scholarly journals Research on Medical Knowledge Graph for Stroke

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Binjie Cheng ◽  
Jin Zhang ◽  
Hong Liu ◽  
Meiling Cai ◽  
Ying Wang
Keyword(s):  
Medical Knowledge ◽  
Similarity Measures ◽  
Graph Model ◽  
Knowledge Graph ◽  
Medical Field ◽  
Graph Models ◽  
Experimental Part ◽  
External Data ◽  
Embedded Model ◽  
Knowledge Graphs

Knowledge graph can effectively analyze and construct the essential characteristics of data. At present, scholars have proposed many knowledge graph models from different perspectives, especially in the medical field, but there are still relatively few studies on stroke diseases using medical knowledge graphs. Therefore, this paper will build a medical knowledge graph model for stroke. Firstly, a stroke disease dictionary and an ontology database are built through the international standard medical term sets and semiautomatic extraction-based crowdsourcing website data. Secondly, the external data are linked to the nodes of the existing knowledge graph via the entity similarity measures and the knowledge representation is performed by the knowledge graph embedded model. Thirdly, the structure of the established knowledge graph is modified continuously through iterative updating. Finally, in the experimental part, the proposed stroke medical knowledge graph is applied to the real stroke data and the performance of the proposed knowledge graph approach on the series of Trans ∗ models is compared.

scholarly journals Path-based knowledge reasoning with textual semantic information for medical knowledge graph completion

2021 ◽  
Vol 21 (S9) ◽  
Author(s):  
Yinyu Lan ◽  
Shizhu He ◽  
Kang Liu ◽  
Xiangrong Zeng ◽  
Shengping Liu ◽  
...  
Keyword(s):  
Semantic Information ◽  
State Of The Art ◽  
Semantic Representation ◽  
Medical Knowledge ◽  
The State ◽  
Language Models ◽  
Knowledge Graph ◽  
Knowledge Reasoning ◽  
Numerical Computing ◽  
Knowledge Graphs

Abstract Background Knowledge graphs (KGs), especially medical knowledge graphs, are often significantly incomplete, so it necessitating a demand for medical knowledge graph completion (MedKGC). MedKGC can find new facts based on the existed knowledge in the KGs. The path-based knowledge reasoning algorithm is one of the most important approaches to this task. This type of method has received great attention in recent years because of its high performance and interpretability. In fact, traditional methods such as path ranking algorithm take the paths between an entity pair as atomic features. However, the medical KGs are very sparse, which makes it difficult to model effective semantic representation for extremely sparse path features. The sparsity in the medical KGs is mainly reflected in the long-tailed distribution of entities and paths. Previous methods merely consider the context structure in the paths of knowledge graph and ignore the textual semantics of the symbols in the path. Therefore, their performance cannot be further improved due to the two aspects of entity sparseness and path sparseness. Methods To address the above issues, this paper proposes two novel path-based reasoning methods to solve the sparsity issues of entity and path respectively, which adopts the textual semantic information of entities and paths for MedKGC. By using the pre-trained model BERT, combining the textual semantic representations of the entities and the relationships, we model the task of symbolic reasoning in the medical KG as a numerical computing issue in textual semantic representation. Results Experiments results on the publicly authoritative Chinese symptom knowledge graph demonstrated that the proposed method is significantly better than the state-of-the-art path-based knowledge graph reasoning methods, and the average performance is improved by 5.83% for all relations. Conclusions In this paper, we propose two new knowledge graph reasoning algorithms, which adopt textual semantic information of entities and paths and can effectively alleviate the sparsity problem of entities and paths in the MedKGC. As far as we know, it is the first method to use pre-trained language models and text path representations for medical knowledge reasoning. Our method can complete the impaired symptom knowledge graph in an interpretable way, and it outperforms the state-of-the-art path-based reasoning methods.

scholarly journals A Method to Learn Embedding of a Probabilistic Medical Knowledge Graph: Algorithm Development (Preprint)

