An Integrated Multi-Model Framework Utilizing Convolutional Neural Networks Coupled with Feature Extraction for Identification of 4mC Sites in DNA Sequences.

N4-methylcytosine (4mC) is a chemical modification that occurs on one of the four nucleotide bases in DNA and plays a vital role in DNA expression, repair, and replication. It also actively participates in the regulation of cell differentiation and gene expression. Consequently, it is important to comprehend the role of 4mC in the epigenetic regulation for revealing the complications of the gene expression and their associated governing cellular operations. However, the inherent resource requirements and time constraints of the experimental procedure, present challenges to the cellular culture process. While data-driven methodologies present promising solutions to mitigate the demand for extensive experimental efforts, their performance relies on the suitability and existence of high-quality data. This study presents a multi-model framework that integrates convolutional neural network (CNN) with the distributed k-mer and embedding feature extraction techniques to enhance the identification of 4mC sites in DNA sequences. The integration of k-mers ensures the effective representation of the local sequence patterns, while the utilization of embedding enables a more holistic encoding by considering the broader context and semantics of the sequence data. Following the initial step, the obtained distributed representation of the DNA sequence seamlessly enters the CNN, triggering a crucial convolution operation wherein a set of adaptable filters systematically convolves across the sequence to detect vital local patterns. The proposed integrated multi-model framework was applied to six publicly available datasets and evaluated against the cutting-edge 4mCPred, 4mCCNN, iDNA4mC, Meta-4mCpred, DeepTorrent, 4mCPred-SVM, and DMKL-HFIS methods. The evaluation was based on accuracy, specificity, sensitivity, and Matthews Correlation Coefficient. The results demonstrated that the proposed multi-model framework outperformed the state-of-the-art methods, as well as one-hot encoding and the hybrid of one-hot & TNC features, in accurately identifying 4mC sites.

StackedEnC-AOP: prediction of antioxidant proteins using transform evolutionary and sequential features based multi-scale vector with stacked ensemble learning.

BACKGROUND: Antioxidant proteins are involved in several biological processes and can protect DNA and cells from the damage of free radicals. These proteins regulate the body's oxidative stress and perform a significant role in many antioxidant-based drugs. The current invitro-based medications are costly, time-consuming, and unable to efficiently screen and identify the targeted motif of antioxidant proteins. METHODS: In this model, we proposed an accurate prediction method to discriminate antioxidant proteins namely StackedEnC-AOP. The training sequences are formulation encoded via incorporating a discrete wavelet transform (DWT) into the evolutionary matrix to decompose the PSSM-based images via two levels of DWT to form a Pseudo position-specific scoring matrix (PsePSSM-DWT) based embedded vector. Additionally, the Evolutionary difference formula and composite physiochemical properties methods are also employed to collect the structural and sequential descriptors. Then the combined vector of sequential features, evolutionary descriptors, and physiochemical properties is produced to cover the flaws of individual encoding schemes. To reduce the computational cost of the combined features vector, the optimal features are chosen using Minimum redundancy and maximum relevance (mRMR). The optimal feature vector is trained using a stacking-based ensemble meta-model. RESULTS: Our developed StackedEnC-AOP method reported a prediction accuracy of 98.40% and an AUC of 0.99 via training sequences. To evaluate model validation, the StackedEnC-AOP training model using an independent set achieved an accuracy of 96.92% and an AUC of 0.98. CONCLUSION: Our proposed StackedEnC-AOP strategy performed significantly better than current computational models with a ~ 5% and ~ 3% improved accuracy via training and independent sets, respectively. The efficacy and consistency of our proposed StackedEnC-AOP make it a valuable tool for data scientists and can execute a key role in research academia and drug design.

Compromise optimum allocation in neutrosophic multi-character survey under stratified random sampling using neutrosophic fuzzy programming.

