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Ma Y, Pei Y, Li C. Predictive Recognition of DNA-binding Proteins Based on Pre-trained Language Model BERT. J Bioinform Comput Biol 2023; 21:2350028. [PMID: 38248912 DOI: 10.1142/s0219720023500282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Identifying proteins is crucial for disease diagnosis and treatment. With the increase of known proteins, large-scale batch predictions are essential. However, traditional biological experiments being time-consuming and expensive are difficult to accomplish this task efficiently. Nevertheless, deep learning algorithms based on big data analysis have manifested potential in this aspect. In recent years, language representation models, especially BERT, have made significant advancements in natural language processing. In this paper, using three protein segmentation methods and three encoder numbers, nine BERT models with different sizes are constructed to predict whether known proteins are DNA-binding proteins or not. Furthermore, based on the concept of protein motifs, multi-scale convolutional networks are fused into the models to extract the local features of DNA-binding proteins. Finally, we find that the larger the number of encoders, the better the model predictions under the condition of considering each amino acid in the protein as a word. Our proposed algorithm achieves 81.88% sensitivity and 0.39 MCC value on the test set. Furthermore, it achieves 62.41% accuracy on the independent test set PDB2272. It is evident that our proposed method can be a tool to assist in the identification of DNA-binding proteins.
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Affiliation(s)
- Yue Ma
- School of Computer Science and Technology, Tiangong University, Tianjin, P. R. China
| | - Yongzhen Pei
- School of Mathematical Sciences, Tiangong University, Tianjin, P. R. China
| | - Changguo Li
- Department of Basic Science, Army Military Transportation University, Tianjin, P. R. China
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Ou YY, Ho QT, Chang HT. Recent advances in features generation for membrane protein sequences: From multiple sequence alignment to pre-trained language models. Proteomics 2023; 23:e2200494. [PMID: 37863817 DOI: 10.1002/pmic.202200494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/22/2023]
Abstract
Membrane proteins play a crucial role in various cellular processes and are essential components of cell membranes. Computational methods have emerged as a powerful tool for studying membrane proteins due to their complex structures and properties that make them difficult to analyze experimentally. Traditional features for protein sequence analysis based on amino acid types, composition, and pair composition have limitations in capturing higher-order sequence patterns. Recently, multiple sequence alignment (MSA) and pre-trained language models (PLMs) have been used to generate features from protein sequences. However, the significant computational resources required for MSA-based features generation can be a major bottleneck for many applications. Several methods and tools have been developed to accelerate the generation of MSAs and reduce their computational cost, including heuristics and approximate algorithms. Additionally, the use of PLMs such as BERT has shown great potential in generating informative embeddings for protein sequence analysis. In this review, we provide an overview of traditional and more recent methods for generating features from protein sequences, with a particular focus on MSAs and PLMs. We highlight the advantages and limitations of these approaches and discuss the methods and tools developed to address the computational challenges associated with features generation. Overall, the advancements in computational methods and tools provide a promising avenue for gaining deeper insights into the function and properties of membrane proteins, which can have significant implications in drug discovery and personalized medicine.
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Affiliation(s)
- Yu-Yen Ou
- Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, Taiwan
- Graduate Program in Biomedical Informatics, Yuan Ze University, Chung-Li, Taiwan
| | - Quang-Thai Ho
- Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, Taiwan
| | - Heng-Ta Chang
- Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, Taiwan
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Thafar MA, Albaradei S, Uludag M, Alshahrani M, Gojobori T, Essack M, Gao X. OncoRTT: Predicting novel oncology-related therapeutic targets using BERT embeddings and omics features. Front Genet 2023; 14:1139626. [PMID: 37091791 PMCID: PMC10117673 DOI: 10.3389/fgene.2023.1139626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/24/2023] [Indexed: 04/08/2023] Open
Abstract
Late-stage drug development failures are usually a consequence of ineffective targets. Thus, proper target identification is needed, which may be possible using computational approaches. The reason being, effective targets have disease-relevant biological functions, and omics data unveil the proteins involved in these functions. Also, properties that favor the existence of binding between drug and target are deducible from the protein’s amino acid sequence. In this work, we developed OncoRTT, a deep learning (DL)-based method for predicting novel therapeutic targets. OncoRTT is designed to reduce suboptimal target selection by identifying novel targets based on features of known effective targets using DL approaches. First, we created the “OncologyTT” datasets, which include genes/proteins associated with ten prevalent cancer types. Then, we generated three sets of features for all genes: omics features, the proteins’ amino-acid sequence BERT embeddings, and the integrated features to train and test the DL classifiers separately. The models achieved high prediction performances in terms of area under the curve (AUC), i.e., AUC greater than 0.88 for all cancer types, with a maximum of 0.95 for leukemia. Also, OncoRTT outperformed the state-of-the-art method using their data in five out of seven cancer types commonly assessed by both methods. Furthermore, OncoRTT predicts novel therapeutic targets using new test data related to the seven cancer types. We further corroborated these results with other validation evidence using the Open Targets Platform and a case study focused on the top-10 predicted therapeutic targets for lung cancer.
