Real-World Medical Knowledge Graph and Clinical Event Graph Construction

Real-World Medical Knowledge Graph and Clinical Event Graph Construction
Due to historical reasons, the characteristics of medical information systems vary among different vendors, and patient information is stored in different internal systems. To use data scattered across various systems, effective governance of the data is required to extract and combine data for the same patient and the same visit into a comprehensive view of patient and visit dimensions.
Based on the comprehensive patient data and existing medical knowledge, a disease knowledge graph can be constructed, which can be applied in scenarios such as CDSS clinical decision support, hospital case search ranking, intelligent consultation, and knowledge integration combined with deep learning. Using this knowledge graph, further processing of each patient’s comprehensive data can extract clinical treatment events, forming a patient dimension and a specialty disease-focused event graph. The event graph can be used for specialty treatment views, automatic generation of medical records, event searches, and causal analysis.
Real-World Medical Knowledge Graph and Clinical Event Graph Construction
This article will introduce how to construct a disease knowledge graph based on real-world electronic medical records and illustrate the value and significance of constructing knowledge graphs based on data through various applications.

Construction and Application of Medical Knowledge Graph

First, with authorization, information from different systems and visits is integrated based on the same patient, same visit, and same onset dimensions. Initially, data mining was based on visit dimension data, but later it was found that some data analysis and mining needs to be based on patient and onset dimensions. For example, a cancer patient may visit the hospital multiple times after diagnosis, and their overall treatment plan needs to combine information from multiple visits to calculate, referred to as one onset. The data for one onset includes the patient’s basic information, chief complaint at the first visit, current medical history, examination and test results at that time, doctor’s diagnosis, medication orders, surgical records, etc.
Based on this raw information, through entity extraction and standardization processes, standard entities are formed. Relationships between entities are constructed to form a graph. Once the links between entities are established, property calculations are performed.
Considering that the graph is built based on a large number of cases, there may be data quality issues, so graph cleaning is necessary, followed by some entity sorting. If entities need to be applied to deep learning, graph embedding is also required.
Real-World Medical Knowledge Graph and Clinical Event Graph Construction
To complete the above pipeline, Yidu Cloud has developed data ETL platforms, medical dictionary management platforms, structured extraction platforms, annotation platforms, quality control platforms, and machine learning platforms. Yidu Cloud has provided big data platforms and knowledge graph technology for many hospitals.
Since each hospital’s original information system comes from different vendors, the data table fields are also different, so a unified data model must be defined first. This data model can cover the records of common disease diagnosis and treatment processes, and each patient’s data will be standardized. Yidu Cloud will first map the original database table structures of various hospitals to this universal model, and subsequent data quality control, structured normalization, data mining, etc., will follow a unified process.
Real-World Medical Knowledge Graph and Clinical Event Graph Construction

Application of Real-World Knowledge Graph in Intelligent Diagnosis

Based on the disease probability knowledge graph, the application of intelligent diagnosis will be more convenient. We apply it in clinical decision support scenarios. When a patient first visits the hospital, the doctor writes the chief complaint, current medical history, and other information in the case. Using NLP technology, symptoms and characteristics of onset from the patient’s chief complaint and current medical history are extracted and input into an improved Bayesian model to infer the most likely list of diseases for the patient. Once the doctor selects a diagnosis, the system automatically recommends examination and testing items based on the doctor’s selected diagnosis, with the recommendations sourced from the constructed medical knowledge graph.

Real-World Medical Knowledge Graph and Clinical Event Graph Construction

Application of Real-World Knowledge Graph in Information Retrieval Ranking

During hospitalization, patients use many medications; for example, a diabetic patient may use dozens of medications during hospitalization. When doctors want to check the patient’s main medications during hospitalization or after discharge, the traditional approach is to flip through medication orders from front to back. Based on the above knowledge graph, we match the medications related to the patient’s main diagnosis in the knowledge graph with the medications used during hospitalization, using the PSR indicator to rank the medications. As shown, the main medications for this type 2 diabetes patient are Repaglinide tablets, Voglibose tablets, and Aspart insulin injection. This greatly saves the doctor’s time and improves work efficiency.

Real-World Medical Knowledge Graph and Clinical Event Graph Construction

Application of Real-World Knowledge Graph in Neural Network Combination

In the field of medical informatics, predictions of the next medication for patients are often based on the public database MIMIC. Since it is time-series data from the ICU, deep learning algorithms based on Bi-LSTM as the basic model have achieved good results. We added a graph embedding layer to the Bi-LSTM model to predict the next medication for patients, and experimental results show that both the convergence speed and accuracy of the model have improved. This indicates that the combination of graph embedding and deep learning is very helpful for model optimization. However, prediction models based on vector representation are often challenged due to their poor interpretability in serious medical scenarios such as drug recommendations, making them more suitable for medical text NLP and intelligent triage scenarios.

Real-World Medical Knowledge Graph and Clinical Event Graph Construction

It is precisely based on the in-depth exploration of knowledge graphs that Yidu Cloud’s “method, device, storage medium, and electronic equipment for constructing knowledge graphs” (Patent No. ZL201811601675.6) was awarded the Excellent Patent Award in the 23rd China Patent Award announced by the National Intellectual Property Administration.
Yidu Cloud constructs a large-scale medical knowledge graph based on desensitized multi-source heterogeneous data, and continuously updates, improves, and iterates the medical knowledge graph through various knowledge graph and artificial intelligence technologies such as semantic computing, knowledge integration, logical reasoning, and data mining, endowing intelligent applications of medical data with breakthrough value. The awarded patented technology has been applied to several self-developed platforms of Yidu Technology, including “Medical Data Intelligent Platform”, “Special Disease Intelligent Research Platform”, “Clinical Decision Support System”, “Single Disease Reporting and Quality Control System”, and “Intelligent Underwriting Application Platform”, successfully achieving commercial operation.
In the next article, we will share the construction of clinical event graphs and their value and significance.
Real-World Medical Knowledge Graph and Clinical Event Graph Construction

Li Linfeng

Vice President of Technical Innovation at Yidu Cloud, AI Architect

Li Linfeng, Ph.D., Vice President of Technical Innovation at Yidu Cloud, AI Architect. He joined Yidu Cloud in 2017, focusing on medical big data mining technology and innovative applications of artificial intelligence, including the construction of medical knowledge graphs, medical knowledge representation and reasoning methods, predictive models, and clinical decision support systems based on AI technology. He holds multiple patents and papers in the field of medical artificial intelligence. He previously served as the head of medical algorithms at Baidu, responsible for knowledge graph construction, intelligent consultation, and algorithms for Baidu Medicine.

Further Reading

Xinhua News Agency | Yidu Technology Wins China Patent Award for the First Time, Related Technology Applied to Several Self-Developed Platforms

Focus on CCKS 2020 | Yidu Cloud Utilizes Knowledge Graph Technology to Better Leverage the Dual Advantages of “Black Box” and “Logic”

Yidu Cloud’s Single Disease Quality Monitoring and Reporting Program Promotes High-Quality Development of Hospitals

Knowledge Graph

Real-World Medical Knowledge Graph and Clinical Event Graph Construction
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