DeepDBS: Identification of DNA-binding sites in protein sequences by using deep representations and random forest.

Interactions of biological molecules in organisms are considered to be primary factors for the lifecycle of that organism. Various important biological functions are dependent on such interactions and among different kinds of interactions, the protein DNA interactions are very important for the processes of transcription, regulation of gene expression, DNA repairing and packaging. Thus, keeping the knowledge of such interactions and the sites of those interactions is necessary to study the mechanism of various biological processes. As experimental identification through biological assays is quite resource-demanding, costly and error-prone, scientists opt for the computational methods for efficient and accurate identification of such DNA-protein interaction sites. Thus, herein, we propose a novel and accurate method namely DeepDBS for the identification of DNA-binding sites in proteins, using primary amino acid sequences of proteins under study. From protein sequences, deep representations were computed through a one-dimensional convolution neural network (1D-CNN), recurrent neural network (RNN) and long short-term memory (LSTM) network and were further used to train a Random Forest classifier. Random Forest with LSTM-based features outperformed the other models, as well as the existing state-of-the-art methods with an accuracy score of 0.99 for self-consistency test, 10-fold cross-validation, 5-fold cross-validation, and jackknife validation while 0.92 for independent dataset testing. It is concluded based on results that the DeepDBS can help accurate and efficient identification of DNA binding sites (DBS) in proteins.

A systematic review on deep learning-based automated cancer diagnosis models.

Deep learning is gaining importance due to its wide range of applications. Many researchers have utilized deep learning (DL) models for the automated diagnosis of cancer patients. This paper provides a systematic review of DL models for automated diagnosis of cancer patients. Initially, various DL models for cancer diagnosis are presented. Five major categories of cancers such as breast, lung, liver, brain and cervical cancer are considered. As these categories of cancers have a very high percentage of occurrences with high mortality rate. The comparative analysis of different types of DL models is drawn for the diagnosis of cancer at early stages by considering the latest research articles from 2016 to 2022. After comprehensive comparative analysis, it is found that most of the researchers achieved appreciable accuracy with implementation of the convolutional neural network model. These utilized the pretrained models for automated diagnosis of cancer patients. Various shortcomings with the existing DL-based automated cancer diagnosis models are also been presented. Finally, future directions are discussed to facilitate further research for automated diagnosis of cancer patients.

Recurrent neural network for predicting absence of heterozygosity from low pass WGS with ultra-low depth.

BACKGROUND: The absence of heterozygosity (AOH) is a kind of genomic change characterized by a long contiguous region of homozygous alleles in a chromosome, which may cause human genetic disorders. However, no method of low-pass whole genome sequencing (LP-WGS) has been reported for the detection of AOH in a low-pass setting of less than onefold. We developed a method, termed CNVseq-AOH, for predicting the absence of heterozygosity using LP-WGS with ultra-low sequencing data, which overcomes the sparse nature of typical LP-WGS data by combing population-based haplotype information, adjustable sliding windows, and recurrent neural network (RNN). We tested the feasibility of CNVseq-AOH for the detection of AOH in 409 cases (11 AOH regions for model training and 863 AOH regions for validation) from the 1000 Genomes Project (1KGP). AOH detection using CNVseq-AOH was also performed on 6 clinical cases with previously ascertained AOHs by whole exome sequencing (WES). RESULTS: Using SNP-based microarray results as reference (AOHs detected by CNVseq-AOH with at least a 50% overlap with the AOHs detected by chromosomal microarray analysis), 409 samples (863 AOH regions) in the 1KGP were used for concordant analysis. For 784 AOHs on autosomes and 79 AOHs on the X chromosome, CNVseq-AOH can predict AOHs with a concordant rate of 96.23% and 59.49% respectively based on the analysis of 0.1-fold LP-WGS data, which is far lower than the current standard in the field. Using 0.1-fold LP-WGS data, CNVseq-AOH revealed 5 additional AOHs (larger than 10 Mb in size) in the 409 samples. We further analyzed AOHs larger than 10 Mb, which is recommended for reporting the possibility of UPD. For the 291 AOH regions larger than 10 Mb, CNVseq-AOH can predict AOHs with a concordant rate of 99.66% with only 0.1-fold LP-WGS data. In the 6 clinical cases, CNVseq-AOH revealed all 15 known AOH regions. CONCLUSIONS: Here we reported a method for analyzing LP-WGS data to accurately identify regions of AOH, which possesses great potential to improve genetic testing of AOH.

