MOTIVATION: The goal of molecular representation learning is to automate the extraction of molecular features, a critical task in cheminformatics and drug discovery. While pretraining models using multiple views like SMILES, 2D graphs, and 3D conformations have advanced the field, integrating them effectively to produce superior representations remains a challenge. RESULTS: To bridge this gap, we propose a novel multi-view molecular pretraining method termed MMPCS, which explicitly factorizes representations into consistency and specific information. Our approach utilizes the Graph Isomorphism Network and the RoBERTa model to encode 2D molecular topological graphs and SMILES sequences, respectively. Each resulting molecular embedding is decomposed into a shared consistency component and a view-specific remainder. An autoencoder then aligns the consistency information across views. The combined consistency and view-specific representations serve as input for downstream tasks, enabling precise and task-aware predictions. When benchmarked against 16 state-of-the-art molecular pretraining methods, MMPCS achieved the highest average performance across both classification and regression tasks for molecular property prediction. It also delivered outstanding results in predicting drug-target binding affinity and cancer drug response, demonstrating its robustness and broad applicability. Additionally, a case study on the SARS-CoV-2 Omicron variant highlights the potential of MMPCS in facilitating drug repurposing efforts. AVAILABILITY AND IMPLEMENTATION: The source code and datasets supporting this study are publicly available at GitHub (https://github.com/xmubiocode/MMPCS) and Zenodo (https://doi.org/10.5281/zenodo.18182748).

Drug-target binding affinity (DTA) is a critical criterion for drug screening. Accurate affinity prediction will significantly cut the cost of new drug development and accelerate the drug discovery process. However, most existing approaches frequently utilize sequence or structure information without incorporating any additional information. At the same time, they encode drugs and targets separately, ignoring the important existing drug-target relationships. In this study, we propose a novel DTA prediction approach, named HSGCL-DTA, which is based on hybrid-scale graph contrastive learning. To completely capture the global information and discriminative properties of the heterogeneous graphs, HSGCL-DTA divides the drug-target affinity graph into two subgraphs with stronger and weaker affinities respectively, and the node embeddings of the two subgraphs are obtained based on node-graph level contrastive learning. Afterwards, graph convolutional network (GCN) is used to encode the molecular graph of drugs and targets, and the node embeddings in the strong affinity subgraph are fused with molecule graph embeddings to fully utilize the distinct information in two different views. Another node-node level contrastive learning is performed between the affinity graph and molecular graphs, thereby filtering out task-independent noise that only appears in one graph. The final drug-target embeddings are put into a multilayer perceptron (MLP) for affinity prediction. Experiments on two widely-used datasets have shown that HSGCL-DTA achieves better prediction performance and generalization than the state-of-the-art DTA prediction methods.

Identifying new disease indications for the approved drugs can help reduce the cost and time of drug development. Most of the recent methods focus on exploiting the various information related to drugs and diseases for predicting the candidate drug-disease associations. However, the previous methods failed to deeply integrate the neighborhood topological structure and the node attributes of an interested drug-disease node pair. We propose a new prediction method, ANPred, to learn and integrate pairwise attribute information and neighbor topology information from the similarities and associations related to drugs and diseases. First, a bi-layer heterogeneous network with intra-layer and inter-layer connections is established to combine the drug similarities, the disease similarities, and the drug-disease associations. Second, the embedding of a pair of drug and disease is constructed based on integrating multiple biological premises about drugs and diseases. The learning framework based on multi-layer convolutional neural networks is designed to learn the attribute representation of the pair of drug and disease nodes from its embedding. The sequences composed of neighbor nodes are formed based on random walk on the heterogeneous network. A framework based on fully-connected autoencoder and skip-gram module is constructed to learn the neighbor topological representations of nodes. The cross-validation results indicate the performance of ANPred is superior to several state-of-the-art methods. The case studies on 5 drugs further confirm the ability of ANPred in discovering the potential drug-disease association candidates.

This paper proposes a hyperspectral image deconvolution algorithm for the online restoration of hyperspectral images as provided by wiskbroom and pushbroom scanning systems. We introduce a least-mean-squares (LMS)-based framework accounting for the convolution kernel noncausality and including nonquadratic (zero attracting and piecewise constant) regularization terms. This results in the so-called sliding block regularized LMS (SBR-LMS), which maintains a linear complexity compatible with real-time processing in industrial applications. A model for the algorithm mean and mean-squares transient behavior is derived and the stability condition is studied. Experiments are conducted to assess the role of each hyper-parameter. A key feature of the proposed SBR-LMS is that it outperforms standard approaches in low SNR scenarios such as ultra-fast scanning.

This work aims at studying a method to automatically estimate regularization parameters of hyperspectral images deconvolution methods. The deconvolution problem is formulated as a multi-objective optimization problem and the properties of the corresponding response surface are studied. Based on these properties, the minimum distance criterion (MDC) is proposed to estimate regularization parameters. It has good theoretical properties (uniqueness, robustness) from which a grid search based approach is proposed. It results in a fast approach to estimate the regularization parameters.

Zero-attracting least-mean-square (ZA-LMS) algorithm has been widely used for online sparse system identification. It combines the LMS framework and l1-norm regularization to promote sparsity, and relies on subgradient iterations. Despite the significant interest in ZA-LMS, few works analyzed its transient behavior. The main difficulty lies in the nonlinearity of the update rule. In this study, a detailed analysis in the mean and mean-square sense is carried out in order to examine the behavior of the algorithm. Simulation results illustrate the accuracy of the model and highlight its performance through comparisons with an existing model.

This paper aims at studying a method to automatically estimate the regularization parameters of non-negative hyperspectral image deconvolution methods. The deconvolution problem is formulated as a multi-objective optimization problem and the properties of the corresponding response surface are studied. Based on these properties, the minimum distance criterion (MDC) and the maximum curvature criterion (MCC) are proposed to estimate regularization parameters especially for the non-negativity constrained deconvolution problem. MDC has good theoretical properties (convexity and uniqueness) but requires to choose a reference point. On the contrary, MCC does not need to choose any reference point but does not have interesting theoretical properties. A grid-search-based approach to minimize the computational cost of MDC and MCC is proposed. It results in fast approaches to estimate the regularization parameters. Based on simulated 2D images, the proposed approaches are compared with the state-of-the-art methods, confirming the effectiveness of the MDC and MCC for the non-negativity constrained image deconvolution problem. In the case of non-negative hyperpsectral image deconvolution, the fast MDC yields better performances than the fast MCC. An application to real-world hyperspectral fluorescence microscopy images is also provided; it confirms the superiority of MDC.