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.

Covid-19上的知识图（KGS）已建立在加速Covid-19的研究过程中。然而，KGs总是不完整，特别是新建造的Covid-19公斤。链路预测任务旨在预测（e，r，t）或（h，r，e）的丢失实体，其中H和t是某些实体，E是需要预测的实体，R是关系。这项任务还有可能解决Covid-19相关的KGS的不完全问题。虽然已经提出了各种知识图形嵌入（KGE）方法的链路预测任务，但这些现有方法遭受了使用单个评分函数的限制，这不能捕获Covid-19 Kgs的丰富特征。在这项工作中，我们提出了利用多个评分函数来提取来自现有三元组的更多特征的MDistmult模型。我们在CCKS2020 Covid-19抗病毒药物知识图（CADKG）上采用实验。实验结果表明，我们的MDistmult在CADKG数据集上的链路预测任务中实现了最先进的性能

事实证明，信息提取方法可有效从结构化或非结构化数据中提取三重。以（头部实体，关系，尾部实体）形式组织这样的三元组的组织称为知识图（kgs）。当前的大多数知识图都是不完整的。为了在下游任务中使用kgs，希望预测kgs中缺少链接。最近，通过将实体和关系嵌入到低维的矢量空间中，旨在根据先前访问的三元组来预测三元组，从而对KGS表示不同的方法。根据如何独立或依赖对三元组进行处理，我们将知识图完成的任务分为传统和图形神经网络表示学习，并更详细地讨论它们。在传统的方法中，每个三重三倍将独立处理，并在基于GNN的方法中进行处理，三倍也考虑了他们的当地社区。查看全文

学术知识图（KGS）提供了代表科学出版物编码的知识的丰富的结构化信息来源。随着出版的科学文学的庞大，包括描述科学概念的过多的非均匀实体和关系，这些公斤本质上是不完整的。我们呈现Exbert，一种利用预先训练的变压器语言模型来执行学术知识图形完成的方法。我们将知识图形的三元组模型为文本并执行三重分类（即，属于KG或不属于KG）。评估表明，在三重分类，链路预测和关系预测的任务中，Exbert在三个学术kg完成数据集中表现出其他基线。此外，我们将两个学术数据集作为研究界的资源，从公共公共公报和在线资源中收集。

Biomedical knowledge graphs (KG) are heterogenous networks consisting of biological entities as nodes and relations between them as edges. These entities and relations are extracted from millions of research papers and unified in a single resource. The goal of biomedical multi-hop question-answering over knowledge graph (KGQA) is to help biologist and scientist to get valuable insights by asking questions in natural language. Relevant answers can be found by first understanding the question and then querying the KG for right set of nodes and relationships to arrive at an answer. To model the question, language models such as RoBERTa and BioBERT are used to understand context from natural language question. One of the challenges in KGQA is missing links in the KG. Knowledge graph embeddings (KGE) help to overcome this problem by encoding nodes and edges in a dense and more efficient way. In this paper, we use a publicly available KG called Hetionet which is an integrative network of biomedical knowledge assembled from 29 different databases of genes, compounds, diseases, and more. We have enriched this KG dataset by creating a multi-hop biomedical question-answering dataset in natural language for testing the biomedical multi-hop question-answering system and this dataset will be made available to the research community. The major contribution of this research is an integrated system that combines language models with KG embeddings to give highly relevant answers to free-form questions asked by biologists in an intuitive interface. Biomedical multi-hop question-answering system is tested on this data and results are highly encouraging.

近年来，人们对少量知识图（FKGC）的兴趣日益增加，该图表旨在推断出关于该关系的一些参考三元组，从而推断出不见了的查询三倍。现有FKGC方法的主要重点在于学习关系表示，可以反映查询和参考三元组共享的共同信息。为此，这些方法从头部和尾部实体的直接邻居中学习实体对表示，然后汇总参考实体对的表示。但是，只有从直接邻居那里学到的实体对代表可能具有较低的表现力，当参与实体稀疏直接邻居或与其他实体共享一个共同的当地社区。此外，仅仅对头部和尾部实体的语义信息进行建模不足以准确推断其关系信息，尤其是当它们具有多个关系时。为了解决这些问题，我们提出了一个特定于关系的上下文学习（RSCL）框架，该框架利用了三元组的图形上下文，以学习全球和本地关系特定的表示形式，以使其几乎没有相关关系。具体而言，我们首先提取每个三倍的图形上下文，这可以提供长期实体关系依赖性。为了编码提取的图形上下文，我们提出了一个分层注意网络，以捕获三元组的上下文信息并突出显示实体的有价值的本地邻里信息。最后，我们设计了一个混合注意聚合器，以评估全球和本地级别的查询三元组的可能性。两个公共数据集的实验结果表明，RSCL的表现优于最先进的FKGC方法。

