Scoring alignments by embedding vector similarity.

Sequence similarity is of paramount importance in biology, as similar sequences tend to have similar function and share common ancestry. Scoring matrices, such as PAM or BLOSUM, play a crucial role in all bioinformatics algorithms for identifying similarities, but have the drawback that they are fixed, independent of context. We propose a new scoring method for amino acid similarity that remedies this weakness, being contextually dependent. It relies on recent advances in deep learning architectures that employ self-supervised learning in order to leverage the power of enormous amounts of unlabelled data to generate contextual embeddings, which are vector representations for words. These ideas have been applied to protein sequences, producing embedding vectors for protein residues. We propose the E-score between two residues as the cosine similarity between their embedding vector representations. Thorough testing on a wide variety of reference multiple sequence alignments indicate that the alignments produced using the new $E$-score method, especially ProtT5-score, are significantly better than those obtained using BLOSUM matrices. The new method proposes to change the way alignments are computed, with far-reaching implications in all areas of textual data that use sequence similarity. The program to compute alignments based on various $E$-scores is available as a web server at e-score.csd.uwo.ca. The source code is freely available for download from github.com/lucian-ilie/E-score.

Deepstacked-AVPs: predicting antiviral peptides using tri-segment evolutionary profile and word embedding based multi-perspective features with deep stacking model.

BACKGROUND: Viral infections have been the main health issue in the last decade. Antiviral peptides (AVPs) are a subclass of antimicrobial peptides (AMPs) with substantial potential to protect the human body against various viral diseases. However, there has been significant production of antiviral vaccines and medications. Recently, the development of AVPs as an antiviral agent suggests an effective way to treat virus-affected cells. Recently, the involvement of intelligent machine learning techniques for developing peptide-based therapeutic agents is becoming an increasing interest due to its significant outcomes. The existing wet-laboratory-based drugs are expensive, time-consuming, and cannot effectively perform in screening and predicting the targeted motif of antiviral peptides. METHODS: In this paper, we proposed a novel computational model called Deepstacked-AVPs to discriminate AVPs accurately. The training sequences are numerically encoded using a novel Tri-segmentation-based position-specific scoring matrix (PSSM-TS) and word2vec-based semantic features. Composition/Transition/Distribution-Transition (CTDT) is also employed to represent the physiochemical properties based on structural features. Apart from these, the fused vector is formed using PSSM-TS features, semantic information, and CTDT descriptors to compensate for the limitations of single encoding methods. Information gain (IG) is applied to choose the optimal feature set. The selected features are trained using a stacked-ensemble classifier. RESULTS: The proposed Deepstacked-AVPs model achieved a predictive accuracy of 96.60%%, an area under the curve (AUC) of 0.98, and a precision-recall (PR) value of 0.97 using training samples. In the case of the independent samples, our model obtained an accuracy of 95.15%, an AUC of 0.97, and a PR value of 0.97. CONCLUSION: Our Deepstacked-AVPs model outperformed existing models with a ~ 4% and ~ 2% higher accuracy using training and independent samples, respectively. The reliability and efficacy of the proposed Deepstacked-AVPs model make it a valuable tool for scientists and may perform a beneficial role in pharmaceutical design and research academia.

S2DV: converting SMILES to a drug vector for predicting the activity of anti-HBV small molecules.

In the past few decades, chronic hepatitis B caused by hepatitis B virus (HBV) has been one of the most serious diseases to human health. The development of innovative systems is essential for preventing the complex pathogenesis of hepatitis B and reducing side effects caused by drugs. HBV inhibitory drugs have been developed through various compounds, and they are often limited by routine experimental screening and delay drug development. More recently, virtual screening of compounds has gradually been used in drug research with strong computational capability and is further applied in anti-HBV drug screening, thus facilitating a reliable drug screening process. However, the lack of structural information in traditional compound analysis is an important hurdle for unsatisfactory efficiency in drug screening. Here, a natural language processing technique was adopted to analyze compound simplified molecular input line entry system strings. By using the targeted optimized word2vec model for pretraining, we can accurately represent the relationship between the compound and its substructure. The machine learning model based on training results can effectively predict the inhibitory effect of compounds on HBV and liver toxicity. The reliability of the model is verified by the results of wet-lab experiments. In addition, a tool has been published to predict potential compounds. Hence, this article provides a new perspective on the prediction of compound properties for anti-HBV drugs that can help improve hepatitis B diagnosis and further develop human health in the future.

