Prediction of Peptide Detectability Based on CapsNet and Convolutional Block Attention Module

DbyDeep: Exploration of MS-Detectable Peptides via Deep Learning

Predicting peptide detectability is useful in a variety of mass spectrometry (MS)-based proteomics applications, particularly targeted proteomics. However, most machine learning-based computational methods have relied solely on information from the peptide itself, such as its amino acid sequences or physicochemical properties, despite the fact that peptides detected by MS are dependent on many factors, including protein sample preparation, digestion, separation, ionization, and precursor selection during MS experiments. DbyDeep (Detectability by Deep learning) is an innovative end-to-end LSTM network model for peptide detectability prediction that incorporates sequence contexts of peptides and their cleavage sites (by protease). Utilizing the cleavage site contexts could improve the performance of prediction, and DbyDeep outperformed existing methods in predicting peptides recognizable from multiple MS/MS data sets with diverse species and MS instruments. We argue for the necessity of a learning model that encompasses several contexts associated with peptide detection, as opposed to depending just on peptide sequences. There is a Python implementation of DbyDeep at https://github.com/BISCodeRepo/DbyDeep.

PD-BertEDL: An Ensemble Deep Learning Method Using BERT and Multivariate Representation to Predict Peptide Detectability

Peptide detectability is defined as the probability of identifying a peptide from a mixture of standard samples, which is a key step in protein identification and analysis. Exploring effective methods for predicting peptide detectability is helpful for disease treatment and clinical research. However, most existing computational methods for predicting peptide detectability rely on a single information. With the increasing complexity of feature representation, it is necessary to explore the influence of multivariate information on peptide detectability. Thus, we propose an ensemble deep learning method, PD-BertEDL. Bidirectional encoder representations from transformers (BERT) is introduced to capture the context information of peptides. Context information, sequence information, and physicochemical information of peptides were combined to construct the multivariate feature space of peptides. We use different deep learning methods to capture the high-quality features of different categories of peptides information and use the average fusion strategy to integrate three model prediction results to solve the heterogeneity problem and to enhance the robustness and adaptability of the model. The experimental results show that PD-BertEDL is superior to the existing prediction methods, which can effectively predict peptide detectability and provide strong support for protein identification and quantitative analysis, as well as disease treatment.

A Hierarchical Approach toward Prediction of Human Biological Age from Masked Facial Image Leveraging Deep Learning Techniques

The lifestyle of humans has changed noticeably since the contagious COVID-19 disease struck globally. People should wear a face mask as a protective measure to curb the spread of the contagious disease. Consequently, real-world applications (i.e., electronic customer relationship management) dealing with human ages extracted from face images must migrate to a robust system proficient to estimate the age of a person wearing a face mask. In this paper, we proposed a hierarchical age estimation model from masked facial images in a group-to-specific manner rather than a single regression model because age progression across different age groups is quite dissimilar. Our intention was to squeeze the feature space among limited age classes so that the model could fairly discern age. We generated a synthetic masked face image dataset over the IMDB-WIKI face image dataset to train and validate our proposed model due to the absence of a benchmark masked face image dataset with real age annotations. We somewhat mitigated the data sparsity problem of the large public IMDB-WIKI dataset using off-the-shelf down-sampling and up-sampling techniques as required. The age estimation task was fully modeled like a deep classification problem, and expected ages were formulated from SoftMax probabilities. We performed a classification task by deploying multiple low-memory and higher-accuracy-based convolutional neural networks (CNNs). Our proposed hierarchical framework demonstrated marginal improvement in terms of mean absolute error (MAE) compared to the one-off model approach for masked face real age estimation. Moreover, this research is perhaps the maiden attempt to estimate the real age of a person from his/her masked face image.