2019 ◽  
Author(s):  
Linfeng Li ◽  
Peng Wang ◽  
Yao Wang ◽  
Shenghui Wang ◽  
Jun Yan ◽  
...  
Keyword(s):  
Medical Records ◽  
Large Scale ◽  
Semantic Representation ◽  
Medical Knowledge ◽  
Mapping Function ◽  
Graph Algorithm ◽  
Knowledge Graph ◽  
Knowledge Graphs ◽  
Representation Method ◽  
Better Than

BACKGROUND Knowledge graph embedding is an effective semantic representation method for entities and relations in knowledge graphs. Several translation-based algorithms, including TransE, TransH, TransR, TransD, and TranSparse, have been proposed to learn effective embedding vectors from typical knowledge graphs in which the relations between head and tail entities are deterministic. However, in medical knowledge graphs, the relations between head and tail entities are inherently probabilistic. This difference introduces a challenge in embedding medical knowledge graphs. OBJECTIVE We aimed to address the challenge of how to learn the probability values of triplets into representation vectors by making enhancements to existing TransX (where X is E, H, R, D, or Sparse) algorithms, including the following: (1) constructing a mapping function between the score value and the probability, and (2) introducing probability-based loss of triplets into the original margin-based loss function. METHODS We performed the proposed PrTransX algorithm on a medical knowledge graph that we built from large-scale real-world electronic medical records data. We evaluated the embeddings using link prediction task. RESULTS Compared with the corresponding TransX algorithms, the proposed PrTransX performed better than the TransX model in all evaluation indicators, achieving a higher proportion of corrected entities ranked in the top 10 and normalized discounted cumulative gain of the top 10 predicted tail entities, and lower mean rank. CONCLUSIONS The proposed PrTransX successfully incorporated the uncertainty of the knowledge triplets into the embedding vectors.

scholarly journals Improving rare disease classification using imperfect knowledge graph

2019 ◽  
Vol 19 (S5) ◽  
Author(s):  
Xuedong Li ◽  
Yue Wang ◽  
Dongwu Wang ◽  
Walter Yuan ◽  
Dezhong Peng ◽  
...  
Keyword(s):  
Rare Disease ◽  
Rare Diseases ◽  
Medical Knowledge ◽  
Classification Algorithm ◽  
Disease Classification ◽  
Knowledge Graph ◽  
Data Set ◽  
Wide Range ◽  
Imperfect Knowledge ◽  
Knowledge Graphs

Abstract Background Accurately recognizing rare diseases based on symptom description is an important task in patient triage, early risk stratification, and target therapies. However, due to the very nature of rare diseases, the lack of historical data poses a great challenge to machine learning-based approaches. On the other hand, medical knowledge in automatically constructed knowledge graphs (KGs) has the potential to compensate the lack of labeled training examples. This work aims to develop a rare disease classification algorithm that makes effective use of a knowledge graph, even when the graph is imperfect. Method We develop a text classification algorithm that represents a document as a combination of a “bag of words” and a “bag of knowledge terms,” where a “knowledge term” is a term shared between the document and the subgraph of KG relevant to the disease classification task. We use two Chinese disease diagnosis corpora to evaluate the algorithm. The first one, HaoDaiFu, contains 51,374 chief complaints categorized into 805 diseases. The second data set, ChinaRe, contains 86,663 patient descriptions categorized into 44 disease categories. Results On the two evaluation data sets, the proposed algorithm delivers robust performance and outperforms a wide range of baselines, including resampling, deep learning, and feature selection approaches. Both classification-based metric (macro-averaged F1 score) and ranking-based metric (mean reciprocal rank) are used in evaluation. Conclusion Medical knowledge in large-scale knowledge graphs can be effectively leveraged to improve rare diseases classification models, even when the knowledge graph is incomplete.

scholarly journals A Method to Learn Embedding of a Probabilistic Medical Knowledge Graph: Algorithm Development