Surfing the OCEAN: The machine learning psycholexical approach 2.0 to detect personality traits in texts.

OBJECTIVE: We aimed to develop a machine learning model to infer OCEAN traits from text. BACKGROUND: The psycholexical approach allows retrieving information about personality traits from human language. However, it has rarely been applied because of methodological and practical issues that current computational advancements could overcome. METHOD: Classical taxonomies and a large Yelp corpus were leveraged to learn an embedding for each personality trait. These embeddings were used to train a feedforward neural network for predicting trait values. Their generalization performances have been evaluated through two external validation studies involving experts (N = 11) and laypeople (N = 100) in a discrimination task about the best markers of each trait and polarity. RESULTS: Intrinsic validation of the model yielded excellent results, with R2 values greater than 0.78. The validation studies showed a high proportion of matches between participants' choices and model predictions, confirming its efficacy in identifying new terms related to the OCEAN traits. The best performance was observed for agreeableness and extraversion, especially for their positive polarities. The model was less efficient in identifying the negative polarity of openness and conscientiousness. CONCLUSIONS: This innovative methodology can be considered a "psycholexical approach 2.0," contributing to research in personality and its practical applications in many fields.

Identifying the Risk Factors of Allergic Rhinitis Based on Zhihu Comment Data Using a Topic-Enhanced Word-Embedding Model: Mixed Method Study and Cluster Analysis.

BACKGROUND: Allergic rhinitis (AR) is a chronic disease, and several risk factors predispose individuals to the condition in their daily lives, including exposure to allergens and inhalation irritants. Analyzing the potential risk factors that can trigger AR can provide reference material for individuals to use to reduce its occurrence in their daily lives. Nowadays, social media is a part of daily life, with an increasing number of people using at least 1 platform regularly. Social media enables users to share experiences among large groups of people who share the same interests and experience the same afflictions. Notably, these channels promote the ability to share health information. OBJECTIVE: This study aims to construct an intelligent method (TopicS-ClusterREV) for identifying the risk factors of AR based on these social media comments. The main questions were as follows: How many comments contained AR risk factor information? How many categories can these risk factors be summarized into? How do these risk factors trigger AR? METHODS: This study crawled all the data from May 2012 to May 2022 under the topic of allergic rhinitis on Zhihu, obtaining a total of 9628 posts and 33,747 comments. We improved the Skip-gram model to train topic-enhanced word vector representations (TopicS) and then vectorized annotated text items for training the risk factor classifier. Furthermore, cluster analysis enabled a closer look into the opinions expressed in the category, namely gaining insight into how risk factors trigger AR. RESULTS: Our classifier identified more comments containing risk factors than the other classification models, with an accuracy rate of 96.1% and a recall rate of 96.3%. In general, we clustered texts containing risk factors into 28 categories, with season, region, and mites being the most common risk factors. We gained insight into the risk factors expressed in each category; for example, seasonal changes and increased temperature differences between day and night can disrupt the body's immune system and lead to the development of allergies. CONCLUSIONS: Our approach can handle the amount of data and extract risk factors effectively. Moreover, the summary of risk factors can serve as a reference for individuals to reduce AR in their daily lives. The experimental data also provide a potential pathway that triggers AR. This finding can guide the development of management plans and interventions for AR.

RB-GAT: A Text Classification Model Based on RoBERTa-BiGRU with Graph ATtention Network.

