Pattern Recognition or Adnexal MR Scoring System: Which Is More Accurate in Evaluating Adnexal Lesions?

PURPOSE: This study aims to compare the accuracy of the ADNEX MR scoring system and pattern recognition system to evaluate adnexal lesions indeterminate on the US exam. METHODS: In this cross-sectional retrospective study, pelvic DCE-MRI of 245 patients with 340 adnexal masses was studied based on the ADNEX MR scoring system and pattern recognition system. RESULTS: ADNEX MR scoring system with a sensitivity of 96.6% and specificity of 91% has an accuracy of 92.9%. The pattern recognition system's sensitivity, specificity, and accuracy are 95.8%, 93.3%, and 94.7%, respectively. PPV and NPV for the ADNEX MR scoring system were 85.1 and 98.1, respectively. PPV and NPV for the pattern recognition system were 89.7% and 97.7%, respectively. The area under the ROC curve for the ADNEX MR scoring system and pattern recognition system is 0.938 (95% CI, 0.909-0.967) and 0.950 (95% CI, 0.922-0.977). Pairwise comparison of these AUCs showed no significant difference (p = 0.052). CONCLUSION: The pattern recognition system is less sensitive than the ADNEX MR scoring system, yet more specific.

Detecting mental and physical disorders using multi-task learning equipped with knowledge graph attention network.

Mental and physical disorders (MPD) are inextricably linked in many medical cases; psychosomatic diseases can be induced by mental concerns and psychological discomfort can ensue from physiological diseases. However, existing medical informatics studies focus on identifying mental or physical disorders from a unilateral perspective. Consequently, no existing domain knowledge base, corpus, or detection modeling approach considers mental as well as physical aspects concurrently. This paper proposes a joint modeling approach to detect MPD. First, we crawl through online medical consultation records of patients from websites and build an MPD knowledge ontology by extracting the core conceptual features of the text. Based on the ontology, an MPD knowledge graph containing 12,673 nodes and 82,195 relations is obtained using term matching with a domain thesaurus of each concept. Subsequently, an MPD corpus with fine-grained severities (None, Mild, Moderate, Severe, Dangerous) and 8909 records is constructed by formulating MPD classification criteria and a data annotation process under the guidance of domain experts. Taking the knowledge graph and corpus as the dataset, we design a multi-task learning model to detect the MPD severity, in which a knowledge graph attention network (KGAT) is embedded to better extract knowledge features. Experiments are performed to demonstrate the effectiveness of our model. Furthermore, we employ ontology-based and centrality-based methods to discover additional potential inferred knowledge, which can be captured by KGAT so as to improve the prediction performance and interpretability of our model. Our dataset has been made publicly available, so it can be further used as a medical informatics reference in the fields of psychosomatic medicine, psychiatrics, physical co-morbidity, and so on.

GC-CDSS: Personalized gastric cancer treatment recommendations system based on knowledge graph.

BACKGROUND: Gastric cancer (GC) is one of the most common malignant tumors in the world, posing a serious threat to human health. Currently, gastric cancer treatment strategies emphasize a multidisciplinary team (MDT) consultation approach. However, there are numerous treatment guidelines and insights from clinical trials. The application of AI-based Clinical Decision Support System (CDSS) in tumor diagnosis and screening is increasing rapidly. OBJECTIVE: The purpose of this study is to (1) summarize the treatment decision process for GC according to the treatment guidelines in China, and then create a knowledge graph (KG) for GC, (2) based on aforementioned KG, built a CDSS and conducted an initial feasibility evaluation for the current system. METHODS: Firstly, we summarized the decision-making process for treatment of GC. Then, we extracted relevant decision nodes and relationships and utilized Neo4j to create the KG. After obtaining the initial node features for building the graph embedding model, graph embedding algorithm, such as Node2Vec and GraphSAGE, were used to construct the GC-CDSS. At last, a retrospective cohort study was used to compare the consistency between GC-CDSS and MDT in treatment decision making. RESULTS: In current study, we introduce a GC-CDSS, which is constructed based on Chinese GC treatment guidelines knowledge graph (KG). In the KG, we define four types of nodes and four types of relationships, and it comprise a total of 207 nodes and 300 relationships. Regarding GC-CDSS, the system is capable of providing dynamic and personalized diagnostic and treatment recommendations based on the patient's condition. Furthermore, a retrospective cohort study is conducted to compare GC-CDSS recommendations with those of the MDT group, the overall consistency rate of treatment recommendations between the auxiliary decision system and MDT team is 92.96%. CONCLUSIONS: We construct a GC treatment support system, GC-CDSS, based on KG. The GC-CDSS may help oncologists make treatment decisions more efficient and promote standardization in primary healthcare settings.

