DECAF: An interpretable deep cascading framework for ICU mortality prediction.

Medical risk detection is an important topic and a challenging task to improve the performance of clinical practices in Intensive Care Units (ICU). Although many bio-statistical learning and deep learning approaches have provided patient-specific mortality predictions, these existing methods lack interpretability that is crucial to gain adequate insight on why such predictions would work. In this paper, we introduce cascading theory to model the physiological domino effect and provide a novel approach to dynamically simulate the deterioration of patients' conditions. We propose a general DEep CAscading Framework (DECAF) to predict the potential risks of all physiological functions at each clinical stage. Compared with other feature-based and/or score-based models, our approach has a range of desirable properties, such as being interpretable, applicable with multi prediction tasks, and learnable from medical common sense and/or clinical experience knowledge. Experiments on a medical dataset (MIMIC-III) of 21,828 ICU patients show that DECAF reaches up to 89.30 % on AUROC, which surpasses the best competing methods for mortality prediction.

Comparison of machine learning models for predicting the risk of breast cancer-related lymphedema in Chinese women.

Objective: Predictive models for the occurrence of cancer symptoms by using machine learning (ML) algorithms could be used to aid clinical decision-making in order to enhance the quality of cancer care. This study aimed to develop and validate a selection of classification models that used ML algorithms to predict the occurrence of breast cancer-related lymphedema (BCRL) among Chinese women. Methods: This was a retrospective cohort study of consecutive cases that had been diagnosed with breast cancer, stages I-IV. Forty-eight variables were grouped into five feature sets. Five classification models with ML algorithms were developed, and the models' performance and the variables' relative importance were assessed accordingly. Results: Of 370 eligible female participants, 91 had BCRL (24.6%). The mean age of this study sample was 49.89 (SD â€‹= â€‹7.45). All participants had had breast cancer surgery, and more than half of them had had a modified radical mastectomy (n â€‹= â€‹206, 55.5%). The mean follow-up time after breast cancer surgery was 28.73 months (SD â€‹= â€‹11.71). Most of the tumors were either stage I (n â€‹= â€‹49, 31.2%) or stage II (n â€‹= â€‹252, 68.1%). More than half of the sample had had postoperative chemotherapy (n â€‹= â€‹227, 61.4%). Overall, the logistic regression model achieved the best performance in terms of accuracy (91.6%), precision (82.1%), and recall (91.4%) for BCRL. Although this study included 48 predicting variables, we found that the five models required only 22 variables to achieve predictive performance. The most important variable was the number of positive lymph nodes, followed in descending order by the BCRL occurring on the same side as the surgery, a history of sentinel lymph node biopsy, a dietary preference for meat and fried food, and an exercise frequency of less than three times per week. These factors were the most influential predictors for enhancing the ML models' performance. Conclusions: This study found that in the ML training dataset, the multilayer perceptron model and the logistic regression model were the best discrimination models for predicting the outcome of BCRL, and the k-nearest neighbors and support vector machine models demonstrated good calibration performance in the ML validation dataset. Future research will need to use large-sample datasets to establish a more robust ML model for predicting BCRL deeply and reliably.

The use of immersive virtual reality for cancer-related cognitive impairment assessment and rehabilitation: A clinical feasibility study.

Objective: This brief study aimed to examine the potential effects of virtual reality (VR)-assisted cognitive rehabilitation intervention on the health outcomes of patients with cancer. Methods: A single group of pre-test and post-test study designs were used. An innovative VR system was developed to assess cancer-related cognitive impairment and provide cognitive rehabilitation. The potential effects of the system were determined by measuring changes in cognitive function (learning and memory, information processing speed, executive function, and verbal fluency) and the severity of depression, anxiety, and insomnia. Results: Nine subjects completed the entire VR intervention and were included in the analysis. The participants' mean age was 43.3 years (standard deviation, 8.9 years). The VR-based cognitive intervention significantly improved the subjective cognitive measures of perceived cognitive impairment and perceived cognitive ability (P â€‹= â€‹0.01 and P â€‹< â€‹0.01, respectively). The intervention also improved the objective cognitive measures of verbal learning memory as measured using the Auditory Verbal Learning Test (eg., P â€‹< â€‹0.01 for 5-min delay recall), information processing speed as measured using the trail-making test-A (P â€‹= â€‹0.02) and executive function as measured using the trail-making test-B (P â€‹= â€‹0.03). Only the subtest of delayed recall showed no statistically significant difference after the intervention (P â€‹= â€‹0.69). The VR-based psychological intervention significantly reduced the severity of sleep disorders (P â€‹< â€‹0.01). Conclusions: The use of immersive VR was shown to have potential effects on improving cognitive function for patients with cancer. Future studies will require a larger sample size to examine the effects of immersive VR-assisted cognitive rehabilitation on the health outcomes of patients with cancer.

