Potential neutralizing antibodies discovered for novel corona virus using machine learning

The fast and untraceable virus mutations take lives of thousands of people before the immune system can produce the inhibitory antibody. The recent outbreak of COVID-19 infected and killed thousands of people in the world. Rapid methods in finding peptides or antibody sequences that can inhibit the viral epitopes of SARS-CoV-2 will save the life of thousands. To predict neutralizing antibodies for SARS-CoV-2 in a high-throughput manner, in this paper, we use different machine learning (ML) model to predict the possible inhibitory synthetic antibodies for SARS-CoV-2. We collected 1933 virus-antibody sequences and their clinical patient neutralization response and trained an ML model to predict the antibody response. Using graph featurization with variety of ML methods, like XGBoost, Random Forest, Multilayered Perceptron, Support Vector Machine and Logistic Regression, we screened thousands of hypothetical antibody sequences and found nine stable antibodies that potentially inhibit SARS-CoV-2. We combined bioinformatics, structural biology, and Molecular Dynamics (MD) simulations to verify the stability of the candidate antibodies that can inhibit SARS-CoV-2.

Artificial Synapse with Mnemonic Functionality using GSST-based Photonic Integrated Memory

Here we present a multi-level discrete-state nonvolatile photonic memory based on an ultra-compact (<4μm) hybrid phase change material GSST-silicon Mach Zehnder modulator, with low insertion losses (3dB), to serve as node in a photonic neural network. Emulating an opportunely trained 100 × 100 fully connected multilayered perceptron neural network with this weighting functionality embedded as photonic memory, shows up to 92% inference accuracy and robustness towards noise when performing predictions of unseen data.

Machine Learning-Based Microclimate Model for Indoor Air Temperature and Relative Humidity Prediction in a Swine Building

Indoor air temperature (IAT) and indoor relative humidity (IRH) are the prominent microclimatic variables; still, potential contributors that influence the homeostasis of livestock animals reared in closed barns. Further, predicting IAT and IRH encourages farmers to think ahead actively and to prepare the optimum solutions. Therefore, the primary objective of the current literature is to build and investigate extensive performance analysis between popular ML models in practice used for IAT and IRH predictions. Meanwhile, multiple linear regression (MLR), multilayered perceptron (MLP), random forest regression (RFR), decision tree regression (DTR), and support vector regression (SVR) models were utilized for the prediction. This study used accessible factors such as external environmental data to simulate the models. In addition, three different input datasets named S1, S2, and S3 were used to assess the models. From the results, RFR models performed better results in both IAT (R2 = 0.9913; RMSE = 0.476; MAE = 0.3535) and IRH (R2 = 0.9594; RMSE = 2.429; MAE = 1.47) prediction among other models particularly with S3 input datasets. In addition, it has been proven that selecting the right features from the given input data builds supportive conditions under which the expected results are available. Overall, the current study demonstrates a better model among other models to predict IAT and IRH of a naturally ventilated swine building containing animals with fewer input attributes.

Identification of 4-carboxyglutamate residue sites based on position based statistical feature and multiple classification

Glutamic acid is an alpha-amino acid used by all living beings in protein biosynthesis. One of the important glutamic acid modifications is post-translationally modified 4-carboxyglutamate. It has a significant role in blood coagulation. 4-carboxyglumates are required for the binding of calcium ions. On the contrary, this modification can also cause different diseases such as bone resorption, osteoporosis, papilloma, and plaque atherosclerosis. Considering its importance, it is necessary to predict the occurrence of glutamic acid carboxylation in amino acid stretches. As there is no computational based prediction model available to identify 4-carboxyglutamate modification, this study is, therefore, designed to predict 4-carboxyglutamate sites with a less computational cost. A machine learning model is devised with a Multilayered Perceptron (MLP) classifier using Chou’s 5-step rule. It may help in learning statistical moments and based on this learning, the prediction is to be made accurately either it is 4-carboxyglutamate residue site or detected residue site having no 4-carboxyglutamate. Prediction accuracy of the proposed model is 94% using an independent set test, while obtained prediction accuracy is 99% by self-consistency tests.