Utilizing nanotechnology and advanced machine learning for early detection of gastric cancer surgery.

Nanotechnology has emerged as a promising frontier in revolutionizing the early diagnosis and surgical management of gastric cancers. The primary factors influencing curative efficacy in GIC patients are drug inefficacy and high surgical and pharmacological therapy recurrence rates. Due to its unique optical features, good biocompatibility, surface effects, and small size effects, nanotechnology is a developing and advanced area of study for detecting and treating cancer. Considering the limitations of GIC MRI and endoscopy and the complexity of gastric surgery, the early diagnosis and prompt treatment of gastric illnesses by nanotechnology has been a promising development. Nanoparticles directly target tumor cells, allowing their detection and removal. It also can be engineered to carry specific payloads, such as drugs or contrast agents, and enhance the efficacy and precision of cancer treatment. In this research, the boosting technique of machine learning was utilized to capture nonlinear interactions between a large number of input variables and outputs by using XGBoost and RNN-CNN as a classification method. The research sample included 350 patients, comprising 200 males and 150 females. The patients' mean ± SD was 50.34 ± 13.04 with a mean age of 50.34 ± 13.04. High-risk behaviors (P = 0.070), age at diagnosis (P = 0.034), distant metastasis (P = 0.004), and tumor stage (P = 0.014) were shown to have a statistically significant link with GC patient survival. AUC was 93.54%, Accuracy 93.54%, F1-score 93.57%, Precision 93.65%, and Recall 93.87% when analyzing stomach pictures. Integrating nanotechnology with advanced machine learning techniques holds promise for improving the diagnosis and treatment of gastric cancer, providing new avenues for precision medicine and better patient outcomes.

Multi-Class Detection of Neurodegenerative Diseases from EEG Signals Using Lightweight LSTM Neural Networks.

Neurodegenerative diseases severely impact the life of millions of patients worldwide, and their occurrence is more and more increasing proportionally to longer life expectancy. Electroencephalography has become an important diagnostic tool for these diseases, due to its relatively simple procedure, but it requires analyzing a large number of data, often carrying a small fraction of informative content. For this reason, machine learning tools have gained a considerable relevance as an aid to classify potential signs of a specific disease, especially in its early stages, when treatments can be more effective. In this work, long short-term memory-based neural networks with different numbers of units were properly designed and trained after accurate data pre-processing, in order to perform a multi-class detection. To this end, a custom dataset of EEG recordings from subjects affected by five neurodegenerative diseases (Alzheimer's disease, frontotemporal dementia, dementia with Lewy bodies, progressive supranuclear palsy, and vascular dementia) was acquired. Experimental results show that an accuracy up to 98% was achieved with data belonging to different classes of disease, up to six including the control group, while not requiring particularly heavy computational resources.

Confining Pressure Forecasting of Shield Tunnel Lining Based on GRU Model and RNN Model.

The confining pressure has a great effect on the internal force of the tunnel. During construction, the confining pressure which has a crucial impact on tunnel construction changes due to the variation of groundwater level and applied load. Therefore, the safety of tunnels must have the magnitude of confining pressure accurately estimated. In this study, a complete tunnel confining pressure time axis was obtained through high-frequency field monitoring, the data are segmented into a training set and a testing set. Using GRU and RNN models, a confining pressure prediction model was established, and the prediction results were analyzed. The results indicate that the GRU model has a fast-training speed and higher accuracy. On the other hand, the training speed of the RNN model is slow, with lower accuracy. The dynamic characteristics of soil pressure during tunnel construction require accurate prediction models to maintain the safety of the tunnel. The comparison between GRU and RNN models not only highlights the advantages of the GRU model but also emphasizes the necessity of balancing speed accuracy in tunnel construction confining pressure prediction modeling. This study is helpful in improving the understanding of soil pressure dynamics and developing effective prediction tools to promote safer and more reliable tunnel construction practices.

An Enhanced Transportation System for People of Determination.

