graph generative models are highly important for sharing surrogate data and benchmarking purposes. Real-world complex systems often exhibit dynamic nature, where the interactions among nodes change over time in the fo...
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(纸本)9798400701030
graph generative models are highly important for sharing surrogate data and benchmarking purposes. Real-world complex systems often exhibit dynamic nature, where the interactions among nodes change over time in the form of a temporal network. Most temporal network generation models extend the static graph generation models by incorporating temporality in the generation process. More recently, temporal motifs are used to generate temporal networks with better success. However, existing models are often restricted to a small set of predefined motif patterns due to the high computational cost of counting temporal motifs. In this work, we develop a practical temporal graph generator, Motif Transition model (MTM), to generate synthetic temporal networks with realistic global and local features. Our key idea is modeling the arrival of new events as temporal motif transition processes. We first calculate the transition properties from the input graph and then simulate the motif transition processes based on the transition probabilities and transition rates. We demonstrate that our model consistently outperforms the baselines with respect to preserving various global and local temporal graph statistics and runtime performance.
Alignment is the cornerstone of many long-read pipelines and plays an essential role in resolving structural variants (SVs). However, forced alignments of SVs embedded in long reads, inflexibility of integrating novel...
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Alignment is the cornerstone of many long-read pipelines and plays an essential role in resolving structural variants (SVs). However, forced alignments of SVs embedded in long reads, inflexibility of integrating novel SVs models and computational inefficiency remain problems. Here, we investigate the feasibility of resolving long-read SVs with alignment-free algorithms. We ask: (1) Is it possible to resolve long-read SVs with alignment-free approaches? and (2) Does it provide an advantage over existing approaches? To this end, we implemented the framework named Linear, which can flexibly integrate alignment-free algorithms such as the generativemodel for long-read SV detection. Furthermore, Linear addresses the problem of compatibility of alignment-free approaches with existing software. It takes as input long reads and outputs standardized results existing software can directly process. We conducted large-scale assessments in this work and the results show that the sensitivity, and flexibility of Linear outperform alignment-based pipelines. Moreover, the computational efficiency is orders of magnitude faster.
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