An Improved k-Nearest Neighbor Algorithm for Recognition and Classification of Thyroid Nodules.

OBJECTIVES: To complete the task of automatic recognition and classification of thyroid nodules and solve the problem of high classification error rates when the samples are imbalanced. METHODS: An improved k-nearest neighbor (KNN) algorithm is proposed and a method for automatic thyroid nodule classification based on the improved KNN algorithm is established. In the improved KNN algorithm, we consider not only the number of class labels for various classes of data in KNNs, but also the corresponding weights. And we use the Minkowski distance measure instead of the Euclidean distance measure. RESULTS: A total of 508 ultrasound images of thyroid nodules, including 415 benign nodules and 93 malignant nodules, were used in the paper. Experimental results show the improved KNN has 0.872549 accuracy, 0.867347 precision, 1 recall, and 0.928962 F1-score. At the same time, we also considered the influence of different distance weights, the value of k, different distance measures on the classification results. CONCLUSIONS: A comparison result shows that our method has a better performance than the traditional KNN and other classical machine learning methods.

Knowledge graph construction based on granulosa cells transcriptome from polycystic ovary syndrome with normoandrogen and hyperandrogen.

PCOS is a widespread disease that primarily caused in-pregnancy in pregnant-age women. Normoandrogen (NA) and Hyperandrogen (HA) PCOS are distinct subtypes of PCOS, while bio-markers and expression patterns for NA PCOS and HA PCOS have not been disclosed. We performed microarray analysis on granusola cells from NA PCOS, HA PCOS and normal tissue from 12 individuals. Afterwards, microarray data were processed and specific genes for NA PCOS and HA PCOS were identified. Further functional analysis selected IL6R and CD274 as new NA PCOS functional markers, and meanwhile selected CASR as new HA PCOS functional marker. IL6R, CD274 and CASR were afterwards experimentally validated on mRNA and protein level. Subsequent causal relationship analysis based on Apriori Rules Algorithm and co-occurrence methods identified classification markers for NA PCOS and HA PCOS. According to classification markers, downloaded transcriptome datasets were merged with our microarray data. Based on merged data, causal knowledge graph was constructed for NA PCOS or HA PCOS and female infertility on NA PCOS and HA PCOS. Gene-drug interaction analysis was then performed and drugs for HA PCOS and NA PCOS were predicted. Our work was among the first to indicate the NA PCOS and HA PCOS functional and classification markers and using markers to construct knowledge graphs and afterwards predict drugs for NA PCOS and HA PCOS based on transcriptome data. Thus, our study possessed biological and clinical value on further understanding the inner mechanism on the difference between NA PCOS and HA PCOS.

Standigm ASK™: knowledge graph and artificial intelligence platform applied to target discovery in idiopathic pulmonary fibrosis.

Standigm ASK™ revolutionizes healthcare by addressing the critical challenge of identifying pivotal target genes in disease mechanisms-a fundamental aspect of drug development success. Standigm ASK™ integrates a unique combination of a heterogeneous knowledge graph (KG) database and an attention-based neural network model, providing interpretable subgraph evidence. Empowering users through an interactive interface, Standigm ASK™ facilitates the exploration of predicted results. Applying Standigm ASK™ to idiopathic pulmonary fibrosis (IPF), a complex lung disease, we focused on genes (AMFR, MDFIC and NR5A2) identified through KG evidence. In vitro experiments demonstrated their relevance, as TGFß treatment induced gene expression changes associated with epithelial-mesenchymal transition characteristics. Gene knockdown reversed these changes, identifying AMFR, MDFIC and NR5A2 as potential therapeutic targets for IPF. In summary, Standigm ASK™ emerges as an innovative KG and artificial intelligence platform driving insights in drug target discovery, exemplified by the identification and validation of therapeutic targets for IPF.