Visually Impaired Persons (VIPs) have difficulty in recognizing vehicles used for navigation. Additionally, they may not be able to identify the bus to their desired destination. However, the bus bay in which the designated bus stops has not been analyzed in the existing literature. Thus, a guidance system for VIPs that identifies the correct bus for transportation is presented in this paper. Initially, speech data indicating the VIP's destination are pre-processed and converted to text. Next, utilizing the Arctan Gradient-activated Recurrent Neural Network (ArcGRNN) model, the number of bays at the location is detected with the help of a Global Positioning System (GPS), input text, and bay location details. Then, the optimal bay is chosen from the detected bays by utilizing the Experienced Perturbed Bacteria Foraging Triangular Optimization Algorithm (EPBFTOA), and an image of the selected bay is captured and pre-processed. Next, the bus is identified utilizing a You Only Look Once (YOLO) series model. Utilizing the Sub-pixel Shuffling Convoluted Encoder-ArcGRNN Decoder (SSCEAD) framework, the text is detected and segmented for the buses identified in the image. From the segmented output, the text is extracted, based on the destination and route of the bus. Finally, regarding the similarity value with respect to the VIP's destination, a decision is made utilizing the Multi-characteristic Non-linear S-Curve-Fuzzy Rule (MNC-FR). This decision informs the bus conductor about the VIP, such that the bus can be stopped appropriately to pick them up. During testing, the proposed system selected the optimal bay in 247,891 ms, which led to deciding the bus stop for the VIP with a fuzzification time of 34,197 ms. Thus, the proposed model exhibits superior performance over those utilized in prevailing works.

Attention-Based Variational Autoencoder Models for Human-Human Interaction Recognition via Generation.

The remarkable human ability to predict others' intent during physical interactions develops at a very early age and is crucial for development. Intent prediction, defined as the simultaneous recognition and generation of human-human interactions, has many applications such as in assistive robotics, human-robot interaction, video and robotic surveillance, and autonomous driving. However, models for solving the problem are scarce. This paper proposes two attention-based agent models to predict the intent of interacting 3D skeletons by sampling them via a sequence of glimpses. The novelty of these agent models is that they are inherently multimodal, consisting of perceptual and proprioceptive pathways. The action (attention) is driven by the agent's generation error, and not by reinforcement. At each sampling instant, the agent completes the partially observed skeletal motion and infers the interaction class. It learns where and what to sample by minimizing the generation and classification errors. Extensive evaluation of our models is carried out on benchmark datasets and in comparison to a state-of-the-art model for intent prediction, which reveals that classification and generation accuracies of one of the proposed models are comparable to those of the state of the art even though our model contains fewer trainable parameters. The insights gained from our model designs can inform the development of efficient agents, the future of artificial intelligence (AI).

Progress on deep learning in genomics.

With the rapid growth of data driven by high-throughput sequencing technologies, genomics has entered an era characterized by big data, which presents significant challenges for traditional bioinformatics methods in handling complex data patterns. At this critical juncture of technological progress, deep learning-an advanced artificial intelligence technology-offers powerful capabilities for data analysis and pattern recognition, revitalizing genomic research. In this review, we focus on four major deep learning models: Convolutional Neural Network(CNN), Recurrent Neural Network(RNN), Long Short-Term Memory(LSTM), and Generative Adversarial Network(GAN). We outline their core principles and provide a comprehensive review of their applications in DNA, RNA, and protein research over the past five years. Additionally, we also explore the use of deep learning in livestock genomics, highlighting its potential benefits and challenges in genetic trait analysis, disease prevention, and genetic enhancement. By delivering a thorough analysis, we aim to enhance precision and efficiency in genomic research through deep learning and offer a framework for developing and applying livestock genomic strategies, thereby advancing precision livestock farming and genetic breeding technologies.

A novel artificial intelligence approach to detect the breast cancer using KNNet technique with EPM gene profiling.

