Efficacy of Chinese Medicine Treatment Based on Syndrome Differentiation for Primary Insomnia: A Randomized Placebo Controlled Triple-Blinded Trial.

OBJECTIVE: To assess efficacy of Chinese medicine (CM) on insomnia considering characteristics of treatment based on syndrome differentiation. METHODS: A total of 116 participants aged 18 to 65 years with moderate and severe primary insomnia were randomized to the placebo (n=20) or the CM group (n=96) for a 4-week treatment and a 4-week follow-up. Three CM clinicians independently prescribed treatments for each patient based on syndromes differentiation. The primary outcome was change in total sleep time (TST) from baseline. Secondary endpoints included sleep onset latency (SOL), wake time after sleep onset (WASO), sleep efficiency, Pittsburgh Sleep Quality Index (PSQI) and CM symptoms. RESULTS: The CM group had an average 0.6 h more (95% confidence interval (CI): 0.3-0.9, P<0.001) TST and 34.1% (10.3%-58.0%, P=0.005) more patients beyond 0.5 h TST increment than that of the placebo group. PSQI was changed -3.3 (-3.8 to -2.7) in the CM group, a -2.0 (-3.2 to -0.8, P<0.001) difference from the placebo group. The CM symptom score in the CM group decreased -2.0 (-3.3 to -0.7, P=0.003) more than the placebo group. SOL and WASO changes were not significantly different between groups. The analysis of prescriptions by these clinicians revealed blood deficiency and Liver stagnation as the most common syndromes. Prescriptions for these clinicians displayed relative stability, while the herbs varied. All adverse events were mild and were not related to study treatment. CONCLUSION: CM treatment based on syndrome differentiation can increase TST and improve sleep quality of primary insomnia. It is effective and safe for primary insomnia. In future studies, the long-term efficacy validation and the exploratory of eutherapeutic clinicians' fixed herb formulas should be addressed (Registration No. NCT01613183).

Intelligent quality control of traditional chinese medical tongue diagnosis images based on deep learning.

BACKGROUND: Computer-aided tongue and face diagnosis technology can make Traditional Chinese Medicine (TCM) more standardized, objective and quantified. However, many tongue images collected by the instrument may not meet the standard in clinical applications, which affects the subsequent quantitative analysis. The common tongue diagnosis instrument cannot determine whether the patient has fully extended the tongue or collected the face. OBJECTIVE: This paper proposes an image quality control algorithm based on deep learning to verify the eligibility of TCM tongue diagnosis images. METHODS: We firstly gathered enough images and categorized them into five states. Secondly, we preprocessed the training images. Thirdly, we built a ResNet34 model and trained it by the transfer learning method. Finally, we input the test images into the trained model and automatically filter out unqualified images and point out the reasons. RESULTS: Experimental results show that the model's quality control accuracy rate of the test dataset is as high as 97.06%. Our methods have the strong discriminative power of the learned representation. Compared with previous studies, it can guarantee subsequent tongue image processing. CONCLUSIONS: Our methods can guarantee the subsequent quantitative analysis of tongue shape, tongue state, tongue spirit, and facial complexion.

PresRecST: a novel herbal prescription recommendation algorithm for real-world patients with integration of syndrome differentiation and treatment planning.

OBJECTIVES: Herbal prescription recommendation (HPR) is a hot topic and challenging issue in field of clinical decision support of traditional Chinese medicine (TCM). However, almost all previous HPR methods have not adhered to the clinical principles of syndrome differentiation and treatment planning of TCM, which has resulted in suboptimal performance and difficulties in application to real-world clinical scenarios. MATERIALS AND METHODS: We emphasize the synergy among diagnosis and treatment procedure in real-world TCM clinical settings to propose the PresRecST model, which effectively combines the key components of symptom collection, syndrome differentiation, treatment method determination, and herb recommendation. This model integrates a self-curated TCM knowledge graph to learn the high-quality representations of TCM biomedical entities and performs 3 stages of clinical predictions to meet the principle of systematic sequential procedure of TCM decision making. RESULTS: To address the limitations of previous datasets, we constructed the TCM-Lung dataset, which is suitable for the simultaneous training of the syndrome differentiation, treatment method determination, and herb recommendation. Overall experimental results on 2 datasets demonstrate that the proposed PresRecST outperforms the state-of-the-art algorithm by significant improvements (eg, improvements of P@5 by 4.70%, P@10 by 5.37%, P@20 by 3.08% compared with the best baseline). DISCUSSION: The workflow of PresRecST effectively integrates the embedding vectors of the knowledge graph for progressive recommendation tasks, and it closely aligns with the actual diagnostic and treatment procedures followed by TCM doctors. A series of ablation experiments and case study show the availability and interpretability of PresRecST, indicating the proposed PresRecST can be beneficial for assisting the diagnosis and treatment in real-world TCM clinical settings. CONCLUSION: Our technology can be applied in a progressive recommendation scenario, providing recommendations for related items in a progressive manner, which can assist in providing more reliable diagnoses and herbal therapies for TCM clinical task.