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Affiliation(s)
- Maha A. Thafar
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center, Computer (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- College of Computers and Information Technology, Computer Science Department, Taif University, Taif, Saudi Arabia
| | - Somayah Albaradei
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center, Computer (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mahmut Uludag
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center, Computer (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mona Alshahrani
- National Center for Artificial Intelligence (NCAI), Saudi Data and Artificial Intelligence Authority (SDAIA), Riyadh, Saudi Arabia
| | - Takashi Gojobori
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center, Computer (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Magbubah Essack
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center, Computer (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- *Correspondence: Xin Gao, ; Magbubah Essack,
| | - Xin Gao
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center, Computer (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- *Correspondence: Xin Gao, ; Magbubah Essack,
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Zhang Y, Liu M, Zhang L, Wang L, Zhao K, Hu S, Chen X, Xie X. Comparison of Chest Radiograph Captions Based on Natural Language Processing vs Completed by Radiologists. JAMA Netw Open 2023; 6:e2255113. [PMID: 36753278 PMCID: PMC9909497 DOI: 10.1001/jamanetworkopen.2022.55113] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
IMPORTANCE Artificial intelligence (AI) can interpret abnormal signs in chest radiography (CXR) and generate captions, but a prospective study is needed to examine its practical value. OBJECTIVE To prospectively compare natural language processing (NLP)-generated CXR captions and the diagnostic findings of radiologists. DESIGN, SETTING, AND PARTICIPANTS A multicenter diagnostic study was conducted. The training data set included CXR images and reports retrospectively collected from February 1, 2014, to February 28, 2018. The retrospective test data set included consecutive images and reports from April 1 to July 31, 2019. The prospective test data set included consecutive images and reports from May 1 to September 30, 2021. EXPOSURES A bidirectional encoder representation from a transformers model was used to extract language entities and relationships from unstructured CXR reports to establish 23 labels of abnormal signs to train convolutional neural networks. The participants in the prospective test group were randomly assigned to 1 of 3 different caption generation models: a normal template, NLP-generated captions, and rule-based captions based on convolutional neural networks. For each case, a resident drafted the report based on the randomly assigned captions and an experienced radiologist finalized the report blinded to the original captions. A total of 21 residents and 19 radiologists were involved. MAIN OUTCOMES AND MEASURES Time to write reports based on different caption generation models. RESULTS The training data set consisted of 74 082 cases (39 254 [53.0%] women; mean [SD] age, 50.0 [17.1] years). In the retrospective (n = 8126; 4345 [53.5%] women; mean [SD] age, 47.9 [15.9] years) and prospective (n = 5091; 2416 [47.5%] women; mean [SD] age, 45.1 [15.6] years) test data sets, the mean (SD) area under the curve of abnormal signs was 0.87 (0.11) in the retrospective data set and 0.84 (0.09) in the prospective data set. The residents' mean (SD) reporting time using the NLP-generated model was 283 (37) seconds-significantly shorter than the normal template (347 [58] seconds; P < .001) and the rule-based model (296 [46] seconds; P < .001). The NLP-generated captions showed the highest similarity to the final reports with a mean (SD) bilingual evaluation understudy score of 0.69 (0.24)-significantly higher than the normal template (0.37 [0.09]; P < .001) and the rule-based model (0.57 [0.19]; P < .001). CONCLUSIONS AND RELEVANCE In this diagnostic study of NLP-generated CXR captions, prior information provided by NLP was associated with greater efficiency in the reporting process, while maintaining good consistency with the findings of radiologists.