Global trends in PANoptosis research: bibliometrics and knowledge graph analysis.

PANoptosis has recently been discovered as a new type of cell death. PANoptosis mainly refers to the significant interaction among the three programmed cell death pathways of apoptosis, necroptosis, and pyroptosis. Despite this, only a few studies have examined the systematic literature in this area. By analyzing the bibliometric data for PANoptosis, we can visualize the current hotspots and predicted trends in research. This study analyzed bibliometric indicators using the Histcite Pro 2.0 tool, which searches the Web of Science for PANoptosis literature published between 2016 and 2022. A bibliometric analysis was performed using Histcite Pro 2.0, while research trends and hotspots were visualized using VOSviewer, CiteSpace and BioBERT. The output of related literature was low in the four years from the first presentation of PANoptosis in 2016 to 2020. The volume of relevant literature grew exponentially between 2020 and 2022. The United States and China play a leading role in this field. Although China started late, its research in this field is developing rapidly. As research progressed, more focus was placed on the relationship between PANoptosis and pyroptosis, as well as apoptosis and necrosis. Now is a rapid development stage of PANoptosis research. Most of the research focuses on the cellular level, and the focus is more on the treatment of tumor-related diseases. The current focus of this area is PANoptosis mechanisms in cancer and inflammation. It can be seen from the burst analysis of keywords that caspase1 and host defense have consistently been research hotspots in the field of PANoptosis, while the frequency of NLRC4, causes of autoinflammation, recognition, NLRP3, and Gasdermin D has gradually increased, all of which have become research hotspots in recent years. Finally, we used the BioBERT biomedical language model to mine the most documented genes and diseases in the PANoptosis field articles, pointing out the direction for subsequent research steps. According to a bibliometric analysis, researchers have shown an increased interest in PANoptosis over the past few years. Researchers initially focused on the molecular mechanism of PANoptosis and pyroptosis, apoptosis, and necroptosis. The role of PANoptosis in diseases and conditions such as inflammation and tumors is one of the current research hotspots in this area. The focus is more on treating inflammation-related diseases, which will become the key development direction of future research.

Not without Context-A Multiple Methods Study on Evaluation and Correction of Automated Brain Tumor Segmentations by Experts.

RATIONALE AND OBJECTIVES: Brain tumor segmentations are integral to the clinical management of patients with glioblastoma, the deadliest primary brain tumor in adults. The manual delineation of tumors is time-consuming and highly provider-dependent. These two problems must be addressed by introducing automated, deep-learning-based segmentation tools. This study aimed to identify criteria experts use to evaluate the quality of automatically generated segmentations and their thought processes as they correct them. MATERIALS AND METHODS: Multiple methods were used to develop a detailed understanding of the complex factors that shape experts' perception of segmentation quality and their thought processes in correcting proposed segmentations. Data from a questionnaire and semistructured interview with neuro-oncologists and neuroradiologists were collected between August and December 2021 and analyzed using a combined deductive and inductive approach. RESULTS: Brain tumors are highly complex and ambiguous segmentation targets. Therefore, physicians rely heavily on the given context related to the patient and clinical context in evaluating the quality and need to correct brain tumor segmentation. Most importantly, the intended clinical application determines the segmentation quality criteria and editing decisions. Physicians' personal beliefs and preferences about the capabilities of AI algorithms and whether questionable areas should not be included are additional criteria influencing the perception of segmentation quality and appearance of an edited segmentation. CONCLUSION: Our findings on experts' perceptions of segmentation quality will allow the design of improved frameworks for expert-centered evaluation of brain tumor segmentation models. In particular, the knowledge presented here can inspire the development of brain tumor-specific metrics for segmentation model training and evaluation.

