Deep learning-based methods significantly advance the exploration of associations among triple-wise biological entities (e.g., drug-target protein-adverse reaction), thereby facilitating drug discovery and safeguarding human health. However, existing researches only focus on entity-centric information mapping and aggregation, neglecting the crucial role of potential association patterns among different entities. To address the above limitation, we propose a novel association pattern-aware fusion method for biological entity relationship prediction, which effectively integrates the related association pattern information into entity representation learning. Additionally, to enhance the missing information of the low-order message passing, we devise a bind-relation module that considers the strong bind of low-order entity associations. Extensive experiments conducted on three biological datasets quantitatively demonstrate that the proposed method achieves about 4%-23% hit@1 improvements compared with state-of-the-art baselines. Furthermore, the interpretability of association patterns is elucidated in detail, thus revealing the intrinsic biological mechanisms and promoting it to be deployed in real-world scenarios.

Similar yet distinct, hypergraph-based methods employ the hypergraph structure toobtain entity representations using thecomplexfeature aggregation strategy.

We introduce the Randomized Dependence Coefficient (RDC), a measure of nonlinear dependence between random variables of arbitrary dimension based on the Hirschfeld-Gebelein-Rényi Maximum Correlation Coefficient. RDC is defined in terms of correlation of random non-linear copula projections; it is invariant with respect to marginal distribution transformations, has low computational cost and is easy to implement: just five lines of R code, included at the end of the paper.

This paper introduces a nonparametric copula-based index for detecting the strength and monotonicity structure of linear and nonlinear statistical dependence between pairs of random variables or stochastic signals. Our index, termed Copula Index for Detecting Dependence and Monotonicity (CIM), satisfies several desirable properties of measures of association, including R\'enyi's properties, the data processing inequality (DPI), and consequently self-equitability. Synthetic data simulations reveal that the statistical power of CIM compares favorably to other state-of-the-art measures of association that are proven to satisfy the DPI. Simulation results with real-world data reveal the CIM's unique ability to detect the monotonicity structure among stochastic signals to find interesting dependencies in large datasets. Additionally, simulations show that the CIM shows favorable performance to estimators of mutual information when discovering Markov network structure.

Conventional multi-label classification algorithms treat the target labels of the classification task as mere symbols that are void of an inherent semantics. However, in many cases textual descriptions of these labels are available or can be easily constructed from public document sources such as Wikipedia. In this paper, we investigate an approach for embedding documents and labels into a joint space while sharing word representations between documents and labels. For finding such embeddings, we rely on the text of documents as well as descriptions for the labels. The use of such label descriptions not only lets us expect an increased performance on conventional multi-label text classification tasks, but can also be used to make predictions for labels that have not been seen during the training phase. The potential of our method is demonstrated on the multi-label classification task of assigning keywords from the Medical Subject Headings (MeSH) to publications in biomedical research, both in a conventional and in a zero-shot learning setting.

We introduce the Randomized Dependence Coefficient (RDC), a measure of non-linear dependence between random variables of arbitrary dimension based on the Hirschfeld-Gebelein-Rényi Maximum Correlation Coefficient. RDC is defined in terms of correlation of random non-linear copula projections; it is invariant with respect to marginal distribution transformations, has low computational cost and is easy to implement: just five lines of R code, included at the end of the paper.

We introduce the Randomized Dependence Coefficient (RDC), a measure of non-linear dependence between random variables of arbitrary dimension based on the Hirschfeld-Gebelein-R\'enyi Maximum Correlation Coefficient. RDC is defined in terms of correlation of random non-linear copula projections; it is invariant with respect to marginal distribution transformations, has low computational cost and is easy to implement: just five lines of R code, included at the end of the paper.