Efficient Chromosome Parallelization for Precision Medicine Genomic Workflows
This work addresses resource inefficiencies in genomic data processing for precision medicine applications, representing an incremental improvement in optimization techniques.
The paper tackled the problem of high memory spikes and poor resource utilization in large-scale genomic workflows for precision medicine by proposing adaptive RAM-efficient parallelization methods, achieving faster end-to-end execution in simulations and real-world pipelines.
Large-scale genomic workflows used in precision medicine can process datasets spanning tens to hundreds of gigabytes per sample, leading to high memory spikes, intensive disk I/O, and task failures due to out-of-memory errors. Simple static resource allocation methods struggle to handle the variability in per-chromosome RAM demands, resulting in poor resource utilization and long runtimes. In this work, we propose multiple mechanisms for adaptive, RAM-efficient parallelization of chromosome-level bioinformatics workflows. First, we develop a symbolic regression model that estimates per-chromosome memory consumption for a given task and introduces an interpolating bias to conservatively minimize over-allocation. Second, we present a dynamic scheduler that adaptively predicts RAM usage with a polynomial regression model, treating task packing as a Knapsack problem to optimally batch jobs based on predicted memory requirements. Additionally, we present a static scheduler that optimizes chromosome processing order to minimize peak memory while preserving throughput. Our proposed methods, evaluated on simulations and real-world genomic pipelines, provide new mechanisms to reduce memory overruns and balance load across threads. We thereby achieve faster end-to-end execution, showcasing the potential to optimize large-scale genomic workflows.