Electrocardiogram profiling of myocardial infarction history using MLP and HMLP networks

<span>Narrowing of coronary arteries caused by cholesterol deposits deprives heart tissues of oxygen. In prolonged conditions, these will result in myocardium infarction. The presence of damage tissues modifies the normal sinus rhythm and this can be detected using electrocardiogram (ECG). Hence, this paper characterized history of myocardial infarction from survivors using QRS power ratio features from the ECG. Subsequent profiling is performed using multilayered perceptron (MLP) and hybrid multilayered perceptron (HMLP) networks. ECG with history of anterior and inferior infarctions, along with healthy controls is obtained from PTB Diagnostic ECG Database. The signal is initially pre-processed and the power ratio features are extracted for low- and mid-frequency components. The features are then used as input vector to the MLP and HMLP networks. The optimized MLP has attained accuracies of 99.2% for training and 98.0% for testing. Meanwhile, the optimized HMLP managed to achieve accuracies of 99.4% for training and 97.8% for testing. Despite the similarities in network performance, MLP provides a better alternative due to the reduced computational requirements by as much as 30%.</span>

Diagnostic Gene Biomarker Selection for Alzheimer’s Classification using Machine Learning

Alzheimer’s disease (AD), also referred to as Alzheimer’s is a neurodegenerative disease and most common type of dementia. It starts at an older age and slowly progressive over time. It is a brain disease which causes loss of memory, reasoning and thinking capability of a person. Short-term memory loss is one of the main symptoms of the AD. Other common symptoms are said to be mood-swings, difficulty in understanding language and its interpretation etc. The major problem in the AD is, it can’t be reverted, but controllable with proper treatment. Genetic factors have a high impact on developing an AD, which can be inherited through genes. According to recent studies, gene therapy shows better results for Alzheimer’s patients than other common medications. It reduces the risk effect of the AD and has a gradual improvement on the patient’s condition. So, identification of gene biomarkers, having high involvement in developing AD could improve positive response over the treatment. In this paper, gene expressions of AD patients and normal peoples are analyzed using statistical approaches and Machine Learning (ML) algorithms. Differential Gene Expression (DEG) identification has an important part in the selection of most informative genes. Potential gene biomarkers are selected using a meta-heuristic global optimization algorithm called Rhinoceros Search Algorithm (RSA). As an outcome from RSA, 24 novel gene biomarkers are identified. Four supervised ML algorithms such as Support Vector Machines (SVM), Random Forest (RF), Naïve Bayes (NB) and Multilayered Perceptron Neural Network (MLP-NN) are used for the classification of two different group of samples. Among them, RSA-MLP-NN model achieved 100% accuracy on identifying the distinction between AD and normal genes and proved its efficacy.

Trochoidal Milling and Neural Networks Simulation of Magnesium Alloys

This paper set out to investigate the effect of cutting speed vc and trochoidal step str modification on selected machinability parameters (the cutting force components and vibration). In addition, for a more detailed analysis, selected surface roughness parameters were investigated. The research was carried out for two grades of magnesium alloys—AZ91D and AZ31—and aimed to determine stable machining parameters and to investigate the dynamics of the milling process, i.e., the resulting change in the cutting force components and in vibration. The tests were performed for the specified range of cutting parameters: vc = 400–1200 m/min and str = 5–30%. The results demonstrate a significant effect of cutting data modification on the parameter under scrutiny—the increase in vc resulted in the reduction of the cutting force components and the displacement and level of vibration recorded in tests. Selected cutting parameters were modelled by means of Statistica Artificial Neural Networks (Radial Basis Function and Multilayered Perceptron), which, furthermore, confirmed the suitability of neural networks as a tool for prediction of the cutting force and vibration in milling of magnesium alloys.

FPGA-based architecture of hybrid multilayered perceptron neural network

<span lang="EN-MY">The HMLP is an ANN similar to the MLP, but with extra weighted connections that connect the input nodes directly to the output nodes. The architecture of the HMLP neural network for implementation on FPGA is proposed. The HMLP architecture is designed to be concurrent to demonstrate the parallel nature of the HMLP where each hidden or output node within the same hidden or output layer of the HMLP can calculate its output independently. The HMLP architecture is designed to be modular as well, such that if modification to a module is necessary, only the specific module need to be modified and all other modules can be retained. This modularity will be especially helpful when different activation function is to be swapped in to replace current activation function. All calculations in the HMLP are performed in floating-point arithmetic. The HMLP architecture is compiled, simulated and finally implemented on the Cyclone V FPGA of DE1-SoC board. The simulation outcome and FPGA outputs showed that the developed HMLP architecture is able to calculate correct output values for all test datasets.</span>