The occurrence of multiple strains of a bacterial pathogen such as M. tuberculosis or C. difficile within a single human host, referred to as a mixed infection, has important implications for both healthcare and public health. However, methods for detecting it, and especially determining the proportion and identities of the underlying strains, from WGS (whole-genome sequencing) data, have been limited. In this paper we introduce SplitStrains, a novel method for addressing these challenges. Grounded in a rigorous statistical model, SplitStrains not only demonstrates superior performance in proportion estimation to other existing methods on both simulated as well as real M. tuberculosis data, but also successfully determines the identity of the underlying strains. We conclude that SplitStrains is a powerful addition to the existing toolkit of analytical methods for data coming from bacterial pathogens and holds the promise of enabling previously inaccessible conclusions to be drawn in the realm of public health microbiology.

An essential consideration in urban transit facility planning is service efficiency and accessibility. Previous research has shown that reducing the number of facilities along a route may increase efficiency but decrease accessibility. Striking a balance between these two is a critical consideration in transit planning. Transit facility consolidation is a cost-effective way to improve the quality of service by strategically determining the desirable allocation of a limited number of facilities. This paper develops an optimization framework that integrates Geographical Information systems (GIS), decision-making analysis, and quantum technologies for addressing the problem of facility consolidation. Our proposed framework includes a novel mathematical model that captures non-linear interactions between facilities and surrounding demand nodes, inter-facility competition, ridership demand and spatial coverage. The developed model can harness the power of quantum effects such as superposition and quantum tunnelling and enables transportation planners to utilize the most recent hardware solutions such as quantum and digital annealers, coherent Ising Machines and gate-based universal quantum computers. This study presents a real-world application of the framework to the public transit facility redundancy problem in the British Columbia Vancouver metropolitan area. We demonstrate the effectiveness of our framework by reducing the number of facilities by 40% while maintaining the same service accessibility. Additionally, we showcase the ability of the proposed mathematical model to take advantage of quantum annealing and classical optimization techniques.