Effective molecular representation learning is very important for Artificial Intelligence-driven Drug Design because it affects the accuracy and efficiency of molecular property prediction and other molecular modeling relevant tasks. However, previous molecular representation learning studies often suffer from limitations, such as over-reliance on a single molecular representation, failure to fully capture both local and global information in molecular structure, and ineffective integration of multiscale features from different molecular representations. These limitations restrict the complete and accurate representation of molecular structure and properties, ultimately impacting the accuracy of predicting molecular properties. To this end, we propose a novel multi-view molecular representation learning method called MvMRL, which can incorporate feature information from multiple molecular representations and capture both local and global information from different views well, thus improving molecular property prediction. Specifically, MvMRL consists of four parts: a multiscale CNN-SE Simplified Molecular Input Line Entry System (SMILES) learning component and a multiscale Graph Neural Network encoder to extract local feature information and global feature information from the SMILES view and the molecular graph view, respectively; a Multi-Layer Perceptron network to capture complex non-linear relationship features from the molecular fingerprint view; and a dual cross-attention component to fuse feature information on the multi-views deeply for predicting molecular properties. We evaluate the performance of MvMRL on 11 benchmark datasets, and experimental results show that MvMRL outperforms state-of-the-art methods, indicating its rationality and effectiveness in molecular property prediction. The source code of MvMRL was released in https://github.com/jedison-github/MvMRL.

The evaluation of absorption, distribution, metabolism, exclusion, and toxicity (ADMET) properties plays a key role in a variety of domains including industrial chemicals, agrochemicals, cosmetics, environmental science, food chemistry, and particularly drug development. Since molecules are often intrinsically described as molecular graphs, graph neural networks have recently been studied to improve the prediction of ADMET properties. Among many graph neural networks published in recent years, Graph Isomorphism Network (GIN) is a relatively recent and very promising one. In this paper, we propose an enhanced GIN, called MolGIN, via exploiting the bond features and differences influence of the atom neighbors to end-to-end predict ADMET properties. Based on GIN, MolGIN concatenates the bond feature together with node feature in the feature aggregator and applies a gate unit to adjust the atomic neighborhood weights to map the differences in the interaction strength between the central atom and its neighbors, such that more meaningful structural patterns of molecules can be explored toward better molecular modeling. Extensive experiments were conducted on seven public datasets to evaluate MolGIN against four baseline models with benchmark metrics. Experimental results of MolGIN were also compared with state-of-the-art results published in the last three years on each dataset. Experimental results in terms of RMSE and AUC show that MolGIN significantly boosts the prediction performance of GIN and markedly outperforms the baseline models, and achieves comparable or superior performance to state-of-the-art results.

Multi-view learning is a machine learning paradigm that utilizes multiple feature sets or data sources to improve learning performance and generalization. However, existing multi-view learning methods often do not capture and utilize information from different views very well, especially when the relationships between views are complex and of varying quality. In this paper, we propose a novel multi-view learning framework for the multi-view classification task, called Gated Cross-Correlation Network (GCCNet), which addresses these challenges by integrating the three key operational levels in multi-view learning: representation, fusion, and decision-making. Specifically, GCCNet contains a novel component called the Multi-View Gated Information Distributor (MVGID) to enhance noise filtering and optimize the retention of critical information. In addition, GCCNet uses cross-correlation analysis to reveal dependencies and interactions between different views, as well as integrates an adaptive weighted joint decision strategy to mitigate the interference of low-quality views. Thus, GCCNet can not only comprehensively capture and utilize information from different views, but also facilitate information exchange and synergy between views, ultimately improving the overall performance of the model. Extensive experimental results on ten benchmark datasets show GCCNet's outperforms state-of-the-art methods on eight out of ten datasets, validating its effectiveness and superiority in multi-view learning.

Causal partitioning is an effective approach for causal discovery based on the divide-and-conquer strategy. Up to now, various heuristic methods based on conditional independence (CI) tests have been proposed for causal partitioning. However, most of these methods fail to achieve satisfactory partitioning without violating $d$ -separation, leading to poor inference performance. In this work, we transform causal partitioning into an alternative problem that can be more easily solved. Concretely, we first construct a superstructure $G$ of the true causal graph $G_{\mathcal {T}}$ by performing a set of low-order CI tests on the observed data $D$ . Then, we leverage point-line duality to obtain a graph $G_\mathcal {A}$ adjoint to $G$ . We show that the solution of minimizing edge-cut ratio on $G_\mathcal {A}$ can lead to a valid causal partitioning with smaller causal-cut ratio on $G$ and without violating $d$d-separation . We design an efficient algorithm to solve this problem. Extensive experiments show that the proposed method can achieve significantly better causal partitioning without violating $d$ -separation than the existing methods.