Matthews Correlation Coefficient Value Research Articles

Phosphate binding sites prediction in phosphorylation-dependent protein-protein interactions.

Phosphate binding plays an important role in modulating protein-protein interactions, which are ubiquitous in various biological processes. Accurate prediction of phosphate binding sites is an important but challenging task. Small size and diversity of phosphate binding sites lead to a substantial challenge for developing accurate prediction methods. Here, we present the phosphate binding site predictor (PBSP), a novel and accurate approach to identifying phosphate binding sites from protein structures. PBSP combines an energy-based ligand-binding sites identification method with reverse focused docking using a phosphate probe. We show that PBSP outperforms not only general ligand binding sites predictors but also other existing phospholigand-specific binding sites predictors. It achieves ∼95% success rate for top 10 predicted sites with an average Matthews correlation coefficient value of 0.84 for successful predictions. PBSP can accurately predict phosphate binding modes, with average position error of 1.4 and 2.4 Å in bound and unbound datasets, respectively. Lastly, visual inspection of the predictions is conducted. Reasons for failed predictions are further analyzed and possible ways to improve the performance are provided. These results demonstrate a novel and accurate approach to phosphate binding sites identification in protein structures. The software and benchmark datasets are freely available at http://web.pkusz.edu.cn/wu/PBSP/. Supplementary data are available at Bioinformatics online.

Identification of subtypes of anticancer peptides based on sequential features and physicochemical properties

Anticancer peptides (ACPs) are a kind of bioactive peptides which could be used as a novel type of anticancer drug that has several advantages over chemistry-based drug, including high specificity, strong tumor penetration capacity, and low toxicity to normal cells. As the number of experimentally verified bioactive peptides has increased significantly, various of in silico approaches are imperative for investigating the characteristics of ACPs. However, the lack of methods for investigating the differences in physicochemical properties of ACPs. In this study, we compared the N- and C-terminal amino acid composition for each peptide, there are three major subtypes of ACPs that are defined based on the distribution of positively charged residues. For the first time, we were motivated to develop a two-step machine learning model for identification of the subtypes of ACPs, which classify the input data into the corresponding group before applying the classifier. Further, to improve the predictive power, the hybrid feature sets were considered for prediction. Evaluation by five-fold cross-validation showed that the two-step model trained with sequence-based features and physicochemical properties was most effective in discriminating between ACPs and non-ACPs. The two-step model trained with the hybrid features performed well, with a sensitivity of 86.75%, a specificity of 85.75%, an accuracy of 86.08%, and a Matthews Correlation Coefficient value of 0.703. Furthermore, the model also consistently provides the effective performance in independent testing set, with sensitivity of 77.6%, specificity of 94.74%, accuracy of 88.99% and the MCC value reached 0.75. Finally, the two-step model has been implemented as a web-based tool, namely iDACP, which is now freely available at http://mer.hc.mmh.org.tw/iDACP/.

Molecular insights on ABL kinase activation using tree-based machine learning models and molecular docking.

Abelson kinase (c-Abl) is a non-receptor tyrosine kinase involved in several biological processes essential for cell differentiation, migration, proliferation, and survival. This enzyme's activation might be an alternative strategy for treating diseases such as neutropenia induced by chemotherapy, prostate, and breast cancer. Recently, a series of compounds that promote the activation of c-Abl has been identified, opening a promising ground for c-Abl drug development. Structure-based drug design (SBDD) and ligand-based drug design (LBDD) methodologies have significantly impacted recent drug development initiatives. Here, we combined SBDD and LBDD approaches to characterize critical chemical properties and interactions of identified c-Abl's activators. We used molecular docking simulations combined with tree-based machine learning models—decision tree, AdaBoost, and random forest to understand the c-Abl activators' structural features required for binding to myristoyl pocket, and consequently, to promote enzyme and cellular activation. We obtained predictive and robust models with Matthews correlation coefficient values higher than 0.4 for all endpoints and identified characteristics that led to constructing a structure–activity relationship model (SAR).Graphic abstract Supplementary InformationThe online version contains supplementary material available at 10.1007/s11030-021-10261-z.

