of KGNNs is largely reduced with negligible accuracy loss. To evaluate the performance of our TinyKG, we conduct comprehensive experiments on real-world datasets. We found that our TinyKG with INT2 quantization aggressively reduces the memory footprint of activation maps with $7 \times$, only with $2\%$ loss in accuracy, allowing us to deploy KGNNs on memory-constrained devices.
Knowledge graph (KG) is used to represent data in terms of entities and structural relations between the entities. This representation can be used to solve complex problems such as recommendation systems and question answering. In this study, a set of candidate drugs for COVID-19 are proposed by using Drug repurposing knowledge graph (DRKG). DRKG is a biological knowledge graph constructed using a vast amount of open source biomedical knowledge to understand the mechanism of compounds and the related biological functions. Node and relation embeddings are learned using knowledge graph embedding models and neural network and attention related models. Different models are used to get the node embedding by changing the objective of the model. These embeddings are later used to predict if a candidate drug is effective to treat a disease or how likely it is for a drug to bind to a protein associated to a disease which can be modelled as a link prediction task between two nodes. RESCAL performed the best on the test dataset in terms of MR, MRR and Hits@3.
Knowledge base completion (KBC) aims to predict the missing links in knowledge graphs. Previous KBC tasks and approaches mainly focus on the setting where all test entities and relations have appeared in the training set. However, there has been limited research on the zero-shot KBC settings, where we need to deal with unseen entities and relations that emerge in a constantly growing knowledge base. In this work, we systematically examine different possible scenarios of zero-shot KBC and develop a comprehensive benchmark, ZeroKBC, that covers these scenarios with diverse types of knowledge sources. Our systematic analysis reveals several missing yet important zero-shot KBC settings. Experimental results show that canonical and state-of-the-art KBC systems cannot achieve satisfactory performance on this challenging benchmark. By analyzing the strength and weaknesses of these systems on solving ZeroKBC, we further present several important observations and promising future directions.
Incorporating external knowledge into the response generation process is essential to building more helpful and reliable dialog agents. However, collecting knowledge-grounded conversations is often costly, calling for a better pre-trained model for grounded dialog generation that generalizes well w.r.t. different types of knowledge. In this work, we propose KPT (Keyword-guided Pre-Training), a novel self-supervised pre-training method for grounded dialog generation without relying on extra knowledge annotation. Specifically, we use a pre-trained language model to extract the most uncertain tokens in the dialog as keywords. With these keywords, we construct two kinds of knowledge and pre-train a knowledge-grounded response generation model, aiming at handling two different scenarios: (1) the knowledge should be faithfully grounded; (2) it can be selectively used. For the former, the grounding knowledge consists of keywords extracted from the response. For the latter, the grounding knowledge is additionally augmented with keywords extracted from other utterances in the same dialog. Since the knowledge is extracted from the dialog itself, KPT can be easily performed on a large volume and variety of dialogue data. We considered three data sources (open-domain, task-oriented, conversational QA) with a total of 2.5M dialogues. We conduct extensive experiments on various few-shot knowledge-grounded generation tasks, including grounding on dialog acts, knowledge graphs, persona descriptions, and Wikipedia passages. Our comprehensive experiments and analyses demonstrate that KPT consistently outperforms state-of-the-art methods on these tasks with diverse grounding knowledge.
Over the past few years, large knowledge bases have been constructed to store massive amounts of knowledge. However, these knowledge bases are highly incomplete, for example, over 70% of people in Freebase have no known place of birth. To solve this problem, we propose a query-driven knowledge base completion system with multimodal fusion of unstructured and structured information. To effectively fuse unstructured information from the Web and structured information in knowledge bases to achieve good performance, our system builds multimodal knowledge graphs based on question answering and rule inference. We propose a multimodal path fusion algorithm to rank candidate answers based on different paths in the multimodal knowledge graphs, achieving much better performance than question answering, rule inference and a baseline fusion algorithm. To improve system efficiency, query-driven techniques are utilized to reduce the runtime of our system, providing fast responses to user queries. Extensive experiments have been conducted to demonstrate the effectiveness and efficiency of our system.