With the development of deep learning, several graph neural network (GNN)-based approaches have been utilized for text classification. However, GNNs encounter challenges when capturing contextual text information within a document sequence. To address this, a novel text classification model, RB-GAT, is proposed by combining RoBERTa-BiGRU embedding and a multi-head Graph ATtention Network (GAT). First, the pre-trained RoBERTa model is exploited to learn word and text embeddings in different contexts. Second, the Bidirectional Gated Recurrent Unit (BiGRU) is employed to capture long-term dependencies and bidirectional sentence information from the text context. Next, the multi-head graph attention network is applied to analyze this information, which serves as a node feature for the document. Finally, the classification results are generated through a Softmax layer. Experimental results on five benchmark datasets demonstrate that our method can achieve an accuracy of 71.48%, 98.45%, 80.32%, 90.84%, and 95.67% on Ohsumed, R8, MR, 20NG and R52, respectively, which is superior to the existing nine text classification approaches.

A Richer Vocabulary of Chinese Personality Traits: Leveraging Word Embedding Technology for Mining Personality Descriptors.

This study uses a data-driven approach to mine the distribution of personality traits among Chinese people in the Chinese social context. Based on the hypothesis of personality lexicology, word embedding technology was employed in machine learning to mine personality vocabulary from Tencent's word embedding database. More than 10,000 Chinese personality descriptors were extracted and analyzed using Gaussian Mixture Model Cluster and Hierarchical clustering analysis. The data was collected from 658 Chinese people randomly from all parts of China through an online questionnaire method. The results reveal six personality traits in the Chinese context, expanding the personality thesaurus and providing examples to illustrate each trait. The findings coincide with previous research on the five-factor model, which partially describes the personality traits of Chinese people, but does not offer a complete explanation of their typical social behavior patterns. Additionally, the study supports the notion of cultural particularity in personality traits. The approach used in this study offers a richer personality vocabulary than traditional personality mining methods, and word embedding technology captures richer semantic information in Chinese. The six Chinese personality traits identified in this study will also be used to explore how to quantify and evaluate personality traits based on word embedding and personality descriptors.

[A medical visual question answering approach based on co-attention networks].

Recent studies have introduced attention models for medical visual question answering (MVQA). In medical research, not only is the modeling of "visual attention" crucial, but the modeling of "question attention" is equally significant. To facilitate bidirectional reasoning in the attention processes involving medical images and questions, a new MVQA architecture, named MCAN, has been proposed. This architecture incorporated a cross-modal co-attention network, FCAF, which identifies key words in questions and principal parts in images. Through a meta-learning channel attention module (MLCA), weights were adaptively assigned to each word and region, reflecting the model's focus on specific words and regions during reasoning. Additionally, this study specially designed and developed a medical domain-specific word embedding model, Med-GloVe, to further enhance the model's accuracy and practical value. Experimental results indicated that MCAN proposed in this study improved the accuracy by 7.7% on free-form questions in the Path-VQA dataset, and by 4.4% on closed-form questions in the VQA-RAD dataset, which effectively improves the accuracy of the medical vision question answer.

pLMSNOSite: an ensemble-based approach for predicting protein S-nitrosylation sites by integrating supervised word embedding and embedding from pre-trained protein language model.

