Single-residue linear and conformational B cell epitopes prediction using random and ESM-2 based projections.

B cell epitope prediction methods are separated into linear sequence-based predictors and conformational epitope predictions that typically use the measured or predicted protein structure. Most linear predictions rely on the translation of the sequence to biologically based representations and the applications of machine learning on these representations. We here present CALIBER 'Conformational And LInear B cell Epitopes pRediction', and show that a bidirectional long short-term memory with random projection produces a more accurate prediction (test set AUC=0.789) than all current linear methods. The same predictor when combined with an Evolutionary Scale Modeling-2 projection also improves on the state of the art in conformational epitopes (AUC = 0.776). The inclusion of the graph of the 3D distances between residues did not increase the prediction accuracy. However, the long-range sequence information was essential for high accuracy. While the same model structure was applicable for linear and conformational epitopes, separate training was required for each. Combining the two slightly increased the linear accuracy (AUC 0.775 versus 0.768) and reduced the conformational accuracy (AUC = 0.769).

iAMP-Attenpred: a novel antimicrobial peptide predictor based on BERT feature extraction method and CNN-BiLSTM-Attention combination model.

As a kind of small molecule protein that can fight against various microorganisms in nature, antimicrobial peptides (AMPs) play an indispensable role in maintaining the health of organisms and fortifying defenses against diseases. Nevertheless, experimental approaches for AMP identification still demand substantial allocation of human resources and material inputs. Alternatively, computing approaches can assist researchers effectively and promptly predict AMPs. In this study, we present a novel AMP predictor called iAMP-Attenpred. As far as we know, this is the first work that not only employs the popular BERT model in the field of natural language processing (NLP) for AMPs feature encoding, but also utilizes the idea of combining multiple models to discover AMPs. Firstly, we treat each amino acid from preprocessed AMPs and non-AMP sequences as a word, and then input it into BERT pre-training model for feature extraction. Moreover, the features obtained from BERT method are fed to a composite model composed of one-dimensional CNN, BiLSTM and attention mechanism for better discriminating features. Finally, a flatten layer and various fully connected layers are utilized for the final classification of AMPs. Experimental results reveal that, compared with the existing predictors, our iAMP-Attenpred predictor achieves better performance indicators, such as accuracy, precision and so on. This further demonstrates that using the BERT approach to capture effective feature information of peptide sequences and combining multiple deep learning models are effective and meaningful for predicting AMPs.

N-GlycoPred: A hybrid deep learning model for accurate identification of N-glycosylation sites.

Studies have shown that protein glycosylation in cells reflects the real-time dynamics of biological processes, and the occurrence and development of many diseases are closely related to protein glycosylation. Abnormal protein glycosylation can be used as a potential diagnostic and prognostic marker of a disease, as well as a therapeutic target and a new breakthrough point for exploring pathogenesis. To address the issue of significant differences in the prediction results of previous models for different species, we constructed a hybrid deep learning model N-GlycoPred on the basis of dual-layer convolution, a paired attention mechanism and BiLSTM for accurate identification of N-glycosylation sites. By adopting one-hot encoding or the AAindex, we specifically selected the optimum combination of features and deep learning frameworks for human and mouse to refine the models. Based on six independent test datasets, our N-GlycoPred model achieved an average AUC of 0.9553, which is 0.23% higher than MusiteDeep. The comparison results indicate that our model can serve as a powerful tool for N-glycosylation site prescreening for biological researchers.

APEX-pHLA: A novel method for accurate prediction of the binding between exogenous short peptides and HLA class I molecules.