Survey sampling has wide range of applications in social and scientific investigation to draw inference about the unknown parameter of interest. In complex surveys, the sample information about the study variable cannot be expressed by a precise number under uncertain environment due fuzziness and indeterminacy. Therefore, this information is expressed by neutrosophic numbers rather than the classical numbers. The neutrosophic statistics, which is generalization of classical statistics, deals with the neutrosophic data that has some degree of indeterminacy and fuzziness. In this study, we investigate the compromise optimum allocation problem for estimating the population means of the neutrosophic study variables in a multi-character stratified random sampling under uncertain per unit measurement cost. We proposed the intuitionistic fuzzy cost function, modeling the fuzzy uncertainty in stratum per unit measurement cost. The compromise optimum allocation problem is formulated as a multi-objective intuitionistic fuzzy optimization problem. The solution methodology is suggested using neutrosophic fuzzy programming and intuitionistic fuzzy programming approaches. A numerical study includes the means estimation of atmospheric variables is presented to explore the real-life application, explain the mathematical formulation, and efficiency comparison with some existing methods. The results show that the suggested methods produce more precise estimates with less utilization of survey resources as compared to some existing methods. The Python is used for statistical analysis, graphical designing and numerical optimization problems are solved using GAMS.

iAFPs-Mv-BiTCN: Predicting antifungal peptides using self-attention transformer embedding and transform evolutionary based multi-view features with bidirectional temporal convolutional networks.

Globally, fungal infections have become a major health concern in humans. Fungal diseases generally occur due to the invading fungus appearing on a specific portion of the body and becoming hard for the human immune system to resist. The recent emergence of COVID-19 has intensely increased different nosocomial fungal infections. The existing wet-laboratory-based medications are expensive, time-consuming, and may have adverse side effects on normal cells. In the last decade, peptide therapeutics have gained significant attention due to their high specificity in targeting affected cells without affecting healthy cells. Motivated by the significance of peptide-based therapies, we developed a highly discriminative prediction scheme called iAFPs-Mv-BiTCN to predict antifungal peptides correctly. The training peptides are encoded using word embedding methods such as skip-gram and attention mechanism-based bidirectional encoder representation using transformer. Additionally, transform-based evolutionary features are generated using the Pseduo position-specific scoring matrix using discrete wavelet transform (PsePSSM-DWT). The fused vector of word embedding and evolutionary descriptors is formed to compensate for the limitations of single encoding methods. A Shapley Additive exPlanations (SHAP) based global interpolation approach is applied to reduce training costs by choosing the optimal feature set. The selected feature set is trained using a bi-directional temporal convolutional network (BiTCN). The proposed iAFPs-Mv-BiTCN model achieved a predictive accuracy of 98.15 % and an AUC of 0.99 using training samples. In the case of the independent samples, our model obtained an accuracy of 94.11 % and an AUC of 0.98. Our iAFPs-Mv-BiTCN model outperformed existing models with a ~4 % and ~5 % higher accuracy using training and independent samples, respectively. The reliability and efficacy of the proposed iAFPs-Mv-BiTCN model make it a valuable tool for scientists and may perform a beneficial role in pharmaceutical design and research academia.

Recent Advances in Machine Learning-Based Models for Prediction of Antiviral Peptides.

Viruses have killed and infected millions of people across the world. It causes several chronic diseases like COVID-19, HIV, and hepatitis. To cope with such diseases and virus infections, antiviral peptides (AVPs) have been applied in the design of drugs. Keeping in view the significant role in pharmaceutical industry and other research fields, identification of AVPs is highly indispensable. In this connection, experimental and computational methods were proposed to identify AVPs. However, more accurate predictors for boosting AVPs identification are highly desirable. This work presents a thorough study and reports the available predictors of AVPs. We explained applied datasets, feature representation approaches, classification algorithms, and evaluation parameters of performance. In this study, the limitations of the existing studies and the best methods were emphasized. Provided the pros and cons of the applied classifiers. The future insights demonstrate efficient feature encoding approaches, best feature optimization schemes, and effective classification techniques that can improve the performance of novel method for accurate prediction of AVPs.

Target-AMP: Computational prediction of antimicrobial peptides by coupling sequential information with evolutionary profile.

