MOTIVATION: Multiplex PCR-based enrichment is widely used in viral genome sequencing and pathogen surveillance. However, designing large sets of primers that maximize genome coverage while minimizing primer-primer interactions remains a major computational challenge. Existing methods such as SADDLE and Olivar use heuristics to optimize a Badness score for primer dimers but lack theoretical guarantees on solution quality. RESULTS: We introduce PRISM, a new framework that formulates multiplex primer design as a constrained submodular maximization problem. Our method defines an objective that balances genome coverage and dimer risk, and applies a local search algorithm with a constant-factor approximation guarantee. Evaluations on viral genome datasets demonstrate that PRISM consistently achieves lower Badness scores compared to PrimalScheme, Olivar, and primerJinn. These results highlight the scalability and theoretical rigor of submodular optimization in primer design. AVAILABILITY: PRISM is open-source and available at https://github.com/yhhan19/PRISM-new. The experimental data, scripts, and results used in this paper are archived on Figshare at https://doi.org/10.6084/m9.figshare.32806499.

OBJECTIVE: The COVID-19 pandemic emphasized the value of geospatial visual analytics for both epidemiologists and the general public. However, systems struggled to encode temporal and geospatial trends of multiple, potentially interacting variables, such as active cases, deaths, and vaccinations. We sought to ask (1) how epidemiologists interact with visual analytics tools, (2) how multiple, time-varying, geospatial variables can be conveyed in a unified view, and (3) how complex spatiotemporal encodings affect utility for both experts and non-experts. MATERIALS AND METHODS: We propose encoding variables with animated, concentric, hollow circles, allowing multiple variables via color encoding and avoiding occlusion problems, and we implement this method in a browser-based tool called CoronaViz. We conduct task-based evaluations with non-experts, as well as in-depth interviews and observational sessions with epidemiologists, covering a range of tools and encodings. RESULTS: Sessions with epidemiologists confirmed the importance of multivariate, spatiotemporal queries and the utility of CoronaViz for answering them, while providing direction for future development. Non-experts tasked with performing spatiotemporal queries unanimously preferred animation to multi-view dashboards. DISCUSSION: We find that conveying complex, multivariate data necessarily involves trade-offs. Yet, our studies suggest the importance of complementary visualization strategies, with our animated multivariate spatiotemporal encoding filling important needs for exploration and presentation. CONCLUSION: CoronaViz's unique ability to convey multiple, time-varying, geospatial variables makes it both a valuable addition to interactive COVID-19 dashboards and a platform for empowering experts and the public during future disease outbreaks. CoronaViz is open-source and a live instance is freely hosted at http://coronaviz.umiacs.io.

More and more advanced technologies have become available to collect and integrate an unprecedented amount of data from multiple sources, including GPS trajectories about the traces of moving objects. Given the fact that GPS trajectories are vast in size while the information carried by the trajectories could be redundant, we focus on trajectory compression in this article. As a systematic solution, we propose a comprehensive framework, namely, COMPRESS ( Comprehensive Paralleled Road-Network-Based Trajectory Compression ), to compress GPS trajectory data in an urban road network. In the preprocessing step, COMPRESS decomposes trajectories into spatial paths and temporal sequences, with a thorough justification for trajectory decomposition. In the compression step, COMPRESS performs spatial compression on spatial paths, and temporal compression on temporal sequences in parallel. It introduces two alternative algorithms with different strengths for lossless spatial compression and designs lossy but error-bounded algorithms for temporal compression. It also presents query processing algorithms to support error-bounded location-based queries on compressed trajectories without full decompression. All algorithms under COMPRESS are efficient and have the time complexity of O (| T |), where | T | is the size of the input trajectory T . We have also conducted a comprehensive experimental study to demonstrate the effectiveness of COMPRESS, whose compression ratio is significantly better than related approaches.