Human leukocyte antigen (HLA) molecules play critically significant role within the realm of immunotherapy due to their capacities to recognize and bind exogenous antigens such as peptides, subsequently delivering them to immune cells. Predicting the binding between peptides and HLA molecules (pHLA) can expedite the screening of immunogenic peptides and facilitate vaccine design. However, traditional experimental methods are time-consuming and inefficient. In this study, an efficient method based on deep learning was developed for predicting peptide-HLA binding, which treated peptide sequences as linguistic entities. It combined the architectures of textCNN and BiLSTM to create a deep neural network model called APEX-pHLA. This model operated without limitations related to HLA class I allele variants and peptide segment lengths, enabling efficient encoding of sequence features for both HLA and peptide segments. On the independent test set, the model achieved Accuracy, ROC_AUC, F1, and MCC is 0.9449, 0.9850, 0.9453, and 0.8899, respectively. Similarly, on an external test set, the results were 0.9803, 0.9574, 0.8835, and 0.7863, respectively. These findings outperformed fifteen methods previously reported in the literature. The accurate prediction capability of the APEX-pHLA model in peptide-HLA binding might provide valuable insights for future HLA vaccine design.

O-GlcNAcPRED-DL: Prediction of Protein O-GlcNAcylation Sites Based on an Ensemble Model of Deep Learning.

O-linked ß-N-acetylglucosamine (O-GlcNAc) is a post-translational modification (i.e., O-GlcNAcylation) on serine/threonine residues of proteins, regulating a plethora of physiological and pathological events. As a dynamic process, O-GlcNAc functions in a site-specific manner. However, the experimental identification of the O-GlcNAc sites remains challenging in many scenarios. Herein, by leveraging the recent progress in cataloguing experimentally identified O-GlcNAc sites and advanced deep learning approaches, we establish an ensemble model, O-GlcNAcPRED-DL, a deep learning-based tool, for the prediction of O-GlcNAc sites. In brief, to make a benchmark O-GlcNAc data set, we extracted the information on O-GlcNAc from the recently constructed database O-GlcNAcAtlas, which contains thousands of experimentally identified and curated O-GlcNAc sites on proteins from multiple species. To overcome the imbalance between positive and negative data sets, we selected five groups of negative data sets in humans and mice to construct an ensemble predictor based on connection of a convolutional neural network and bidirectional long short-term memory. By taking into account three types of sequence information, we constructed four network frameworks, with the systematically optimized parameters used for the models. The thorough comparison analysis on two independent data sets of humans and mice and six independent data sets from other species demonstrated remarkably increased sensitivity and accuracy of the O-GlcNAcPRED-DL models, outperforming other existing tools. Moreover, a user-friendly Web server for O-GlcNAcPRED-DL has been constructed, which is freely available at http://oglcnac.org/pred_dl.

HLAB: learning the BiLSTM features from the ProtBert-encoded proteins for the class I HLA-peptide binding prediction.

Human Leukocyte Antigen (HLA) is a type of molecule residing on the surfaces of most human cells and exerts an essential role in the immune system responding to the invasive items. The T cell antigen receptors may recognize the HLA-peptide complexes on the surfaces of cancer cells and destroy these cancer cells through toxic T lymphocytes. The computational determination of HLA-binding peptides will facilitate the rapid development of cancer immunotherapies. This study hypothesized that the natural language processing-encoded peptide features may be further enriched by another deep neural network. The hypothesis was tested with the Bi-directional Long Short-Term Memory-extracted features from the pretrained Protein Bidirectional Encoder Representations from Transformers-encoded features of the class I HLA (HLA-I)-binding peptides. The experimental data showed that our proposed HLAB feature engineering algorithm outperformed the existing ones in detecting the HLA-I-binding peptides. The extensive evaluation data show that the proposed HLAB algorithm outperforms all the seven existing studies on predicting the peptides binding to the HLA-A*01:01 allele in AUC and achieves the best average AUC values on the six out of the seven k-mers (k=8,9,...,14, respectively represent the prediction task of a polypeptide consisting of k amino acids) except for the 9-mer prediction tasks. The source code and the fine-tuned feature extraction models are available at http://www.healthinformaticslab.org/supp/resources.php.

Study on the impact of meteorological factors on influenza in different periods and prediction based on artificial intelligence RF-Bi-LSTM algorithm: to compare the COVID-19 period with the non-COVID-19 period.