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Affiliation(s)
- Yaping Zhang
- Radiology Department, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Lu Zhang
- Radiology Department, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lingyun Wang
- Radiology Department, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Keke Zhao
- Radiology Department, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shundong Hu
- Radiology Department, Shanghai Sixth People Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xu Chen
- Winning Health Technology Ltd, Shanghai, China
| | - Xueqian Xie
- Radiology Department, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Chen D, Li S, Chen Y. ISTRF: Identification of sucrose transporter using random forest. Front Genet 2022; 13:1012828. [PMID: 36171889 PMCID: PMC9511101 DOI: 10.3389/fgene.2022.1012828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/22/2022] [Indexed: 12/05/2022] Open
Abstract
Sucrose transporter (SUT) is a type of transmembrane protein that exists widely in plants and plays a significant role in the transportation of sucrose and the specific signal sensing process of sucrose. Therefore, identifying sucrose transporter is significant to the study of seed development and plant flowering and growth. In this study, a random forest-based model named ISTRF was proposed to identify sucrose transporter. First, a database containing 382 SUT proteins and 911 non-SUT proteins was constructed based on the UniProt and PFAM databases. Second, k-separated-bigrams-PSSM was exploited to represent protein sequence. Third, to overcome the influence of imbalance of samples on identification performance, the Borderline-SMOTE algorithm was used to overcome the shortcoming of imbalance training data. Finally, the random forest algorithm was used to train the identification model. It was proved by 10-fold cross-validation results that k-separated-bigrams-PSSM was the most distinguishable feature for identifying sucrose transporters. The Borderline-SMOTE algorithm can improve the performance of the identification model. Furthermore, random forest was superior to other classifiers on almost all indicators. Compared with other identification models, ISTRF has the best general performance and makes great improvements in identifying sucrose transporter proteins.
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Affiliation(s)
- Dong Chen
- College of Electrical and Information Engineering, Qu Zhou University, Quzhou, China
| | - Sai Li
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Yu Chen
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
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BERT-PPII: The Polyproline Type II Helix Structure Prediction Model Based on BERT and Multichannel CNN. BIOMED RESEARCH INTERNATIONAL 2022; 2022:9015123. [PMID: 36060139 PMCID: PMC9433275 DOI: 10.1155/2022/9015123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/01/2022] [Accepted: 08/03/2022] [Indexed: 11/26/2022]
Abstract
Predicting the polyproline type II (PPII) helix structure is crucial important in many research areas, such as the protein folding mechanisms, the drug targets, and the protein functions. However, many existing PPII helix prediction algorithms encode the protein sequence information in a single way, which causes the insufficient learning of protein sequence feature information. To improve the protein sequence encoding performance, this paper proposes a BERT-based PPII helix structure prediction algorithm (BERT-PPII), which learns the protein sequence information based on the BERT model. The BERT model's CLS vector can fairly fuse sample's each amino acid residue information. Thus, we utilize the CLS vector as the global feature to represent the sample's global contextual information. As the interactions among the protein chains' local amino acid residues have an important influence on the formation of PPII helix, we utilize the CNN to extract local amino acid residues' features which can further enhance the information expression of protein sequence samples. In this paper, we fuse the CLS vectors with CNN local features to improve the performance of predicting PPII structure. Compared to the state-of-the-art PPIIPRED method, the experimental results on the unbalanced dataset show that the proposed method improves the accuracy value by 1% on the strict dataset and 2% on the less strict dataset. Correspondingly, the results on the balanced dataset show that the AUCs of the proposed method are 0.826 on the strict dataset and 0.785 on less strict datasets, respectively. For the independent test set, the proposed method has the AUC value of 0.827 on the strict dataset and 0.783 on the less strict dataset. The above experimental results have proved that the proposed BERT-PPII method can achieve a superior performance of predicting the PPII helix.
