Protein fold recognition using an overlapping segmentation approach and a mixture of feature extraction models

Protein Fold Recognition (PFR) is considered as a critical step towards the protein structure prediction problem. PFR has also a profound impact on protein function determination and drug design. Despite all the enhancements achieved by using pattern recognition-based approaches in the protein fold recognition, it still remains unsolved and its prediction accuracy remains limited. In this study, we propose a new model based on the concept of mixture of physicochemical and evolutionary features. We then design and develop two novel overlapping segmented-based feature extraction methods. Our proposed methods capture more local and global discriminatory information than previously proposed approaches for this task. We investigate the impact of our novel approaches using the most promising attributes selected from a wide range of physicochemical-based attributes (117 attributes) which is also explored experimentally in this study. By using Support Vector Machine (SVM) our experimental results demonstrate a significant improvement (up to 5.7%) in the protein fold prediction accuracy compared to previously reported results found in the literature

Gram - positive and gram - negative subcellular localization using rotation forest and physicochemical-based features

The functioning of a protein relies on its location in the cell. Therefore, predicting protein subcellular localization is an important step towards protein function prediction. Recent studies have shown that relying on Gene Ontology (GO) for feature extraction can improve the prediction performance. However, for newly sequenced proteins, the GO is not available. Therefore, for these cases, the prediction performance of GO based methods degrade significantly. Results: In this study, we develop a method to effectively employ physicochemical and evolutionary-based information in the protein sequence. To do this, we propose segmentation based feature extraction method to explore potential discriminatory information based on physicochemical properties of the amino acids to tackle Gram-positive and Gram-negative subcellular localization. We explore our proposed feature extraction techniques using 10 attributes that have been experimentally selected among a wide range of physicochemical attributes. Finally by applying the Rotation Forest classification technique to our extracted features, we enhance Gram-positive and Gram-negative subcellular localization accuracies up to 3.4% better than previous studies which used GO for feature extraction. Conclusion: By proposing segmentation based feature extraction method to explore potential discriminatory information based on physicochemical properties of the amino acids as well as using Rotation Forest classification technique, we are able to enhance the Gram-positive and Gram-negative subcellular localization prediction accuracies, significantly

Temporal - spatial recognizer for multi-label data

Pattern recognition is an important artificial intelligence task with practical applications in many fields such as medical and species distribution. Such application involves overlapping data points which are demonstrated in the multi- label dataset. Hence, there is a need for a recognition algorithm that can separate the overlapping data points in order to recognize the correct pattern. Existing recognition methods suffer from sensitivity to noise and overlapping points as they could not recognize a pattern when there is a shift in the position of the data points. Furthermore, the methods do not implicate temporal information in the process of recognition, which leads to low quality of data clustering. In this study, an improved pattern recognition method based on Hierarchical Temporal Memory (HTM) is proposed to solve the overlapping in data points of multi- label dataset. The imHTM (Improved HTM) method includes improvement in two of its components; feature extraction and data clustering. The first improvement is realized as TS-Layer Neocognitron algorithm which solves the shift in position problem in feature extraction phase. On the other hand, the data clustering step, has two improvements, TFCM and cFCM (TFCM with limit- Chebyshev distance metric) that allows the overlapped data points which occur in patterns to be separated correctly into the relevant clusters by temporal clustering. Experiments on five datasets were conducted to compare the proposed method (imHTM) against statistical, template and structural pattern recognition methods. The results showed that the percentage of success in recognition accuracy is 99% as compared with the template matching method (Featured-Based Approach, Area-Based Approach), statistical method (Principal Component Analysis, Linear Discriminant Analysis, Support Vector Machines and Neural Network) and structural method (original HTM). The findings indicate that the improved HTM can give an optimum pattern recognition accuracy, especially the ones in multi- label dataset

A^2-Net: Molecular Structure Estimation from Cryo-EM Density Volumes

Constructing of molecular structural models from Cryo-Electron Microscopy (Cryo-EM) density volumes is the critical last step of structure determination by Cryo-EM technologies. Methods have evolved from manual construction by structural biologists to perform 6D translation-rotation searching, which is extremely compute-intensive. In this paper, we propose a learning-based method and formulate this problem as a vision-inspired 3D detection and pose estimation task. We develop a deep learning framework for amino acid determination in a 3D Cryo-EM density volume. We also design a sequence-guided Monte Carlo Tree Search (MCTS) to thread over the candidate amino acids to form the molecular structure. This framework achieves 91% coverage on our newly proposed dataset and takes only a few minutes for a typical structure with a thousand amino acids. Our method is hundreds of times faster and several times more accurate than existing automated solutions without any human intervention.Comment: 8 pages, 5 figures, 4 table

Hidden Markov Models

Hidden Markov Models (HMMs), although known for decades, have made a big career nowadays and are still in state of development. This book presents theoretical issues and a variety of HMMs applications in speech recognition and synthesis, medicine, neurosciences, computational biology, bioinformatics, seismology, environment protection and engineering. I hope that the reader will find this book useful and helpful for their own research

Novel image markers for non-small cell lung cancer classification and survival prediction

BACKGROUND: Non-small cell lung cancer (NSCLC), the most common type of lung cancer, is one of serious diseases causing death for both men and women. Computer-aided diagnosis and survival prediction of NSCLC, is of great importance in providing assistance to diagnosis and personalize therapy planning for lung cancer patients. RESULTS: In this paper we have proposed an integrated framework for NSCLC computer-aided diagnosis and survival analysis using novel image markers. The entire biomedical imaging informatics framework consists of cell detection, segmentation, classification, discovery of image markers, and survival analysis. A robust seed detection-guided cell segmentation algorithm is proposed to accurately segment each individual cell in digital images. Based on cell segmentation results, a set of extensive cellular morphological features are extracted using efficient feature descriptors. Next, eight different classification techniques that can handle high-dimensional data have been evaluated and then compared for computer-aided diagnosis. The results show that the random forest and adaboost offer the best classification performance for NSCLC. Finally, a Cox proportional hazards model is fitted by component-wise likelihood based boosting. Significant image markers have been discovered using the bootstrap analysis and the survival prediction performance of the model is also evaluated. CONCLUSIONS: The proposed model have been applied to a lung cancer dataset that contains 122 cases with complete clinical information. The classification performance exhibits high correlations between the discovered image markers and the subtypes of NSCLC. The survival analysis demonstrates strong prediction power of the statistical model built from the discovered image markers