Knowledge graphs (KGs) have attracted more and more attentions because of their fundamental roles in many tasks. Quality evaluation for KGs is thus crucial and indispensable. Existing methods in this field evaluate KGs by either proposing new quality metrics from different dimensions or measuring performances at KG construction stages. However, there are two major issues with those methods. First, they highly rely on raw data in KGs, which makes KGs' internal information exposed during quality evaluation. Second, they consider more about the quality at data level instead of ability level, where the latter one is more important for downstream applications. To address these issues, we propose a knowledge graph quality evaluation framework under incomplete information (QEII). The quality evaluation task is transformed into an adversarial Q&A game between two KGs. Winner of the game is thus considered to have better qualities. During the evaluation process, no raw data is exposed, which ensures information protection. Experimental results on four pairs of KGs demonstrate that, compared with baselines, the QEII implements a reasonable quality evaluation at ability level under incomplete information.
Knowledge graphs, modeling multi-relational data, improve numerous applications such as question answering or graph logical reasoning. Many graph neural networks for such data emerged recently, often outperforming shallow architectures. However, the design of such multi-relational graph neural networks is ad-hoc, driven mainly by intuition and empirical insights. Up to now, their expressivity, their relation to each other, and their (practical) learning performance is poorly understood. Here, we initiate the study of deriving a more principled understanding of multi-relational graph neural networks. Namely, we investigate the limitations in the expressive power of the well-known Relational GCN and Compositional GCN architectures and shed some light on their practical learning performance. By aligning both architectures with a suitable version of the Weisfeiler-Leman test, we establish under which conditions both models have the same expressive power in distinguishing non-isomorphic (multi-relational) graphs or vertices with different structural roles. Further, by leveraging recent progress in designing expressive graph neural networks, we introduce the $k$-RN architecture that provably overcomes the expressiveness limitations of the above two architectures. Empirically, we confirm our theoretical findings in a vertex classification setting over small and large multi-relational graphs.
Commonsense knowledge-graphs (CKGs) are important resources towards building machines that can 'reason' on text or environmental inputs and make inferences beyond perception. While current CKGs encode world knowledge for a large number of concepts and have been effectively utilized for incorporating commonsense in neural models, they primarily encode declarative or single-condition inferential knowledge and assume all conceptual beliefs to have the same likelihood. Further, these CKGs utilize a limited set of relations shared across concepts and lack a coherent knowledge organization structure resulting in redundancies as well as sparsity across the larger knowledge graph. Consequently, today's CKGs, while useful for a first level of reasoning, do not adequately capture deeper human-level commonsense inferences which can be more nuanced and influenced by multiple contextual or situational factors. Accordingly, in this work, we study how commonsense knowledge can be better represented by -- (i) utilizing a probabilistic logic representation scheme to model composite inferential knowledge and represent conceptual beliefs with varying likelihoods and (ii) incorporating a hierarchical conceptual ontology to identify salient concept-relevant relations and organize beliefs at different conceptual levels. Our resulting knowledge representation framework can encode a wider variety of world knowledge and represent beliefs flexibly using grounded concepts as well as free-text phrases. As a result, the framework can be utilized as both a traditional free-text knowledge graph and a grounded logic-based inference system more suitable for neuro-symbolic applications. We describe how we extend the PrimeNet knowledge base with our framework through crowd-sourcing and expert-annotation, and demonstrate its application for more interpretable passage-based semantic parsing and question answering.
Entity Alignment (EA), which aims to detect entity mappings (i.e. equivalent entity pairs) in different Knowledge Graphs (KGs), is critical for KG fusion. Neural EA methods dominate current EA research but still suffer from their reliance on labelled mappings. To solve this problem, a few works have explored boosting the training of EA models with self-training, which adds confidently predicted mappings into the training data iteratively. Though the effectiveness of self-training can be glimpsed in some specific settings, we still have very limited knowledge about it. One reason is the existing works concentrate on devising EA models and only treat self-training as an auxiliary tool. To fill this knowledge gap, we change the perspective to self-training to shed light on it. In addition, the existing self-training strategies have limited impact because they introduce either much False Positive noise or a low quantity of True Positive pseudo mappings. To improve self-training for EA, we propose exploiting the dependencies between entities, a particularity of EA, to suppress the noise without hurting the recall of True Positive mappings. Through extensive experiments, we show that the introduction of dependency makes the self-training strategy for EA reach a new level. The value of self-training in alleviating the reliance on annotation is actually much higher than what has been realised. Furthermore, we suggest future study on smart data annotation to break the ceiling of EA performance.