LMCrot: an enhanced protein crotonylation site predictor by leveraging an interpretable window-level embedding from a transformer-based protein language model.

MOTIVATION: Recent advancements in natural language processing have highlighted the effectiveness of global contextualized representations from protein language models (pLMs) in numerous downstream tasks. Nonetheless, strategies to encode the site-of-interest leveraging pLMs for per-residue prediction tasks, such as crotonylation (Kcr) prediction, remain largely uncharted. RESULTS: Herein, we adopt a range of approaches for utilizing pLMs by experimenting with different input sequence types (full-length protein sequence versus window sequence), assessing the implications of utilizing per-residue embedding of the site-of-interest as well as embeddings of window residues centered around it. Building upon these insights, we developed a novel residual ConvBiLSTM network designed to process window-level embeddings of the site-of-interest generated by the ProtT5-XL-UniRef50 pLM using full-length sequences as input. This model, termed T5ResConvBiLSTM, surpasses existing state-of-the-art Kcr predictors in performance across three diverse datasets. To validate our approach of utilizing full sequence-based window-level embeddings, we also delved into the interpretability of ProtT5-derived embedding tensors in two ways: firstly, by scrutinizing the attention weights obtained from the transformer's encoder block; and secondly, by computing SHAP values for these tensors, providing a model-agnostic interpretation of the prediction results. Additionally, we enhance the latent representation of ProtT5 by incorporating two additional local representations, one derived from amino acid properties and the other from supervised embedding layer, through an intermediate fusion stacked generalization approach, using an n-mer window sequence (or, peptide/fragment). The resultant stacked model, dubbed LMCrot, exhibits a more pronounced improvement in predictive performance across the tested datasets. AVAILABILITY AND IMPLEMENTATION: LMCrot is publicly available at https://github.com/KCLabMTU/LMCrot.

A Novel Approach for Automatic Detection of Driver Fatigue Using EEG Signals Based on Graph Convolutional Networks.

Nowadays, the automatic detection of driver fatigue has become one of the important measures to prevent traffic accidents. For this purpose, a lot of research has been conducted in this field in recent years. However, the diagnosis of fatigue in recent research is binary and has no operational capability. This research presents a multi-class driver fatigue detection system based on electroencephalography (EEG) signals using deep learning networks. In the proposed system, a standard driving simulator has been designed, and a database has been collected based on the recording of EEG signals from 20 participants in five different classes of fatigue. In addition to self-report questionnaires, changes in physiological patterns are used to confirm the various stages of weariness in the suggested model. To pre-process and process the signal, a combination of generative adversarial networks (GAN) and graph convolutional networks (GCN) has been used. The proposed deep model includes five convolutional graph layers, one dense layer, and one fully connected layer. The accuracy obtained for the proposed model is 99%, 97%, 96%, and 91%, respectively, for the four different considered practical cases. The proposed model is compared to one developed through recent methods and research and has a promising performance.

CT-ML: Diagnosis of Breast Cancer Based on Ultrasound Images and Time-Dependent Feature Extraction Methods Using Contourlet Transformation and Machine Learning.

Breast diseases are a group of diseases that appear in different forms. An entire group of these diseases is breast cancer. This disease is one of the most important and common diseases in women. A machine learning system has been trained to identify specific patterns using an algorithm in a machine learning system to diagnose breast cancer. Therefore, designing a feature extraction method is essential to decrease the computation time. In this article, a two-dimensional contourlet is utilized as the input image based on the Breast Cancer Ultrasound Dataset. The sub-banded contourlet coefficients are modeled using the time-dependent model. The features of the time-dependent model are considered the leading property vector. The extracted features are applied separately to determine breast cancer classes based on classification methods. The classification is performed for the diagnosis of tumor types. We used the time-dependent approach to feature contourlet sub-bands from three groups of benign, malignant, and health control test samples. The final feature of 1200 ultrasound images used in three categories is trained based on k-nearest neighbor, support vector machine, decision tree, random forest, and linear discrimination analysis approaches, and the results are recorded. The decision tree results show that the method's sensitivity is 87.8%, 92.0%, and 87.0% for normal, benign, and malignant, respectively. The presented feature extraction method is compatible with the decision tree approach for this problem. Based on the results, the decision tree architecture with the highest accuracy is the more accurate and compatible method for diagnosing breast cancer using ultrasound images.

A universal methodology for reliable predicting the non-steroidal anti-inflammatory drug solubility in supercritical carbon dioxide.

Understanding the drug solubility behavior is likely the first essential requirement for designing the supercritical technology for pharmaceutical processing. Therefore, this study utilizes different machine learning scenarios to simulate the solubility of twelve non-steroidal anti-inflammatory drugs (NSAIDs) in the supercritical carbon dioxide (SCCO2). The considered NSAIDs are Fenoprofen, Flurbiprofen, Ibuprofen, Ketoprofen, Loxoprofen, Nabumetone, Naproxen, Nimesulide, Phenylbutazone, Piroxicam, Salicylamide, and Tolmetin. Physical characteristics of the drugs (molecular weight and melting temperature), operating conditions (pressure and temperature), and solvent property (SCCO2 density) are effectively used to estimate the drug solubility. Monitoring and comparing the prediction accuracy of twelve intelligent paradigms from three categories (artificial neural networks, support vector regression, and hybrid neuro-fuzzy) approves that adaptive neuro-fuzzy inference is the best tool for the considered task. The hybrid optimization strategy adjusts the cluster radius of the subtractive clustering membership function to 0.6111. This model estimates 254 laboratory-measured solubility data with the AAPRE = 3.13%, MSE = 2.58 × 10-9, and R2 = 0.99919. The leverage technique confirms that outliers may poison less than four percent of the experimental data. In addition, the proposed hybrid paradigm is more reliable than the equations of state and available correlations in the literature. Experimental measurements, model predictions, and relevancy analyses justified that the drug solubility in SCCO2 increases by increasing temperature and pressure. The results show that Ibuprofen and Naproxen are the most soluble and insoluble drugs in SCCO2, respectively.