Jingchi Jiang

A study of EMR-based medical knowledge network and its applications

BACKGROUND AND OBJECTIVE Electronic medical records (EMRs) contain an amount of medical knowledge which can be used for clinical decision support. We attempt to integrate this medical knowledge into a complex network, and then implement a diagnosis model based on this network. METHODS The dataset of our study contains 992 records which are uniformly sampled from different departments of the hospital. In order to integrate the knowledge of these records, an EMR-based medical knowledge network (EMKN) is constructed. This network takes medical entities as nodes, and co-occurrence relationships between the two entities as edges. Selected properties of this network are analyzed. To make use of this network, a basic diagnosis model is implemented. Seven hundred records are randomly selected to re-construct the network, and the remaining 292 records are used as test records. The vector space model is applied to illustrate the relationships between diseases and symptoms. Because there may exist more than one actual disease in a record, the recall rate of the first ten results, and the average precision are adopted as evaluation measures. RESULTS Compared with a random network of the same size, this network has a similar average length but a much higher clustering coefficient. Additionally, it can be observed that there are direct correlations between the community structure and the real department classes in the hospital. For the diagnosis model, the vector space model using disease as a base obtains the best result. At least one accurate disease can be obtained in 73.27% of the records in the first ten results. CONCLUSION We constructed an EMR-based medical knowledge network by extracting the medical entities. This network has the small-world and scale-free properties. Moreover, the community structure showed that entities in the same department have a tendency to be self-aggregated. Based on this network, a diagnosis model was proposed. This model uses only the symptoms as inputs and is not restricted to a specific disease. The experiments conducted demonstrated that EMKN is a simple and universal technique to integrate different medical knowledge from EMRs, and can be used for clinical decision support.

De-identification of medical records using conditional random fields and long short-term memory networks

The CEGS N-GRID 2016 Shared Task 1 in Clinical Natural Language Processing focuses on the de-identification of psychiatric evaluation records. This paper describes two participating systems of our team, based on conditional random fields (CRFs) and long short-term memory networks (LSTMs). A pre-processing module was introduced for sentence detection and tokenization before de-identification. For CRFs, manually extracted rich features were utilized to train the model. For LSTMs, a character-level bi-directional LSTM network was applied to represent tokens and classify tags for each token, following which a decoding layer was stacked to decode the most probable protected health information (PHI) terms. The LSTM-based system attained an i2b2 strict micro-F1 measure of 0.8986, which was higher than that of the CRF-based system.

Learning and inference in knowledge-based probabilistic model for medical diagnosis

Based on a weighted knowledge graph to represent first-order knowledge and combining it with a probabilistic model, we propose a methodology for creating a medical knowledge network (MKN) in medical diagnosis. When a set of evidence is activated for a specific patient, we can generate a ground medical knowledge network that is composed of evidence nodes and potential disease nodes. By incorporating a Boltzmann machine into the potential function of a Markov network, we investigated the joint probability distribution of the MKN. To consider numerical evidence, a multivariate inference model is presented that uses conditional probability. In addition, the weights for the knowledge graph are efficiently learned from manually annotated Chinese Electronic Medical Records (CEMRs) and Blood Examination Records (BERs). In our experiments, we found numerically that an improved expression of evidence variables is necessary for medical diagnosis. Our experimental results comparing a Markov logic network and six kinds of classic machine learning algorithms on the actual CEMR database and BER database indicate that our method holds promise and that MKN can facilitate studies of intelligent diagnosis.