BACKGROUND: Protein S-nitrosylation (SNO) plays a key role in transferring nitric oxide-mediated signals in both animals and plants and has emerged as an important mechanism for regulating protein functions and cell signaling of all main classes of protein. It is involved in several biological processes including immune response, protein stability, transcription regulation, post translational regulation, DNA damage repair, redox regulation, and is an emerging paradigm of redox signaling for protection against oxidative stress. The development of robust computational tools to predict protein SNO sites would contribute to further interpretation of the pathological and physiological mechanisms of SNO. RESULTS: Using an intermediate fusion-based stacked generalization approach, we integrated embeddings from supervised embedding layer and contextualized protein language model (ProtT5) and developed a tool called pLMSNOSite (protein language model-based SNO site predictor). On an independent test set of experimentally identified SNO sites, pLMSNOSite achieved values of 0.340, 0.735 and 0.773 for MCC, sensitivity and specificity respectively. These results show that pLMSNOSite performs better than the compared approaches for the prediction of S-nitrosylation sites. CONCLUSION: Together, the experimental results suggest that pLMSNOSite achieves significant improvement in the prediction performance of S-nitrosylation sites and represents a robust computational approach for predicting protein S-nitrosylation sites. pLMSNOSite could be a useful resource for further elucidation of SNO and is publicly available at https://github.com/KCLabMTU/pLMSNOSite .

iEnhancer-DCSA: identifying enhancers via dual-scale convolution and spatial attention.

BACKGROUND: Due to the dynamic nature of enhancers, identifying enhancers and their strength are major bioinformatics challenges. With the development of deep learning, several models have facilitated enhancers detection in recent years. However, existing studies either neglect different length motifs information or treat the features at all spatial locations equally. How to effectively use multi-scale motifs information while ignoring irrelevant information is a question worthy of serious consideration. In this paper, we propose an accurate and stable predictor iEnhancer-DCSA, mainly composed of dual-scale fusion and spatial attention, automatically extracting features of different length motifs and selectively focusing on the important features. RESULTS: Our experimental results demonstrate that iEnhancer-DCSA is remarkably superior to existing state-of-the-art methods on the test dataset. Especially, the accuracy and MCC of enhancer identification are improved by 3.45% and 9.41%, respectively. Meanwhile, the accuracy and MCC of enhancer classification are improved by 7.65% and 18.1%, respectively. Furthermore, we conduct ablation studies to demonstrate the effectiveness of dual-scale fusion and spatial attention. CONCLUSIONS: iEnhancer-DCSA will be a valuable computational tool in identifying and classifying enhancers, especially for those not included in the training dataset.

DeepIPs: comprehensive assessment and computational identification of phosphorylation sites of SARS-CoV-2 infection using a deep learning-based approach.

The rapid spread of SARS-CoV-2 infection around the globe has caused a massive health and socioeconomic crisis. Identification of phosphorylation sites is an important step for understanding the molecular mechanisms of SARS-CoV-2 infection and the changes within the host cells pathways. In this study, we present DeepIPs, a first specific deep-learning architecture to identify phosphorylation sites in host cells infected with SARS-CoV-2. DeepIPs consists of the most popular word embedding method and convolutional neural network-long short-term memory network architecture to make the final prediction. The independent test demonstrates that DeepIPs improves the prediction performance compared with other existing tools for general phosphorylation sites prediction. Based on the proposed model, a web-server called DeepIPs was established and is freely accessible at http://lin-group.cn/server/DeepIPs. The source code of DeepIPs is freely available at the repository https://github.com/linDing-group/DeepIPs.

A transformer architecture based on BERT and 2D convolutional neural network to identify DNA enhancers from sequence information.

Recently, language representation models have drawn a lot of attention in the natural language processing field due to their remarkable results. Among them, bidirectional encoder representations from transformers (BERT) has proven to be a simple, yet powerful language model that achieved novel state-of-the-art performance. BERT adopted the concept of contextualized word embedding to capture the semantics and context of the words in which they appeared. In this study, we present a novel technique by incorporating BERT-based multilingual model in bioinformatics to represent the information of DNA sequences. We treated DNA sequences as natural sentences and then used BERT models to transform them into fixed-length numerical matrices. As a case study, we applied our method to DNA enhancer prediction, which is a well-known and challenging problem in this field. We then observed that our BERT-based features improved more than 5-10% in terms of sensitivity, specificity, accuracy and Matthews correlation coefficient compared to the current state-of-the-art features in bioinformatics. Moreover, advanced experiments show that deep learning (as represented by 2D convolutional neural networks; CNN) holds potential in learning BERT features better than other traditional machine learning techniques. In conclusion, we suggest that BERT and 2D CNNs could open a new avenue in biological modeling using sequence information.

