A CNN-CBAM-BIGRU model for protein function prediction.

Understanding a protein's function based solely on its amino acid sequence is a crucial but intricate task in bioinformatics. Traditionally, this challenge has proven difficult. However, recent years have witnessed the rise of deep learning as a powerful tool, achieving significant success in protein function prediction. Their strength lies in their ability to automatically learn informative features from protein sequences, which can then be used to predict the protein's function. This study builds upon these advancements by proposing a novel model: CNN-CBAM+BiGRU. It incorporates a Convolutional Block Attention Module (CBAM) alongside BiGRUs. CBAM acts as a spotlight, guiding the CNN to focus on the most informative parts of the protein data, leading to more accurate feature extraction. BiGRUs, a type of Recurrent Neural Network (RNN), excel at capturing long-range dependencies within the protein sequence, which are essential for accurate function prediction. The proposed model integrates the strengths of both CNN-CBAM and BiGRU. This study's findings, validated through experimentation, showcase the effectiveness of this combined approach. For the human dataset, the suggested method outperforms the CNN-BIGRU+ATT model by +1.0 % for cellular components, +1.1 % for molecular functions, and +0.5 % for biological processes. For the yeast dataset, the suggested method outperforms the CNN-BIGRU+ATT model by +2.4 % for the cellular component, +1.2 % for molecular functions, and +0.6 % for biological processes.

Sharma L ，Deepak A ，Ranjan A ，Krishnasamy G ... -  《-》

Recognition of sports and daily activities through deep learning and convolutional block attention.

Portable devices like accelerometers and physiological trackers capture movement and biometric data relevant to sports. This study uses data from wearable sensors to investigate deep learning techniques for recognizing human behaviors associated with sports and fitness. The proposed CNN-BiGRU-CBAM model, a unique hybrid architecture, combines convolutional neural networks (CNNs), bidirectional gated recurrent unit networks (BiGRUs), and convolutional block attention modules (CBAMs) for accurate activity recognition. CNN layers extract spatial patterns, BiGRU captures temporal context, and CBAM focuses on informative BiGRU features, enabling precise activity pattern identification. The novelty lies in seamlessly integrating these components to learn spatial and temporal relationships, prioritizing significant features for activity detection. The model and baseline deep learning models were trained on the UCI-DSA dataset, evaluating with 5-fold cross-validation, including multi-class classification accuracy, precision, recall, and F1-score. The CNN-BiGRU-CBAM model outperformed baseline models like CNN, LSTM, BiLSTM, GRU, and BiGRU, achieving state-of-the-art results with 99.10% accuracy and F1-score across all activity classes. This breakthrough enables accurate identification of sports and everyday activities using simplified wearables and advanced deep learning techniques, facilitating athlete monitoring, technique feedback, and injury risk detection. The proposed model's design and thorough evaluation significantly advance human activity recognition for sports and fitness.

Mekruksavanich S ，Phaphan W ，Hnoohom N ，Jitpattanakul A ... -  《PeerJ Computer Science》

A novel hybrid CNN and BiGRU-Attention based deep learning model for protein function prediction.

Sharma L ，Deepak A ，Ranjan A ，Krishnasamy G ... -  《-》

Deep_CNN_LSTM_GO: Protein function prediction from amino-acid sequences.

Protein amino acid sequences can be used to determine the functions of the protein. However, determining the function of a single protein requires many resources and a tremendous amount of time. Computational Intelligence methods such as Deep learning have been shown to predict the proteins' functions. This paper proposes a hybrid deep neural network model to predict an unknown protein's functions from sequences. The proposed model is named Deep_CNN_LSTM_GO. Deep_CNN_LSTM_GO is an Integration between Convolutional Neural network (CNN) and Long Short-Term Memory (LSTM) Neural Network to learn features from amino acid sequences and outputs the three different Gene Ontology (GO). The gene ontology represents the protein functions in the three sub-ontologies: Molecular Functions (MF), Biological Process (BP), and Cellular Component (CC). The proposed model has been trained and tested using UniProt-SwissProt's dataset. Another test has been done using Computational Assessment of Function Annotation (CAFA) on the three sub-ontologies. The proposed model outperforms different methods proposed in the field with better performance using three different evaluation metrics (Fmax, Smin, and AUPR) in the three sub-ontologies (MF, BP, CC).

Elhaj-Abdou MEM ，El-Dib H ，El-Helw A ，El-Habrouk M ... -  《-》

BERT-TFBS: a novel BERT-based model for predicting transcription factor binding sites by transfer learning.

Transcription factors (TFs) are proteins essential for regulating genetic transcriptions by binding to transcription factor binding sites (TFBSs) in DNA sequences. Accurate predictions of TFBSs can contribute to the design and construction of metabolic regulatory systems based on TFs. Although various deep-learning algorithms have been developed for predicting TFBSs, the prediction performance needs to be improved. This paper proposes a bidirectional encoder representations from transformers (BERT)-based model, called BERT-TFBS, to predict TFBSs solely based on DNA sequences. The model consists of a pre-trained BERT module (DNABERT-2), a convolutional neural network (CNN) module, a convolutional block attention module (CBAM) and an output module. The BERT-TFBS model utilizes the pre-trained DNABERT-2 module to acquire the complex long-term dependencies in DNA sequences through a transfer learning approach, and applies the CNN module and the CBAM to extract high-order local features. The proposed model is trained and tested based on 165 ENCODE ChIP-seq datasets. We conducted experiments with model variants, cross-cell-line validations and comparisons with other models. The experimental results demonstrate the effectiveness and generalization capability of BERT-TFBS in predicting TFBSs, and they show that the proposed model outperforms other deep-learning models. The source code for BERT-TFBS is available at https://github.com/ZX1998-12/BERT-TFBS.

Wang K ，Zeng X ，Zhou J ，Liu F ，Luan X ，Wang X ... -  《-》