A Hierarchy-driven Multi-label Network with Label Constraints for Post-operative Complication Prediction of Lung Cancer.

Lung cancer is one of the most dangerous cancers all over the world. Surgical resection remains the only potentially curative option for patients with lung cancer. However, this invasive treatment often causes various complications, which seriously endanger patient health. In this study, we proposed a novel multi-label network, namely a hierarchy-driven multi-label network with label constraints (HDMN-LC), to predict the risk of complications of lung cancer patients. In this method, we first divided all complications into pulmonary and cardiovascular complication groups and employed the hierarchical cluster algorithm to analyze the hierarchies between these complications. After that, we employed the hierarchies to drive the network architecture design so that related complications could share more hidden features. And then, we combined all complications and employed an auxiliary task to predict whether any complications would occur to impose the bottom layer to learn general features. Finally, we proposed a regularization term to constrain the relationship between specific and combined complication labels to improve performance. We conducted extensive experiments on real clinical data of 593 patients. Experimental results indicate that the proposed method outperforms the single-label, multi-label baseline methods, with an average AUC value of 0.653. And the results also prove the effectiveness of hierarchy-driven network architecture and label constraints. We conclude that the proposed method can predict complications for lung cancer patients more effectively than the baseline methods.Clinical relevance-This study presents a novel multi-label network that can more accurately predict the risk of specific postoperative complications for lung cancer patients. The method can help clinicians identify high-risk patients more accurately and timely so that interventions can be implemented in advance to ensure patient safety.

Statistical shape modeling of mean shape and principal variability of the human talar bone in the Chinese population.

PURPOSE: The talar bone plays a crucial role in ankle biomechanics and stability. Understanding the shape variability of the talar bone within specific populations is essential for various clinical applications. In this study, we aimed to investigate the mean shape and principal variability of the human talar bone in the Chinese population using statistical shape modeling (SSM). METHODS: CT scans of 214 tali were included to create SSM models. Principal component analysis was used to describe shape variation among the male, female, and overall groups. RESULTS: The largest amount of variation among three groups ranges from 17.2%-18.8% of each variation. The first seven principal components (modes) captured 62.4%-67.5% of the cumulative variance. No dominant shape of the talus was found. Male tali generally have a larger size than the female tali, with the exception of the articular surface of the anterior subtalar joint. CONCLUSIONS: SSM is an effective method of finding mean shape and principal variability. Considerable variabilities were noticed among these three groups and all principal modes of variation. No dominant talar model was found to represent the majority of tali, regardless the gender. Such information is crucial to improve the current understanding of talar pathologies and their treatment strategies.

[Knowledge Graph-Based Prediction of Potentially Inappropriate Medication].

Objective: To improve the accuracy of potentially inappropriate medication (PIM) prediction, a PIM prediction model that combines knowledge graph and machine learning was proposed. Methods: Firstly, based on Beers criteria 2019 and using the knowledge graph as the basic structure, a PIM knowledge representation framework with logical expression capabilities was constructed, and a PIM inference process was implemented from patient information nodes to PIM nodes. Secondly, a machine learning prediction model for each PIM label was established based on the classifier chain algorithm, to learn the potential feature associations from the data. Finally, based on a threshold of sample size, a portion of reasoning results from the knowledge graph was used as output labels on the classifier chain to enhance the reliability of the prediction results of low-frequency PIMs. Results: 11 741 prescriptions from 9 medical institutions in Chengdu were used to evaluate the effectiveness of the model. Experimental results show that the accuracy of the model for PIM quantity prediction is 98.10%, the F1 is 93.66%, the Hamming loss for PIM multi-label prediction is 0.06%, and the macroF1 is 66.09%, which has higher prediction accuracy than the existing models. Conclusion: The method proposed has better prediction performance for potentially inappropriate medication and significantly improves the recognition of low-frequency PIM labels.

Semi-supervised enhanced discriminative local constraint preserving projection for dimensionality reduction of medical hyperspectral images.

