No abstract

No abstract

No abstract

The COVID-19 pandemic has emphasized the importance of accurate detection of known and emerging pathogens. However, robust characterization of pathogenic sequences remains an open challenge. To address this need we developed SeqScreen, which accurately characterizes short nucleotide sequences using taxonomic and functional labels and a customized set of curated Functions of Sequences of Concern (FunSoCs) specific to microbial pathogenesis. We show our ensemble machine learning model can label protein-coding sequences with FunSoCs with high recall and precision. SeqScreen is a step towards a novel paradigm of functionally informed synthetic DNA screening and pathogen characterization, available for download at www.gitlab.com/treangenlab/seqscreen.

Run-time monitoring can provide important insights about a program's behavior and, for simple properties, it can be done efficiently. Monitoring properties describing sequences of program states and events, however, can result in significant run-time overhead. In this paper we present a novel approach to reducing the cost of run-time monitoring of path properties. Properties are composed to form a single integrated property that is then systematically decomposed into a set of properties that encode necessary conditions for property violations. The resulting set of properties forms a lattice whose structure is exploited to select a sample of properties that can lower monitoring cost, while preserving violation detection power relative to the original properties. Preliminary studies for a widely used Java API reveal that our approach produces a rich, structured set of properties that enables control of monitoring overhead, while detecting more violations than alternative techniques 1 .