KDGene: knowledge graph completion for disease gene prediction using interactional tensor decomposition.

The accurate identification of disease-associated genes is crucial for understanding the molecular mechanisms underlying various diseases. Most current methods focus on constructing biological networks and utilizing machine learning, particularly deep learning, to identify disease genes. However, these methods overlook complex relations among entities in biological knowledge graphs. Such information has been successfully applied in other areas of life science research, demonstrating their effectiveness. Knowledge graph embedding methods can learn the semantic information of different relations within the knowledge graphs. Nonetheless, the performance of existing representation learning techniques, when applied to domain-specific biological data, remains suboptimal. To solve these problems, we construct a biological knowledge graph centered on diseases and genes, and develop an end-to-end knowledge graph completion framework for disease gene prediction using interactional tensor decomposition named KDGene. KDGene incorporates an interaction module that bridges entity and relation embeddings within tensor decomposition, aiming to improve the representation of semantically similar concepts in specific domains and enhance the ability to accurately predict disease genes. Experimental results show that KDGene significantly outperforms state-of-the-art algorithms, whether existing disease gene prediction methods or knowledge graph embedding methods for general domains. Moreover, the comprehensive biological analysis of the predicted results further validates KDGene's capability to accurately identify new candidate genes. This work proposes a scalable knowledge graph completion framework to identify disease candidate genes, from which the results are promising to provide valuable references for further wet experiments. Data and source codes are available at https://github.com/2020MEAI/KDGene.

Construction of a clinical prediction model for the impact of acupuncture on pregnancy outcomes in poor ovarian response (POR) patients based on a patient registry research platform. / åŸºäºŽç— ä¾‹æ³¨å†Œç™»è®°ç ”ç©¶å¹³å°æž„å»ºé’ˆç¸å¯¹åµå·¢ä½Žååº”æ‚£è€ å¦Šå¨ ç»“å±€çš„ä¸´åºŠé¢„æµ‹æ¨¡åž‹.

OBJECTIVES: To construct a clinical prediction model for the impact of acupuncture on pregnancy outcomes in poor ovarian response (POR) patients, providing insights and methods for predicting pregnancy outcomes in POR patients undergoing acupuncture treatment. METHODS: Clinical data of 268 POR patients (2 cases were eliminated) primarily treated with "thirteen needle acupuncture for Tiaojing Cuyun (regulating menstruation and promoting pregnancy)" was collected from the international patient registry platform of acupuncture moxibustion (IPRPAM) from September 19, 2017 to April 30, 2023, involving 24 clinical centers including Acupuncture-Moxibustion Hospital of China Academy of Chinese Medical Sciences. LASSO and univariate Cox regression were used to screen factors influencing pregnancy outcomes, and a multivariate Cox regression model was established based on the screening results. The best model was selected using the Akaike information criterion (AIC), and a nomogram for clinical pregnancy prediction was constructed. The prediction model was evaluated using receiver operating characteristic (ROC) curves and calibration curves, and internal validation was performed using the Bootstrap method. RESULTS: (1) Age, level of anti-Müllerian hormone (AMH), and total treatment numbers of acupuncture were independent predictors of pregnancy outcomes in POR patients receiving acupuncture (P<0.05). (2) The AIC value of the best subset-Cox multivariate model (560.6) was the smallest, indicating it as the optimal model. (3) The areas under curve (AUCs) of the clinical prediction model after 6, 12, 24, and 36 months treatment were 0.627, 0.719, 0.770, and 0.766, respectively, and in the validation group, they were 0.620, 0.704, 0.759, and 0.765, indicating good discrimination and repeatability of the prediction model. (4) The calibration curve showed that the prediction curve of the clinical prediction model was close to the ideal model's prediction curve, indicating good calibration of the prediction model. CONCLUSIONS: The clinical prediction model for the impact of acupuncture on pregnancy outcomes in POR patients based on the IPRPAM platform has good clinical application value and provides insights into predicting pregnancy outcomes in POR patients undergoing acupuncture treatment.