Women's most frequent type of cancer is breast cancer, second only to lung cancer. This paper summarizes changes in genomics and epigenetics and incremental biological activities. A tumour develops through a series of phases involving a separate abnormal gene. Even though many diseases cause DNA mutations, most treatments are designed to relieve symptoms rather than change the DNA. Clustering short palindromic repeats (CRISPR) or Cas9 is the primary approach for discovering and confirming tumorigenic genomic targets. A Kohonen neural network with an expression programming model was developed for gene selection. The main problem in genetic selection is reducing the number of features chosen while maintaining accuracy. This purpose is accomplished systematically. In the end, the approach method performed better than the existing quantum squirrel-inspired algorithm and the recurrent neural network oppositional call search algorithm for genetic selection. The KNNet-EPM model used an expression programming approach to identify gene biomarkers for breast cancer. This method was achieved with RAE of 42%, sensitivity of 93%, f1 score of 88%, accuracy of 98%, kappa score of 83%, specificity of 92% and MAE of 30%.

Combined CNN and RNN Neural Networks for GPR Detection of Railway Subgrade Diseases.

Vehicle-mounted ground-penetrating radar (GPR) has been used to non-destructively inspect and evaluate railway subgrade conditions. However, existing GPR data processing and interpretation methods mostly rely on time-consuming manual interpretation, and limited studies have applied machine learning methods. GPR data are complex, high-dimensional, and redundant, in particular with non-negligible noises, for which traditional machine learning methods are not effective when applied to GPR data processing and interpretation. To solve this problem, deep learning is more suitable to process large amounts of training data, as well as to perform better data interpretation. In this study, we proposed a novel deep learning method to process GPR data, the CRNN network, which combines convolutional neural networks (CNN) and recurrent neural networks (RNN). The CNN processes raw GPR waveform data from signal channels, and the RNN processes features from multiple channels. The results show that the CRNN network achieves a higher precision at 83.4%, with a recall of 77.3%. Compared to the traditional machine learning method, the CRNN is 5.2 times faster and has a smaller size of 2.6 MB (traditional machine learning method: 104.0 MB). Our research output has demonstrated that the developed deep learning method improves the efficiency and accuracy of railway subgrade condition evaluation.

Optimization of Deep Learning Parameters for Magneto-Impedance Sensor in Metal Detection and Classification.

Deep learning technology is generally applied to analyze periodic data, such as the data of electromyography (EMG) and acoustic signals. Conversely, its accuracy is compromised when applied to the anomalous and irregular nature of the data obtained using a magneto-impedance (MI) sensor. Thus, we propose and analyze a deep learning model based on recurrent neural networks (RNNs) optimized for the MI sensor, such that it can detect and classify data that are relatively irregular and diverse compared to the EMG and acoustic signals. Our proposed method combines the long short-term memory (LSTM) and gated recurrent unit (GRU) models to detect and classify metal objects from signals acquired by an MI sensor. First, we configured various layers used in RNN with a basic model structure and tested the performance of each layer type. In addition, we succeeded in increasing the accuracy by processing the sequence length of the input data and performing additional work in the prediction process. An MI sensor acquires data in a non-contact mode; therefore, the proposed deep learning approach can be applied to drone control, electronic maps, geomagnetic measurement, autonomous driving, and foreign object detection.

Fixed-Time Recurrent NN Learning Control of Uncertain Robotic Manipulators with Time-Varying Constraints: Experimental Verification.

This paper proposes a learning control framework for the robotic manipulator's dynamic tracking task demanding fixed-time convergence and constrained output. In contrast with model-dependent methods, the proposed solution deals with unknown manipulator dynamics and external disturbances by virtue of a recurrent neural network (RNN)-based online approximator. First, a time-varying tangent-type barrier Lyapunov function (BLF) is introduced to construct a fixed-time virtual controller. Then, the RNN approximator is embedded in the closed-loop system to compensate for the lumped unknown term in the feedforward loop. Finally, we devise a novel fixed-time, output-constrained neural learning controller by integrating the BLF and RNN approximator into the main framework of the dynamic surface control (DSC). The proposed scheme not only guarantees the tracking errors converge to the small neighborhoods about the origin in a fixed time, but also preserves the actual trajectories always within the prescribed ranges and thus improves the tracking accuracy. Experiment results illustrate the excellent tracking performance and verify the effectiveness of the online RNN estimate for unknown dynamics and external disturbances.

Cardiac Magnetic Resonance Image Segmentation Method Based on Multi-Scale Feature Fusion and Sequence Relationship Learning.

