Optimizing the order of actions in a model of contact tracing.

Contact tracing is a key tool for managing epidemic diseases like HIV, tuberculosis, COVID-19, and monkeypox. Manual investigations by human-contact tracers remain a dominant way in which this is carried out. This process is limited by the number of contact tracers available, who are often overburdened during an outbreak or epidemic. As a result, a crucial decision in any contact tracing strategy is, given a set of contacts, which person should a tracer trace next? In this work, we develop a formal model that articulates these questions and provides a framework for comparing contact tracing strategies. Through analyzing our model, we give provably optimal prioritization policies via a clean connection to a tool from operations research called a "branching bandit". Examining these policies gives qualitative insight into trade-offs in contact tracing applications.

Mining TCGA data using Boolean implications.

Boolean implications (if-then rules) provide a conceptually simple, uniform and highly scalable way to find associations between pairs of random variables. In this paper, we propose to use Boolean implications to find relationships between variables of different data types (mutation, copy number alteration, DNA methylation and gene expression) from the glioblastoma (GBM) and ovarian serous cystadenoma (OV) data sets from The Cancer Genome Atlas (TCGA). We find hundreds of thousands of Boolean implications from these data sets. A direct comparison of the relationships found by Boolean implications and those found by commonly used methods for mining associations show that existing methods would miss relationships found by Boolean implications. Furthermore, many relationships exposed by Boolean implications reflect important aspects of cancer biology. Examples of our findings include cis relationships between copy number alteration, DNA methylation and expression of genes, a new hierarchy of mutations and recurrent copy number alterations, loss-of-heterozygosity of well-known tumor suppressors, and the hypermethylation phenotype associated with IDH1 mutations in GBM. The Boolean implication results used in the paper can be accessed at http://crookneck.stanford.edu/microarray/TCGANetworks/.