As post-transcriptional regulators of gene expression, micro-ribonucleic acids (miRNAs) are regarded as potential biomarkers for a variety of diseases. Hence, the prediction of miRNA-disease associations (MDAs) is of great significance for an in-depth understanding of disease pathogenesis and progression. Existing prediction models are mainly concentrated on incorporating different sources of biological information to perform the MDA prediction task while failing to consider the fully potential utility of MDA network information at the motif-level. To overcome this problem, we propose a novel motif-aware MDA prediction model, namely MotifMDA, by fusing a variety of high- and low-order structural information. In particular, we first design several motifs of interest considering their ability to characterize how miRNAs are associated with diseases through different network structural patterns. Then, MotifMDA adopts a two-layer hierarchical attention to identify novel MDAs. Specifically, the first attention layer learns high-order motif preferences based on their occurrences in the given MDA network, while the second one learns the final embeddings of miRNAs and diseases through coupling high- and low-order preferences. Experimental results on two benchmark datasets have demonstrated the superior performance of MotifMDA over several state-of-the-art prediction models. This strongly indicates that accurate MDA prediction can be achieved by relying solely on MDA network information. Furthermore, our case studies indicate that the incorporation of motif-level structure information allows MotifMDA to discover novel MDAs from different perspectives. The data and codes are available at https://github.com/stevejobws/MotifMDA.

Motif-Aware miRNA-Disease Association Prediction Via Hierarchical Attention Network.

Abstract Herbs applicability in disease treatment has been verified through experiences over thousands of years. The understanding of herb–disease associations (HDAs) is yet far from complete due to the complicated mechanism inherent in multi-target and multi-component (MTMC) botanical therapeutics. Most of the existing prediction models fail to incorporate the MTMC mechanism. To overcome this problem, we propose a novel dual-channel hypergraph convolutional network, namely HGHDA, for HDA prediction. Technically, HGHDA first adopts an autoencoder to project components and target protein onto a low-dimensional latent space so as to obtain their embeddings by preserving similarity characteristics in their original feature spaces. To model the high-order relations between herbs and their components, we design a channel in HGHDA to encode a hypergraph that describes the high-order patterns of herb-component relations via hypergraph convolution. The other channel in HGHDA is also established in the same way to model the high-order relations between diseases and target proteins. The embeddings of drugs and diseases are then aggregated through our dual-channel network to obtain the prediction results with a scoring function. To evaluate the performance of HGHDA, a series of extensive experiments have been conducted on two benchmark datasets, and the results demonstrate the superiority of HGHDA over the state-of-the-art algorithms proposed for HDA prediction. Besides, our case study on Chuan Xiong and Astragalus membranaceus is a strong indicator to verify the effectiveness of HGHDA, as seven and eight out of the top 10 diseases predicted by HGHDA for Chuan-Xiong and Astragalus-membranaceus, respectively, have been reported in literature.

Dual-channel hypergraph convolutional network for predicting herb–disease associations

The pharmaceutical industry is continually striving to innovate drug development and formulation processes. Orally disintegrating tablets (ODTs) have gained popularity due to their quick release and patient-friendly characteristics. The choice of excipients in tablet formulations plays a critical role in ensuring product quality, highlighting its importance in tablet creation. The traditional trial-and-error approach to this process is both expensive and time-intensive. To tackle these obstacles, we introduce a fresh approach leveraging machine learning and deep learning methods to automate and enhance pre-formulation drug design.We collected a comprehensive dataset of 1983 formulations, including excipient names, quantities, active ingredient details, and various physicochemical attributes. Our study focused on predicting two critical control test parameters: tablet disintegration time and hardness. We compared a range of models like deep learning, artificial neural networks, support vector machines, decision trees, multiple linear regression, and random forests.A 12-layer deep neural network, as a form of deep learning, surpassed alternative techniques by achieving 73% accuracy for disintegration time and 99% for tablet hardness. This success underscores its efficacy in predicting complex pharmaceutical factors. Such an approach streamlines the drug formulation process, reducing iterations and material consumption.Our findings highlight the deep learning potential in pharmaceutical formulations, particularly for tablet hardness prediction. Future work should focus on enlarging the dataset to improve model effectiveness and extend its application in pharmaceutical product development and assessment. 

A prediction model based on artificial intelligence techniques for disintegration time and hardness of fast disintegrating tablets in pre-formulation tests

Large scale interaction data are frequently found in industrial applications related with Big Data. Due to the fact that few interactions commonly happen among numerous nodes in real scenes, such data can be quantified into a High-Dimensional and Incomplete (HDI) matrix where most entries are unknown. An alternating-direction-method-based nonnegative latent factor model can perform efficient and accurate representation leaning to an HDI matrix, while its multiple hyper-parameters greatly limit its scalability for real applications. Aiming at implementing a highly-scalable and efficient latent factor model, this paper adopts the principle of particle swarm optimization and the tree-structured parzen estimator algorithm to facilitate the hyper-parameter adaptation mechanism, thereby building an Alternating-direction-method-based Adaptive Nonnegative Latent Factor (A2NLF) model. Its theoretical convergence is rigorously proved. Empirical studies on several nonnegative HDI matrices from real applications demonstrate that the proposed A2NLF model obtains higher computational and storage efficiency than several state-of-the-art models, along with significant accuracy gain. Its hyper-parameter adaptation is implemented smoothly, thereby greatly boosting its scalability in real problems.