Network medicine framework reveals generic herb-symptom effectiveness of traditional Chinese medicine.

Understanding natural and traditional medicine can lead to world-changing drug discoveries. Despite the therapeutic effectiveness of individual herbs, traditional Chinese medicine (TCM) lacks a scientific foundation and is often considered a myth. In this study, we establish a network medicine framework and reveal the general TCM treatment principle as the topological relationship between disease symptoms and TCM herb targets on the human protein interactome. We find that proteins associated with a symptom form a network module, and the network proximity of an herb's targets to a symptom module is predictive of the herb's effectiveness in treating the symptom. These findings are validated using patient data from a hospital. We highlight the translational value of our framework by predicting herb-symptom treatments with therapeutic potential. Our network medicine framework reveals the scientific foundation of TCM and establishes a paradigm for understanding the molecular basis of natural medicine and predicting disease treatments.

Pro-angiogenic photo-crosslinked silk fibroin hydrogel: a potential candidate for repairing alveolar bone defects.

OBJECTIVE: This study aimed to develop a pro-angiogenic hydrogel with in situ gelation ability for alveolar bone defects repair. METHODOLOGY: Silk fibroin was chemically modified by Glycidyl Methacrylate (GMA), which was evaluated by proton nuclear magnetic resonance (1H-NMR). Then, the photo-crosslinking ability of the modified silk fibroin was assessed. Scratch and transwell-based migration assays were conducted to investigate the effect of the photo-crosslinked silk fibroin hydrogel on the migration of human umbilical vein endothelial cells (HUVECs). In vitro angiogenesis was conducted to examine whether the photo-crosslinked silk fibroin hydrogel would affect the tube formation ability of HUVECs. Finally, subcutaneous implantation experiments were conducted to further examine the pro-angiogenic ability of the photo-crosslinked silk fibroin hydrogel, in which the CD31 and α-smooth muscle actin (α-SMA) were stained to assess neovascularization. The tumor necrosis factor-α (TNF-α) and interleukin-1ß (IL-1ß) were also stained to evaluate inflammatory responses after implantation. RESULTS: GMA successfully modified the silk fibroin, which we verified by our 1H-NMR and in vitro photo-crosslinking experiment. Scratch and transwell-based migration assays proved that the photo-crosslinked silk fibroin hydrogel promoted HUVEC migration. The hydrogel also enhanced the tube formation of HUVECs in similar rates to Matrigel®. After subcutaneous implantation in rats for one week, the hydrogel enhanced neovascularization without triggering inflammatory responses. CONCLUSION: This study found that photo-crosslinked silk fibroin hydrogel showed pro-angiogenic and inflammation inhibitory abilities. Its photo-crosslinking ability makes it suitable for matching irregular alveolar bone defects. Thus, the photo-crosslinkable silk fibroin-derived hydrogel is a potential candidate for constructing scaffolds for alveolar bone regeneration.

Add-on Chinese medicine for hospitalized chronic obstructive pulmonary disease (CHOP): A cohort study of hospital registry.