Accurate segmentation of the left atrial structure using magnetic resonance images provides an important basis for the diagnosis of atrial fibrillation (AF) and its treatment using robotic surgery. In this study, an image segmentation method based on sequence relationship learning and multi-scale feature fusion is proposed for 3D to 2D sequence conversion in cardiac magnetic resonance images and the varying scales of left atrial structures within different slices. Firstly, a convolutional neural network layer with an attention module was designed to extract and fuse contextual information at different scales in the image, to strengthen the target features using the correlation between features in different regions within the image, and to improve the network's ability to distinguish the left atrial structure. Secondly, a recurrent neural network layer oriented to two-dimensional images was designed to capture the correlation of left atrial structures in adjacent slices by simulating the continuous relationship between sequential image slices. Finally, a combined loss function was constructed to reduce the effect of positive and negative sample imbalance and improve model stability. The Dice, IoU, and Hausdorff distance values reached 90.73%, 89.37%, and 4.803 mm, respectively, based on the LASC2013 (left atrial segmentation challenge in 2013) dataset; the corresponding values reached 92.05%, 89.41% and 9.056 mm, respectively, based on the ASC2018 (atrial segmentation challenge at 2018) dataset.

Crowd-Aware Mobile Robot Navigation Based on Improved Decentralized Structured RNN via Deep Reinforcement Learning.

Efficient navigation in a socially compliant manner is an important and challenging task for robots working in dynamic dense crowd environments. With the development of artificial intelligence, deep reinforcement learning techniques have been widely used in the robot navigation. Previous model-free reinforcement learning methods only considered the interactions between robot and humans, not the interactions between humans and humans. To improve this, we propose a decentralized structured RNN network with coarse-grained local maps (LM-SRNN). It is capable of modeling not only Robot-Human interactions through spatio-temporal graphs, but also Human-Human interactions through coarse-grained local maps. Our model captures current crowd interactions and also records past interactions, which enables robots to plan safer paths. Experimental results show that our model is able to navigate efficiently in dense crowd environments, outperforming state-of-the-art methods.

Development of a Soil Moisture Prediction Model Based on Recurrent Neural Network Long Short-Term Memory (RNN-LSTM) in Soybean Cultivation.

Due to climate change, soil moisture may increase, and outflows could become more frequent, which will have a considerable impact on crop growth. Crops are affected by soil moisture; thus, soil moisture prediction is necessary for irrigating at an appropriate time according to weather changes. Therefore, the aim of this study is to develop a future soil moisture (SM) prediction model to determine whether to conduct irrigation according to changes in soil moisture due to weather conditions. Sensors were used to measure soil moisture and soil temperature at a depth of 10 cm, 20 cm, and 30 cm from the topsoil. The combination of optimal variables was investigated using soil moisture and soil temperature at depths between 10 cm and 30 cm and weather data as input variables. The recurrent neural network long short-term memory (RNN-LSTM) models for predicting SM was developed using time series data. The loss and the coefficient of determination (R2) values were used as indicators for evaluating the model performance and two verification datasets were used to test various conditions. The best model performance for 10 cm depth was an R2 of 0.999, a loss of 0.022, and a validation loss of 0.105, and the best results for 20 cm and 30 cm depths were an R2 of 0.999, a loss of 0.016, and a validation loss of 0.098 and an R2 of 0.956, a loss of 0.057, and a validation loss of 2.883, respectively. The RNN-LSTM model was used to confirm the SM predictability in soybean arable land and could be applied to supply the appropriate moisture needed for crop growth. The results of this study show that a soil moisture prediction model based on time-series weather data can help determine the appropriate amount of irrigation required for crop cultivation.

In-City Rain Mapping from Commercial Microwave Links-Challenges and Opportunities.

Obtaining accurate rainfall measurements is highly important in urban areas, having a significant impact on different aspects in city life. Opportunistic rainfall sensing utilizing measurements collected by existing microwave and mmWave-based wireless networks has been researched in the last two decades and can be considered as an opportunistic integrated sensing and communication (ISAC) approach. In this paper, we compare two methods that utilize received signal level (RSL) measurements obtained by an existing smart-city wireless network deployed in the city of Rehovot, Israel, for rain estimation. The first method is a model-based approach using the RSL measurements from short links, in which two design parameters are calibrated empirically. This method is combined with a known wet/dry classification method, which is based on the rolling standard deviation of the RSL. The second method is a data-driven approach, based on a recurrent neural network (RNN), which is trained to estimate rainfall and classify wet/dry periods. We compare the results of rainfall classification and estimation from both methods and show that the data-driven approach slightly outperforms the empirical model and that the improvement is most significant for light rainfall events. Furthermore, we apply both methods to construct high-resolution 2D maps of accumulated rainfall in the city of Rehovot. The ground-level rainfall maps constructed over the city area are compared for the first time with weather radar rainfall maps obtained from the Israeli Meteorological Service (IMS). The rain maps generated by the smart-city network are found to be in agreement with the average rainfall depth obtained from the radar, demonstrating the potential of using existing smart-city networks as a source for constructing 2D high-resolution rainfall maps.