Gated Tree-based Graph Attention Network (GTGAT) for medical knowledge graph reasoning.

Knowledge graph (KG) is a multi-relational data that has proven valuable for many tasks including decision making and semantic search. In this paper, we present GTGAT (Gated Tree-based Graph Attention), a method for tackling the problems of transductive and inductive reasoning in generalized KGs. Based on recent advancement of graph attention network (GAT), we develop a gated tree-based method to distill valuable information in neighborhood via hierarchical-aware and semantic-aware attention mechanism. Our approach not only addresses several key challenges of GAT but is also capable of undertaking multiple downstream tasks. Experimental results have revealed that our proposed GTGAT has matched state-of-the-art approaches across transductive benchmarks on the Cora, Citeseer, and electronic medical record networks (EMRNet). Meanwhile, the inductive experiments on medical knowledge graphs show that GTGAT surpasses the best competing methods for personalized disease diagnosis.

PercolationDF: A percolation-based medical diagnosis framework.

Goal: With the continuing shortage and unequal distribution of medical resources, our objective is to develop a general diagnosis framework that utilizes a smaller amount of electronic medical records (EMRs) to alleviate the problem that the data volume requirement of prevailing models is too vast for medical institutions to afford. Methods: The framework proposed contains network construction, network expansion, and disease diagnosis methods. In the first two stages above, the knowledge extracted from EMRs is utilized to build and expense an EMR-based medical knowledge network (EMKN) to model and represent the medical knowledge. Then, percolation theory is modified to diagnose EMKN. Result: Facing the lack of data, our framework outperforms naïve Bayes networks, neural networks and logistic regression, especially in the top-10 recall. Out of 207 test cases, 51.7% achieved 100% in the top-10 recall, 21% better than what was achieved in one of our previous studies. Conclusion: The experimental results show that the proposed framework may be useful for medical knowledge representation and diagnosis. The framework effectively alleviates the lack of data volume by inferring the knowledge modeled in EMKN. Significance: The proposed framework not only has applications for diagnosis but also may be extended to other domains to represent and model the knowledge and inference on the representation.

KIEGLFN: A unified acne grading framework on face images.

BACKGROUND AND OBJECTIVE: Grading the severity level is an extremely important procedure for correct diagnoses and personalized treatment schemes for acne. However, the acne grading criteria are not unified in the medical field. This work aims to develop an acne diagnosis system that can be generalized to various criteria. METHODS: A unified acne grading framework that can be generalized to apply referring to different grading criteria is developed. It imitates the global estimation of the dermatologist diagnosis in two steps. First, an adaptive image preprocessing method effectively filters meaningless information and enhances key information. Next, an innovative network structure fuses global deep features with local features to simulate the dermatologists' comparison of local skin and global observation. In addition, a transfer fine-tuning strategy is proposed to transfer prior knowledge on one criterion to another criterion, which effectively improves the framework performance in case of insufficient data. RESULTS: The Preprocessing method effectively filters meaningless areas and improves the performance of downstream models.The framework reaches accuracies of 84.52% and 59.35% on two datasets separately. CONCLUSIONS: The application of the framework on acne grading exceeds the state-of-the-art method by 1.71%, reaches the diagnostic level of a professional dermatologist and the transfer fine-tuning strategy improves the accuracy of 6.5% on the small data.

Clinical decision-making framework against over-testing based on modeling implicit evaluation criteria.

Different statistical methods include various subjective criteria that can prevent over-testing. However, no unified framework that defines generalized objective criteria for various diseases is available to determine the appropriateness of diagnostic tests recommended by doctors. We present the clinical decision-making framework against over-testing based on modeling the implicit evaluation criteria (CDFO-MIEC). The CDFO-MIEC quantifies the subjective evaluation process using statistics-based methods to identify over-testing. Furthermore, it determines the test's appropriateness with extracted entities obtained via named entity recognition and entity alignment. More specifically, implicit evaluation criteria are defined-namely, the correlation among the diagnostic tests, symptoms, and diseases, confirmation function, and exclusion function. Additionally, four evaluation strategies are implemented by applying statistical methods, including the multi-label k-nearest neighbor and the conditional probability algorithms, to model the implicit evaluation criteria. Finally, they are combined into a classification and regression tree to make the final decision. The CDFO-MIEC also provides interpretability by decision conditions for supporting each clinical decision of over-testing. We tested the CDFO-MIEC on 2,860 clinical texts obtained from a single respiratory medicine department in China with the appropriate confirmation by physicians. The dataset was supplemented with random inappropriate tests. The proposed framework excelled against the best competing text classification methods with a Mean_F1 of 0.9167. This determined whether the appropriate and inappropriate tests were properly classified. The four evaluation strategies captured the features effectively, and they were imperative. Therefore, the proposed CDFO-MIEC is feasible because it exhibits high performance and can prevent over-testing.