OBJECTIVE: At different times, public health faces various challenges and the degree of intervention measures varies. The research on the impact and prediction of meteorology factors on influenza is increasing gradually, however, there is currently no evidence on whether its research results are affected by different periods. This study aims to provide limited evidence to reveal this issue. METHODS: Daily data on influencing factors and influenza in Xiamen were divided into three parts: overall period (phase AB), non-COVID-19 epidemic period (phase A), and COVID-19 epidemic period (phase B). The association between influencing factors and influenza was analysed using generalized additive models (GAMs). The excess risk (ER) was used to represent the percentage change in influenza as the interquartile interval (IQR) of meteorology factors increases. The 7-day average daily influenza cases were predicted using the combination of bi-directional long short memory (Bi-LSTM) and random forest (RF) through multi-step rolling input of the daily multifactor values of the previous 7-day. RESULTS: In periods A and AB, air temperature below 22 °C was a risk factor for influenza. However, in phase B, temperature showed a U-shaped effect on it. Relative humidity had a more significant cumulative effect on influenza in phase AB than in phase A (peak: accumulate 14d, AB: ER = 281.54, 95% CI = 245.47 ~ 321.37; A: ER = 120.48, 95% CI = 100.37 ~ 142.60). Compared to other age groups, children aged 4-12 were more affected by pressure, precipitation, sunshine, and day light, while those aged ≥ 13 were more affected by the accumulation of humidity over multiple days. The accuracy of predicting influenza was highest in phase A and lowest in phase B. CONCLUSIONS: The varying degrees of intervention measures adopted during different phases led to significant differences in the impact of meteorology factors on influenza and in the influenza prediction. In association studies of respiratory infectious diseases, especially influenza, and environmental factors, it is advisable to exclude periods with more external interventions to reduce interference with environmental factors and influenza related research, or to refine the model to accommodate the alterations brought about by intervention measures. In addition, the RF-Bi-LSTM model has good predictive performance for influenza.

Identification of adaptor proteins by incorporating deep learning and PSSM profiles.

Adaptor proteins, also known as signal transduction adaptor proteins, are important proteins in signal transduction pathways, and play a role in connecting signal proteins for signal transduction between cells. Studies have shown that adaptor proteins are closely related to some diseases, such as tumors and diabetes. Therefore, it is very meaningful to construct a relevant model to accurately identify adaptor proteins. In recent years, many studies have used a position-specific scoring matrix (PSSM) and neural network methods to identify adaptor proteins. However, ordinary neural network models cannot correlate the contextual information in PSSM profiles well, so these studies usually process 20×N (N > 20) PSSM into 20×20 dimensions, which results in the loss of a large amount of protein information; This research proposes an efficient method that combines one-dimensional convolution (1-D CNN) and a bidirectional long short-term memory network (biLSTM) to identify adaptor proteins. The complete PSSM profiles are the input of the model, and the complete information of the protein is retained during the training process. We perform cross-validation during model training and test the performance of the model on an independent test set; in the data set with 1224 adaptor proteins and 11,078 non-adaptor proteins, five indicators including specificity, sensitivity, accuracy, area under the receiver operating characteristic curve (AUC) metric and Matthews correlation coefficient (MCC), were employed to evaluate model performance. On the independent test set, the specificity, sensitivity, accuracy and MCC were 0.817, 0.865, 0.823 and 0.465, respectively. Those results show that our method is better than the state-of-the art methods. This study is committed to improve the accuracy of adaptor protein identification, and laid a foundation for further research on diseases related to adaptor protein. This research provided a new idea for the application of deep learning related models in bioinformatics and computational biology.

Optimizing protein sequence classification: integrating deep learning models with Bayesian optimization for enhanced biological analysis.