Antimicrobial peptides (AMPs) are gaining a lot of attention as cutting-edge treatments for many infectious disorders. The effectiveness of AMPs against bacteria, fungi, and viruses has persisted for a long period, making them the greatest option for addressing the growing problem of antibiotic resistance. Due to their wide-ranging actions, AMPs have become more prominent, particularly in therapeutic applications. The prediction of AMPs has become a difficult task for academics due to the explosive increase of AMPs documented in databases. Wet-lab investigations to find anti-microbial peptides are exceedingly costly, time-consuming, and even impossible for some species. Therefore, in order to choose the optimal AMPs candidate before to the in-vitro trials, an efficient computational method must be developed. In this study, an effort was made to develop a machine learning-based classification system that is effective, accurate, and can distinguish between anti-microbial peptides. The position-specific-scoring-matrix (PSSM), Pseudo Amino acid composition, di-peptide composition, and combination of these three were utilized in the suggested scheme to extract salient aspects from AMPs sequences. The classification techniques K-nearest neighbor (KNN), Random Forest (RF), and Support Vector Machine (SVM) were employed. On the independent dataset and training dataset, the accuracy levels achieved by the suggested predictor (Target-AMP) are 97.07% and 95.71%, respectively. The results show that, when compared to other techniques currently used in the literature, our Target-AMP had the best success rate.

NLP-BCH-Ens: NLP-based intelligent computational model for discrimination of malaria parasite.

Plasmodium falciparum causes malaria, which is an infectious and fatal disease. In early days, malaria-infected cells were diagnosed using a microscope. owing to a huge number of instances for analysis and intricacy of time, it may lead to false detection. Automated parasite detection technologies are in high demand due to increased time consumption and erroneous detection. To create effective cures and treatments, it is critical to use an accurate approach for predicting malaria parasite. Here, numerous protein sequences formulation techniques namely: discrete methods, Biochemical, physiochemical and Natural language processing techniques are applied for transformation of protein sequences in to numerical descriptors. Four classification algorithms are utilized and the anticipated results of these classifiers were then fused to establish ensemble classification model via simple majority and genetic algorithm. In addition, BCH error correction code is incorporated with support vector machine using all the feature spaces. The simulated results demonstrate the remarkable achievement of proposed compared to previous models. Thus, our proposed model may be an effective tool for discriminating the secretory and non-secretory proteins of malaria parasite.

cACP-DeepGram: Classification of anticancer peptides via deep neural network and skip-gram-based word embedding model.

Cancer is a Toxic health concern worldwide, it happens when cellular modifications cause the irregular growth and division of human cells. Several traditional approaches such as therapies and wet laboratory-based methods have been applied to treat cancer cells. However, these methods are considered less effective due to their high cost and diverse side effects. According to recent advancements, peptide-based therapies have attracted the attention of scientists because of their high selectivity. Peptide therapy can efficiently treat the targeted cells, without affecting the normal cells. Due to the rapid increase of peptide sequences, an accurate prediction model has become a challenging task. Keeping the significance of anticancer peptides (ACPs) in cancer treatment, an intelligent and reliable prediction model is highly indispensable. In this paper, a FastText-based word embedding strategy has been employed to represent each peptide sample via a skip-gram model. After extracting the peptide embedding descriptors, the deep neural network (DNN) model was applied to accurately discriminate the ACPs. The optimized parameters of DNN achieved an accuracy of 96.94 %, 93.41 %, and 94.02 % using training, alternate, and independent samples, respectively. It was observed that our proposed cACP-DeepGram model outperformed and reported ~10 % highest prediction accuracy than existing predictors. It is suggested that the cACP-DeepGram model will be a reliable tool for scientists and might play a valuable role in academic research and drug discovery. The source code and the datasets are publicly available at https://github.com/shahidakbarcs/cACP-DeepGram.

Hybrid Clustering and Routing Algorithm with Threshold-Based Data Collection for Heterogeneous Wireless Sensor Networks.

