Pathogen detection from biological and environmental samples is important for global disease control. Despite advances in pathogen detection using deep learning, current algorithms have limitations in processing long genomic sequences. Through the deep cross-fusion of cross, residual and deep neural networks, we developed DCiPatho for accurate pathogen detection based on the integrated frequency features of 3-to-7 k-mers. Compared with the existing state-of-the-art algorithms, DCiPatho can be used to accurately identify distinct pathogenic bacteria infecting humans, animals and plants. We evaluated DCiPatho on both learned and unlearned pathogen species using both genomics and metagenomics datasets. DCiPatho is an effective tool for the genomic-scale identification of pathogens by integrating the frequency of k-mers into deep cross-fusion networks. The source code is publicly available at https://github.com/LorMeBioAI/DCiPatho.

When running in Parameter Server (PS), the Distributed Stochastic Gradient Descent (D-SGD) incurs significant communication delays and huge communication overhead due to the model synchronization. Moreover, considering the heterogeneity of computational capability among workers, traditional synchronization modes incur under-utilization of computational resources because fast workers have to wait for slow ones finishing the computation. Although our previous work OSP can effectively solve these problems by overlapping the computation and communication procedures and allowing adaptive multiple local updates in distributed training, it causes the staleness problem brought by the overlap, yielding a performance degradation. In this paper, we propose a new method named LOSP by introducing local compensation to our previous synchronization mechanism, which mitigates adverse effects caused by the overlapping synchronization. We theoretically prove that LOSP (1) preserves the same convergence rate as the sequential SGD for non-convex problems, and (2) exhibits good scalability due to the linear speedup property with respect to both the number of workers and the average number of local updates. Evaluations show that LOSP significantly improves performance over the state-of-the-art ones in terms of both convergence accuracy and communication cost.