Efforts to enhance the accuracy of protein sequence classification are of utmost importance in driving forward biological analyses and facilitating significant medical advancements. This study presents a cutting-edge model called ProtICNN-BiLSTM, which combines attention-based Improved Convolutional Neural Networks (ICNN) and Bidirectional Long Short-Term Memory (BiLSTM) units seamlessly. Our main goal is to improve the accuracy of protein sequence classification by carefully optimizing performance through Bayesian Optimisation. ProtICNN-BiLSTM combines the power of CNN and BiLSTM architectures to effectively capture local and global protein sequence dependencies. In the proposed model, the ICNN component uses convolutional operations to identify local patterns. Captures long-range associations by analyzing sequence data forward and backwards. In advanced biological studies, Bayesian Optimisation optimizes model hyperparameters for efficiency and robustness. The model was extensively confirmed with PDB-14,189 and other protein data. We found that ProtICNN-BiLSTM outperforms traditional categorization models. Bayesian Optimization's fine-tuning and seamless integration of local and global sequence information make it effective. The precision of ProtICNN-BiLSTM improves comparative protein sequence categorization. The study improves computational bioinformatics for complex biological analysis. Good results from the ProtICNN-BiLSTM model improve protein sequence categorization. This powerful tool could improve medical and biological research. The breakthrough protein sequence classification model is ProtICNN-BiLSTM. Bayesian optimization, ICNN, and BiLSTM analyze biological data accurately.

DEL-Thyroid: deep ensemble learning framework for detection of thyroid cancer progression through genomic mutation.

Genes, expressed as sequences of nucleotides, are susceptible to mutations, some of which can lead to cancer. Machine learning and deep learning methods have emerged as vital tools in identifying mutations associated with cancer. Thyroid cancer ranks as the 5th most prevalent cancer in the USA, with thousands diagnosed annually. This paper presents an ensemble learning model leveraging deep learning techniques such as Long Short-Term Memory (LSTM), Gated Recurrent Units (GRUs), and Bi-directional LSTM (Bi-LSTM) to detect thyroid cancer mutations early. The model is trained on a dataset sourced from asia.ensembl.org and IntOGen.org, consisting of 633 samples with 969 mutations across 41 genes, collected from individuals of various demographics. Feature extraction encompasses techniques including Hahn moments, central moments, raw moments, and various matrix-based methods. Evaluation employs three testing methods: self-consistency test (SCT), independent set test (IST), and 10-fold cross-validation test (10-FCVT). The proposed ensemble learning model demonstrates promising performance, achieving 96% accuracy in the independent set test (IST). Statistical measures such as training accuracy, testing accuracy, recall, sensitivity, specificity, Mathew's Correlation Coefficient (MCC), loss, training accuracy, F1 Score, and Cohen's kappa are utilized for comprehensive evaluation.

Aircraft Engine Fault Diagnosis Model Based on 1DCNN-BiLSTM with CBAM.

As the operational status of aircraft engines evolves, their fault modes also undergo changes. In response to the operational degradation trend of aircraft engines, this paper proposes an aircraft engine fault diagnosis model based on 1DCNN-BiLSTM with CBAM. The model can be directly applied to raw monitoring data without the need for additional algorithms to extract fault degradation features. It fully leverages the advantages of 1DCNN in extracting local features along the spatial dimension and incorporates CBAM, a channel and spatial attention mechanism. CBAM could assign higher weights to features relevant to fault categories and make the model pay more attention to them. Subsequently, it utilizes BiLSTM to handle nonlinear time feature sequences and bidirectional contextual feature information. Finally, experimental validation is conducted on the publicly available CMAPSS dataset from NASA, categorizing fault modes into three types: faultless, HPC fault (the single fault), and HPC&Fan fault (the mixed fault). Comparative analysis with other models reveals that the proposed model has a higher classification accuracy, which is of practical significance in improving the reliability of aircraft engine operations and for Remaining Useful Life (RUL) prediction.

A Low-Cost Inertial Measurement Unit Motion Capture System for Operation Posture Collection and Recognition.