Learning an expandable EMR-based medical knowledge network to enhance clinical diagnosis.

Electronic medical records (EMRs) contain a wealth of knowledge that can be used to assist doctors in making clinical decisions like disease diagnosis. Constructing a medical knowledge network (MKN) to link medical concepts in EMRs is an effective way to manage this knowledge. The quality of the diagnostic result made by MKN-based clinical decision support system depends on the accuracy of medical knowledge and the completeness of the network. However, collecting knowledge is a long-lasting and cumulative process, which means it's hard to construct a complete MKN with limited data. This study was conducted with the objective of developing an expandable EMR-based MKN to enhance capabilities in making an initial clinical diagnosis. A network of symptom-indicate-disease knowledge in 992 Chinese EMRs (CEMRs) was manually constructed as Original-MKN, and an incremental expansion framework was applied to it to obtain an expandable MKN based on new CEMRs. The framework was composed by: (1) integrating external knowledge extracted from the medical information websites and (2) mining potential knowledge with new EMRs. The framework also adopts a diagnosis-driven learning method to estimate the effectiveness of each knowledge in clinical practice. Experimental results indicate that our expanded MKN achieves a precision of 0.837 for a recall of 0.719 in clinical diagnosis, which outperforms Original-MKN and four classical machine learning methods. Furthermore, both external medical knowledge and potential medical knowledge benefit MKN expansion and disease diagnosis. The proposed incremental expansion framework sustains the MKN learning new knowledge.

Medical knowledge embedding based on recursive neural network for multi-disease diagnosis.

The representation of knowledge based on first-order logic captures the richness of natural language and supports multiple probabilistic inference models. Although symbolic representation enables quantitative reasoning with statistical probability, it is difficult to utilize with machine learning models as they perform numerical operations. In contrast, knowledge embedding (i.e., high-dimensional and continuous vectors) is a feasible approach to complex reasoning that can not only retain the semantic information of knowledge, but also establish the quantifiable relationship among embeddings. In this paper, we propose a recursive neural knowledge network (RNKN), which combines medical knowledge based on first-order logic with a recursive neural network for multi-disease diagnosis. After the RNKN is efficiently trained using manually annotated Chinese Electronic Medical Records (CEMRs), diagnosis-oriented knowledge embeddings and weight matrixes are learned. The experimental results confirm that the diagnostic accuracy of the RNKN is superior to those of four machine learning models, four classical neural networks and Markov logic network. The results also demonstrate that the more explicit the evidence extracted from CEMRs, the better the performance. The RNKN gradually reveals the interpretation of knowledge embeddings as the number of training epochs increases.

Extraction of risk factors for cardiovascular diseases from Chinese electronic medical records.

BACKGROUND AND OBJECTIVE: Early prevention of cardiovascular diseases (CVDs) can effectively prevent later loss of health, and the detection of CVDs risk factors is a simple method to achieve early prevention. Personal health records play a prominent role in the field of health information extraction because of their factuality and reliability. This present study describes how to extract risk factors for CVDs from Chinese electronic medical records (CEMRs). METHODS: The extraction process involves two tasks: (a) CVDs risk factor recognition and (b) risk factor time and assertion classification. We considered risk factor recognition as a named entity recognition (NER) task and time and assertion classification as a textual classification task. An information extraction pipeline system consisting of NER and textual classification modules with machine learning models was developed. In the risk factor recognition module, bidirectional long short term memory (BLSTM) with extra risk factor textual feature input was built, as well, convolutional neural networks (CNNs) with risk factor type and section label input and support vector machine (SVM) were built for time and assertion classification. RESULTS: We have achieved the best performance of risk factor recognition with F1 value of 0.9609, time and assertion classification with F1 of 0.9812 and 0.9612, respectively. The experimental results showed that our system achieved a high performance and can extract risk factors from CEMRs efficiently. CONCLUSIONS: The proposed system is the first system for CVDs risk factors extraction from CEMRs and shows competition to risk factor extraction systems that developed on English EMRs. Further, its good performance should have a strong influence on CVDs prevention.

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.

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.

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.

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

BACKGROUND: Cardiovascular 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. RESULTS: We 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. CONCLUSION: To 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.

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.