A study on pharmaceutical text relationship extraction based on heterogeneous graph neural networks.

Effective information extraction of pharmaceutical texts is of great significance for clinical research. The ancient Chinese medicine text has streamlined sentences and complex semantic relationships, and the textual relationships may exist between heterogeneous entities. The current mainstream relationship extraction model does not take into account the associations between entities and relationships when extracting, resulting in insufficient semantic information to form an effective structured representation. In this paper, we propose a heterogeneous graph neural network relationship extraction model adapted to traditional Chinese medicine (TCM) text. First, the given sentence and predefined relationships are embedded by bidirectional encoder representation from transformers (BERT fine-tuned) word embedding as model input. Second, a heterogeneous graph network is constructed to associate words, phrases, and relationship nodes to obtain the hidden layer representation. Then, in the decoding stage, two-stage subject-object entity identification method is adopted, and the identifier adopts a binary classifier to locate the start and end positions of the TCM entities, identifying all the subject-object entities in the sentence, and finally forming the TCM entity relationship group. Through the experiments on the TCM relationship extraction dataset, the results show that the precision value of the heterogeneous graph neural network embedded with BERT is 86.99% and the F1 value reaches 87.40%, which is improved by 8.83% and 10.21% compared with the relationship extraction models CNN, Bert-CNN, and Graph LSTM.

Multiple prescription pattern recognition model based on Siamese network.

Prescription data is an important focus and breakthrough in the study of clinical treatment rules, and the complex multidimensional relationships between Traditional Chinese medicine (TCM) prescription data increase the difficulty of extracting knowledge from clinical data. This paper proposes a complex prescription recognition algorithm (MTCMC) based on the classification and matching of TCM prescriptions with classical prescriptions to identify the classical prescriptions contained in the prescriptions and provide a reference for mining TCM knowledge. The MTCMC algorithm first calculates the importance level of each drug in the complex prescriptions and determines the core prescription combinations of patients through the Analytic Hierarchy Process (AHP) combined with drug dosage. Secondly, a drug attribute tagging strategy was used to quantify the functional features of each drug in the core prescriptions; finally, a Bidirectional Long Short-Term Memory Network (BiLSTM) was used to extract the relational features of the core prescriptions, and a vector representation similarity matrix was constructed in combination with the Siamese network framework to calculate the similarity between the core prescriptions and the classical prescriptions. The experimental results show that the accuracy and F1 score of the prescription matching dataset constructed based on this paper reach 94.45% and 94.34% respectively, which is a significant improvement compared with the models of existing methods.

Dose-effect relationship analysis of TCM based on deep Boltzmann machine and partial least squares.

A dose-effect relationship analysis of traditional Chinese Medicine (TCM) is crucial to the modernization of TCM. However, due to the complex and nonlinear nature of TCM data, such as multicollinearity, it can be challenging to conduct a dose-effect relationship analysis. Partial least squares can be applied to multicollinearity data, but its internally extracted principal components cannot adequately express the nonlinear characteristics of TCM data. To address this issue, this paper proposes an analytical model based on a deep Boltzmann machine (DBM) and partial least squares. The model uses the DBM to extract nonlinear features from the feature space, replaces the components in partial least squares, and performs a multiple linear regression. Ultimately, this model is suitable for analyzing the dose-effect relationship of TCM. The model was evaluated using experimental data from Ma Xing Shi Gan Decoction and datasets from the UCI Machine Learning Repository. The experimental results demonstrate that the prediction accuracy of the model based on the DBM and partial least squares method is on average 10% higher than that of existing methods.

BA-GCA Net: Boundary-Aware Grid Contextual Attention Net in Osteosarcoma MRI Image Segmentation.

Osteosarcoma is one of the most common bone tumors that occurs in adolescents. Doctors often use magnetic resonance imaging (MRI) through biosensors to diagnose and predict osteosarcoma. However, a number of osteosarcoma MRI images have the problem of the tumor shape boundary being vague, complex, or irregular, which causes doctors to encounter difficulties in diagnosis and also makes some deep learning methods lose segmentation details as well as fail to locate the region of the osteosarcoma. In this article, we propose a novel boundary-aware grid contextual attention net (BA-GCA Net) to solve the problem of insufficient accuracy in osteosarcoma MRI image segmentation. First, a novel grid contextual attention (GCA) is designed to better capture the texture details of the tumor area. Then the statistical texture learning block (STLB) and the spatial transformer block (STB) are integrated into the network to improve its ability to extract statistical texture features and locate tumor areas. Over 80,000 MRI images of osteosarcoma from the Second Xiangya Hospital are adopted as a dataset for training, testing, and ablation studies. Results show that our proposed method achieves higher segmentation accuracy than existing methods with only a slight increase in the number of parameters and computational complexity.

Traditional Chinese Medicine Text Similarity Calculation Model Based on the Bidirectional Temporal Siamese Network.

The text similarity calculation plays a crucial role as the core work of artificial intelligence commercial applications such as traditional Chinese medicine (TCM) auxiliary diagnosis, intelligent question and answer, and prescription recommendation. However, TCM texts have problems such as short sentence expression, inaccurate word segmentation, strong semantic relevance, high feature dimension, and sparseness. This study comprehensively considers the temporal information of sentence context and proposes a TCM text similarity calculation model based on the bidirectional temporal Siamese network (BTSN). We used the enhanced representation through knowledge integration (ERNIE) pretrained language model to train character vectors instead of word vectors and solved the problem of inaccurate word segmentation in TCM. In the Siamese network, the traditional fully connected neural network was replaced by a deep bidirectional long short-term memory (BLSTM) to capture the contextual semantics of the current word information. The improved similarity BLSTM was used to map the sentence that is to be tested into two sets of low-dimensional numerical vectors. Then, we performed similarity calculation training. Experiments on the two datasets of financial and TCM show that the performance of the BTSN model in this study was better than that of other similarity calculation models. When the number of layers of the BLSTM reached 6 layers, the accuracy of the model was the highest. This verifies that the text similarity calculation model proposed in this study has high engineering value.