The concept of the internet of things (IoT) motivates us to connect bulk isolated heterogeneous devices to automate report generation without human interaction. Energy-efficient routing algorithms help to prolong the network lifetime of these energy-restricted smart devices that are connected by means of wireless sensor networks (WSNs). Current vendor-level advancements enable algorithm-level flexibility to design protocols to concurrently collect multiple application data while enforcing the reduction of energy expenditure to gain commercial success in the industrial stage. In this paper, we propose a hybrid clustering and routing algorithm with threshold-based data collection for heterogeneous wireless sensor networks. In our proposed model, homogeneous and heterogeneous nodes are deployed within specific regions. To reduce unnecessary data transmission, threshold-based conditions are presented to prevent unnecessary transmission when minor or no change is observed in the simulated and real-world applications. We further extend our proposed multi-hop model to achieve more network stability in dense and larger network areas. Our proposed model shows enhancement in terms of load balancing and end-to-end delay as compared to the other threshold-based energy-efficient routing protocols, such as the threshold-sensitive stable election protocol (TSEP), threshold distributed energy-efficient clustering (TDEEC), low-energy adaptive clustering hierarchy (LEACH), and energy-efficient sensor network (TEEN).

Users' Rating Predictions Using Collaborating Filtering Based on Users and Items Similarity Measures.

The social media has made the world a global world and we, in addition to, as part of physical society, are now part of the virtual society as well. There has been the generation of a large amount of information over the social web. By way of increasing online information, new opportunities emerged, and diverse issues have been raised, which have attracted researchers to address these research problems. In this current age, where online business and e-commerce are part of our daily lives, recommender systems (RSs) are very effective for information filtering. RSs play a significant role in our lives by assisting users in recommending items and services what they may be interesting in to purchase or avail. In this research work, our goal is to predict the users' ratings for various items, which are an active research area in collaborative filtering (CF). In this work, we have explored various similarity measures based on user-user and item-item rating predictions on different datasets by applying collaborative filtering approaches. The comparison of item-item and user-user CF algorithms such as user K-Nearest Neighbour using cosine; similarity, Pearson correlation as well as item-based K-NN using these measures with baseline approaches and matrix-based methods such as Matrix factorization (MF), biased MF, and factor wise MF has been carried out. For empirical-based comparison analysis, diverse approaches have been selected such as slope one, random, and global average, and it revealed that item-item K-NN using Pearson correlation has outperformed all other applied approaches. For the experiments, three real world and widely used datasets of MovieLens 1M, CiaoDVD, and MovieLens 100k have been used. The empirical-based results have been evaluated by using standard performance evaluation measures of RMSE and MAE.

Theoretical Analysis on Absorption of Carbon Dioxide (CO2) into Solutions of Phenyl Glycidyl Ether (PGE) Using Nonlinear Autoregressive Exogenous Neural Networks.

In this paper, we analyzed the mass transfer model with chemical reactions during the absorption of carbon dioxide (CO2) into phenyl glycidyl ether (PGE) solution. The mathematical model of the phenomenon is governed by a coupled nonlinear differential equation that corresponds to the reaction kinetics and diffusion. The system of differential equations is subjected to Dirichlet boundary conditions and a mixed set of Neumann and Dirichlet boundary conditions. Further, to calculate the concentration of CO2, PGE, and the flux in terms of reaction rate constants, we adopt the supervised learning strategy of a nonlinear autoregressive exogenous (NARX) neural network model with two activation functions (Log-sigmoid and Hyperbolic tangent). The reference data set for the possible outcomes of different scenarios based on variations in normalized parameters (α1, α2, ß1, ß2, k) are obtained using the MATLAB solver "pdex4". The dataset is further interpreted by the Levenberg-Marquardt (LM) backpropagation algorithm for validation, testing, and training. The results obtained by the NARX-LM algorithm are compared with the Adomian decomposition method and residual method. The rapid convergence of solutions, smooth implementation, computational complexity, absolute errors, and statistics of the mean square error further validate the design scheme's worth and efficiency.