Use of multiple LIDAR-derived digital terrain indices and machine learning for high-resolution national-scale soil moisture mapping of the Swedish forest landscape

Spatially extensive high-resolution soil moisture mapping is valuable in practical forestry and land management, but challenging. Here we present a novel technique involving use of LIDAR-derived terrain indices and machine learning (ML) algorithms capable of accurately modeling soil moisture at 2 m spatial resolution across the entire Swedish forest landscape. We used field data from about 20,000 sites across Sweden to train and evaluate multiple ML models. The predictor features (variables) included a suite of terrain indices generated from a national LIDAR digital elevation model and ancillary environmental features, including surficial geology, climate and land use, enabling adjustment of soil moisture class maps to regional or local conditions. Extreme gradient boosting (XGBoost) provided better performance for a 2-class model, manifested by Cohen’s Kappa and Matthews Correlation Coefficient (MCC) values of 0.69 and 0.68, respectively, than the other tested ML methods: Artificial Neural Network, Random Forest, Support Vector Machine, and Naïve Bayes classification. The depth to water index, topographic wetness index, and ‘wetland’ categorization derived from Swedish property maps were the most important predictors for all models. The presented technique enabled generation of a 3-class model with Cohen’s Kappa and MCC values of 0.58. In addition to the classified moisture maps, we investigated the technique’s potential for producing continuous soil moisture maps. We argue that the probability of a pixel being classified as wet from a 2-class model can be used as a 0–100% index (dry to wet) of soil moisture, and the resulting maps could provide more valuable information for practical forest management than classified maps.

Diagnosis of multiple sclerosis using multifocal ERG data feature fusion

The purpose of this paper is to implement a computer-aided diagnosis (CAD) system for multiple sclerosis (MS) based on analysing the outer retina as assessed by multifocal electroretinograms (mfERGs). MfERG recordings taken with the RETI‐port/scan 21 (Roland Consult) device from 15 eyes of patients diagnosed with incipient relapsing-remitting MS and without prior optic neuritis, and from 6 eyes of control subjects, are selected. The mfERG recordings are grouped (whole macular visual field, five rings, and four quadrants). For each group, the correlation with a normative database of adaptively filtered signals, based on empirical model decomposition (EMD) and three features from the continuous wavelet transform (CWT) domain, are obtained. Of the initial 40 features, the 4 most relevant are selected in two stages: a) using a filter method and b) using a wrapper-feature selection method. The Support Vector Machine (SVM) is used as a classifier. With the optimal CAD configuration, a Matthews correlation coefficient value of 0.89 (accuracy = 0.95, specificity = 1.0 and sensitivity = 0.93) is obtained. This study identified an outer retina dysfunction in patients with recent MS by analysing the outer retina responses in the mfERG and employing an SVM as a classifier. In conclusion, a promising new electrophysiological-biomarker method based on feature fusion for MS diagnosis was identified.

Identifying Protein Subcellular Locations With Embeddings-Based node2loc.

Identifying protein subcellular locations is an important topic in protein function prediction. Interacting proteins may share similar locations. Thus, it is imperative to infer protein subcellular locations by taking protein-protein interactions (PPIs)into account. In this study, we present a network embedding-based method, node2loc, to identify protein subcellular locations. node2loc first learns distributed embeddings of proteins in a protein-protein interaction (PPI)network using node2vec. Then the learned embeddings are further fed into a recurrent neural network (RNN). To resolve the severe class imbalance of different subcellular locations, Synthetic Minority Over-sampling Technique (SMOTE)is applied to artificially synthesize proteins for minority classes. node2loc is evaluated on our constructed human benchmark dataset with 16 subcellular locations and yields a Matthews correlation coefficient (MCC)value of 0.800, which is superior to baseline methods. In addition, node2loc yields a better performance on a Yeast benchmark dataset with 17 locations. The results demonstrate that the learned representations from a PPI network have certain discriminative ability for classifying protein subcellular locations. However, node2loc is a transductive method, it only works for proteins connected in a PPI network, and it needs to be retrained for new proteins. In addition, the PPI network needs be annotated to some extent with location information. node2loc is freely available at https://github.com/xypan1232/node2loc.