BACKGROUND: Chronic obstructive pulmonary disease (COPD) is the third leading cause of death globally. The effect of Chinese medicine (CM) on mortality during acute exacerbation of COPD is unclear. We evaluated the real-world effectiveness of add-on personalized CM in hospitalized COPD patients with acute exacerbation. METHODS: This is a retrospective cohort study with new-user design. All electronic medical records of hospitalized adult COPD patients (n = 4781) between July 2011 and November 2019 were extracted. Personalized CM exposure was defined as receiving CM that were prescribed, and not in a fixed form and dose at baseline. A 1:1 matching control cohort was generated from the same source and matched by propensity score. Primary endpoint was mortality. Multivariable Cox regression models were used to estimate the hazard ratio (HR) adjusting the same set of covariates (most prevalent with significant inter-group difference) used in propensity score calculation. Secondary endpoints included the change in hematology and biochemistry, and the association between the use of difference CMs and treatment effect. The prescription pattern was also assessed and the putative targets of the CMs on COPD was analyzed with network pharmacology approach. RESULTS: 4325 (90.5%) patients were included in the analysis. The mean total hospital stay was 16.7 ± 11.8 days. In the matched cohort, the absolute risk reduction by add-on personalized CM was 5.2% (3.9% vs 9.1%). The adjusted HR of mortality was 0.13 (95% CI: 0.03 to 0.60, p = 0.008). The result remained robust in the sensitivity analyses. The change in hematology and biochemistry were comparable between groups. Among the top 10 most used CMs, Poria (Fu-ling), Citri Reticulatae Pericarpium (Chen-pi) and Glycyrrhizae Radix Et Rhizoma (Gan-cao) were associated with significant hazard reduction in mortality. The putative targets of the CM used in this cohort on COPD were related to Jak-STAT, Toll-like receptor, and TNF signaling pathway which shares similar mechanism with a range of immunological disorders and infectious diseases. CONCLUSION: Our results suggest that add-on personalized Chinese medicine was associated with significant mortality reduction in hospitalized COPD patients with acute exacerbation in real-world setting with minimal adverse effect on liver and renal function. Further randomized trials are warranted.

The mechanisms of Qizhu Tangshen formula in the treatment of diabetic kidney disease: Network pharmacology, machine learning, molecular docking and experimental assessment.

BACKGROUND: Qizhu Tangshen Formula (QZTS) has been shown therapeutic effects on diabetic kidney disease (DKD). However, to date, the pharmacological mechanisms remain vague. METHODS: To explore the underlying mechanisms of QZTS in treating DKD using network pharmacology, machine learning, molecular docking and experimental assessment. RESULTS: First, we found that QZTS improved glycolipid metabolism disorder, decreased proteinuria and alleviated kidney tissue injury in DKD model KKAy mice. Then, by integrating multiple databases, a total of 96 targets of 74 active compounds in QZTS and 759 DKD-related genes were acquired. Next, we identified 13 hub targets of QZTS in DKD by three rank algorithms, including functional similarity, topological similarity and shortest path. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses demonstrated that the pathways mainly centered on the processes of glycolipid metabolism disorder, inflammation and angiogenesis. Among them, VEGF signaling pathway was significantly enriched. Molecular docking showed that key active compounds of QZTS all had relatively good binding affinity with predicted hub targets. Finally, animal experiments found that QZTS significantly inhibited the secretion of plasma VEGF and downregulated the protein and mRNA expression levels of AKT, p38MAPK and VEGFR2. CONCLUSION: Our results indicated that QZTS treated DKD via multiple targets and pathways and the VEGF signaling pathway may be highly involved in this process.

DRONet: effectiveness-driven drug repositioning framework using network embedding and ranking learning.

As one of the most vital methods in drug development, drug repositioning emphasizes further analysis and research of approved drugs based on the existing large amount of clinical and experimental data to identify new indications of drugs. However, the existing drug repositioning methods didn't achieve enough prediction performance, and these methods do not consider the effectiveness information of drugs, which make it difficult to obtain reliable and valuable results. In this study, we proposed a drug repositioning framework termed DRONet, which make full use of effectiveness comparative relationships (ECR) among drugs as prior information by combining network embedding and ranking learning. We utilized network embedding methods to learn the deep features of drugs from a heterogeneous drug-disease network, and constructed a high-quality drug-indication data set including effectiveness-based drug contrast relationships. The embedding features and ECR of drugs are combined effectively through a designed ranking learning model to prioritize candidate drugs. Comprehensive experiments show that DRONet has higher prediction accuracy (improving 87.4% on Hit@1 and 37.9% on mean reciprocal rank) than state of the art. The case analysis also demonstrates high reliability of predicted results, which has potential to guide clinical drug development.

