3,857 research outputs found
Robust Principal Component Analysis-based Prediction of Protein-Protein Interaction Hot spots ( {RBHS} )
Proteins often exert their function by binding to other cellular partners. The hot spots are key residues for protein-protein binding. Their identification may shed light on the impact of disease associated mutations on protein complexes and help design protein-protein interaction inhibitors for therapy. Unfortunately, current machine learning methods to predict hot spots, suffer from limitations caused by gross errors in the data matrices. Here, we present a novel data pre-processing pipeline that overcomes this problem by recovering a low rank matrix with reduced noise using Robust Principal Component Analysis. Application to existing databases shows the predictive power of the method
IDENTIFYING MOLECULAR FUNCTIONS OF DYNEIN MOTOR PROTEINS USING EXTREME GRADIENT BOOSTING ALGORITHM WITH MACHINE LEARNING
The majority of cytoplasmic proteins and vesicles move actively primarily to dynein motor proteins, which are the cause of muscle contraction. Moreover, identifying how dynein are used in cells will rely on structural knowledge. Cytoskeletal motor proteins have different molecular roles and structures, and they belong to three superfamilies of dynamin, actin and myosin. Loss of function of specific molecular motor proteins can be attributed to a number of human diseases, such as Charcot-Charcot-Dystrophy and kidney disease. It is crucial to create a precise model to identify dynein motor proteins in order to aid scientists in understanding their molecular role and designing therapeutic targets based on their influence on human disease. Therefore, we develop an accurate and efficient computational methodology is highly desired, especially when using cutting-edge machine learning methods. In this article, we proposed a machine learning-based superfamily of cytoskeletal motor protein locations prediction method called extreme gradient boosting (XGBoost). We get the initial feature set All by extraction the protein features from the sequence and evolutionary data of the amino acid residues named BLOUSM62. Through our successful eXtreme gradient boosting (XGBoost), accuracy score 0.8676%, Precision score 0.8768%, Sensitivity score 0.760%, Specificity score 0.9752% and MCC score 0.7536%. Our method has demonstrated substantial improvements in the performance of many of the evaluation parameters compared to other state-of-the-art methods. This study offers an effective model for the classification of dynein proteins and lays a foundation for further research to improve the efficiency of protein functional classification
A Comparative Analysis of Ensemble Classifiers: Case Studies in Genomics
The combination of multiple classifiers using ensemble methods is
increasingly important for making progress in a variety of difficult prediction
problems. We present a comparative analysis of several ensemble methods through
two case studies in genomics, namely the prediction of genetic interactions and
protein functions, to demonstrate their efficacy on real-world datasets and
draw useful conclusions about their behavior. These methods include simple
aggregation, meta-learning, cluster-based meta-learning, and ensemble selection
using heterogeneous classifiers trained on resampled data to improve the
diversity of their predictions. We present a detailed analysis of these methods
across 4 genomics datasets and find the best of these methods offer
statistically significant improvements over the state of the art in their
respective domains. In addition, we establish a novel connection between
ensemble selection and meta-learning, demonstrating how both of these disparate
methods establish a balance between ensemble diversity and performance.Comment: 10 pages, 3 figures, 8 tables, to appear in Proceedings of the 2013
International Conference on Data Minin
Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening
This work introduces a number of algebraic topology approaches, such as
multicomponent persistent homology, multi-level persistent homology and
electrostatic persistence for the representation, characterization, and
description of small molecules and biomolecular complexes. Multicomponent
persistent homology retains critical chemical and biological information during
the topological simplification of biomolecular geometric complexity.
Multi-level persistent homology enables a tailored topological description of
inter- and/or intra-molecular interactions of interest. Electrostatic
persistence incorporates partial charge information into topological
invariants. These topological methods are paired with Wasserstein distance to
characterize similarities between molecules and are further integrated with a
variety of machine learning algorithms, including k-nearest neighbors, ensemble
of trees, and deep convolutional neural networks, to manifest their descriptive
and predictive powers for chemical and biological problems. Extensive numerical
experiments involving more than 4,000 protein-ligand complexes from the PDBBind
database and near 100,000 ligands and decoys in the DUD database are performed
to test respectively the scoring power and the virtual screening power of the
proposed topological approaches. It is demonstrated that the present approaches
outperform the modern machine learning based methods in protein-ligand binding
affinity predictions and ligand-decoy discrimination
Robust principal component analysis-based prediction of protein-protein interaction hot spots.
AbstractProteins often exert their function by binding to other cellular partners. The hot spots are key residues for protein‐protein binding. Their identification may shed light on the impact of disease associated mutations on protein complexes and help design protein‐protein interaction inhibitors for therapy. Unfortunately, current machine learning methods to predict hot spots, suffer from limitations caused by gross errors in the data matrices. Here, we present a novel data pre‐processing pipeline that overcomes this problem by recovering a low rank matrix with reduced noise using Robust Principal Component Analysis. Application to existing databases shows the predictive power of the method
Machine Learning and Integrative Analysis of Biomedical Big Data.
Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues
Classification of IGF1R ligand compounds for Identification of herbal extracts using extreme gradient boosting
Diabetes Mellitus is a serious disease that requires serious treatment. The cause of this disease is due to malfunctions in insulin and insulin-producing organs. One of the proteins that become insulin signaling receptors is IGF1R, which has an important role in activating and maximizing insulin performance. In this study, we aimed to obtain herbal compounds that can activate the function of the IGF1R protein by utilizing compound data in an open database and modeling it using the ensemble method, namely extreme gradient boosting. We found that this method produces the best classification model than with other algorithms. We predicted 844 data for herbal compounds, but only 15 data met the threshold of 0.6. We got one plant from the fifteen herbal compounds, namely Zostera Marine, which was confirmed to have compounds that bind to IGF1R. These compounds have the highest probability value in the classification model that we formed compared to others
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