Accurate prediction of protein-ATP binding residues using position-specific frequency matrix

Knowledge of protein-ATP interaction can help for protein functional annotation and drug discovery. Accurately identifying protein-ATP binding residues is an important but challenging task to gain the knowledge of protein-ATP interactions, especially for the case where only protein sequence information is given. In this study, we propose a novel method, named DeepATPseq, to predict protein-ATP binding residues without using any information about protein three-dimension structure or sequence-derived structural information. In DeepATPseq, the HHBlits-generated position-specific frequency matrix (PSFM) profile is first employed to extract the feature information of each residue. Then, for each residue, the PSFM-based feature is fed into two prediction models, which are generated by the algorithms of deep convolutional neural network (DCNN) and support vector machine (SVM) separately. The final ATP-binding probability of the corresponding residue is calculated by the weighted sum of the outputted values of DCNN-based and SVM-based models. Experimental results on the independent validation data set demonstrate that DeepATPseq could achieve an accuracy of 77.71%, covering 57.42% of all ATP-binding residues, while achieving a Matthew's correlation coefficient value (0.655) that is significantly higher than that of existing sequence-based methods and comparable to that of the state-of-the-art structure-based predictors. Detailed data analysis show that the major advantage of DeepATPseq lies at the combination utilization of DCNN and SVM that helps dig out more discriminative information from the PSFM profiles. The online server and standalone package of DeepATPseq are freely available at: https://jun-csbio.github.io/DeepATPseq/for academic use.

Screening for Core Genes Related to Pathogenesis of Alzheimer's Disease.

Alzheimer’s disease (AD), a nervous system disease, lacks effective therapies at present. RNA expression is the basic way to regulate life activities, and identifying related characteristics in AD patients may aid the exploration of AD pathogenesis and treatment. This study developed a classifier that could accurately classify AD patients and healthy people, and then obtained 3 core genes that may be related to the pathogenesis of AD. To this end, RNA expression data of the middle temporal gyrus of AD patients were firstly downloaded from GEO database, and the data were then normalized using limma package following a supplementation of missing data by k-Nearest Neighbor (KNN) algorithm. Afterwards, the top 500 genes of the most feature importance were obtained through Max-Relevance and Min-Redundancy (mRMR) analysis, and based on these genes, a series of AD classifiers were constructed through Support Vector Machine (SVM), Random Forest (RF), and KNN algorithms. Then, the KNN classifier with the highest Matthews correlation coefficient (MCC) value composed of 14 genes in incremental feature selection (IFS) analysis was identified as the best AD classifier. As analyzed, the 14 genes played a pivotal role in determination of AD and may be core genes associated with the pathogenesis of AD. Finally, protein-protein interaction (PPI) network and Random Walk with Restart (RWR) analysis were applied to obtain core gene-associated genes, and key pathways related to AD were further analyzed. Overall, this study contributed to a deeper understanding of AD pathogenesis and provided theoretical guidance for related research and experiments.

MeerCRAB: MeerLICHT classification of real and bogus transients using deep learning

Astronomers require efficient automated detection and classification pipelines when conducting large-scale surveys of the (optical) sky for variable and transient sources. Such pipelines are fundamentally important, as they permit rapid follow-up and analysis of those detections most likely to be of scientific value. We therefore present a deep learning pipeline based on the convolutional neural network architecture called $\texttt{MeerCRAB}$. It is designed to filter out the so called 'bogus' detections from true astrophysical sources in the transient detection pipeline of the MeerLICHT telescope. Optical candidates are described using a variety of 2D images and numerical features extracted from those images. The relationship between the input images and the target classes is unclear, since the ground truth is poorly defined and often the subject of debate. This makes it difficult to determine which source of information should be used to train a classification algorithm. We therefore used two methods for labelling our data (i) thresholding and (ii) latent class model approaches. We deployed variants of $\texttt{MeerCRAB}$ that employed different network architectures trained using different combinations of input images and training set choices, based on classification labels provided by volunteers. The deepest network worked best with an accuracy of 99.5$\%$ and Matthews correlation coefficient (MCC) value of 0.989. The best model was integrated to the MeerLICHT transient vetting pipeline, enabling the accurate and efficient classification of detected transients that allows researchers to select the most promising candidates for their research goals.

