Prostate cancer is one of the most common and fatal diseases among men, and its early diagnosis can have a significant impact on the treatment process and prevent mortality. Since it does not have apparent clinical symptoms in the early stages, it is difficult to diagnose. In addition, the disagreement of experts in the analysis of magnetic resonance images is also a significant challenge. In recent years, various research has shown that deep learning, especially convolutional neural networks, has appeared successfully in machine vision (especially in medical image analysis). In this research, a deep learning approach was used on multi-parameter magnetic resonance images, and the synergistic effect of clinical and pathological data on the accuracy of the model was investigated. The data were collected from Trita Hospital in Tehran, which included 343 patients (data augmentation and learning transfer methods were used during the process). In the designed model, four different types of images are analyzed with four separate ResNet50 deep convolutional networks, and their extracted features are transferred to a fully connected neural network and combined with clinical and pathological features. In the model without clinical and pathological data, the maximum accuracy reached 88%, but by adding these data, the accuracy increased to 96%, which shows the significant impact of clinical and pathological data on the accuracy of diagnosis.

The measurement of chemical oxygen demand (COD) is very important in the process of sewage treatment. The value of COD reflects the effectiveness and trend of sewage treatment to a certain extent, but obtaining accurate data requires high cost and labor intensity. To1 solve this problem, this paper proposes an online soft measurement method for COD based on Convolutional Neural Network-Bidirectional Long Short-Term Memory Network-Attention Mechanism (CNN-BiLSTM-Attention) algorithm. Firstly, by analyzing the mechanism of the aerobic tank stage in the Anaerobic-Anoxic-Oxic (A2O) wastewater treatment process, the selection range of input variables was preliminarily determined, and the collected sample dataset was subjected to correlation analysis. Finally, pH, dissolved oxygen (DO), electrical conductivity (EC), and water temperature (T) were determined as input variables for soft measurement prediction of COD.Then, based on the feature extraction ability of CNN and the advantage that BiLSTM is able to capture the backward and forward dependencies in time series data, combined with the attention mechanism that can assign higher weights to the key data, a CNN-BiLSTM-Attention algorithm model was established to soft measure COD in the effluent from the aerobic zone of the A2O wastewater treatment process. At the same time, root mean square error (RMSE), mean absolute error (MAE), mean absolute percentage error (MAPE) and coefficient of determination (R2) were utilized Three indicators were used to evaluate the model, and the results showed that the model can accurately predict the value of COD and has a high accuracy. At the same time, compared with models such as CNN-LSTM-Attention, CNN-BiLSTM, CNN-LSTM, LSTM, RNN, BP, SVM, XGBoost, and RF etc., the results showed that the CNN-BiLSTM Attention model performed the best, proving the superiority of the algorithm model.The Wilcoxon signed-rank test indicates significant differences between the CNN-BiLSTM-Attention model and other models.

This study develops a \"Skill Talent Ecological Evaluation Model\" across cultivation, potential energy, kinetic energy, innovation, and service and support ecologies. AHP-entropy determines indicator weights, Hopfield neural network assesses talent ecology levels, and the PVAR model analyzes digital transformation effects. Findings reveal: Cultivation ecology rates A, potential ecology rates B+, kinetic ecology rates B-, service and support ecology rates B-, and innovation ecology rates C. Digital transformation spurs skill demand, impacting talent and economic contributions. Kinetic ecology sees increased demand, potentially impacting traditional industries positively. Innovation ecology necessitates continuous skill learning. Service and support ecology witnesses growth in digital entrepreneurship, requiring policy incentives and incubation center support.

To explore the application effect of the deep learning (DL) network model in the Internet of Things (IoT) database query and optimization. This study first analyzes the architecture of IoT database queries, then explores the DL network model, and finally optimizes the DL network model through optimization strategies. The advantages of the optimized model in this study are verified through experiments. Experimental results show that the optimized model has higher efficiency than other models in the model training and parameter optimization stages. Especially when the data volume is 2000, the model training time and parameter optimization time of the optimized model are remarkably lower than that of the traditional model. In terms of resource consumption, the Central Processing Unit and Graphics Processing Unit usage and memory usage of all models have increased as the data volume rises. However, the optimized model exhibits better performance on energy consumption. In throughput analysis, the optimized model can maintain high transaction numbers and data volumes per second when handling large data requests, especially at 4000 data volumes, and its peak time processing capacity exceeds that of other models. Regarding latency, although the latency of all models increases with data volume, the optimized model performs better in database query response time and data processing latency. The results of this study not only reveal the optimized model\'s superior performance in processing IoT database queries and their optimization but also provide a valuable reference for IoT data processing and DL model optimization. These findings help to promote the application of DL technology in the IoT field, especially in the need to deal with large-scale data and require efficient processing scenarios, and offer a vital reference for the research and practice in related fields.