Analysis of Chinese Medical Syndrome Features of Ischemic Stroke Based on Similarity of Symptoms Subgroup.

OBJECTIVE: To derive the Chinese medicine (CM) syndrome classification and subgroup syndrome characteristics of ischemic stroke patients. METHODS: By extracting the CM clinical electronic medical records (EMRs) of 7,170 hospitalized patients with ischemic stroke from 2016 to 2018 at Weifang Hospital of Traditional Chinese Medicine, Shandong Province, China, a patient similarity network (PSN) was constructed based on the symptomatic phenotype of the patients. Thereafter the efficient community detection method BGLL was used to identify subgroups of patients. Finally, subgroups with a large number of cases were selected to analyze the specific manifestations of clinical symptoms and CM syndromes in each subgroup. RESULTS: Seven main subgroups of patients with specific symptom characteristics were identified, including M3, M2, M1, M5, M0, M29 and M4. M3 and M0 subgroups had prominent posterior circulatory symptoms, while M3 was associated with autonomic disorders, and M4 manifested as anxiety; M2 and M4 had motor and motor coordination disorders; M1 had sensory disorders; M5 had more obvious lung infections; M29 had a disorder of consciousness. The specificity of CM syndromes of each subgroup was as follows. M3, M2, M1, M0, M29 and M4 all had the same syndrome as wind phlegm pattern; M3 and M0 both showed hyperactivity of Gan (Liver) yang pattern; M2 and M29 had similar syndromes, which corresponded to intertwined phlegm and blood stasis pattern and phlegm-stasis obstructing meridians pattern, respectively. The manifestations of CM syndromes often appeared in a combination of 2 or more syndrome elements. The most common combination of these 7 subgroups was wind-phlegm. The 7 subgroups of CM syndrome elements were specifically manifested as pathogenic wind, pathogenic phlegm, and deficiency pathogens. CONCLUSIONS: There were 7 main symptom similarity-based subgroups in ischemic stroke patients, and their specific characteristics were obvious. The main syndromes were wind phlegm pattern and hyperactivity of Gan yang pattern.

Pro-angiogenic photo-crosslinked silk fibroin hydrogel: a potential candidate for repairing alveolar bone defects

Abstract Objective: This study aimed to develop a pro-angiogenic hydrogel with in situ gelation ability for alveolar bone defects repair. Methodology: Silk fibroin was chemically modified by Glycidyl Methacrylate (GMA), which was evaluated by proton nuclear magnetic resonance (1H-NMR). Then, the photo-crosslinking ability of the modified silk fibroin was assessed. Scratch and transwell-based migration assays were conducted to investigate the effect of the photo-crosslinked silk fibroin hydrogel on the migration of human umbilical vein endothelial cells (HUVECs). In vitro angiogenesis was conducted to examine whether the photo-crosslinked silk fibroin hydrogel would affect the tube formation ability of HUVECs. Finally, subcutaneous implantation experiments were conducted to further examine the pro-angiogenic ability of the photo-crosslinked silk fibroin hydrogel, in which the CD31 and α-smooth muscle actin (α-SMA) were stained to assess neovascularization. The tumor necrosis factor-α (TNF-α) and interleukin-1β (IL-1β) were also stained to evaluate inflammatory responses after implantation. Results: GMA successfully modified the silk fibroin, which we verified by our 1H-NMR and in vitro photo-crosslinking experiment. Scratch and transwell-based migration assays proved that the photo-crosslinked silk fibroin hydrogel promoted HUVEC migration. The hydrogel also enhanced the tube formation of HUVECs in similar rates to Matrigel®. After subcutaneous implantation in rats for one week, the hydrogel enhanced neovascularization without triggering inflammatory responses. Conclusion: This study found that photo-crosslinked silk fibroin hydrogel showed pro-angiogenic and inflammation inhibitory abilities. Its photo-crosslinking ability makes it suitable for matching irregular alveolar bone defects. Thus, the photo-crosslinkable silk fibroin-derived hydrogel is a potential candidate for constructing scaffolds for alveolar bone regeneration.

Phenonizer: A Fine-Grained Phenotypic Named Entity Recognizer for Chinese Clinical Texts.