Using deep neural networks and biological subwords to detect protein S-sulfenylation sites.

Protein S-sulfenylation is one kind of crucial post-translational modifications (PTMs) in which the hydroxyl group covalently binds to the thiol of cysteine. Some recent studies have shown that this modification plays an important role in signaling transduction, transcriptional regulation and apoptosis. To date, the dynamic of sulfenic acids in proteins remains unclear because of its fleeting nature. Identifying S-sulfenylation sites, therefore, could be the key to decipher its mysterious structures and functions, which are important in cell biology and diseases. However, due to the lack of effective methods, scientists in this field tend to be limited in merely a handful of some wet lab techniques that are time-consuming and not cost-effective. Thus, this motivated us to develop an in silico model for detecting S-sulfenylation sites only from protein sequence information. In this study, protein sequences served as natural language sentences comprising biological subwords. The deep neural network was consequentially employed to perform classification. The performance statistics within the independent dataset including sensitivity, specificity, accuracy, Matthews correlation coefficient and area under the curve rates achieved 85.71%, 69.47%, 77.09%, 0.5554 and 0.833, respectively. Our results suggested that the proposed method (fastSulf-DNN) achieved excellent performance in predicting S-sulfenylation sites compared to other well-known tools on a benchmark dataset.

DapNet-HLA: Adaptive dual-attention mechanism network based on deep learning to predict non-classical HLA binding sites.

Human leukocyte antigen (HLA) plays a vital role in immunomodulatory function. Studies have shown that immunotherapy based on non-classical HLA has essential applications in cancer, COVID-19, and allergic diseases. However, there are few deep learning methods to predict non-classical HLA alleles. In this work, an adaptive dual-attention network named DapNet-HLA is established based on existing datasets. Firstly, amino acid sequences are transformed into digital vectors by looking up the table. To overcome the feature sparsity problem caused by unique one-hot encoding, the fused word embedding method is used to map each amino acid to a low-dimensional word vector optimized with the training of the classifier. Then, we use the GCB (group convolution block), SENet attention (squeeze-and-excitation networks), BiLSTM (bidirectional long short-term memory network), and Bahdanau attention mechanism to construct the classifier. The use of SENet can make the weight of the effective feature map high, so that the model can be trained to achieve better results. Attention mechanism is an Encoder-Decoder model used to improve the effectiveness of RNN, LSTM or GRU (gated recurrent neural network). The ablation experiment shows that DapNet-HLA has the best adaptability for five datasets. On the five test datasets, the ACC index and MCC index of DapNet-HLA are 4.89% and 0.0933 higher than the comparison method, respectively. According to the ROC curve and PR curve verified by the 5-fold cross-validation, the AUC value of each fold has a slight fluctuation, which proves the robustness of the DapNet-HLA. The codes and datasets are accessible at https://github.com/JYY625/DapNet-HLA.

Deep-4mCW2V: A sequence-based predictor to identify N4-methylcytosine sites in Escherichia coli.

N4-methylcytosine (4mC) is a type of DNA modification which could regulate several biological progressions such as transcription regulation, replication and gene expressions. Precisely recognizing 4mC sites in genomic sequences can provide specific knowledge about their genetic roles. This study aimed to develop a deep learning-based model to predict 4mC sites in the Escherichia coli. In the model, DNA sequences were encoded by word embedding technique 'word2vec'. The obtained features were inputted into 1-D convolutional neural network (CNN) to discriminate 4mC sites from non-4mC sites in Escherichia coli genome. The examination on independent dataset showed that our model could yield the overall accuracy of 0.861, which was about 4.3% higher than the existing model. To provide convenience to scholars, we provided the data and source code of the model which can be freely download from https://github.com/linDing-groups/Deep-4mCW2V.