In this study, we employed various machine learning models to predict metabolic phenotypes, focusing on thyroid function, using a dataset from the National Health and Nutrition Examination Survey (NHANES) from 2007 to 2012. Our analysis utilized laboratory parameters relevant to thyroid function or metabolic dysregulation in addition to demographic features, aiming to uncover potential associations between thyroid function and metabolic phenotypes by various machine learning methods. Multinomial Logistic Regression performed best to identify the relationship between thyroid function and metabolic phenotypes, achieving an area under receiver operating characteristic curve (AUROC) of 0.818, followed closely by Neural Network (AUROC: 0.814). Following the above, the performance of Random Forest, Boosted Trees, and K Nearest Neighbors was inferior to the first two methods (AUROC 0.811, 0.811, and 0.786, respectively). In Random Forest, homeostatic model assessment for insulin resistance, serum uric acid, serum albumin, gamma glutamyl transferase, and triiodothyronine/thyroxine ratio were positioned in the upper ranks of variable importance. These results highlight the potential of machine learning in understanding complex relationships in health data. However, it\'s important to note that model performance may vary depending on data characteristics and specific requirements. Furthermore, we emphasize the significance of accounting for sampling weights in complex survey data analysis and the potential benefits of incorporating additional variables to enhance model accuracy and insights. Future research can explore advanced methodologies combining machine learning, sample weights, and expanded variable sets to further advance survey data analysis.

The present research endeavors to examine the effectiveness of four gridded precipitation datasets, namely Integrated Multi-satellite Retrievals for GPM (IMERG), Tropical Precipitation Measuring Mission (TRMM), Modern-Era Retrospective Analysis for Research and Applications Version 2 (MERRA-2), and Precipitation Estimation from Remotely Sensed Information using Artificial Neural Networks (PERSIANN), with the observed rainfall data of eight rain gauge stations of India Meteorological Department (IMD) from 2001 to 2019 in Kosi River basin, India. Various statistical metrics, contingency tests, trend analysis, and rainfall anomaly index were utilized at daily, monthly, seasonal, and annual time scales. The categorical metrics namely probability of detection (POD) and false alarm ratio (FAR) indicate that MERRA-2 and IMERG datasets have the highest level of concurrence with the observed daily data. Statistical analysis of gridded datasets with observed dataset of IMD showed that the performance of the IMERG dataset is better than MERRA-2, PERSIANN, and TRMM datasets with \"very good\" coefficient of determination (R2) and Nash-Sutcliffe Efficiency values for monthly data. Trend analysis of gridded seasonal data of IMERG showed similar trends of observed seasonal data whereas other dataset differs. IMERG also performed well in identifying wet and dry years based on annual data. Discrepancies of the satellite sensor in capturing the precipitation have also been discussed. Thus, the IMERG dataset can be effectively used for hydro-meteorological and climatological investigations in cases of lack of observed datasets.

BACKGROUND: Electronic health records (EHRs) represent a comprehensive resource of a patient\'s medical history. EHRs are essential for utilizing advanced technologies such as deep learning (DL), enabling healthcare providers to analyze extensive data, extract valuable insights, and make precise and data-driven clinical decisions. DL methods such as recurrent neural networks (RNN) have been utilized to analyze EHR to model disease progression and predict diagnosis. However, these methods do not address some inherent irregularities in EHR data such as irregular time intervals between clinical visits. Furthermore, most DL models are not interpretable. In this study, we propose two interpretable DL architectures based on RNN, namely time-aware RNN (TA-RNN) and TA-RNN-autoencoder (TA-RNN-AE) to predict patient\'s clinical outcome in EHR at the next visit and multiple visits ahead, respectively. To mitigate the impact of irregular time intervals, we propose incorporating time embedding of the elapsed times between visits. For interpretability, we propose employing a dual-level attention mechanism that operates between visits and features within each visit.
RESULTS: The results of the experiments conducted on Alzheimer\'s Disease Neuroimaging Initiative (ADNI) and National Alzheimer\'s Coordinating Center (NACC) datasets indicated the superior performance of proposed models for predicting Alzheimer\'s Disease (AD) compared to state-of-the-art and baseline approaches based on F2 and sensitivity. Additionally, TA-RNN showed superior performance on the Medical Information Mart for Intensive Care (MIMIC-III) dataset for mortality prediction. In our ablation study, we observed enhanced predictive performance by incorporating time embedding and attention mechanisms. Finally, investigating attention weights helped identify influential visits and features in predictions.
METHODS: https://github.com/bozdaglab/TA-RNN.