Biomedical named entity recognition (BioNER) from clinical texts is a fundamental task for clinical data analysis due to the availability of large volume of electronic medical record data, which are mostly in free text format, in real-world clinical settings. Clinical text data incorporates significant phenotypic medical entities (e.g., symptoms, diseases, and laboratory indexes), which could be used for profiling the clinical characteristics of patients in specific disease conditions (e.g., Coronavirus Disease 2019 (COVID-19)). However, general BioNER approaches mostly rely on coarse-grained annotations of phenotypic entities in benchmark text dataset. Owing to the numerous negation expressions of phenotypic entities (e.g., "no fever," "no cough," and "no hypertension") in clinical texts, this could not feed the subsequent data analysis process with well-prepared structured clinical data. In this paper, we developed Human-machine Cooperative Phenotypic Spectrum Annotation System (http://www.tcmai.org/login, HCPSAS) and constructed a fine-grained Chinese clinical corpus. Thereafter, we proposed a phenotypic named entity recognizer: Phenonizer, which utilized BERT to capture character-level global contextual representation, extracted local contextual features combined with bidirectional long short-term memory, and finally obtained the optimal label sequences through conditional random field. The results on COVID-19 dataset show that Phenonizer outperforms those methods based on Word2Vec with an F1-score of 0.896. By comparing character embeddings from different data, it is found that character embeddings trained by clinical corpora can improve F-score by 0.0103. In addition, we evaluated Phenonizer on two kinds of granular datasets and proved that fine-grained dataset can boost methods' F1-score slightly by about 0.005. Furthermore, the fine-grained dataset enables methods to distinguish between negated symptoms and presented symptoms. Finally, we tested the generalization performance of Phenonizer, achieving a superior F1-score of 0.8389. In summary, together with fine-grained annotated benchmark dataset, Phenonizer proposes a feasible approach to effectively extract symptom information from Chinese clinical texts with acceptable performance.

HFCF-Net: A hybrid-feature cross fusion network for COVID-19 lesion segmentation from CT volumetric images.

BACKGROUND: The coronavirus disease 2019 (COVID-19) spreads rapidly across the globe, seriously threatening the health of people all over the world. To reduce the diagnostic pressure of front-line doctors, an accurate and automatic lesion segmentation method is highly desirable in clinic practice. PURPOSE: Many proposed two-dimensional (2D) methods for sliced-based lesion segmentation cannot take full advantage of spatial information in the three-dimensional (3D) volume data, resulting in limited segmentation performance. Three-dimensional methods can utilize the spatial information but suffer from long training time and slow convergence speed. To solve these problems, we propose an end-to-end hybrid-feature cross fusion network (HFCF-Net) to fuse the 2D and 3D features at three scales for the accurate segmentation of COVID-19 lesions. METHODS: The proposed HFCF-Net incorporates 2D and 3D subnets to extract features within and between slices effectively. Then the cross fusion module is designed to bridge 2D and 3D decoders at the same scale to fuse both types of features. The module consists of three cross fusion blocks, each of which contains a prior fusion path and a context fusion path to jointly learn better lesion representations. The former aims to explicitly provide the 3D subnet with lesion-related prior knowledge, and the latter utilizes the 3D context information as the attention guidance of the 2D subnet, which promotes the precise segmentation of the lesion regions. Furthermore, we explore an imbalance-robust adaptive learning loss function that includes image-level loss and pixel-level loss to tackle the problems caused by the apparent imbalance between the proportions of the lesion and non-lesion voxels, providing a learning strategy to dynamically adjust the learning focus between 2D and 3D branches during the training process for effective supervision. RESULT: Extensive experiments conducted on a publicly available dataset demonstrate that the proposed segmentation network significantly outperforms some state-of-the-art methods for the COVID-19 lesion segmentation, yielding a Dice similarity coefficient of 74.85%. The visual comparison of segmentation performance also proves the superiority of the proposed network in segmenting different-sized lesions. CONCLUSIONS: In this paper, we propose a novel HFCF-Net for rapid and accurate COVID-19 lesion segmentation from chest computed tomography volume data. It innovatively fuses hybrid features in a cross manner for lesion segmentation, aiming to utilize the advantages of 2D and 3D subnets to complement each other for enhancing the segmentation performance. Benefitting from the cross fusion mechanism, the proposed HFCF-Net can segment the lesions more accurately with the knowledge acquired from both subnets.