Deep transformers and convolutional neural network in identifying DNA N6-methyladenine sites in cross-species genomes.

As one of the most common post-transcriptional epigenetic modifications, N6-methyladenine (6 mA), plays an essential role in various cellular processes and disease pathogenesis. Therefore, accurately identifying 6 mA modifications is necessary for a deep understanding of cellular processes and other possible functional mechanisms. Although a few computational methods have been proposed, their respective models were developed with small training datasets. Hence, their practical application is quite limited in genome-wide detection. To overcome the existing limitations, we present a novel model based on transformer architecture and deep learning to identify DNA 6 mA sites from the cross-species genome. The model is constructed on a benchmark dataset and explored a feature derived from pre-trained transformer word embedding approaches. Subsequently, a convolutional neural network was employed to learn the generated features and generate the prediction outcomes. As a result, our predictor achieved excellent performance during independent test with the accuracy and Matthews correlation coefficient (MCC) of 79.3% and 0.58, respectively. Overall, its performance achieved better accuracy than the baseline models and significantly outperformed the existing predictors, demonstrating the effectiveness of our proposed hybrid framework. Furthermore, our model is expected to assist biologists in accurately identifying 6mAs and formulate the novel testable biological hypothesis. We also release source codes and datasets freely at https://github.com/khanhlee/bert-dna for front-end users.

Examining Rural and Urban Sentiment Difference in COVID-19-Related Topics on Twitter: Word Embedding-Based Retrospective Study.

BACKGROUND: By the end of 2022, more than 100 million people were infected with COVID-19 in the United States, and the cumulative death rate in rural areas (383.5/100,000) was much higher than in urban areas (280.1/100,000). As the pandemic spread, people used social media platforms to express their opinions and concerns about COVID-19-related topics. OBJECTIVE: This study aimed to (1) identify the primary COVID-19-related topics in the contiguous United States communicated over Twitter and (2) compare the sentiments urban and rural users expressed about these topics. METHODS: We collected tweets containing geolocation data from May 2020 to January 2022 in the contiguous United States. We relied on the tweets' geolocations to determine if their authors were in an urban or rural setting. We trained multiple word2vec models with several corpora of tweets based on geospatial and timing information. Using a word2vec model built on all tweets, we identified hashtags relevant to COVID-19 and performed hashtag clustering to obtain related topics. We then ran an inference analysis for urban and rural sentiments with respect to the topics based on the similarity between topic hashtags and opinion adjectives in the corresponding urban and rural word2vec models. Finally, we analyzed the temporal trend in sentiments using monthly word2vec models. RESULTS: We created a corpus of 407 million tweets, 350 million (86%) of which were posted by users in urban areas, while 18 million (4.4%) were posted by users in rural areas. There were 2666 hashtags related to COVID-19, which clustered into 20 topics. Rural users expressed stronger negative sentiments than urban users about COVID-19 prevention strategies and vaccination (P<.001). Moreover, there was a clear political divide in the perception of politicians by urban and rural users; these users communicated stronger negative sentiments about Republican and Democratic politicians, respectively (P<.001). Regarding misinformation and conspiracy theories, urban users exhibited stronger negative sentiments about the "covidiots" and "China virus" topics, while rural users exhibited stronger negative sentiments about the "Dr. Fauci" and "plandemic" topics. Finally, we observed that urban users' sentiments about the economy appeared to transition from negative to positive in late 2021, which was in line with the US economic recovery. CONCLUSIONS: This study demonstrates there is a statistically significant difference in the sentiments of urban and rural Twitter users regarding a wide range of COVID-19-related topics. This suggests that social media can be relied upon to monitor public sentiment during pandemics in disparate types of regions. This may assist in the geographically targeted deployment of epidemic prevention and management efforts.

Deep Artificial Neural Networks Reveal a Distributed Cortical Network Encoding Propositional Sentence-Level Meaning.