Microscopic hyperspectral images has the advantage of containing rich spatial and spectral information. However, the large number of spectral bands provides a significant amount of spectral features, but also leads to data redundancy and noise, which seriously affect the recognition and classification performance of the images, as well as increasing the requirements for computation and storage. To address this issue, we propose a dimensionality reduction algorithm named enhanced discriminant local constraint preserving projection (EDLCPP). Specifically, the global spectral attention mechanism focuses on important bands, the high discriminability sample selection module measures the discriminability of samples using a modified average neighborhood margin, the graph construction module preserves the local geometric relationship and discriminant information, and the graph embedding module embeds the constructed graphs into a low-dimensional space to obtain the projection matrices. Experimental results on eight cholangiocarcinoma (CCA) hyperspectral images, Bloodcell1-3, and Bloodcell2-2 datasets have demonstrated the effectiveness of the proposed method.

Construction of a knowledge graph for breast cancer diagnosis based on Chinese electronic medical records: development and usability study.

BACKGROUND: Electronic medical records (EMRs) contain a wealth of information related to breast cancer diagnosis and treatment. Extracting relevant features from these medical records and constructing a knowledge graph can significantly contribute to an efficient data analysis and decision support system for breast cancer diagnosis. METHODS: An approach was proposed to develop a workflow for effectively extracting breast cancer-related features from Chinese breast cancer mammography reports and constructing a knowledge graph for breast cancer diagnosis. Firstly, the concept layer of the knowledge graph for breast cancer diagnosis was constructed based on breast cancer diagnosis and treatment guidelines, along with insights from clinical experts. .Next, a BiLSTM-Highway-CRF model was designed to extract the mammography features, which formed the data layer of the knowledge graph. Finally, the knowledge graph was constructed by combining the concept layer and the data layer in a Neo4j graph data platform, and then applied in visualization analysis, semantic query and computer assisted diagnosis. RESULTS: Mammographic features were extracted from a total of 1171 mammography examination reports. The overall extraction performance of the model achieved an accuracy rate of 97.16%, a recall rate of 98.06%, and a F1 score of 97.61%. Additionally, 47,660 relationships between entities were identified based on the four different types of relationships defined in the concept layer. The knowledge graph for breast cancer diagnosis was constructed after inputting mammographic features and relationships into the Neo4j graph data platform. The model was assessed from the concept layer, data layer, and application layer perspectives, and showed promising results. CONCLUSIONS: The proposed workflow is applicable for constructing knowledge graphs for breast cancer diagnosis based on Chinese EMRs. This study serves as a reference for the rapid design, construction, and application of knowledge graphs for diagnosis and treatment of other diseases. Furthermore, it offers a potential solution to address the issues of limited data sharing and format inconsistencies present in Chinese EMR data.

Visual analysis of lung neuroendocrine tumors based on CiteSpace knowledge graph.

Objective: The relevant literatures in the field of pulmonary neuroendocrine tumor were analyzed to understand the lineage, hot spots and development trends of research in this tumor. Method: The Web of Science core collection was searched for English-language literature about neuroendocrine tumors of the lung published between 2000 and 2022. CiteSpace software was imported for visualization analysis of countries, institutions, co-cited authors and co-cited journals and sorting of high-frequency keywords, as well as co-cited references and keyword co-occurrence, clustering and bursting display. Results: A total of 594 publications on neuroendocrine tumours of the lung were available, from 2000 to 2022, with an overall upward trend of annual publications in the literature. Authors or institutions from the United States, Italy, Japan and China were more active in this field, but there was little cooperation among the major countries. Co-cited references and keyword co-occurrence and cluster analysis showed that research on diagnostic instruments, pathogenesis, ectopic ACTH signs, staging and prognosis and treatment was a current research hotspot. The keyword bursts suggested that therapeutic approaches might be a key focus of future research into the field for pulmonary neuroendocrine tumors. Conclusion: Over these 20 years, research related to neuroendocrine tumors of the lung has increased in fervour, with research on diagnostic instruments, pathogenesis, ectopic ACTH signs, staging and prognosis, and treatment being the main focus of research. Therapeutic treatments may be the future research trend in this field.

Laparoscopic Image-Based Critical Action Recognition and Anticipation With Explainable Features.