In factories, human posture recognition facilitates human-machine collaboration, human risk management, and workflow improvement. Compared to optical sensors, inertial sensors have the advantages of portability and resistance to obstruction, making them suitable for factories. However, existing product-level inertial sensing solutions are generally expensive. This paper proposes a low-cost human motion capture system based on BMI 160, a type of six-axis inertial measurement unit (IMU). Based on WIFI communication, the collected data are processed to obtain the displacement of human joints' rotation angles around XYZ directions and the displacement in XYZ directions, then the human skeleton hierarchical relationship was combined to calculate the real-time human posture. Furthermore, the digital human model was been established on Unity3D to synchronously visualize and present human movements. We simulated assembly operations in a virtual reality environment for human posture data collection and posture recognition experiments. Six inertial sensors were placed on the chest, waist, knee joints, and ankle joints of both legs. There were 16,067 labeled samples obtained for posture recognition model training, and the accumulated displacement and the rotation angle of six joints in the three directions were used as input features. The bi-directional long short-term memory (BiLSTM) model was used to identify seven common operation postures: standing, slightly bending, deep bending, half-squatting, squatting, sitting, and supine, with an average accuracy of 98.24%. According to the experiment result, the proposed method could be used to develop a low-cost and effective solution to human posture recognition for factory operation.

Track Irregularity Identification Method of High-Speed Railway Based on CNN-Bi-LSTM.

Track smoothness has become an important factor in the safe operation of high-speed trains. In order to ensure the safety of high-speed operations, studies on track smoothness detection methods are constantly improving. This paper presents a track irregularity identification method based on CNN-Bi-LSTM and predicts track irregularity through car body acceleration detection, which is easy to collect and can be obtained by passenger trains, so the model proposed in this paper provides an idea for the development of track irregularity identification method based on conventional vehicles. The first step is construction of the data set required for model training. The model input is the car body acceleration detection sequence, and the output is the irregularity sequence of the same length. The fluctuation trend of the irregularity data is extracted by the HP filtering (Hodrick Prescott Filter) algorithm as the prediction target. The second is a prediction model based on the CNN-Bi-LSTM network, extracting features from the car body acceleration data and realizing the point-by-point prediction of irregularities. Meanwhile, this paper proposes an exponential weighted mean square error with priority inner fitting (EIF-MSE) as the loss function, improving the accuracy of big value data prediction, and reducing the risk of false alarms. In conclusion, the model is verified based on the simulation data and the real data measured by the high-speed railway comprehensive inspection train.

Hour-Ahead Photovoltaic Power Prediction Combining BiLSTM and Bayesian Optimization Algorithm, with Bootstrap Resampling for Interval Predictions.

Photovoltaic (PV) power prediction plays a critical role amid the accelerating adoption of renewable energy sources. This paper introduces a bidirectional long short-term memory (BiLSTM) deep learning (DL) model designed for forecasting photovoltaic power one hour ahead. The dataset under examination originates from a small PV installation located at the Polytechnic School of the University of Alcala. To improve the quality of historical data and optimize model performance, a robust data preprocessing algorithm is implemented. The BiLSTM model is synergistically combined with a Bayesian optimization algorithm (BOA) to fine-tune its primary hyperparameters, thereby enhancing its predictive efficacy. The performance of the proposed model is evaluated across diverse meteorological and seasonal conditions. In deterministic forecasting, the findings indicate its superiority over alternative models employed in this research domain, specifically a multilayer perceptron (MLP) neural network model and a random forest (RF) ensemble model. Compared with the MLP and RF reference models, the proposed model achieves reductions in the normalized mean absolute error (nMAE) of 75.03% and 77.01%, respectively, demonstrating its effectiveness in this type of prediction. Moreover, interval prediction utilizing the bootstrap resampling method is conducted, with the acquired prediction intervals carefully adjusted to meet the desired confidence levels, thereby enhancing the robustness and flexibility of the predictions.

Advancing Phishing Email Detection: A Comparative Study of Deep Learning Models.

