Relationship between B-factor and average shortest path in the protein structure

Protein structural flexibility is important for catalysis, binding, protein design, and allostery. Some simple methods have recently been introduced to compute protein flexibility directly from the protein structure without any mechanical models. For example the atomic mean square displacement (or B-factor) is related to the number of neighboring atoms. The protein structure can be modeled as a graph where nodes represent atoms and edges can be defined by Delaunay tessellation procedure with weight equal to d2 where d is the Euclidean distance between pair of atoms. In this study, we show that the average of shortest path for each atom in this graph is related to the B-factor.

A hybrid approach for categorizing images based on complex networks and neural networks

There are several methods for categorizing images, the most of which are statistical, geometric, model-based and structural methods. In this paper, a new method for describing images based on complex network models is presented. Each image contains a number of key points that can be identified through standard edge detection algorithms. To understand each image better, we can use these points to create a graph of the image. In order to facilitate the use of graphs, generated graphs are created in the form of a complex network of small-worlds. Complex grid features such as topological and dynamic features can be used to display image-related features. After generating this information, it normalizes them and uses them as suitable features for categorizing images. For this purpose, the generated information is given to the neural network. Based on these features and the use of neural networks, comparisons between new images are performed. The results of the article show that this method has a good performance in identifying similarities and finally categorizing them

Predicting the status of COVID-19 active cases using a neural network time series

The design of intelligent systems for analyzing information and predicting the epidemiological trends of the disease is rapidly expanding because of the coronavirus disease (COVID-19) pandemic. The COVID-19 datasets provided by Johns Hopkins University were included in the analysis. This dataset contains some missing data that is imputed using the multi-objective particle swarm optimization method. A time series model based on nonlinear autoregressive exogenou (NARX) neural network is proposed to predict the recovered and death COVID-19 cases. This model is trained and evaluated for two modes: predicting the situation of the affected areas for the next day and the next month. After training the model based on the data from January 22 to February 27, 2020, the performance of the proposed model was evaluated in predicting the situation of the areas in the coming two weeks. The error rate was less than 5%. The prediction of the proposed model for April 9, 2020, was compared with the actual data for that day. The absolute percentage error (AE) worldwide was 12%. The lowest mean absolute error (MAE) of the model was for South America and Australia with 3 and 3.3, respectively. In this paper, we have shown that geographical areas with mortality and recovery of COVID-19 cases can be predicted using a neural network-based model

The Studies of Decision Tree in Estimation of Breast Cancer Risk by Using Polymorphism Nucleotide

Abstract Introduction:   Decision tree is the data mining tools to collect, accurate prediction and sift information from massive amounts of data that are used widely in the field of computational biology and bioinformatics. In bioinformatics can be predict on diseases, including breast cancer. The use of genomic data including single nucleotide polymorphisms is a very important factor in predicting the risk of diseases. The number of seven important SNP among hundreds of thousands genetic markers were identified as factors associated with breast cancer. The objective of this study is to evaluate the training data on decision tree predictor error of the risk of breast cancer by using single nucleotide polymorphism genotype. Methods: The risk of breast cancer were calculated associated with the use of SNP formula:xj = fo * In human,  The decision tree can be used To predict the probability of disease using single nucleotide polymorphisms .Seven SNP with different odds ratio associated with breast cancer considered and coding and design of decision tree model, C4.5, by  Csharp2013 programming language were done. In the decision tree created with the coding, the four important associated SNP was considered. The decision tree error in two case of coding and using WEKA were assessment and percentage of decision tree accuracy in prediction of breast cancer were calculated. The number of trained samples was obtained with systematic sampling. With coding, two scenarios as well as software WEKA, three scenarios with different sets of data and the number of different learning and testing, were evaluated. Results: In both scenarios of coding, by increasing the training percentage from 66/66 to 86/42, the error reduced from 55/56 to 9/09. Also by running of WEKA on three scenarios with different sets of data, the number of different education, and different tests by increasing records number from 81 to 2187, the error rate decreased from 48/15 to 13/46. Also in the majority of scenarios, prevalence of the disease, had no effect on errors in the WEKA and code. Conclusion: The results suggest that with increased training, and thus the accuracy of prediction error decision tree to reduce the risk of breast cancer increases with the use of decision trees. In Biological data, decision trees error is high even with a 66/66% training. On the other hand by increasing the number of SNP from 4 to 7 decision tree, decision tree error dramatically decreased at 70/1% training. In general we can say that with increased training and increasing the number of SNP in the decision tree, the prediction accuracy increased and errors reduced. In the CODING and WEKA, percentage of disease prevalence had no significant effect on errors,” Because of selecting set of training and testing by systemic method “

A Medical Decision Support System to Assess Risk Factors for Gastric Cancer Based on Fuzzy Cognitive Map

Gastric cancer (GC), one of the most common cancers around the world, is a multifactorial disease and there are many risk factors for this disease. Assessing the risk of GC is essential for choosing an appropriate healthcare strategy. There have been very few studies conducted on the development of risk assessment systems for GC. This study is aimed at providing a medical decision support system based on soft computing using fuzzy cognitive maps (FCMs) which will help healthcare professionals to decide on an appropriate individual healthcare strategy based on the risk level of the disease. FCMs are considered as one of the strongest artificial intelligence techniques for complex system modeling. In this system, an FCM based on Nonlinear Hebbian Learning (NHL) algorithm is used. The data used in this study are collected from the medical records of 560 patients referring to Imam Reza Hospital in Tabriz City. 27 effective features in gastric cancer were selected using the opinions of three experts. The prediction accuracy of the proposed method is 95.83%. The results show that the proposed method is more accurate than other decision-making algorithms, such as decision trees, Naïve Bayes, and ANN. From the perspective of healthcare professionals, the proposed medical decision support system is simple, comprehensive, and more effective than previous models for assessing the risk of GC and can help them to predict the risk factors for GC in the clinical setting