Surgical workflow analysis integrates perception, comprehension, and prediction of the surgical workflow, which helps real-time surgical support systems provide proper guidance and assistance for surgeons. This article promotes the idea of critical actions, which refer to the essential surgical actions that progress towards the fulfillment of the operation. Fine-grained workflow analysis involves recognizing current critical actions and previewing the moving tendency of instruments in the early stage of critical actions. Aiming at this, we propose a framework that incorporates operational experience to improve the robustness and interpretability of action recognition in in-vivo situations. High-dimensional images are mapped into an experience-based explainable feature space with low dimensions to achieve critical action recognition through a hierarchical classification structure. To forecast the instrument's motion tendency, we model the motion primitives in the polar coordinate system (PCS) to represent patterns of complex trajectories. Given the laparoscopy variance, the adaptive pattern recognition (APR) method, which adapts to uncertain trajectories by modifying model parameters, is designed to improve prediction accuracy. The in-vivo dataset validations show that our framework fulfilled the surgical awareness tasks with exceptional accuracy and real-time performance.

Feature-aware unsupervised lesion segmentation for brain tumor images using fast data density functional transform.

We demonstrate that isomorphically mapping gray-level medical image matrices onto energy spaces underlying the framework of fast data density functional transform (fDDFT) can achieve the unsupervised recognition of lesion morphology. By introducing the architecture of geometric deep learning and metrics of graph neural networks, gridized density functionals of the fDDFT establish an unsupervised feature-aware mechanism with global convolutional kernels to extract the most likely lesion boundaries and produce lesion segmentation. An AutoEncoder-assisted module reduces the computational complexity from [Formula: see text] to [Formula: see text], thus efficiently speeding up global convolutional operations. We validate their performance utilizing various open-access datasets and discuss limitations. The inference time of each object in large three-dimensional datasets is 1.76 s on average. The proposed gridized density functionals have activation capability synergized with gradient ascent operations, hence can be modularized and embedded in pipelines of modern deep neural networks. Algorithms of geometric stability and similarity convergence also raise the accuracy of unsupervised recognition and segmentation of lesion images. Their performance achieves the standard requirement for conventional deep neural networks; the median dice score is higher than 0.75. The experiment shows that the synergy of fDDFT and a naïve neural network improves the training and inference time by 58% and 51%, respectively, and the dice score raises to 0.9415. This advantage facilitates fast computational modeling in interdisciplinary applications and clinical investigation.

An efficient multi-level pre-processing algorithm for the enhancement of dermoscopy images in melanoma detection.

In this paper, a multi-level algorithm for pre-processing of dermoscopy images is proposed, which helps in improving the quality of the raw images, making it suitable for skin lesion detection. This multi-level pre-processing method has a positive impact on automated skin lesion segmentation using Regularized Extreme Learning Machine. Raw images are subjected to de-noising, illumination correction, contrast enhancement, sharpening, reflection removal, and virtual shaving before the skin lesion segmentation. The Non-Local Means (NLM) filter with lowest Blind Reference less Image Spatial Quality Evaluator (BRISQUE) score exhibits better de-noising of dermoscopy images. To suppress uneven illumination, gamma correction is subjected to the denoised image. The Robust Image Contrast Enhancement (RICE) algorithm is used for contrast enhancement, and produces enhanced images with better structural preservation and negligible loss of information. Unsharp masking for sharpening exhibits low BRISQUE scores for better sharpening of fine details in an image. Output images produced by the phase congruency-based method in virtual shaving show high similarity with ground truth images as the hair is removed completely from the input images. Obtained scores at each stage of pre-processing framework show that the performance is superior compared to all the existing methods, both qualitatively and quantitatively, in terms of uniform contrast, preservation of information content, removal of undesired information, and elimination of artifacts in melanoma images. The output of the proposed system is assessed qualitatively and quantitatively with and without pre-processing of dermoscopy images. From the overall evaluation results, it is found that the segmentation of skin lesion is more efficient using Regularized Extreme Learning Machine if the multi-level pre-processing steps are used in proper sequence.