Phishing is one of the most dangerous attacks targeting individuals, organizations, and nations. Although many traditional methods for email phishing detection exist, there is a need to improve accuracy and reduce false-positive rates. Our work investigates one-dimensional CNN-based models (1D-CNNPD) to detect phishing emails in order to address these challenges. Additionally, further improvement is achieved with the augmentation of the base 1D-CNNPD model with recurrent layers, namely, LSTM, Bi-LSTM, GRU, and Bi-GRU, and experimented with the four resulting models. Two benchmark datasets were used to evaluate the performance of our models: Phishing Corpus and Spam Assassin. Our results indicate that, in general, the augmentations improve the performance of the 1D-CNNPD base model. Specifically, the 1D-CNNPD with Bi-GRU yields the best results. Overall, the performance of our models is comparable to the state of the art of CNN-based phishing email detection. The Advanced 1D-CNNPD with Leaky ReLU and Bi-GRU achieved 100% precision, 99.68% accuracy, an F1 score of 99.66%, and a recall of 99.32%. We observe that increasing model depth typically leads to an initial performance improvement, succeeded by a decline. In conclusion, this study highlights the effectiveness of augmented 1D-CNNPD models in detecting phishing emails with improved accuracy. The reported performance measure values indicate the potential of these models in advancing the implementation of cybersecurity solutions to combat email phishing attacks.

Enhancing Classification Accuracy with Integrated Contextual Gate Network: Deep Learning Approach for Functional Near-Infrared Spectroscopy Brain-Computer Interface Application.

Brain-computer interface (BCI) systems include signal acquisition, preprocessing, feature extraction, classification, and an application phase. In fNIRS-BCI systems, deep learning (DL) algorithms play a crucial role in enhancing accuracy. Unlike traditional machine learning (ML) classifiers, DL algorithms eliminate the need for manual feature extraction. DL neural networks automatically extract hidden patterns/features within a dataset to classify the data. In this study, a hand-gripping (closing and opening) two-class motor activity dataset from twenty healthy participants is acquired, and an integrated contextual gate network (ICGN) algorithm (proposed) is applied to that dataset to enhance the classification accuracy. The proposed algorithm extracts the features from the filtered data and generates the patterns based on the information from the previous cells within the network. Accordingly, classification is performed based on the similar generated patterns within the dataset. The accuracy of the proposed algorithm is compared with the long short-term memory (LSTM) and bidirectional long short-term memory (Bi-LSTM). The proposed ICGN algorithm yielded a classification accuracy of 91.23 ± 1.60%, which is significantly (p < 0.025) higher than the 84.89 ± 3.91 and 88.82 ± 1.96 achieved by LSTM and Bi-LSTM, respectively. An open access, three-class (right- and left-hand finger tapping and dominant foot tapping) dataset of 30 subjects is used to validate the proposed algorithm. The results show that ICGN can be efficiently used for the classification of two- and three-class problems in fNIRS-based BCI applications.

Sentiment analysis of online reviews of energy-saving products based on transfer learning and LBBA model.

With the exacerbation of global climate change and the growing environmental awareness among the general public, the concept of green consumption has gained significant attention across various sectors of society. As a representative example of green consumer products, energy-saving products play a crucial role in the timely realization of dual carbon goals. However, an analysis of online comments regarding energy-saving products reveals that the majority of these products still exhibit shortcomings in terms of efficacy, noise level, cost-effectiveness, and particularly, energy-saving appliances. This study focuses on the user-generated online comments data from the Taobao e-commerce platform for Grade 1 energy-saving refrigerators. By employing text mining techniques, the study aims to extract the essential information and sentiments expressed in the comments, in order to explore the consumption characteristics of Grade 1 energy-saving refrigerators. Moreover, the LBBA (LDA-Bert-BiLSTM-Attention) model is utilized to investigate the consumer topics of interest and emotional features. Initially, the LDA model is adopted to identify the attributes and weights of consumer concerns. Subsequently, the Bert model is pre-trained with the online comment data, and combined with the BiLSTM algorithm and Attention mechanism to predict sentiment categories. Finally, a transfer learning approach is utilized to determine the sentiment inclination of user-generated online comments and to identify the primary driving factors behind each sentiment category. This research employs sentiment analysis on online comments data regarding energy-saving products to uncover consumer sentiment attributes and emotional characteristics. It provides decision-makers with a comprehensive and systematic understanding of public consumption intentions, offering decision support for the efficient operation and management of the energy-saving product market.

