MOTIVATION: Computational prediction of drug-target affinity (DTA) plays a critical role in modern drug discovery. However, the limited interpretability of traditional deep learning models and the heterogeneity of multimodal data from compounds and proteins hinder their reliability in practical drug development applications. RESULTS: We propose a novel Uncertainty-aware Multimodal Representation Learning (UAMRL) framework to address these challenges. UAMRL employs a dual-stream encoder to learn cross-modal association mappings between drugs and targets in a latent space and integrates heterogeneous information from different modalities. Moreover, an uncertainty quantification mechanism based on the Normal-Inverse-Gamma distribution is introduced to model the reliability of heterogeneous information and suppress less trustworthy contributions during fusion. Experiments show that UAMRL achieves superior predictive accuracy on multiple public DTA datasets, improving both prediction performance and decision transparency. AVAILABILITY AND IMPLEMENTATION: The source code is available at https://github.com/Astraea2xu/UAMRL.

Predicting the metabolic pathway classes of compounds in the human body is an important problem in drug research and development. For this purpose, we propose a Multi-Scale Graph Neural Network framework, named MSGNN. The framework includes a subgraph encoder, a feature encoder and a global feature processor, and a graph augmentation strategy is adopted. The subgraph encoder is responsible for extracting the local structural features of the compound, the feature encoder learns the characteristics of the atoms, and the global feature processor processes the information from the pre-training model and the two molecular fingerprints, while the graph augmentation strategy is to expand the train set through a scientific and reasonable method. The experiment result illustrates that the accuracy, precision, recall and F1 metrics of MSGNN reach 98.17%, 94.18%, 94.43% and 94.30%, respectively, which is superior to the similar models we have known. In addition, the ablation experiment demonstrates the indispensability of MSGNN modules.

Multi-view clustering research is a hot topic in the field of data mining, where complementary information between views can better describe data objects and improve the clustering performance. Non-negative matrix factorization (NMF) based multi-view clustering algorithm suffers from weak feature extraction, slow convergence speed and low accuracy. To solve these problems, this paper proposes a generalized deep learning multi-view clustering (GDLMC) algorithm based on NMF. Firstly, via decoupling the elements in the matrix, the matrix elements are non-negatively restricted using an activation function with a non-negative value domain, and the elements are updated employing stochastic gradient descent with learning rate guidance. Then, the corresponding gradients when the elements update are transformed into generalized weights and generalized biases, followed by combining the generalized weights and generalized biases with activation functions to construct generalized deep learning (GDL). Further, GDL is adopted to learn the corresponding low-dimensional matrix of each view and consensus matrix for obtaining the GDLMC algorithm. In addition, the detailed reasoning of the GDLMC algorithm are given. Finally, extensive experiments are conducted on four public datasets including regular and large-scale datasets, and the experimental results show that GDLMC has significant advantages.

The main goal of most information quality (IQ)-based measures is to combine data provided by multiple information sources to enhance the quality of information essential for decision makers to perform their tasks. However, there is few work to fuse multisource information from the perspective of possibility distribution (PD) and use IQ as the evaluation criteria for feature selection. The PD is one of important concepts in the possibility theory, which is a generally acknowledged method for describing a kind of uncertain knowledge. In this article, we propose a novel representation model of PDs based on FMs, namely, a possibility distribution information system (PDIS). Then, several IQ measures are defined in the PDIS, including Gini entropy, compatibility, conflict, credibility, and separability degrees. In view of this, a minimal-separability-minimal-uncertainty-based unsupervised feature selection algorithm (UmSMU) is designed. The proposed UmSMU can sufficiently fuse multiple possibilistic information. Meanwhile, the selected features maintain as much information as possible while minimizing the uncertainty of information. The experimental results show that the proposed algorithm performs well, especially when it comes to selecting fewer features and improving performance.

Clustering is a popular research topic in the field of data mining, in which the clustering method based on non-negative matrix factorization (NMF) has been widely employed. However, in the update process of NMF, there is no learning rate to guide the update as well as the update depends on the data itself, which leads to slow convergence and low clustering accuracy. To solve these problems, a generalized deep learning clustering (GDLC) algorithm based on NMF is proposed in this article. Firstly, a nonlinear constrained NMF (NNMF) algorithm is constructed to achieve sequential updates of the elements in the matrix guided by the learning rate. Then, the gradient values corresponding to the element update are transformed into generalized weights and generalized biases, by inputting the elements as well as their corresponding generalized weights and generalized biases into the nonlinear activation function to construct the GDLC algorithm. In addition, for improving the understanding of the GDLC algorithm, its detailed inference procedure and algorithm design are provided. Finally, the experimental results on eight datasets show that the GDLC algorithm has efficient performance.