Surgical Instrument Signaling Gesture Recognition Using Surface Electromyography Signals.

Surgical Instrument Signaling (SIS) is compounded by specific hand gestures used by the communication between the surgeon and surgical instrumentator. With SIS, the surgeon executes signals representing determined instruments in order to avoid error and communication failures. This work presented the feasibility of an SIS gesture recognition system using surface electromyographic (sEMG) signals acquired from the Myo armband, aiming to build a processing routine that aids telesurgery or robotic surgery applications. Unlike other works that use up to 10 gestures to represent and classify SIS gestures, a database with 14 selected gestures for SIS was recorded from 10 volunteers, with 30 repetitions per user. Segmentation, feature extraction, feature selection, and classification were performed, and several parameters were evaluated. These steps were performed by taking into account a wearable application, for which the complexity of pattern recognition algorithms is crucial. The system was tested offline and verified as to its contribution for all databases and each volunteer individually. An automatic segmentation algorithm was applied to identify the muscle activation; thus, 13 feature sets and 6 classifiers were tested. Moreover, 2 ensemble techniques aided in separating the sEMG signals into the 14 SIS gestures. Accuracy of 76% was obtained for the Support Vector Machine classifier for all databases and 88% for analyzing the volunteers individually. The system was demonstrated to be suitable for SIS gesture recognition using sEMG signals for wearable applications.

A knowledge graph-based analytical model for mining clinical value of drug stress echocardiography for diagnosis, risk stratification and prognostic evaluation of coronary artery disease.

The three major techniques for clinically diagnosing coronary heart disease, including angina associated with myocardial ischemia, are coronary angiography, myocardial perfusion imaging, and drug stress echocardiography. Compared to the first two methods, which are invasive or involve the use of radionuclides, drug stress echocardiography is increasingly used in clinical practice due to its non-invasive, low-risk, and controllable nature, and wide applicability. We developed a novel methodology to demonstrate knowledge graph-based efficacy analysis of drug stress echocardiography as a complement to traditional meta-analysis. By measuring coronary flow reserve (CFR), we discovered that regional ventricular wall abnormalities (RVWA) and drug-loaded cardiac ultrasound can be used to detect coronary artery disease. Additionally, drug-loaded cardiac ultrasound can be used to identify areas of cardiac ischemia, stratify risks, and determine prognosis. Furthermore, adenosine stress echocardiography(ASE) can determine atypical symptoms of coronary heart disease with associated cardiac events through CFR and related quantitative indices for risk stratification. Using a knowledge graph-based approach, we investigated the positive and negative effects of three drugs - Dipyridamole, Dobutamine, and Adenosine - for coronary artery disease analysis. Our findings show that Adenosine has the highest positive effect and the lowest negative effect among the three drugs. Due to its minimal and controlled side effects, and high sensitivity for diagnosing coronary microcirculation disorders and multiple lesions, adenosine is frequently used in clinical practice.

Biomedical knowledge graph learning for drug repurposing by extending guilt-by-association to multiple layers.

Computational drug repurposing aims to identify new indications for existing drugs by utilizing high-throughput data, often in the form of biomedical knowledge graphs. However, learning on biomedical knowledge graphs can be challenging due to the dominance of genes and a small number of drug and disease entities, resulting in less effective representations. To overcome this challenge, we propose a "semantic multi-layer guilt-by-association" approach that leverages the principle of guilt-by-association - "similar genes share similar functions", at the drug-gene-disease level. Using this approach, our model DREAMwalk: Drug Repurposing through Exploring Associations using Multi-layer random walk uses our semantic information-guided random walk to generate drug and disease-populated node sequences, allowing for effective mapping of both drugs and diseases in a unified embedding space. Compared to state-of-the-art link prediction models, our approach improves drug-disease association prediction accuracy by up to 16.8%. Moreover, exploration of the embedding space reveals a well-aligned harmony between biological and semantic contexts. We demonstrate the effectiveness of our approach through repurposing case studies for breast carcinoma and Alzheimer's disease, highlighting the potential of multi-layer guilt-by-association perspective for drug repurposing on biomedical knowledge graphs.