Data imputation and machine learning improve association analysis and genomic prediction for resistance to fish photobacteriosis in the gilthead sea bream

Disease resistance represents a key trait for breeding programs in aquaculture species. Here we re-analysed 2bRAD sequence data from two experimental challenges of gilthead sea bream with Photobacterium damsealae piscicida. Using a high quality reference genome, we carried out variant calling and data imputation with Beagle to obtain a large set of SNPs (80,744). This allowed the identification of eight novel QTLs for resistance to photobacteriosis across different chromosomes and revealed a highly polygenic genetic architecture.Bayesian regression approaches and machine learning methods (support vector machines and linear bagging) were compared to evaluate relative performance to classify susceptible-resistant individuals. Both data sets showed higher Matthew Correlation Coefficient (MCC) and accuracy values for machine learning methods, particularly linear bagging, with 20–70 % increase in prediction performance. Overall, machine learning methods should be explored in parallel with parametric regression approaches to increase the chances of highly effective genomic prediction.

A Comparative Study of Window Size and Channel Arrangement on EEG-Emotion Recognition Using Deep CNN.

Emotion recognition based on electroencephalograms has become an active research area. Yet, identifying emotions using only brainwaves is still very challenging, especially the subject-independent task. Numerous studies have tried to propose methods to recognize emotions, including machine learning techniques like convolutional neural network (CNN). Since CNN has shown its potential in generalization to unseen subjects, manipulating CNN hyperparameters like the window size and electrode order might be beneficial. To our knowledge, this is the first work that extensively observed the parameter selection effect on the CNN. The temporal information in distinct window sizes was found to significantly affect the recognition performance, and CNN was found to be more responsive to changing window sizes than the support vector machine. Classifying the arousal achieved the best performance with a window size of ten seconds, obtaining 56.85% accuracy and a Matthews correlation coefficient (MCC) of 0.1369. Valence recognition had the best performance with a window length of eight seconds at 73.34% accuracy and an MCC value of 0.4669. Spatial information from varying the electrode orders had a small effect on the classification. Overall, valence results had a much more superior performance than arousal results, which were, perhaps, influenced by features related to brain activity asymmetry between the left and right hemispheres.

4mCPred-CNN-Prediction of DNA N4-Methylcytosine in the Mouse Genome Using a Convolutional Neural Network.

Among DNA modifications, N4-methylcytosine (4mC) is one of the most significant ones, and it is linked to the development of cell proliferation and gene expression. To know different its biological functions, the accurate detection of 4mC sites is required. Although we have several techniques for the prediction of 4mC sites in different genomes based on both machine learning (ML) and convolutional neural networks (CNNs), there is no CNN-based tool for the identification of 4mC sites in the mouse genome. In this article, a CNN-based model named 4mCPred-CNN was developed to classify 4mC locations in the mouse genome. Until now, we had only two ML-based models for this purpose; they utilized several feature encoding schemes, and thus still had a lot of space available to improve the prediction accuracy. Utilizing only a single feature encoding scheme—one-hot encoding—we outperformed both of the previous ML-based techniques. In a ten-fold validation test, the proposed model, 4mCPred-CNN, achieved an accuracy of 85.71% and Matthews correlation coefficient (MCC) of 0.717. On an independent dataset, the achieved accuracy was 87.50% with an MCC value of 0.750. The attained results exhibit that the proposed model can be of great use for researchers in the fields of biology and bioinformatics.

Prediction of Protein–ATP Binding Residues Based on Ensemble of Deep Convolutional Neural Networks and LightGBM Algorithm

Accurately identifying protein–ATP binding residues is important for protein function annotation and drug design. Previous studies have used classic machine-learning algorithms like support vector machine (SVM) and random forest to predict protein–ATP binding residues; however, as new machine-learning techniques are being developed, the prediction performance could be further improved. In this paper, an ensemble predictor that combines deep convolutional neural network and LightGBM with ensemble learning algorithm is proposed. Three subclassifiers have been developed, including a multi-incepResNet-based predictor, a multi-Xception-based predictor, and a LightGBM predictor. The final prediction result is the combination of outputs from three subclassifiers with optimized weight distribution. We examined the performance of our proposed predictor using two datasets: a classic ATP-binding benchmark dataset and a newly proposed ATP-binding dataset. Our predictor achieved area under the curve (AUC) values of 0.925 and 0.902 and Matthews Correlation Coefficient (MCC) values of 0.639 and 0.642, respectively, which are both better than other state-of-art prediction methods.