Alternating-Direction-Method of Multipliers-Based Adaptive Nonnegative Latent Factor Analysis

Fetal cardiac ultrasound is a valuable tool for screening fetal cardiac health during pregnancy. Ultrasound standard section testing is an essential part of fetal heart ultrasound diagnosis. Due to the many scattered and partially similar anatomical structures in standard ultrasound views of the fetal heart, the results strongly depend on the clinical experience and knowledge of the sonographer. To improve detection efficiency and reduce misdiagnosis and omission, we propose a single-stage fetal cardiac ultrasound standard plane detection model (FCUM) based on multitask learning and a hybrid attention mechanism to assist sonographers in diagnosis. The feature fusion pyramids of the backbone and detection networks of this model are each embedded with a hybrid attention mechanism module of our design, which enables the multitasking network to extract shared features more accurately and efficiently and improves the accuracy of the detection and classification networks. We designed a classification module for multilayer residual network feature fusion that leads to better classification and faster convergence time. We conducted comprehensive experiments on a dataset of fetal cardiac ultrasound images acquired with several types of devices and in different geographic regions. The experimental results show that our model outperforms baseline models such as YOLOv8 and ResNet-50 in terms of detection precision and classification accuracy. 

Fetal cardiac ultrasound standard section detection model based on multitask learning and mixed attention mechanism

As a pivotal post-transcriptional modification of RNA, N6-methyladenosine (m6A) has a substantial influence on gene expression modulation and cellular fate determination. Although a variety of computational models have been developed to accurately identify potential m6A modification sites, few of them are capable of interpreting the identification process with insights gained from consensus knowledge. To overcome this problem, we propose a deep learning model, namely M6A-DCR, by discovering consensus regions for interpretable identification of m6A modification sites. In particular, M6A-DCR first constructs an instance graph for each RNA sequence by integrating specific positions and types of nucleotides. The discovery of consensus regions is then formulated as a graph clustering problem in light of aggregating all instance graphs. After that, M6A-DCR adopts a motif-aware graph reconstruction optimization process to learn high-quality embeddings of input RNA sequences, thus achieving the identification of m6A modification sites in an end-to-end manner. Experimental results demonstrate the superior performance of M6A-DCR by comparing it with several state-of-the-art identification models. The consideration of consensus regions empowers our model to make interpretable predictions at the motif level. The analysis of cross validation through different species and tissues further verifies the consistency between the identification results of M6A-DCR and the evolutionary relationships among species.

Discovering consensus regions for interpretable identification of RNA N6-methyladenosine modification sites via graph contrastive clustering.

The abundance of artificial intelligence AI algorithms and growing computing power has brought a disruptive revolution to the smart medical industry. Its powerful data abstraction and representation capabilities enable the modeling of hundreds of millions of medical data, such as sub-Computed Tomography tumor identification, retinal lesion screening, and survival curve analysis. However, all of these applications demonstrate AI’s use of unimodal data for specific tasks. In contrast, clinicians deal with multi-modal data from multiple sources when diagnosing, performing prognostic assessments, and deciding on treatment plans. These requirements have facilitated the development of multi-modal AI solutions and improved the performance of AI models in handling complex medical scenarios and data. In this paper, we provide an overview of the current state of the art and research in multi-modal biomedical AI, including applications, data, methods, and analytics. Additionally, we summarize potential research directions for multi-modal AI technologies in the future of healthcare. 

Artificial intelligence accelerates multi-modal biomedical process: A Survey

Abstract Background The site information of substrates that can be cleaved by human immunodeficiency virus 1 proteases (HIV-1 PRs) is of great significance for designing effective inhibitors against HIV-1 viruses. A variety of machine learning-based algorithms have been developed to predict HIV-1 PR cleavage sites by extracting relevant features from substrate sequences. However, only relying on the sequence information is not sufficient to ensure a promising performance due to the uncertainty in the way of separating the datasets used for training and testing. Moreover, the existence of noisy data, i.e., false positive and false negative cleavage sites, could negatively influence the accuracy performance. Results In this work, an ensemble learning algorithm for predicting HIV-1 PR cleavage sites, namely EM-HIV, is proposed by training a set of weak learners, i.e., biased support vector machine classifiers, with the asymmetric bagging strategy. By doing so, the impact of data imbalance and noisy data can thus be alleviated. Besides, in order to make full use of substrate sequences, the features used by EM-HIV are collected from three different coding schemes, including amino acid identities, chemical properties and variable-length coevolutionary patterns, for the purpose of constructing more relevant feature vectors of octamers. Experiment results on three independent benchmark datasets demonstrate that EM-HIV outperforms state-of-the-art prediction algorithm in terms of several evaluation metrics. Hence, EM-HIV can be regarded as a useful tool to accurately predict HIV-1 PR cleavage sites. 

https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04999-y

Effectively predicting HIV-1 protease cleavage sites by using an ensemble learning approach

The utilization of web social media for depression detection has been proven effective in recent years since the multimedia signal on web can reflect users’ emotions, feelings, and personality traits in advance. However, most earlier studies simply used users’ submitted words or user profiles to predict depression risk. The implicit information accessible in users’ posted images, which can be effective in depression detection, still remains unexplored. In this paper, an implicit and explicit multi-modal feature fusion (IEMFF) model is proposed for depression detection. We successfully make the implicit information inherent in users’ posted images explicit and further incorporate such explicit features with the textual features directly extracted from user-posted texts. A multi-modal feature fusion approach is applied for depression detection. Extensive experiments have been conducted on public Twitter datasets. Experimental results show that our approach has achieved state-of-the-art performance for depression detection.

Making the Implicit Explicit: Depression Detection in Web across Posted Texts and Images

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Discovering consensus regions for interpretable identification of RNA N6-methyladenosine modification sites via graph contrastive clustering.

Artificial intelligence accelerates multi-modal biomedical process: A Survey

Effectively predicting HIV-1 protease cleavage sites by using an ensemble learning approach

Making the Implicit Explicit: Depression Detection in Web across Posted Texts and Images