Atmospheric Turbulence Degraded Video Restoration with Recurrent GAN (ATVR-GAN).

Atmospheric turbulence (AT) can change the path and direction of light during video capturing of a target in space due to the random motion of the turbulent medium, a phenomenon that is most noticeable when shooting videos at long ranges, resulting in severe video dynamic distortion and blur. To mitigate geometric distortion and reduce spatially and temporally varying blur, we propose a novel Atmospheric Turbulence Video Restoration Generative Adversarial Network (ATVR-GAN) with a specialized Recurrent Neural Network (RNN) generator, which is trained to predict the scene's turbulent optical flow (OF) field and utilizes a recurrent structure to catch both spatial and temporal dependencies. The new architecture is trained using a newly combined loss function that counts for the spatiotemporal distortions, specifically tailored to the AT problem. Our network was tested on synthetic and real imaging data and compared against leading algorithms in the field of AT mitigation and image restoration. The proposed method outperformed these methods for both synthetic and real data examined.

Network Security Situation Prediction Based on Optimized Clock-Cycle Recurrent Neural Network for Sensor-Enabled Networks.

We propose an optimized Clockwork Recurrent Neural Network (CW-RNN) based approach to address temporal dynamics and nonlinearity in network security situations, improving prediction accuracy and real-time performance. By leveraging the clock-cycle RNN, we enable the model to capture both short-term and long-term temporal features of network security situations. Additionally, we utilize the Grey Wolf Optimization (GWO) algorithm to optimize the hyperparameters of the network, thus constructing an enhanced network security situation prediction model. The introduction of a clock-cycle for hidden units allows the model to learn short-term information from high-frequency update modules while retaining long-term memory from low-frequency update modules, thereby enhancing the model's ability to capture data patterns. Experimental results demonstrate that the optimized clock-cycle RNN outperforms other network models in extracting the temporal and nonlinear features of network security situations, leading to improved prediction accuracy. Furthermore, our approach has low time complexity and excellent real-time performance, ideal for monitoring large-scale network traffic in sensor networks.

Employing Deep-Learning Approach for the Early Detection of Mild Cognitive Impairment Transitions through the Analysis of Digital Biomarkers.

Mild cognitive impairment (MCI) is the precursor to the advanced stage of Alzheimer's disease (AD), and it is important to detect the transition to the MCI condition as early as possible. Trends in daily routines/activities provide a measurement of cognitive/functional status, particularly in older adults. In this study, activity data from longitudinal monitoring through in-home ambient sensors are leveraged in predicting the transition to the MCI stage at a future time point. The activity dataset from the Oregon Center for Aging and Technology (ORCATECH) includes measures representing various domains such as walk, sleep, etc. Each sensor-captured activity measure is constructed as a time series, and a variety of summary statistics is computed. The similarity between one individual's activity time series and that of the remaining individuals is also computed as distance measures. The long short-term memory (LSTM) recurrent neural network is trained with time series statistics and distance measures for the prediction modeling, and performance is evaluated by classification accuracy. The model outcomes are explained using the SHapley Additive exPlanations (SHAP) framework. LSTM model trained using the time series statistics and distance measures outperforms other modeling scenarios, including baseline classifiers, with an overall prediction accuracy of 83.84%. SHAP values reveal that sleep-related features contribute the most to the prediction of the cognitive stage at the future time point, and this aligns with the findings in the literature. Findings from this study not only demonstrate that a practical, less expensive, longitudinal monitoring of older adults' activity routines can benefit immensely in modeling AD progression but also unveil the most contributing features that are medically applicable and meaningful.