Multi-Tier Ensemble Learning Model With Neighborhood Component Analysis to Predict Health Diseases

Various well-known health diseases affect millions of people worldwide. In the early stage, the clinicians may not recognize various clinical symptoms due to lack of reflection or anything else matter. So, such diseases are not easier to identify, and there may have chances to grow these illnesses and affect millions of people worldwide. Whenever an accurate early prediction is possible, the risk factor of such diseases severity can be lessened. This study presents an innovative multi-tier weighted ensemble learning model (MTWEL) for predicting several diseases such as diabetes and hepatocellular carcinoma (HCC) and, therefore, reduces such above-said problems from the sufferers and lessens the chances of mortality. In the MTWEL model, we have utilized two lists of base classifiers in which six various machine learning (ML) classifiers are assigned in each list to develop two weighted ensemble learning (EL) models and combine them to form the proposed model by employing a weighted voting approach. In the MTWEL model, the parameters of all employed classifiers are tuned through the genetic algorithm-enabled hyperparameter optimization technique to form the optimized base models. The weight of each chosen optimized base model and generated EL model(s) is calculated using Matthews correlation coefficient value with the optimized weight value. In this study, neighborhood component analysis is employed to reduce the dimension of the given input dataset. The suggested model’s experimental outcomes are conducted on two real-world datasets to exhibit its performance. The suggested approach receives the best result in AUC values: 1.0 and 1.0, F1-score values: 0.9957 and 0.9947, and accuracy values: 0.9952 and 0.9929. Such outcomes in the form of performance exhibit that the proposed model is the best-suited model to predict several diseases than other techniques, and hence it helps clinicians make accurate decisions.

Avoiding Occupancy Detection From Smart Meter Using Adversarial Machine Learning

More and more conventional electromechanical meters are being replaced with smart meters because of their substantial benefits such as providing faster bi-directional communication between utility services and end users, enabling direct load control for demand response, energy saving and so on. However, the fine-grained usage data provided by smart meter brings additional vulnerabilities from users to companies. Occupancy detection is one such example which causes privacy violation of smart meter users. Detecting the occupancy of a home is straightforward with time of use information as there is a strong correlation between occupancy and electricity usage. In this work, our major contributions are twofold. First, we validate the viability of an occupancy detection attack based on a machine learning technique called Long Short Term Memory (LSTM) method and demonstrate improved results. In addition, we introduce an Adversarial Machine Learning Occupancy Detection Avoidance (AMLODA) framework as a counter attack in order to prevent abuse of energy consumption. Essentially, the proposed privacy-preserving framework is designed to mask real-time or near real-time electricity usage information using calculated optimum noise without compromising users’ billing systems functionality. The results show that without the use of the proposed AMLODA approach, our occupancy detection attack models using LSTM achieve a high detection rate with Matthews Correlation Coefficient (MCC) value of 0.89 on average for the five different households energy consumption data under investigation captured during the winter and summer seasons. With the proposed AMLODA approach working to protect consumers’ privacy, occupancy detection attacks are demonstrated to be mitigated with the MCC values of the attack models converging to zero with no significant change over the actual consumption data and thus protecting needed functionalities of the utility companies.

DeepDILI: Deep Learning-Powered Drug-Induced Liver Injury Prediction Using Model-Level Representation.