BACKGROUND: RNA design shows growing applications in synthetic biology and therapeutics, driven by the crucial role of RNA in various biological processes. A fundamental challenge is to find functional RNA sequences that satisfy given structural constraints, known as the inverse folding problem. Computational approaches have emerged to address this problem based on secondary structures. However, designing RNA sequences directly from 3D structures is still challenging, due to the scarcity of data, the nonunique structure-sequence mapping, and the flexibility of RNA conformation.
RESULTS: In this study, we propose RiboDiffusion, a generative diffusion model for RNA inverse folding that can learn the conditional distribution of RNA sequences given 3D backbone structures. Our model consists of a graph neural network-based structure module and a Transformer-based sequence module, which iteratively transforms random sequences into desired sequences. By tuning the sampling weight, our model allows for a trade-off between sequence recovery and diversity to explore more candidates. We split test sets based on RNA clustering with different cut-offs for sequence or structure similarity. Our model outperforms baselines in sequence recovery, with an average relative improvement of 11% for sequence similarity splits and 16% for structure similarity splits. Moreover, RiboDiffusion performs consistently well across various RNA length categories and RNA types. We also apply in silico folding to validate whether the generated sequences can fold into the given 3D RNA backbones. Our method could be a powerful tool for RNA design that explores the vast sequence space and finds novel solutions to 3D structural constraints.
METHODS: The source code is available at https://github.com/ml4bio/RiboDiffusion.

BACKGROUND: Genetic perturbations (e.g. knockouts, variants) have laid the foundation for our understanding of many diseases, implicating pathogenic mechanisms and indicating therapeutic targets. However, experimental assays are fundamentally limited by the number of measurable perturbations. Computational methods can fill this gap by predicting perturbation effects under novel conditions, but accurately predicting the transcriptional responses of cells to unseen perturbations remains a significant challenge.
RESULTS: We address this by developing a novel attention-based neural network, AttentionPert, which accurately predicts gene expression under multiplexed perturbations and generalizes to unseen conditions. AttentionPert integrates global and local effects in a multi-scale model, representing both the nonuniform system-wide impact of the genetic perturbation and the localized disturbance in a network of gene-gene similarities, enhancing its ability to predict nuanced transcriptional responses to both single and multi-gene perturbations. In comprehensive experiments, AttentionPert demonstrates superior performance across multiple datasets outperforming the state-of-the-art method in predicting differential gene expressions and revealing novel gene regulations. AttentionPert marks a significant improvement over current methods, particularly in handling the diversity of gene perturbations and in predicting out-of-distribution scenarios.
METHODS: Code is available at https://github.com/BaiDing1234/AttentionPert.

CONCLUSIONS: Cis-acting mRNA elements play a key role in the regulation of mRNA stability and translation efficiency. Revealing the interactions of these elements and their impact plays a crucial role in understanding the regulation of the mRNA translation process, which supports the development of mRNA-based medicine or vaccines. Deep neural networks (DNN) can learn complex cis-regulatory codes from RNA sequences. However, extracting these cis-regulatory codes efficiently from DNN remains a significant challenge. Here, we propose a method based on our toolkit NeuronMotif and motif mutagenesis, which not only enables the discovery of diverse and high-quality motifs but also efficiently reveals motif interactions. By interpreting deep-learning models, we have discovered several crucial motifs that impact mRNA translation efficiency and stability, as well as some unknown motifs or motif syntax, offering novel insights for biologists. Furthermore, we note that it is challenging to enrich motif syntax in datasets composed of randomly generated sequences, and they may not contain sufficient biological signals.
METHODS: The source code and data used to produce the results and analyses presented in this manuscript are available from GitHub (https://github.com/WangLabTHU/combmotif).