在本文中，我们介绍了一种新的基于GNN的知识图形嵌入模型，命名为WGE，以捕获聚焦的图形结构和关联的图形结构。特别是，鉴于知识图形，WGE构建一个无向实体的聚焦图，该图形将实体视为节点。此外，WGE还从关联的约束构造另一个无向图形，将实体和关系视为节点。然后，WGE提出了一种新的架构，即直接在这两个单个图表上使用两个vanilla GNNS，以更好地更新实体和关系的矢量表示，然后是加权得分函数来返回三重分数。实验结果表明，WGE在三个新的和具有挑战性的基准数据集Codex上获得最先进的表演，用于知识图形完成。

The development of deep neural networks has improved representation learning in various domains, including textual, graph structural, and relational triple representations. This development opened the door to new relation extraction beyond the traditional text-oriented relation extraction. However, research on the effectiveness of considering multiple heterogeneous domain information simultaneously is still under exploration, and if a model can take an advantage of integrating heterogeneous information, it is expected to exhibit a significant contribution to many problems in the world. This thesis works on Drug-Drug Interactions (DDIs) from the literature as a case study and realizes relation extraction utilizing heterogeneous domain information. First, a deep neural relation extraction model is prepared and its attention mechanism is analyzed. Next, a method to combine the drug molecular structure information and drug description information to the input sentence information is proposed, and the effectiveness of utilizing drug molecular structures and drug descriptions for the relation extraction task is shown. Then, in order to further exploit the heterogeneous information, drug-related items, such as protein entries, medical terms and pathways are collected from multiple existing databases and a new data set in the form of a knowledge graph (KG) is constructed. A link prediction task on the constructed data set is conducted to obtain embedding representations of drugs that contain the heterogeneous domain information. Finally, a method that integrates the input sentence information and the heterogeneous KG information is proposed. The proposed model is trained and evaluated on a widely used data set, and as a result, it is shown that utilizing heterogeneous domain information significantly improves the performance of relation extraction from the literature.

The ability of knowledge graphs to represent complex relationships at scale has led to their adoption for various needs including knowledge representation, question-answering, fraud detection, and recommendation systems. Knowledge graphs are often incomplete in the information they represent, necessitating the need for knowledge graph completion tasks, such as link and relation prediction. Pre-trained and fine-tuned language models have shown promise in these tasks although these models ignore the intrinsic information encoded in the knowledge graph, namely the entity and relation types. In this work, we propose the Knowledge Graph Language Model (KGLM) architecture, where we introduce a new entity/relation embedding layer that learns to differentiate distinctive entity and relation types, therefore allowing the model to learn the structure of the knowledge graph. In this work, we show that further pre-training the language models with this additional embedding layer using the triples extracted from the knowledge graph, followed by the standard fine-tuning phase sets a new state-of-the-art performance for the link prediction task on the benchmark datasets.

由于知识图（kgs）的不完整，旨在预测kgs中未观察到的关系的零照片链接预测（ZSLP）引起了研究人员的最新兴趣。一个常见的解决方案是将关系的文本特征（例如表面名称或文本描述）用作辅助信息，以弥合所见关系和看不见的关系之间的差距。当前方法学习文本中每个单词令牌的嵌入。这些方法缺乏稳健性，因为它们遭受了量不足（OOV）的问题。同时，建立在字符n-grams上的模型具有为OOV单词生成表达式表示的能力。因此，在本文中，我们提出了一个为零链接预测（HNZSLP）的层次N-gram框架，该框架考虑了ZSLP的关系n-gram之间的依赖项。我们的方法通过首先在表面名称上构造层次n-gram图来进行起作用，以模拟导致表面名称的N-gram的组织结构。然后，将基于变压器的革兰amtransformer呈现，以建模层次n-gram图，以构建ZSLP的关系嵌入。实验结果表明，提出的HNZSLP在两个ZSLP数据集上实现了最先进的性能。