10.2196/17645 ◽  
2020 ◽  
Vol 8 (5) ◽  
pp. e17645
Author(s):  
Linfeng Li ◽  
Peng Wang ◽  
Yao Wang ◽  
Shenghui Wang ◽  
Jun Yan ◽  
...  
Keyword(s):  
Medical Records ◽  
Large Scale ◽  
Semantic Representation ◽  
Medical Knowledge ◽  
Mapping Function ◽  
Graph Algorithm ◽  
Knowledge Graph ◽  
Knowledge Graphs ◽  
Representation Method ◽  
Better Than

Background Knowledge graph embedding is an effective semantic representation method for entities and relations in knowledge graphs. Several translation-based algorithms, including TransE, TransH, TransR, TransD, and TranSparse, have been proposed to learn effective embedding vectors from typical knowledge graphs in which the relations between head and tail entities are deterministic. However, in medical knowledge graphs, the relations between head and tail entities are inherently probabilistic. This difference introduces a challenge in embedding medical knowledge graphs. Objective We aimed to address the challenge of how to learn the probability values of triplets into representation vectors by making enhancements to existing TransX (where X is E, H, R, D, or Sparse) algorithms, including the following: (1) constructing a mapping function between the score value and the probability, and (2) introducing probability-based loss of triplets into the original margin-based loss function. Methods We performed the proposed PrTransX algorithm on a medical knowledge graph that we built from large-scale real-world electronic medical records data. We evaluated the embeddings using link prediction task. Results Compared with the corresponding TransX algorithms, the proposed PrTransX performed better than the TransX model in all evaluation indicators, achieving a higher proportion of corrected entities ranked in the top 10 and normalized discounted cumulative gain of the top 10 predicted tail entities, and lower mean rank. Conclusions The proposed PrTransX successfully incorporated the uncertainty of the knowledge triplets into the embedding vectors.

Mobile Software Assurance Informed through Knowledge Graph Construction: The OWASP Threat of Insecure Data Storage

2020 ◽  
Vol 2 (2) ◽  
Author(s):  
Suzanna Schmeelk ◽  
Lixin Tao
Keyword(s):  
Data Storage ◽  
Program Analysis ◽  
Web Application ◽  
Security Analysis ◽  
Knowledge Graph ◽  
Healthcare Applications ◽  
Sensitive Data ◽  
Knowledge Graphs ◽  
Mobile Malware Detection ◽  
Software Assurance

Many organizations, to save costs, are movinheg to t Bring Your Own Mobile Device (BYOD) model and adopting applications built by third-parties at an unprecedented rate.  Our research examines software assurance methodologies specifically focusing on security analysis coverage of the program analysis for mobile malware detection, mitigation, and prevention.  This research focuses on secure software development of Android applications by developing knowledge graphs for threats reported by the Open Web Application Security Project (OWASP).  OWASP maintains lists of the top ten security threats to web and mobile applications.  We develop knowledge graphs based on the two most recent top ten threat years and show how the knowledge graph relationships can be discovered in mobile application source code.  We analyze 200+ healthcare applications from GitHub to gain an understanding of their software assurance of their developed software for one of the OWASP top ten moble threats, the threat of “Insecure Data Storage.”  We find that many of the applications are storing personally identifying information (PII) in potentially vulnerable places leaving users exposed to higher risks for the loss of their sensitive data.

scholarly journals TransET: Knowledge Graph Embedding with Entity Types

Electronics ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1407
Author(s):  
Peng Wang ◽  
Jing Zhou ◽  
Yuzhang Liu ◽  
Xingchen Zhou
Keyword(s):  
Link Prediction ◽  
State Of The Art ◽  
Score Function ◽  
Graph Embedding ◽  
Vector Spaces ◽  
Knowledge Graph ◽  
Semantic Features ◽  
Knowledge Graphs ◽  
Real World Datasets ◽  
Low Dimensional

