GCRNN: graph convolutional recurrent neural network for compound-protein interaction prediction.

BACKGROUND: Compound-protein interaction prediction is necessary to investigate health regulatory functions and promotes drug discovery. Machine learning is becoming increasingly important in bioinformatics for applications such as analyzing protein-related data to achieve successful solutions. Modeling the properties and functions of proteins is important but challenging, especially when dealing with predictions of the sequence type. RESULT: We propose a method to model compounds and proteins for compound-protein interaction prediction. A graph neural network is used to represent the compounds, and a convolutional layer extended with a bidirectional recurrent neural network framework, Long Short-Term Memory, and Gate Recurrent unit is used for protein sequence vectorization. The convolutional layer captures regulatory protein functions, while the recurrent layer captures long-term dependencies between protein functions, thus improving the accuracy of interaction prediction with compounds. A database of 7000 sets of annotated compound protein interaction, containing 1000 base length proteins is taken into consideration for the implementation. The results indicate that the proposed model performs effectively and can yield satisfactory accuracy regarding compound protein interaction prediction. CONCLUSION: The performance of GCRNN is based on the classification accordiong to a binary class of interactions between proteins and compounds The architectural design of GCRNN model comes with the integration of the Bi-Recurrent layer on top of CNN to learn dependencies of motifs on protein sequences and improve the accuracy of the predictions.

Physician Knowledge Base: Clinical Decision Support Systems.

With the introduction of electronic medical records (EMRs), it has become possible to accumulate massive amounts of qualitative medical data. As such, EMRs have become increasingly used in clinical decision support systems (CDSSs). While CDSSs aim to reduce medical errors normally occurring in the process of treating patients by physicians, technical maturity and the completeness of CDSSs do not meet standards for medical use yet. As data further accumulates, CDSS algorithms must be continuously updated to allow CDSSs to perform their core functions. Doing so, however, requires extensive time and manpower investments. In current practice, computational systems already perform a wide variety of functions in medical settings to allow medical staff to focus on other tasks. However, no prior research has evaluated the potential effectiveness of future CDSSs nor analyzed possibilities for their further development. In this article, we evaluate CDSS technology with the consideration that medical staff also understand the core functions of such systems.

A pilot study using machine learning methods about factors influencing prognosis of dental implants.

PURPOSE: This study tried to find the most significant factors predicting implant prognosis using machine learning methods. MATERIALS AND METHODS: The data used in this study was based on a systematic search of chart files at Seoul National University Bundang Hospital for one year. In this period, oral and maxillofacial surgeons inserted 667 implants in 198 patients after consultation with a prosthodontist. The traditional statistical methods were inappropriate in this study, which analyzed the data of a small sample size to find a factor affecting the prognosis. The machine learning methods were used in this study, since these methods have analyzing power for a small sample size and are able to find a new factor that has been unknown to have an effect on the result. A decision tree model and a support vector machine were used for the analysis. RESULTS: The results identified mesio-distal position of the inserted implant as the most significant factor determining its prognosis. Both of the machine learning methods, the decision tree model and support vector machine, yielded the similar results. CONCLUSION: Dental clinicians should be careful in locating implants in the patient's mouths, especially mesio-distally, to minimize the negative complications against implant survival.

Development of a cervical cancer progress prediction tool for human papillomavirus-positive Koreans: A support vector machine-based approach.

OBJECTIVES: To develop a Web-based tool to draw attention to patients positive for human papillomavirus (HPV) who have a high risk of progression to cervical cancer, in order to increase compliance with follow-up examinations and facilitate good doctor-patient communication. METHODS: Records were retrospectively analysed from women who were positive for HPV on initial testing (before any treatment). Information concerning age, Papanicolaou (PAP) smear result and presence of 15 high-risk HPV genotypes was used in a support vector machine (SVM) model, to identify the patient features that maximally contributed to progression to high-risk cervical lesions. RESULTS: Data from 731 subjects were analysed. The maximum number of correct cancer predictions was seen when four features (PAP, HPV16, HPV52 and HPV35) were used, giving an accuracy of 74.41%. A web-based high-risk cervical lesion prediction application tool was developed using the SVM model results. CONCLUSIONS: Use of the web-based prediction tool may help to increase patient compliance with physician advice, and may heighten awareness of the significance of regular follow-up HPV examinations for the prevention of cervical cancer, in Korean women predicted to have heightened risk of the disease.

A network perspective on unraveling the role of TRP channels in biology and disease.

Transient receptor potential (TRP) channels are a large family of non-selective cation channels that mediate numerous physiological and pathophysiological processes; however, still largely unknown are the underlying molecular mechanisms. With data generated on an unprecedented scale, network-based approaches have been revolutionizing the way in which we understand biology and disease, discover disease genes, and develop therapeutic strategies. These circumstances have created opportunities to encounter TRP channel research to data-intensive science. In this review, we provide an introduction of network-based approaches in biomedical science, describe the current state of TRP channel network biology, and discuss the future direction of TRP channel research. Network perspective will facilitate the discovery of latent roles and underlying mechanisms of TRP channels in biology and disease.

Application of support vector machine for prediction of medication adherence in heart failure patients.

OBJECTIVES: Heart failure (HF) is a progressive syndrome that marks the end-stage of heart diseases, and it has a high mortality rate and significant cost burden. In particular, non-adherence of medication in HF patients may result in serious consequences such as hospital readmission and death. This study aims to identify predictors of medication adherence in HF patients. In this work, we applied a Support Vector Machine (SVM), a machine-learning method useful for data classification. METHODS: Data about medication adherence were collected from patients at a university hospital through self-reported questionnaire. The data included 11 variables of 76 patients with HF. Mathematical simulations were conducted in order to develop a SVM model for the identification of variables that would best predict medication adherence. To evaluate the robustness of the estimates made with the SVM models, leave-one-out cross-validation (LOOCV) was conducted on the data set. RESULTS: THE TWO MODELS THAT BEST CLASSIFIED MEDICATION ADHERENCE IN THE HF PATIENTS WERE: one with five predictors (gender, daily frequency of medication, medication knowledge, New York Heart Association [NYHA] functional class, spouse) and the other with seven predictors (age, education, monthly income, ejection fraction, Mini-Mental Status Examination-Korean [MMSE-K], medication knowledge, NYHA functional class). The highest detection accuracy was 77.63%. CONCLUSIONS: SVM modeling is a promising classification approach for predicting medication adherence in HF patients. This predictive model helps stratify the patients so that evidence-based decisions can be made and patients managed appropriately. Further, this approach should be further explored in other complex diseases using other common variables.