改善疾病的护理标准是关于更好的治疗方法，反过来依赖于寻找和开发新药。然而，药物发现是一个复杂且昂贵的过程。通过机器学习的方法采用了利用域固有的互连性质的药物发现知识图的创建。基于图形的数据建模，结合知识图形嵌入式提供了更直观的域表示，适用于推理任务，例如预测缺失链路。一个这样的例子将产生对给定疾病的可能相关基因的排名列表，通常被称为目标发现。因此，这是关键的，即这些预测不仅是相关的，而且是生物学上的有意义的。然而，知识图形可以直接偏向，由于集成的底层数据源，或者由于图形构造中的建模选择，其中的一个结果是某些实体可以在拓扑上超越。我们展示了知识图形嵌入模型可能受到这种结构不平衡的影响，导致无论上下文都要高度排名的密集连接实体。我们在不同的数据集，模型和预测任务中提供对此观察的支持。此外，我们展示了如何通过随机，生物学上无意义的信息扰乱图形拓扑结构以人为地改变基因的等级。这表明这种模型可能会受到实体频率而不是在关系中编码的生物学信息的影响，当实体频率不是基础数据的真实反射时，创建问题。我们的结果突出了数据建模选择的重要性，并强调了从业者在解释模型输出和知识图形组合期间时要注意这些问题。

链路预测是预测知识图的实体之间缺失关系的任务。最近的链路预测工作已经尝试通过在神经网络架构中使用更多层来提供增加链路预测精度的模型。在本文中，我们提出了一种精炼知识图的新方法，从而可以使用相对快速的翻译模型更准确地执行链路预测操作。翻译链接预测模型，如Transe，Transh，Transd，而不是深度学习方法的复杂性较小。我们的方法使用知识图中的关系和实体的层次结构将实体信息作为辅助节点添加到图形中，并将它们连接到包含在其层级中的该信息的节点。我们的实验表明，我们的方法可以显着提高H @ 10的翻译链路预测方法的性能，MRR，MRR。

神经网络的最新进步已经解决了常见的图表问题，例如链路预测，节点分类，节点聚类，通过将实体和关系的嵌入和关系开发到向量空间中来看。绘图嵌入式对图中存在的结构信息进行编码。然后，编码嵌入式可用于预测图中的缺失链接。然而，获得图表的最佳嵌入可以是嵌入式系统中的计算具有挑战性的任务。我们在这项工作中专注的两种技术是1）节点嵌入来自随机步行的方法和2）知识图形嵌入。随机播放的嵌入物是计算地廉价的，但是是次优的，而知识图形嵌入物表现更好，但是计算得昂贵。在这项工作中，我们研究了转换从基于随机步行方法获得的节点嵌入的转换模型，以直接从知识图方法获得的嵌入，而不会增加计算成本。广泛的实验表明，所提出的变换模型可用于实时解决链路预测。

链接预测的任务旨在解决由于难以从现实世界中收集事实而引起的不完整知识的问题。基于GCN的模型由于其复杂性而广泛应用于解决链接预测问题，但基于GCN的模型在结构和培训过程中遇到了两个问题。 1）GCN层的转化方法在基于GCN的知识表示模型中变得越来越复杂； 2）由于知识图收集过程的不完整，标记为负样本中有许多未收集的真实事实。因此，本文研究了相邻节点的信息聚合系数（自我注意）的特征，并重新设计了GAT结构的自我注意力。同时，受到人类思维习惯的启发，我们在预训练的模型上设计了一种半监督的自训练方法。基准数据集FB15K-237和WN18RR上的实验结果表明，我们提出的自我发项机制和半监督的自我训练方法可以有效地提高链接预测任务的性能。例如，如果您查看FB15K-237，则建议的方法将@1的命中率提高了约30％。

We study the problem of learning representations of entities and relations in knowledge graphs for predicting missing links. The success of such a task heavily relies on the ability of modeling and inferring the patterns of (or between) the relations. In this paper, we present a new approach for knowledge graph embedding called RotatE, which is able to model and infer various relation patterns including: symmetry/antisymmetry, inversion, and composition. Specifically, the RotatE model defines each relation as a rotation from the source entity to the target entity in the complex vector space. In addition, we propose a novel self-adversarial negative sampling technique for efficiently and effectively training the RotatE model. Experimental results on multiple benchmark knowledge graphs show that the proposed RotatE model is not only scalable, but also able to infer and model various relation patterns and significantly outperform existing state-of-the-art models for link prediction.