Knowledge graph embedding aims to embed entities and relations into low-dimensional vector spaces. Most existing methods only focus on triple facts in knowledge graphs. In addition, models based on translation or distance measurement cannot fully represent complex relations. As well-constructed prior knowledge, entity types can be employed to learn the representations of entities and relations. In this paper, we propose a novel knowledge graph embedding model named TransET, which takes advantage of entity types to learn more semantic features. More specifically, circle convolution based on the embeddings of entity and entity types is utilized to map head entity and tail entity to type-specific representations, then translation-based score function is used to learn the presentation triples. We evaluated our model on real-world datasets with two benchmark tasks of link prediction and triple classification. Experimental results demonstrate that it outperforms state-of-the-art models in most cases.

scholarly journals Development of Knowledge Graph for Data Management Related to Flooding Disasters Using Open Data

2021 ◽  
Vol 13 (5) ◽  
pp. 124
Author(s):  
Jiseong Son ◽  
Chul-Su Lim ◽  
Hyoung-Seop Shim ◽  
Ji-Sun Kang
Keyword(s):  
Artificial Intelligence ◽  
Domain Knowledge ◽  
Open Data ◽  
Heterogeneous Data ◽  
Big Data Analysis ◽  
Knowledge Graph ◽  
Cross Domain ◽  
Disaster Data ◽  
Knowledge Graphs ◽  
Open Datasets

Despite the development of various technologies and systems using artificial intelligence (AI) to solve problems related to disasters, difficult challenges are still being encountered. Data are the foundation to solving diverse disaster problems using AI, big data analysis, and so on. Therefore, we must focus on these various data. Disaster data depend on the domain by disaster type and include heterogeneous data and lack interoperability. In particular, in the case of open data related to disasters, there are several issues, where the source and format of data are different because various data are collected by different organizations. Moreover, the vocabularies used for each domain are inconsistent. This study proposes a knowledge graph to resolve the heterogeneity among various disaster data and provide interoperability among domains. Among disaster domains, we describe the knowledge graph for flooding disasters using Korean open datasets and cross-domain knowledge graphs. Furthermore, the proposed knowledge graph is used to assist, solve, and manage disaster problems.

scholarly journals Research of Personalized Recommendation Technology Based on Knowledge Graphs

2021 ◽  
Vol 11 (15) ◽  
pp. 7104
Author(s):  
Xu Yang ◽  
Ziyi Huan ◽  
Yisong Zhai ◽  
Ting Lin
Keyword(s):  
Neural Network ◽  
Hot Spot ◽  
Experimental Results ◽  
Graph Representation ◽  
Personalized Recommendation ◽  
Knowledge Graph ◽  
Learning Technology ◽  
Data Set ◽  
Model Based ◽  
Knowledge Graphs

Nowadays, personalized recommendation based on knowledge graphs has become a hot spot for researchers due to its good recommendation effect. In this paper, we researched personalized recommendation based on knowledge graphs. First of all, we study the knowledge graphs’ construction method and complete the construction of the movie knowledge graphs. Furthermore, we use Neo4j graph database to store the movie data and vividly display it. Then, the classical translation model TransE algorithm in knowledge graph representation learning technology is studied in this paper, and we improved the algorithm through a cross-training method by using the information of the neighboring feature structures of the entities in the knowledge graph. Furthermore, the negative sampling process of TransE algorithm is improved. The experimental results show that the improved TransE model can more accurately vectorize entities and relations. Finally, this paper constructs a recommendation model by combining knowledge graphs with ranking learning and neural network. We propose the Bayesian personalized recommendation model based on knowledge graphs (KG-BPR) and the neural network recommendation model based on knowledge graphs(KG-NN). The semantic information of entities and relations in knowledge graphs is embedded into vector space by using improved TransE method, and we compare the results. The item entity vectors containing external knowledge information are integrated into the BPR model and neural network, respectively, which make up for the lack of knowledge information of the item itself. Finally, the experimental analysis is carried out on MovieLens-1M data set. The experimental results show that the two recommendation models proposed in this paper can effectively improve the accuracy, recall, F1 value and MAP value of recommendation.

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