Motivation: Understanding chemical–gene interactions (CGIs) is crucial for screening drugs. Wet experiments are usually costly and laborious, which limits relevant studies to a small scale. On the contrary, computational studies enable efficient in-silico exploration. For the CGI prediction problem, a common method is to perform systematic analyses on a heterogeneous network involving various biomedical entities. Recently, graph neural networks become popular in the field of relation prediction. However, the inherent heterogeneous complexity of biological interaction networks and the massive amount of data pose enormous challenges. This paper aims to develop a data-driven model that is capable of learning latent information from the interaction network and making correct predictions. Results: We developed BioNet, a deep biological networkmodel with a graph encoder–decoder architecture. The graph encoder utilizes graph convolution to learn latent information embedded in complex interactions among chemicals, genes, diseases and biological pathways. The learning process is featured by two consecutive steps. Then, embedded information learnt by the encoder is then employed to make multi-type interaction predictions between chemicals and genes with a tensor decomposition decoder based on the RESCAL algorithm. BioNet includes 79 325 entities as nodes, and 34 005 501 relations as edges. To train such a massive deep graph model, BioNet introduces a parallel training algorithm utilizing multiple Graphics Processing Unit (GPUs). The evaluation experiments indicated that BioNet exhibits outstanding prediction performance with a best area under Receiver Operating Characteristic (ROC) curve of 0.952, which significantly surpasses state-of-theart methods. For further validation, top predicted CGIs of cancer and COVID-19 by BioNet were verified by external curated data and published literature.

Background: Interactions of microbes and diseases are of great importance for biomedical research. However, large-scale of microbe–disease interactions are hidden in the biomedical literature. The structured databases for microbe–disease interactions are in limited amounts. In this paper, we aim to construct a large-scale database for microbe–disease interactions automatically. We attained this goal via applying text mining methods based on a deep learning model with a moderate curation cost. We also built a user-friendly web interface that allows researchers to navigate and query required information. Results: Firstly, we manually constructed a golden-standard corpus and a sliver-standard corpus (SSC) for microbe–disease interactions for curation. Moreover, we proposed a text mining framework for microbe–disease interaction extraction based on a pretrained model BERE. We applied named entity recognition tools to detect microbe and disease mentions from the free biomedical texts. After that, we fine-tuned the pretrained model BERE to recognize relations between targeted entities, which was originally built for drug–target interactions or drug–drug interactions. The introduction of SSC for model fine-tuning greatly improved detection performance for microbe–disease interactions, with an average reduction in error of approximately 10%. The MDIDB website offers data browsing, custom searching for specific diseases or microbes, and batch downloading. Conclusions: Evaluation results demonstrate that our method outperform the baseline model (rule-based PKDE4J) with an average $$F_1$$F 1 -score of 73.81%. For further validation, we randomly sampled nearly 1000 predicted interactions by our model, and manually checked the correctness of each interaction, which gives a 73% accuracy. The MDIDB webiste is freely avaliable throuth http://dbmdi.com/index/

Deep cross-modal retrieval, with its effective and efficient search capabilities, has gained widespread adoption in today’s media-sharing practices yet raises concerns regarding potential threats to user data privacy. The cutting-edge data-centric countermeasures usually adopt adversarial learning, i.e., laboriously crafting the proper perturbation for each image, resulting in the noticeable noise in adversarial examples that greatly undermines the aesthetic appeal of image sharing. To address this issue, we propose a novel Model-centric Cross-modal Privacy-preserving framework (MCP), wherein the pre-defined invisible backdoor is seamlessly integrated into the global retrieval model via backdoor learning, thereby effectively preventing shared images containing such triggers from being retrieved. Specifically, we introduce a simple yet effective cross-modal backdoor learning algorithm that alternately optimizes two losses: 1) a privacy-preserving loss for perturbing retrieval with a user-injected trigger and 2) the standard utility loss for maintaining normal retrieval performance. Compared to state-of-the-art methods, MCP excels in providing excellent stealthiness, manifesting in a notable improvement of approximately 100% in SSIM metrics. Furthermore, it achieves an outstanding privacy-preserving (backdoor) success rate, as evidenced by a substantial mAP reduction of 22.3% (for FashionVC), 11.5% (for NUS-WIDE), and 21.8% (for MIRFlickr-25K) in poisoned retrieval, while maintaining similar normal retrieval performance. Additionally, MCP exhibits robust resistance against potential black-box defenses (e.g., trigger filtering) and white-box defenses (e.g., fine-tuning and model pruning). The code and data are available at https://github.com/lqsunshine/MCP.