Knowledge graph embedding (KGE) models learn the representation of entities and relations in knowledge graphs. Distance-based methods show promising performance on link prediction task, which predicts the result by the distance between two entity representations. However, most of these methods represent the head entity and tail entity separately, which limits the model capacity. We propose two novel distance-based methods named InterHT and InterHT+ that allow the head and tail entities to interact better and get better entity representation. Experimental results show that our proposed method achieves the best results on ogbl-wikikg2 dataset.

我们介绍了一个名为Nuge的新型嵌入式模型，旨在将实体和关系之间的共同发生整合到图形神经网络中，以改善知识图形完成（即，链接预测）。鉴于知识图形，Nuge将单个图形构建，考虑实体和关系作为单个节点。然后，Nuge基于实体和关系的共同发生来计算节点之间的边缘的权重。接下来，Nuge提出双季型图形神经网络（DualQGNN），并利用DualQGNN更新实体和关系节点的向量表示。然后采用分数函数来产生三重分数。综合实验结果表明，NOGE在三个新的和困难的基准数据集Codex上获得最先进的结果，用于知识图形完成。

知识图，例如Wikidata，包括结构和文本知识，以表示知识。对于图形嵌入和语言模型的两种方式中的每种方法都可以学习预测新型结构知识的模式。很少有方法与模式结合学习和推断，而这些现有的方法只能部分利用结构和文本知识的相互作用。在我们的方法中，我们以单个方式的现有强烈表示为基础，并使用超复杂代数来表示（i），（i），单模式嵌入以及（ii），不同方式之间的相互作用及其互补的知识表示手段。更具体地说，我们建议4D超复合数的二脑和四个元素表示，以整合四个模态，即结构知识图形嵌入，单词级表示（例如\ word2vec，fastText，fastText），句子级表示（句子transformer）和文档级表示（句子级别）（句子级别）（句子级表示）（句子变压器，doc2vec）。我们的统一矢量表示通过汉密尔顿和二脑产物进行标记的边缘的合理性，从而对不同模态之间的成对相互作用进行建模。对标准基准数据集的广泛实验评估显示了我们两个新模型的优越性，除了稀疏的结构知识外，还可以提高链接预测任务中的性能。

To date, there are no effective treatments for most neurodegenerative diseases. Knowledge graphs can provide comprehensive and semantic representation for heterogeneous data, and have been successfully leveraged in many biomedical applications including drug repurposing. Our objective is to construct a knowledge graph from literature to study relations between Alzheimer's disease (AD) and chemicals, drugs and dietary supplements in order to identify opportunities to prevent or delay neurodegenerative progression. We collected biomedical annotations and extracted their relations using SemRep via SemMedDB. We used both a BERT-based classifier and rule-based methods during data preprocessing to exclude noise while preserving most AD-related semantic triples. The 1,672,110 filtered triples were used to train with knowledge graph completion algorithms (i.e., TransE, DistMult, and ComplEx) to predict candidates that might be helpful for AD treatment or prevention. Among three knowledge graph completion models, TransE outperformed the other two (MR = 13.45, Hits@1 = 0.306). We leveraged the time-slicing technique to further evaluate the prediction results. We found supporting evidence for most highly ranked candidates predicted by our model which indicates that our approach can inform reliable new knowledge. This paper shows that our graph mining model can predict reliable new relationships between AD and other entities (i.e., dietary supplements, chemicals, and drugs). The knowledge graph constructed can facilitate data-driven knowledge discoveries and the generation of novel hypotheses.

实体类型预测是知识图中的一个重要问题（kg）研究。在这项工作中提出了一种新的KG实体类型预测方法，名为Core（复杂的空间回归和嵌入）。所提出的核心方法利用两个复杂空间嵌入模型的表现力;即，旋转和复杂的模型。它使用旋转或复杂地将实体和类型嵌入两个不同的复杂空间中。然后，我们推导了一个复杂的回归模型来链接这两个空格。最后，介绍了一种优化嵌入和回归参数的机制。实验表明，核心优于代表性KG实体型推理数据集的基准测试方法。分析了各种实体型预测方法的强度和弱点。