Drug-induced liver injury (DILI) is the most frequently reported single cause of safety-related withdrawal of marketed drugs. It is essential to identify drugs with DILI potential at the early stages of drug development. In this study, we describe a deep learning-powered DILI (DeepDILI) prediction model created by combining model-level representation generated by conventional machine learning (ML) algorithms with a deep learning framework based on Mold2 descriptors. We conducted a comprehensive evaluation of the proposed DeepDILI model performance by posing several critical questions: (1) Could the DILI potential of newly approved drugs be predicted by accumulated knowledge of early approved ones? (2) is model-level representation more informative than molecule-based representation for DILI prediction? and (3) could improved model explainability be established? For question 1, we developed the DeepDILI model using drugs approved before 1997 to predict the DILI potential of those approved thereafter. As a result, the DeepDILI model outperformed the five conventional ML algorithms and two state-of-the-art ensemble methods with a Matthews correlation coefficient (MCC) value of 0.331. For question 2, we demonstrated that the DeepDILI model's performance was significantly improved (i.e., a MCC improvement of 25.86% in test set) compared with deep neural networks based on molecule-based representation. For question 3, we found 21 chemical descriptors that were enriched, suggesting a strong association with DILI outcome. Furthermore, we found that the DeepDILI model has more discrimination power to identify the DILI potential of drugs belonging to the World Health Organization therapeutic category of 'alimentary tract and metabolism'. Moreover, the DeepDILI model based on Mold2 descriptors outperformed the ones with Mol2vec and MACCS descriptors. Finally, the DeepDILI model was applied to the recent real-world problem of predicting any DILI concern for potential COVID-19 treatments from repositioning drug candidates. Altogether, this developed DeepDILI model could serve as a promising tool for screening for DILI risk of compounds in the preclinical setting, and the DeepDILI model is publicly available through https://github.com/TingLi2016/DeepDILI.

IDPGK: characterization and identification of lysine phosphoglycerylation sites based on sequence-based features

BackgroundProtein phosphoglycerylation, the addition of a 1,3-bisphosphoglyceric acid (1,3-BPG) to a lysine residue of a protein and thus to form a 3-phosphoglyceryl-lysine, is a reversible and non-enzymatic post-translational modification (PTM) and plays a regulatory role in glucose metabolism and glycolytic process. As the number of experimentally verified phosphoglycerylated sites has increased significantly, statistical or machine learning methods are imperative for investigating the characteristics of phosphoglycerylation sites. Currently, research into phosphoglycerylation is very limited, and only a few resources are available for the computational identification of phosphoglycerylation sites.ResultWe present a bioinformatics investigation of phosphoglycerylation sites based on sequence-based features. The TwoSampleLogo analysis reveals that the regions surrounding the phosphoglycerylation sites contain a high relatively of positively charged amino acids, especially in the upstream flanking region. Additionally, the non-polar and aliphatic amino acids are more abundant surrounding phosphoglycerylated lysine following the results of PTM-Logo, which may play a functional role in discriminating between phosphoglycerylation and non-phosphoglycerylation sites. Many types of features were adopted to build the prediction model on the training dataset, including amino acid composition, amino acid pair composition, positional weighted matrix and position-specific scoring matrix. Further, to improve the predictive power, numerous top features ranked by F-score were considered as the final combination for classification, and thus the predictive models were trained using DT, RF and SVM classifiers. Evaluation by five-fold cross-validation showed that the selected features was most effective in discriminating between phosphoglycerylated and non-phosphoglycerylated sites.ConclusionThe SVM model trained with the selected sequence-based features performed well, with a sensitivity of 77.5%, a specificity of 73.6%, an accuracy of 74.9%, and a Matthews Correlation Coefficient value of 0.49. Furthermore, the model also consistently provides the effective performance in independent testing set, yielding sensitivity of 75.7% and specificity of 64.9%. Finally, the model has been implemented as a web-based system, namely iDPGK, which is now freely available at http://mer.hc.mmh.org.tw/iDPGK/.

Meta-i6mA: an interspecies predictor for identifying DNA N6-methyladenine sites of plant genomes by exploiting informative features in an integrative machine-learning framework.