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Indriani F, Mahmudah KR, Purnama B, Satou K. ProtTrans-Glutar: Incorporating Features From Pre-trained Transformer-Based Models for Predicting Glutarylation Sites. Front Genet 2022; 13:885929. [PMID: 35711929 PMCID: PMC9194472 DOI: 10.3389/fgene.2022.885929] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/26/2022] [Indexed: 11/16/2022] Open
Abstract
Lysine glutarylation is a post-translational modification (PTM) that plays a regulatory role in various physiological and biological processes. Identifying glutarylated peptides using proteomic techniques is expensive and time-consuming. Therefore, developing computational models and predictors can prove useful for rapid identification of glutarylation. In this study, we propose a model called ProtTrans-Glutar to classify a protein sequence into positive or negative glutarylation site by combining traditional sequence-based features with features derived from a pre-trained transformer-based protein model. The features of the model were constructed by combining several feature sets, namely the distribution feature (from composition/transition/distribution encoding), enhanced amino acid composition (EAAC), and features derived from the ProtT5-XL-UniRef50 model. Combined with random under-sampling and XGBoost classification method, our model obtained recall, specificity, and AUC scores of 0.7864, 0.6286, and 0.7075 respectively on an independent test set. The recall and AUC scores were notably higher than those of the previous glutarylation prediction models using the same dataset. This high recall score suggests that our method has the potential to identify new glutarylation sites and facilitate further research on the glutarylation process.
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Affiliation(s)
- Fatma Indriani
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan
- Department of Computer Science, Lambung Mangkurat University, Banjarmasin, Indonesia
| | - Kunti Robiatul Mahmudah
- Department of Postgraduate of Mathematics Education, Universitas Ahmad Dahlan, Yogyakarta, Indonesia
| | - Bedy Purnama
- School of Computing, Telkom University, Bandung, Indonesia
| | - Kenji Satou
- Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan
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Taju SW, Shah SMA, Ou YY. Identification of efflux proteins based on contextual representations with deep bidirectional transformer encoders. Anal Biochem 2021; 633:114416. [PMID: 34656612 DOI: 10.1016/j.ab.2021.114416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 10/20/2022]
Abstract
Efflux proteins are the transport proteins expressed in the plasma membrane, which are involved in the movement of unwanted toxic substances through specific efflux pumps. Several studies based on computational approaches have been proposed to predict transport proteins and thereby to understand the mechanism of the movement of ions across cell membranes. However, few methods were developed to identify efflux proteins. This paper presents an approach based on the contextualized word embeddings from Bidirectional Encoder Representations from Transformers (BERT) with the Support Vector Machine (SVM) classifier. BERT is the most effective pre-trained language model that performs exceptionally well on several Natural Language Processing (NLP) tasks. Therefore, the contextualized representations from BERT were implemented to incorporate multiple interpretations of identical amino acids in the sequence. A dataset of efflux proteins with annotations was first established. The feature vectors were extracted by transferring protein data through the hidden layers of the pre-trained model. Our proposed method was trained on complete training datasets to identify efflux proteins and achieved the accuracies of 94.15% and 87.13% in the independent tests on membrane and transport datasets, respectively. This study opens a research avenue for the implementation of contextualized word embeddings in Bioinformatics and Computational Biology.
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Affiliation(s)
- Semmy Wellem Taju
- Department of Computer Science & Engineering, Yuan Ze University, Chungli, 32003, Taiwan
| | - Syed Muazzam Ali Shah
- Department of Computer Science & Engineering, Yuan Ze University, Chungli, 32003, Taiwan
| | - Yu-Yen Ou
- Department of Computer Science & Engineering, Yuan Ze University, Chungli, 32003, Taiwan.
