Drug combinations are widely used in modern medicine but may cause severe adverse drug reactions. Therefore, making effective drug-drug interactions (DDI) prediction is crucial for pharmacovigilance. Existing DDI prediction models are typically built from a structural perspective, assuming that drugs with similar molecular structures may exhibit similar interactions. However, such approaches overlook the biological mechanisms underlying DDI in the human body. This not only weakens the generalization ability of the model, but also makes its interpretability less convincing. Inspired by this, we propose a new method called PC-DDI. Unlike structure-based models, PC-DDI utilizes pharmacophores as basic unit, and designs a complete pharmacophore feature processing framework. It further constructs a pharmacophore-based bipartite graph to model interactions between pharmacophores. This approach allows us to explore the underlying mechanisms of DDI from a functional perspective. We also design a spatial attention weight graph convolution module to optimize the message passing process by integrating pharmacophore position features with node features. Furthermore, we apply causal inference to identify key pharmacophores in pharmacophore bipartite graph, enhancing the interpretability. Compared with the SOTA, PC-DDI achieves an accuracy improvement of 1.84% under the transductive setting and consistently outperforms others in all other experiments.

Drug-drug interactions (DDIs) are crucial in clinical medicine, as they can lead to adverse events. Existing DDI extraction methods focus on sentence-level tasks, limiting their ability to identify cross-sentence DDIs. Moreover, the only document-level method available considers only internal drug features, leading to suboptimal performance. To address this, we propose MF-DocDDI, a document-level DDI extraction model using drug entity multi-feature fusion. We first construct a document-level dataset based on DDI Extraction 2013. Then, we introduce document-entity embeddings to capture internal drug features and employ a simplified U-shaped network to extract external features. Finally, we integrate these features to enhance interaction modeling. Experimental results show MF-DocDDI outperforms existing methods, improving the F1 score by 5.33 %. Case studies confirm its ability to identify cross-sentence DDIs, such as (naloxone, morphine) and (HEXALEN, cisplatin). Beyond DDI extraction, MF-DocDDI can be applied to other biomedical tasks like protein-protein interaction (PPI) extraction.

Developing generalizable seizure prediction models across patients is clinically imperative but challenged by significant inter-subject EEG variability. Prevailing methods still yield poor cross-patient accuracy, failing to overcome this barrier. To address this, we propose dual attention learning on crossfrequency phase-amplitude coupling networks (CFPAC-DAL) for generalized seizure prediction. Firstly, cross-frequency PAC brain networks were constructed to quantify neurodynamic couplings; next, a dual-attention mechanism for spatial extraction: intra-graph attention learns node interactions within individual networks, and inter-graph attention captures cross-frequency dependencies between distinct PAC graphs; Finally, temporal dynamics are modeled to capture long-range dependencies in EEG sequences. Evaluations on CHB-MIT and Siena datasets show 98.27%/98.24% patient-specific accuracy and 86.28%/81.15% cross-patient accuracy, outperforming the existing state-of-the-art methods, substantiating that dual-attention on cross-frequency PAC networks encodes neural signatures resilient to individual differences, establishing a new paradigm for clinical-ready prediction.

Determining drug-drug interactions (DDIs) is an important part of pharmacovigilance and has a vital impact on public health. Compared with drug trials, obtaining DDI information from scientific articles is a faster and lower cost but still a highly credible approach. However, current DDI text extraction methods consider the instances generated from articles to be independent and ignore the potential connections between different instances in the same article or sentence. Effective use of external text data could improve prediction accuracy, but existing methods cannot extract key information from external data accurately and reasonably, resulting in low utilization of external data. In this study, we propose a DDI extraction framework, instance position embedding and key external text for DDI (IK-DDI), which adopts instance position embedding and key external text to extract DDI information. The proposed framework integrates the article-level and sentence-level position information of the instances into the model to strengthen the connections between instances generated from the same article or sentence. Moreover, we introduce a comprehensive similarity-matching method that uses string and word sense similarity to improve the matching accuracy between the target drug and external text. Furthermore, the key sentence search method is used to obtain key information from external data. Therefore, IK-DDI can make full use of the connection between instances and the information contained in external text data to improve the efficiency of DDI extraction. Experimental results show that IK-DDI outperforms existing methods on both macro-averaged and micro-averaged metrics, which suggests our method provides complete framework that can be used to extract relationships between biomedical entities and process external text data.

In the treatment of many diseases, combination drug therapy has been widely used and achieved good clinical efficacy. However, drug-drug interaction (DDI) may occur between multiple drugs and pose a huge threat to the health of patients. Therefore, predicting the presence or absence of DDI among multiple drugs is an important part of pharmacovigilance. Currently, various computational methods for DDI prediction usually use biological information such as molecular structures, targets and enzymes of drugs, or construct heterogeneous networks about drugs, diseases, and genes, so as to obtain abundant information related to drugs. In addition to biological data, pharmacology texts also contain a wealth of information about drug properties, but these texts have not yet been applied to DDI predictions. In this study, we first collect six types of pharmacology texts from DrugBank that can reflect properties of drugs, and propose a novel method named BP-DDI which can combine biological information and pharmacological text to realize DDI event prediction. BP-DDI first extracts biological features (chemical substructure features and target features) from biological data, and then extracts specific types of text features from the collected pharmacology text data. Finally, the biological features are fused with different types of pharmacological text features in order to predict DDI events. Our experiments demonstrate that BP-DDI outperforms existing methods on all three types of prediction tasks. BP-DDI achieves 0.9052 on ACC, and achieves 0.9612 on AUPR.

DDI is an important part of drug-related research and pharmacovigilance. Extracting DDI information from scientific literature has become a low-cost and highly reliable way. Currently, existing works are all sentence-level DDI relation extraction. In fact, the entity relationship is often expressed by multiple sentences. Moreover, the sentence-level DDI relation extraction also causes a large amount of redundancy in the whole dataset with increasing in negative instance data. In this study, we propose a document-level DDI relation extraction method based on document-entity embedding. Our method performs special processing on the DDI Extraction 2013 for the first time, in order to calculate document-level relation extraction. For obtaining document-level entity information, we propose a document-entity embedding method to integrate the information of all same drugs in the same article. The experimental results show that the processing of DDI Extraction 2013 dataset is reasonable. In addition, the proposed method has achieved good performance on document-level DDI dataset, and the best F1 score is 62.51%. This is the first time that DDI Extraction 2013 has been processed into a document-level dataset, and document-level DDI relation extraction has been realized.