BiLSTM- and CNN-Based m6A Modification Prediction Model for circRNAs.

m6A methylation, a ubiquitous modification on circRNAs, exerts a profound influence on RNA function, intracellular behavior, and diverse biological processes, including disease development. While prediction algorithms exist for mRNA m6A modifications, a critical gap remains in the prediction of circRNA m6A modifications. Therefore, accurate identification and prediction of m6A sites are imperative for understanding RNA function and regulation. This study presents a novel hybrid model combining a convolutional neural network (CNN) and a bidirectional long short-term memory network (BiLSTM) for precise m6A methylation site prediction in circular RNAs (circRNAs) based on data from HEK293 cells. This model exploits the synergy between CNN's ability to extract intricate sequence features and BiLSTM's strength in capturing long-range dependencies. Furthermore, the integrated attention mechanism empowers the model to pinpoint critical biological information for studying circRNA m6A methylation. Our model, exhibiting over 78% prediction accuracy on independent datasets, offers not only a valuable tool for scientific research but also a strong foundation for future biomedical applications. This work not only furthers our understanding of gene expression regulation but also opens new avenues for the exploration of circRNA methylation in biological research.

Soft sensing of NOx emission from waste incineration process based on data de-noising and bidirectional long short-term memory neural networks.

Continuous emission monitoring system is commonly employed to monitor NOx emissions in municipal solid waste incineration (MSWI) processes. However, it still encounters the challenges of regular maintenance and measurement lag. These issues significantly impact the accurate and stable control of NOx emissions. Therefore, developing a soft NOx emission sensor to complement hardware monitoring becomes imperative. Considering data noise, dynamic nonlinearity, time series characteristics and volatility in the MSWI process, this article introduces a soft sensor model for NOx emission prediction utilizing the complete ensemble empirical mode decomposition adaptive noise (CEEMDAN)-wavelet threshold (WT) method and bidirectional long short-term memory (Bi-LSTM). Firstly, the original data signal is decomposed into a group of intrinsic mode functions (IMFs) using the CEEMDAN. Subsequently, the WT processes the high-frequency IMFs that are noise-dominant. Then, all IMFs are reconstructed to obtain the denoized signal. Finally, the Bi-LSTM model is employed to predict NOx emissions. Compared to conventional modelling approaches, the model proposed in this article demonstrates the best predictive performance. The mean absolute percentage error, root-mean-squared error and average absolute error on the test set of the proposed model are 3.75%, 5.34 mg m-3 and 4.34 mg m-3, respectively. The proposed model provides a new method to soft sensing NOx emissions. It holds significant practical value for precise and stable monitoring of NOx emissions in MSWI processes and provides a reference for research on modelling key process parameters.

Deep-ABPpred: identifying antibacterial peptides in protein sequences using bidirectional LSTM with word2vec.

The overuse of antibiotics has led to emergence of antimicrobial resistance, and as a result, antibacterial peptides (ABPs) are receiving significant attention as an alternative. Identification of effective ABPs in lab from natural sources is a cost-intensive and time-consuming process. Therefore, there is a need for the development of in silico models, which can identify novel ABPs in protein sequences for chemical synthesis and testing. In this study, we propose a deep learning classifier named Deep-ABPpred that can identify ABPs in protein sequences. We developed Deep-ABPpred using bidirectional long short-term memory algorithm with amino acid level features from word2vec. The results show that Deep-ABPpred outperforms other state-of-the-art ABP classifiers on both test and independent datasets. Our proposed model achieved the precision of approximately 97 and 94% on test dataset and independent dataset, respectively. The high precision suggests applicability of Deep-ABPpred in proposing novel ABPs for synthesis and experimentation. By utilizing Deep-ABPpred, we identified ABPs in the tail protein sequences of Streptococcus bacteriophages, chemically synthesized identified peptides in lab and tested their activity in vitro. These ABPs showed potent antibacterial activity against selected Gram-positive and Gram-negative bacteria, which confirms the capability of Deep-ABPpred in identifying novel ABPs in protein sequences. Based on the proposed approach, an online prediction server is also developed, which is freely accessible at https://abppred.anvil.app/. This web server takes the protein sequence as input and provides ABPs with high probability (>0.95) as output.