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Zhang Y, Liu M, Hu S, Shen Y, Lan J, Jiang B, de Bock GH, Vliegenthart R, Chen X, Xie X. Development and multicenter validation of chest X-ray radiography interpretations based on natural language processing. COMMUNICATIONS MEDICINE 2021; 1:43. [PMID: 35602222 PMCID: PMC9053275 DOI: 10.1038/s43856-021-00043-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/23/2021] [Indexed: 01/01/2023] Open
Abstract
Background Artificial intelligence can assist in interpreting chest X-ray radiography (CXR) data, but large datasets require efficient image annotation. The purpose of this study is to extract CXR labels from diagnostic reports based on natural language processing, train convolutional neural networks (CNNs), and evaluate the classification performance of CNN using CXR data from multiple centers Methods We collected the CXR images and corresponding radiology reports of 74,082 subjects as the training dataset. The linguistic entities and relationships from unstructured radiology reports were extracted by the bidirectional encoder representations from transformers (BERT) model, and a knowledge graph was constructed to represent the association between image labels of abnormal signs and the report text of CXR. Then, a 25-label classification system were built to train and test the CNN models with weakly supervised labeling. Results In three external test cohorts of 5,996 symptomatic patients, 2,130 screening examinees, and 1,804 community clinic patients, the mean AUC of identifying 25 abnormal signs by CNN reaches 0.866 ± 0.110, 0.891 ± 0.147, and 0.796 ± 0.157, respectively. In symptomatic patients, CNN shows no significant difference with local radiologists in identifying 21 signs (p > 0.05), but is poorer for 4 signs (p < 0.05). In screening examinees, CNN shows no significant difference for 17 signs (p > 0.05), but is poorer at classifying nodules (p = 0.013). In community clinic patients, CNN shows no significant difference for 12 signs (p > 0.05), but performs better for 6 signs (p < 0.001). Conclusion We construct and validate an effective CXR interpretation system based on natural language processing. Chest X-rays are accompanied by a report from the radiologist, which contains valuable diagnostic information in text format. Extracting and interpreting information from these reports, such as keywords, is time-consuming, but artificial intelligence (AI) can help with this. Here, we use a type of AI known as natural language processing to extract information about abnormal signs seen on chest X-rays from the corresponding report. We develop and test natural language processing models using data from multiple hospitals and clinics, and show that our models achieve similar performance to interpretation from the radiologists themselves. Our findings suggest that AI might help radiologists to speed up interpretation of chest X-ray reports, which could be useful not only in patient triage and diagnosis but also cataloguing and searching of radiology datasets. Zhang et al. develop a natural language processing approach, based on the BERT model, to extract linguistic information from chest X-ray radiography reports. The authors establish a 25-label classification system for abnormal findings described in the reports and validate their model using data from multiple sites.
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Ali Shah SM, Ou YY. TRP-BERT: Discrimination of transient receptor potential (TRP) channels using contextual representations from deep bidirectional transformer based on BERT. Comput Biol Med 2021; 137:104821. [PMID: 34508974 DOI: 10.1016/j.compbiomed.2021.104821] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 11/16/2022]
Abstract
Transient receptor potential (TRP) channels are non-selective cation channels that act as ion channels and are primarily found on the plasma membrane of numerous animal cells. These channels are involved in the physiology and pathophysiology of a wide variety of biological processes, including inhibition and progression of cancer, pain initiation, inflammation, regulation of pressure, thermoregulation, secretion of salivary fluid, and homeostasis of Ca2+ and Mg2+. Increasing evidences indicate that mutations in the gene encoding TRP channels play an essential role in a broad array of diseases. Therefore, these channels are becoming popular as potential drug targets for several diseases. The diversified role of these channels demands a prediction model to classify TRP channels from other channel proteins (non-TRP channels). Therefore, we presented an approach based on the Support Vector Machine (SVM) classifier and contextualized word embeddings from Bidirectional Encoder Representations from Transformers (BERT) to represent protein sequences. BERT is a deeply bidirectional language model and a neural network approach to Natural Language Processing (NLP) that achieves outstanding performance on various NLP tasks. We apply BERT to generate contextualized representations for every single amino acid in a protein sequence. Interestingly, these representations are context-sensitive and vary for the same amino acid appearing in different positions in the sequence. Our proposed method showed 80.00% sensitivity, 96.03% specificity, 95.47% accuracy, and a 0.56 Matthews correlation coefficient (MCC) for an independent test set. We suggest that our proposed method could effectively classify TRP channels from non-TRP channels and assist biologists in identifying new potential TRP channels.
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Affiliation(s)
- Syed Muazzam Ali Shah
- Department of Computer Science & Engineering, Yuan Ze University, Chungli, 32003, Taiwan
| | - Yu-Yen Ou
- Department of Computer Science & Engineering, Yuan Ze University, Chungli, 32003, Taiwan.
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Weighted graph convolution over dependency trees for nontaxonomic relation extraction on public opinion information. APPL INTELL 2021. [DOI: 10.1007/s10489-021-02596-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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