TCMPR: TCM Prescription Recommendation Based on Subnetwork Term Mapping and Deep Learning.

Traditional Chinese medicine (TCM) has played an indispensable role in clinical diagnosis and treatment. Based on a patient's symptom phenotypes, computation-based prescription recommendation methods can recommend personalized TCM prescription using machine learning and artificial intelligence technologies. However, owing to the complexity and individuation of a patient's clinical phenotypes, current prescription recommendation methods cannot obtain good performance. Meanwhile, it is very difficult to conduct effective representation for unrecorded symptom terms in an existing knowledge base. In this study, we proposed a subnetwork-based symptom term mapping method (SSTM) and constructed a SSTM-based TCM prescription recommendation method (termed TCMPR). Our SSTM can extract the subnetwork structure between symptoms from a knowledge network to effectively represent the embedding features of clinical symptom terms (especially the unrecorded terms). The experimental results showed that our method performs better than state-of-the-art methods. In addition, the comprehensive experiments of TCMPR with different hyperparameters (i.e., feature embedding, feature dimension, subnetwork filter threshold, and feature fusion) demonstrate that our method has high performance on TCM prescription recommendation and potentially promote clinical diagnosis and treatment of TCM precision medicine.

PDGNet: Predicting Disease Genes Using a Deep Neural Network With Multi-View Features.

The knowledge of phenotype-genotype associations is crucial for the understanding of disease mechanisms. Numerous studies have focused on developing efficient and accurate computing approaches to predict disease genes. However, owing to the sparseness and complexity of medical data, developing an efficient deep neural network model to identify disease genes remains a huge challenge. Therefore, we develop a novel deep neural network model that fuses the multi-view features of phenotypes and genotypes to identify disease genes (termed PDGNet). Our model integrated the multi-view features of diseases and genes and leveraged the feedback information of training samples to optimize the parameters of deep neural network and obtain the deep vector features of diseases and genes. The evaluation experiments on a large data set indicated that PDGNet obtained higher performance than the state-of-the-art method (precision and recall improved by 9.55 and 9.63 percent). The analysis results for the candidate genes indicated that the predicted genes have strong functional homogeneity and dense interactions with known genes. We validated the top predicted genes of Parkinson's disease based on external curated data and published medical literatures, which indicated that the candidate genes have a huge potential to guide the selection of causal genes in the 'wet experiment'. The source codes and the data of PDGNet are available at https://github.com/yangkuoone/PDGNet.

TMNP: a transcriptome-based multi-scale network pharmacology platform for herbal medicine.

One of the most difficult problems that hinder the development and application of herbal medicine is how to illuminate the global effects of herbs on the human body. Currently, the chemo-centric network pharmacology methodology regards herbs as a mixture of chemical ingredients and constructs the 'herb-compound-target-disease' connections based on bioinformatics methods, to explore the pharmacological effects of herbal medicine. However, this approach is severely affected by the complexity of the herbal composition. Alternatively, gene-expression profiles induced by herbal treatment reflect the overall biological effects of herbs and are suitable for studying the global effects of herbal medicine. Here, we develop an online transcriptome-based multi-scale network pharmacology platform (TMNP) for exploring the global effects of herbal medicine. Firstly, we build specific functional gene signatures for different biological scales from molecular to higher tissue levels. Then, specific algorithms are designed to measure the correlations of transcriptional profiles and types of gene signatures. Finally, TMNP uses pharmacotranscriptomics of herbal medicine as input and builds associations between herbs and different biological scales to explore the multi-scale effects of herb medicine. We applied TMNP to a single herb Astragalus membranaceus and Xuesaitong injection to demonstrate the power to reveal the multi-scale effects of herbal medicine. TMNP integrating herbal medicine and multiple biological scales into the same framework, will greatly extend the conventional network pharmacology model centering on the chemical components, and provide a window for systematically observing the complex interactions between herbal medicine and the human body. TMNP is available at http://www.bcxnfz.top/TMNP.