Max-margin weight learning for medical knowledge network

BACKGROUND AND OBJECTIVE The application of medical knowledge strongly affects the performance of intelligent diagnosis, and method of learning the weights of medical knowledge plays a substantial role in probabilistic graphical models (PGMs). The purpose of this study is to investigate a discriminative weight-learning method based on a medical knowledge network (MKN). METHODS We propose a training model called the maximum margin medical knowledge network (M3KN), which is strictly derived for calculating the weight of medical knowledge. Using the definition of a reasonable margin, the weight learning can be transformed into a margin optimization problem. To solve the optimization problem, we adopt a sequential minimal optimization (SMO) algorithm and the clique property of a Markov network. Ultimately, M3KN not only incorporates the inference ability of PGMs but also deals with high-dimensional logic knowledge. RESULTS The experimental results indicate that M3KN obtains a higher F-measure score than the maximum likelihood learning algorithm of MKN for both Chinese Electronic Medical Records (CEMRs) and Blood Examination Records (BERs). Furthermore, the proposed approach is obviously superior to some classical machine learning algorithms for medical diagnosis. To adequately manifest the importance of domain knowledge, we numerically verify that the diagnostic accuracy of M3KN is gradually improved as the number of learned CEMRs increase, which contain important medical knowledge. CONCLUSIONS Our experimental results show that the proposed method performs reliably for learning the weights of medical knowledge. M3KN outperforms other existing methods by achieving an F-measure of 0.731 for CEMRs and 0.4538 for BERs. This further illustrates that M3KN can facilitate the investigations of intelligent healthcare.

EMR-based medical knowledge representation and inference via Markov random fields and distributed representation learning

OBJECTIVE Electronic medical records (EMRs) contain medical knowledge that can be used for clinical decision support (CDS). Our objective is to develop a general system that can extract and represent knowledge contained in EMRs to support three CDS tasks-test recommendation, initial diagnosis, and treatment plan recommendation-given the condition of a patient. METHODS We extracted four kinds of medical entities from records and constructed an EMR-based medical knowledge network (EMKN), in which nodes are entities and edges reflect their co-occurrence in a record. Three bipartite subgraphs (bigraphs) were extracted from the EMKN, one to support each task. One part of the bigraph was the given condition (e.g., symptoms), and the other was the condition to be inferred (e.g., diseases). Each bigraph was regarded as a Markov random field (MRF) to support the inference. We proposed three graph-based energy functions and three likelihood-based energy functions. Two of these functions are based on knowledge representation learning and can provide distributed representations of medical entities. Two EMR datasets and three metrics were utilized to evaluate the performance. RESULTS As a whole, the evaluation results indicate that the proposed system outperformed the baseline methods. The distributed representation of medical entities does reflect similarity relationships with respect to knowledge level. CONCLUSION Combining EMKN and MRF is an effective approach for general medical knowledge representation and inference. Different tasks, however, require individually designed energy functions.

Developing a cardiovascular disease risk factor annotated corpus of Chinese electronic medical records

BackgroundCardiovascular disease (CVD) has become the leading cause of death in China, and most of the cases can be prevented by controlling risk factors. The goal of this study was to build a corpus of CVD risk factor annotations based on Chinese electronic medical records (CEMRs). This corpus is intended to be used to develop a risk factor information extraction system that, in turn, can be applied as a foundation for the further study of the progress of risk factors and CVD.ResultsWe designed a light annotation task to capture CVD risk factors with indicators, temporal attributes and assertions that were explicitly or implicitly displayed in the records. The task included: 1) preparing data; 2) creating guidelines for capturing annotations (these were created with the help of clinicians); 3) proposing an annotation method including building the guidelines draft, training the annotators and updating the guidelines, and corpus construction. Meanwhile, we proposed some creative annotation guidelines: (1) the under-threshold medical examination values were annotated for our purpose of studying the progress of risk factors and CVD; (2) possible and negative risk factors were concerned for the same reason, and we created assertions for annotations; (3) we added four temporal attributes to CVD risk factors in CEMRs for constructing long term variations. Then, a risk factor annotated corpus based on de-identified discharge summaries and progress notes from 600 patients was developed. Built with the help of clinicians, this corpus has an inter-annotator agreement (IAA) F1-measure of 0.968, indicating a high reliability.ConclusionTo the best of our knowledge, this is the first annotated corpus concerning CVD risk factors in CEMRs and the guidelines for capturing CVD risk factor annotations from CEMRs were proposed. The obtained document-level annotations can be applied in future studies to monitor risk factors and CVD over the long term.