Understanding how and where in the brain sentence-level meaning is constructed from words presents a major scientific challenge. Recent advances have begun to explain brain activation elicited by sentences using vector models of word meaning derived from patterns of word co-occurrence in text corpora. These studies have helped map out semantic representation across a distributed brain network spanning temporal, parietal, and frontal cortex. However, it remains unclear whether activation patterns within regions reflect unified representations of sentence-level meaning, as opposed to superpositions of context-independent component words. This is because models have typically represented sentences as "bags-of-words" that neglect sentence-level structure. To address this issue, we interrogated fMRI activation elicited as 240 sentences were read by 14 participants (9 female, 5 male), using sentences encoded by a recurrent deep artificial neural-network trained on a sentence inference task (InferSent). Recurrent connections and nonlinear filters enable InferSent to transform sequences of word vectors into unified "propositional" sentence representations suitable for evaluating intersentence entailment relations. Using voxelwise encoding modeling, we demonstrate that InferSent predicts elements of fMRI activation that cannot be predicted by bag-of-words models and sentence models using grammatical rules to assemble word vectors. This effect occurs throughout a distributed network, which suggests that propositional sentence-level meaning is represented within and across multiple cortical regions rather than at any single site. In follow-up analyses, we place results in the context of other deep network approaches (ELMo and BERT) and estimate the degree of unpredicted neural signal using an "experiential" semantic model and cross-participant encoding.SIGNIFICANCE STATEMENT A modern-day scientific challenge is to understand how the human brain transforms word sequences into representations of sentence meaning. A recent approach, emerging from advances in functional neuroimaging, big data, and machine learning, is to computationally model meaning, and use models to predict brain activity. Such models have helped map a cortical semantic information-processing network. However, how unified sentence-level information, as opposed to word-level units, is represented throughout this network remains unclear. This is because models have typically represented sentences as unordered "bags-of-words." Using a deep artificial neural network that recurrently and nonlinearly combines word representations into unified propositional sentence representations, we provide evidence that sentence-level information is encoded throughout a cortical network, rather than in a single region.

iEnhancer-DCLA: using the original sequence to identify enhancers and their strength based on a deep learning framework.

Enhancers are small regions of DNA that bind to proteins, which enhance the transcription of genes. The enhancer may be located upstream or downstream of the gene. It is not necessarily close to the gene to be acted on, because the entanglement structure of chromatin allows the positions far apart in the sequence to have the opportunity to contact each other. Therefore, identifying enhancers and their strength is a complex and challenging task. In this article, a new prediction method based on deep learning is proposed to identify enhancers and enhancer strength, called iEnhancer-DCLA. Firstly, we use word2vec to convert k-mers into number vectors to construct an input matrix. Secondly, we use convolutional neural network and bidirectional long short-term memory network to extract sequence features, and finally use the attention mechanism to extract relatively important features. In the task of predicting enhancers and their strengths, this method has improved to a certain extent in most evaluation indexes. In summary, we believe that this method provides new ideas in the analysis of enhancers.

DeepMHADTA: Prediction of Drug-Target Binding Affinity Using Multi-Head Self-Attention and Convolutional Neural Network.

Drug-target interactions provide insight into the drug-side effects and drug repositioning. However, wet-lab biochemical experiments are time-consuming and labor-intensive, and are insufficient to meet the pressing demand for drug research and development. With the rapid advancement of deep learning, computational methods are increasingly applied to screen drug-target interactions. Many methods consider this problem as a binary classification task (binding or not), but ignore the quantitative binding affinity. In this paper, we propose a new end-to-end deep learning method called DeepMHADTA, which uses the multi-head self-attention mechanism in a deep residual network to predict drug-target binding affinity. On two benchmark datasets, our method outperformed several current state-of-the-art methods in terms of multiple performance measures, including mean square error (MSE), consistency index (CI), rm2, and PR curve area (AUPR). The results demonstrated that our method achieved better performance in predicting the drug-target binding affinity.