DNA N6-methyladenine (6mA) represents important epigenetic modifications, which are responsible for various cellular processes. The accurate identification of 6mA sites is one of the challenging tasks in genome analysis, which leads to an understanding of their biological functions. To date, several species-specific machine learning (ML)-based models have been proposed, but majority of them did not test their model to other species. Hence, their practical application to other plant species is quite limited. In this study, we explored 10 different feature encoding schemes, with the goal of capturing key characteristics around 6mA sites. We selected five feature encoding schemes based on physicochemical and position-specific information that possesses high discriminative capability. The resultant feature sets were inputted to six commonly used ML methods (random forest, support vector machine, extremely randomized tree, logistic regression, naïve Bayes and AdaBoost). The Rosaceae genome was employed to train the above classifiers, which generated 30 baseline models. To integrate their individual strength, Meta-i6mA was proposed that combined the baseline models using the meta-predictor approach. In extensive independent test, Meta-i6mA showed high Matthews correlation coefficient values of 0.918, 0.827 and 0.635 on Rosaceae, rice and Arabidopsis thaliana, respectively and outperformed the existing predictors. We anticipate that the Meta-i6mA can be applied across different plant species. Furthermore, we developed an online user-friendly web server, which is available at http://kurata14.bio.kyutech.ac.jp/Meta-i6mA/.

Analisis Matthew Correlation Coefficient pada K-Nearest Neighbor dalam Klasifikasi Ikan Hias


 
 
 K-Nearest Neighbor (K-NN) is a machine learning algorithm that functions to classify data. This study aims to measure the performance of K-NN algorithm by using Matthew Correlation Coefficient (MCC). The data that used in this study are the ornamental fish which consisting of 3 classes named Premium, Medium, and Low. The analysis results of the Matthew Correlation Coefficient on K-NN using Euclidean Distance obtained the highest MCC value in Medium class which is 0.786542. The second highest MCC value is in Premium class which is 0.567434. The lowest MCC value is in Low class which is 0.435269.
 Overall, the MCC values is statistically which is 0,596415.
 
 

Integrative Network Fusion: A Multi-Omics Approach in Molecular Profiling.

Recent technological advances and international efforts, such as The Cancer Genome Atlas (TCGA), have made available several pan-cancer datasets encompassing multiple omics layers with detailed clinical information in large collection of samples. The need has thus arisen for the development of computational methods aimed at improving cancer subtyping and biomarker identification from multi-modal data. Here we apply the Integrative Network Fusion (INF) pipeline, which combines multiple omics layers exploiting Similarity Network Fusion (SNF) within a machine learning predictive framework. INF includes a feature ranking scheme (rSNF) on SNF-integrated features, used by a classifier over juxtaposed multi-omics features (juXT). In particular, we show instances of INF implementing Random Forest (RF) and linear Support Vector Machine (LSVM) as the classifier, and two baseline RF and LSVM models are also trained on juXT. A compact RF model, called rSNFi, trained on the intersection of top-ranked biomarkers from the two approaches juXT and rSNF is finally derived. All the classifiers are run in a 10x5-fold cross-validation schema to warrant reproducibility, following the guidelines for an unbiased Data Analysis Plan by the US FDA-led initiatives MAQC/SEQC. INF is demonstrated on four classification tasks on three multi-modal TCGA oncogenomics datasets. Gene expression, protein expression and copy number variants are used to predict estrogen receptor status (BRCA-ER, N = 381) and breast invasive carcinoma subtypes (BRCA-subtypes, N = 305), while gene expression, miRNA expression and methylation data is used as predictor layers for acute myeloid leukemia and renal clear cell carcinoma survival (AML-OS, N = 157; KIRC-OS, N = 181). In test, INF achieved similar Matthews Correlation Coefficient (MCC) values and 97% to 83% smaller feature sizes (FS), compared with juXT for BRCA-ER (MCC: 0.83 vs. 0.80; FS: 56 vs. 1801) and BRCA-subtypes (0.84 vs. 0.80; 302 vs. 1801), improving KIRC-OS performance (0.38 vs. 0.31; 111 vs. 2319). INF predictions are generally more accurate in test than one-dimensional omics models, with smaller signatures too, where transcriptomics consistently play the leading role. Overall, the INF framework effectively integrates multiple data levels in oncogenomics classification tasks, improving over the performance of single layers alone and naive juxtaposition, and provides compact signature sizes1.