Massively parallel DNA sequencing technologies are revolutionizing genomics research. Billions of short reads generated at low costs can be assembled for reconstructing the whole genomes. Unfortunately, the large memory footprint of the existing de novo assembly algorithms makes it challenging to get the assembly done for higher eukaryotes like mammals. In this work, we investigate the memory issue of constructing de Bruijn graph, a core task in leading assembly algorithms, which often consumes several hundreds of gigabytes memory for large genomes. We propose a disk-based partition method, called Minimum Substring Partitioning (MSP), to complete the task using less than 10 gigabytes memory, without runtime slowdown. MSP breaks the short reads into multiple small disjoint partitions so that each partition can be loaded into memory, processed individually and later merged with others to form a de Bruijn graph. By leveraging the overlaps among the k-mers (substring of length k), MSP achieves astonishing compression ratio: The total size of partitions is reduced from Θ(kn) to Θ(n), where n is the size of the short read database, and k is the length of a k-mer. Experimental results show that our method can build de Bruijn graphs using a commodity computer for any large-volume sequence dataset.

No abstract

No abstract

Multi-view networks are broadly present in real-world applications. In the meantime, network embedding has emerged as an effective representation learning approach for networked data. Therefore, we are motivated to study the problem of multi-view network embedding with a focus on the optimization objectives that are specific and important in embedding this type of network. In our practice of embedding real-world multi-view networks, we explicitly identify two such objectives, which we refer to as preservation and collaboration. The in-depth analysis of these two objectives is discussed throughout this paper. In addition, the MVN2VEC algorithms are proposed to (i) study how varied extent of preservation and collaboration can impact embedding learning and (ii) explore the feasibility of achieving better embedding quality by modeling them simultaneously. With experiments on a series of synthetic datasets, a large-scale internal Snapchat dataset, and two public datasets, we confirm the validity and importance of preservation and collaboration as two objectives for multi-view network embedding. These experiments further demonstrate that better embedding can be obtained by simultaneously modeling the two objectives, while not over-complicating the model or requiring additional supervision. The code and the processed datasets are available at http://yushi2.web.engr.illinois.edu/.

No abstract