Obese rats intervened with Rhizoma coptidis revealed differential gene expression and microbiota by serum metabolomics.

BACKGROUND: Integrating systems biology is an approach for investigating metabolic diseases in humans. However, few studies use this approach to investigate the mechanism by which Rhizoma coptidis (RC) reduces the effect of lipids and glucose on high-fat induced obesity in rats. METHODS: Twenty-four specific pathogen-free (SPF) male Sprague-Dawley rats (80 ± 10 g) were used in this study. Serum metabolomics were detected by ultra-high-performance liquid chromatography coupled with quadrupole-time-of-flight tandem mass spectrometry. Liver tissue and cecum feces were used for RNA-Seq technology and 16S rRNA gene sequencing, respectively. RESULTS: We identified nine potential biomarkers, which are differential metabolites in the Control, Model and RC groups, including linoleic acid, eicosapentaenoic acid, arachidonic acid, stearic acid, and L-Alloisoleucine (p < 0.01). The liver tissue gene expression profile indicated the circadian rhythm pathway was significantly affected by RC (Q ≤ 0.05). A total of 149 and 39 operational taxonomic units (OTUs), which were highly associated with biochemical indicators and potential biomarkers in the cecum samples (FDR ≤ 0.05), respectively, were identified. CONCLUSION: This work provides information to better understand the mechanism of the effect of RC intervention on hyperlipidemia and hypoglycemic effects in obese rats. The present study demonstrates that integrating systems biology may be a powerful tool to reveal the complexity of metabolic diseases in rats intervened by traditional Chinese medicine.

Design and Evaluation of a Prescription Drug Monitoring Program for Chinese Patent Medicine based on Knowledge Graph.

BACKGROUND: Chinese patent medicines are increasingly used clinically, and the prescription drug monitoring program is an effective tool to promote drug safety and maintain health. METHODS: We constructed a prescription drug monitoring program for Chinese patent medicines based on knowledge graphs. First, we extracted the key information of Chinese patent medicines, diseases, and symptoms from the domain-specific corpus by the information extraction. Second, based on the extracted entities and relationships, a knowledge graph was constructed to form a rule base for the monitoring of data. Then, the named entity recognition model extracted the key information from the electronic medical record to be monitored and matched the knowledge graph to realize the monitoring of the Chinese patent medicines in the prescription. RESULTS: Named entity recognition based on the pretrained model achieved an F1 value of 83.3% on the Chinese patent medicines dataset. On the basis of entity recognition technology and knowledge graph, we implemented a prescription drug monitoring program for Chinese patent medicines. The accuracy rate of combined medication monitoring of three or more drugs of the program increased from 68% to 86.4%. The accuracy rate of drug control monitoring increased from 70% to 97%. The response time for conflicting prescriptions with two drugs was shortened from 1.3S to 0.8S. The response time for conflicting prescriptions with three or more drugs was shortened from 5.2S to 1.4S. CONCLUSIONS: The program constructed in this study can respond quickly and improve the efficiency of monitoring prescriptions. It is of great significance to ensure the safety of patients' medication.

Research on Hybrid Feature Selection Method Based on Iterative Approximation Markov Blanket.

The basic experimental data of traditional Chinese medicine are generally obtained by high-performance liquid chromatography and mass spectrometry. The data often show the characteristics of high dimensionality and few samples, and there are many irrelevant features and redundant features in the data, which bring challenges to the in-depth exploration of Chinese medicine material information. A hybrid feature selection method based on iterative approximate Markov blanket (CI_AMB) is proposed in the paper. The method uses the maximum information coefficient to measure the correlation between features and target variables and achieves the purpose of filtering irrelevant features according to the evaluation criteria, firstly. The iterative approximation Markov blanket strategy analyzes the redundancy between features and implements the elimination of redundant features and then selects an effective feature subset finally. Comparative experiments using traditional Chinese medicine material basic experimental data and UCI's multiple public datasets show that the new method has a better advantage to select a small number of highly explanatory features, compared with Lasso, XGBoost, and the classic approximate Markov blanket method.

Feature Selection Method Based on Partial Least Squares and Analysis of Traditional Chinese Medicine Data.

The partial least squares method has many advantages in multivariable linear regression, but it does not include the function of feature selection. This method cannot screen for the best feature subset (referred to in this study as the "Gold Standard") or optimize the model, although contrarily using the L1 norm can achieve the sparse representation of parameters, leading to feature selection. In this study, a feature selection method based on partial least squares is proposed. In the new method, exploiting partial least squares allows extraction of the latent variables required for performing multivariable linear regression, and this method applies the L1 regular term constraint to the sum of the absolute values of the regression coefficients. This technique is then combined with the coordinate descent method to perform multiple iterations to select a better feature subset. Analyzing traditional Chinese medicine data and University of California, Irvine (UCI), datasets with the model, the experimental results show that the feature selection method based on partial least squares exhibits preferable adaptability for traditional Chinese medicine data and UCI datasets.