Background In the search for therapeutic peptides for disease treatments, many efforts have been made to identify various functional peptides from large numbers of peptide sequence databases. In this paper, we propose an effective computational model that uses deep learning and word2vec to predict therapeutic peptides (PTPD). Results Representation vectors of all k-mers were obtained through word2vec based on k-mer co-existence information. The original peptide sequences were then divided into k-mers using the windowing method. The peptide sequences were mapped to the input layer by the embedding vector obtained by word2vec. Three types of filters in the convolutional layers, as well as dropout and max-pooling operations, were applied to construct feature maps. These feature maps were concatenated into a fully connected dense layer, and rectified linear units (ReLU) and dropout operations were included to avoid over-fitting of PTPD. The classification probabilities were generated by a sigmoid function. PTPD was then validated using two datasets: an independent anticancer peptide dataset and a virulent protein dataset, on which it achieved accuracies of 96% and 94%, respectively. Conclusions PTPD identified novel therapeutic peptides efficiently, and it is suitable for application as a useful tool in therapeutic peptide design.

Microorganisms resided in human body play a vital role in metabolism, immune defense, nutrition absorption, cancer control and protection against pathogen colonization. The changes of microbial communities can cause human diseases. Based on the known microbe-disease association, we presented a novel computational model employing Random Walking with Restart optimized by Particle Swarm Optimization (PSO) on the heterogeneous interlinked network of Human Microbe-Disease Associations (PRWHMDA) (see Figure 1). Based on the known human microbe-disease associations, we constructed the heterogeneous interlinked network with Cosine similarity. The extended random walk with restart (RWR) method was derived to get the potential microbe-disease associations. PSO was utilized to get the optimal parameters of RWR. To evaluate the prediction effectiveness, we performed leave one out cross validation (LOOCV) and 5-fold cross validation (CV), which got the AUC (The area under ROC curve) of 0.915 (LOOCV) and the average AUCs of 0.8875 ± 0.0046 (5-fold CV). Moreover, we carried out three case studies of asthma, inflammatory bowel disease (IBD) and type 1 diabetes (T1D) for the further evaluation. The result showed that 10, 10 and 9 of top-10 predicted microbes were verified by previously published experimental results, respectively. It is anticipated that PRWHMDA can be effective to identify the disease-related microbes and maybe helpful to disclose the relationship between microorganisms and their human host.

Extracting stride length and velocity from wearable sensors is traditionally based on the double integration of accelerometer data with zero velocity update (ZUPT) technique. However, this approach might not be suitable for institutionalized older adults, whose clear zero-velocity phase can not be detected accurately. While deep learning models have been proposed to overcome this limitation, these approaches need subject-specific labeled data, which are difficult to collect in practice, to calibrate the models. We show that two-dimensional (2D) deep convolutional neural networks (DCNNs) can be used to extract accurate estimates of stride length and velocity with instrumented footwear. Leave-one-subject-out cross-validation is used to avoid overfitting of the results to deep learning models on data collected from N=95 institutionalized older adults with two different stride definitions during the 6-minute walk test (6MWT). When stride is defined from the initial contact to the next initial contact, DCNNs result in better inter-rater reliability and improved performance by 38.8% and 31.2% relative to conventional techniques (i.e., the double integration method with ZUPT technique) for stride length and velocity, respectively. The performance of DCNNs does not degrade substantially when the stride is defined from the foot-flat phase (i.e., zero-velocity phase) to the next foot-flat phase. Deep learning models are robust to inter-subject variability without requiring subject-specific labeled data, indicating the potential of their use for out-of-the-lab gait analysis. Their performance is independent of stride definitions, making them more suitable for institutionalized older adults than conventional techniques, where initial contacts can be reliably detected even when they do not occur under the hindfoot.

This study presents a novel framework that utilizes instrumented footwear to predict fall risk in institutionalized older adults by leveraging stride-to-stride gait data. The older adults are categorized into fallers and non-fallers using three distinct criteria: retrospective fall history, prospective fall occurrence, and a combination of both retrospective and prospective data. Three types of data collected from N=95 institutionalized older adults are analyzed: traditional timed mobility tests, gait data collected from a validated electronic walkway, and gait data collected with instrumented footwear developed by our team. The importance of each type of data is assessed using a brute-force search method, through which the optimal features are selected. AdaBoost algorithms are then utilized to develop predictive models based on the selected features. The models are evaluated using leave-one-out cross-validation and 10-fold cross-validation. The results show that models using gait data from the instrumented footwear outperformed those based on traditional tests and walkway data, with area under the receiver operating characteristic curve (AUC) values for predicting prospective falls being 0.47, 0.66, and 0.80, respectively. The sensitivity of the models increases when they are trained using both past and future falls data, rather than relying solely on past or future falls data. This study demonstrates the potential of instrumented footwear for fall risk assessment in elderly individuals. The findings provide valuable insights for fall prevention and care, highlighting the superior predictive capabilities of the developed system compared to traditional methods.

Background: Essential proteins play an important role in the process of life, which can be identified by experimental methods and computational approaches. Experimental approaches to identify essential proteins are of high accuracy but with the limitation of time and resource-consuming. Objective: Herein, we present a computational model (PEPRF) to identify essential proteins based on machine learning. Methods: Different features of proteins were extracted. Topological features of Protein-Protein Interaction (PPI) network-based are extracted. Based on the protein sequence, graph theory-based features, information- based features, composition and physichemical features, etc., were extracted. Finally, 282 features are constructed. In order to select the features that contributed most to the identification, ReliefF- based feature selection method was adopted to measure the weights of these features. Results: As a result, 212 features were curated to train random forest classifiers. Finally, PEPRF get the AUC of 0.71 and an accuracy of 0.742. Conclusion: Our results show that PEPRF may be applied as an efficient tool to identify essential proteins.