Background Cardiovascular disease (CVD), as a chronic disease, has been perplexing human beings and is one of the serious diseases endangering life and health. Therefore, using the electronic medical record information of patients to automatically predict CVD has important application value in intelligent auxiliary diagnosis and treatment, and is a hot issue in intelligent medical research. In recent years, attention mechanism has been successfully extended to various tasks of natural language processing. Typically, these methods use attention to focus on a small part of the context and summarize it with a fixed-size vector, coupling attention in time, and/or often forming a uni-directional attention. Methods In this paper, we propose a CVD risk factors powered bi-directional attention (RFPBiA) network, which is a multi-stage hierarchical process, representing information fusion at different granularity levels, and uses the bi-directional attention to obtain the text representation of risk factors without early aggregation. Results The experimental results show that the proposed method can obviously improve the performance of CVD prediction, and the F-score reaches 0.9424, which is better than the existing related methods. Conclusions We propose to extract the risk factors leading to CVD by using the existing mature entity recognition technology, which provides a new idea for disease prediction tasks. Moreover, the memory- less attention mechanism in both directions in our proposed prediction model of RFPBiA can fuse the character sequence and the risk factors contained in the electronic medical record text to predict CVD.

The Overset Grid method is a promising computational approach for tackling the challenging moving boundary problems in Computational Fluid Dynamics (CFD) simulations. The computational efficiency and accuracy of the method are critically dependent on the effectiveness of the Overset Grid Assembly (OGA) process. However, the OGA process is plagued by unavoidable issues of load imbalance and communication overheads, which adversely impact the parallel efficiency of the method, particularly when dealing with sub-grids in motion. This paper proposes an improved parallel assembly approach as an effective alternative to address these challenges. Specifically, we introduce a Balanced Merging After Decomposition (BMAD) approach, which ensures that each processor possesses a uniform number of cells from each sub-grid after partitioning and a consistent donor search time. In addition, we deploy a fine-grained list to reduce the data transfer domain, thereby minimizing communication redundancy and cost. We validate the efficiency of our approach in the case of a moving Autonomous Underwater Vehicle (AUV). Experimental results in 3 × 106 grid cells indicate that the proposed approach reduces the parallel computational cost of the OGA process by an average of 21.9% and the speedup has increased by 23.9% with 128 processors. Additionally, it demonstrated equally effective and stable performance in tests using 6 × 106 grid cells, especially achieving the highest speedup of 55.0 with 256 processors.

With the exponential growth of biomedical knowledge in unstructured text repositories such as PubMed, it is imminent to establish a knowledge graph-style, efficient searchable and targeted database that can support the need of information retrieval from researchers and clinicians. To mine knowledge from graph databases, most previous methods view a triple in a graph (see Fig. 1) as the basic processing unit and embed the triplet element (i.e. drugs/chemicals, proteins/genes and their interaction) as separated embedding matrices, which cannot capture the semantic correlation among triple elements. To remedy the loss of semantic correlation caused by disjoint embeddings, we propose a novel approach to learn triple embeddings by combining entities and interactions into a unified representation. Furthermore, traditional methods usually learn triple embeddings from scratch, which cannot take advantage of the rich domain knowledge embedded in pre-trained models, and is also another significant reason for the fact that they cannot distinguish the differences implied by the same entity in the multi-interaction triples. In this paper, we propose a novel fine-tuning based approach to learn better triple embeddings by creating weakly supervised signals from pre-trained knowledge graph embeddings. The method automatically samples triples from knowledge graphs and estimates their pairwise similarity from pre-trained embedding models. The triples are then fed pairwise into a Siamese-like neural architecture, where the triple representation is fine-tuned in the manner bootstrapped by triple similarity scores. Finally, we demonstrate that triple embeddings learned with our method can be readily applied to several downstream applications (e.g. triple classification and triple clustering). We evaluated the proposed method on two open-source drug-protein knowledge graphs constructed from PubMed abstracts, as provided by BioCreative. Our method achieves consistent improvement in both triple classification and triple clustering tasks when compared to other state-of-the-art triple embedding methods, with an average 35% improvement of F1 score for the multi-interaction triples.