Software is a powerful tool that can be effectively harnessed to achieve optimal results and reduce labor in wet laboratory experiment. As a dedicated team aspiring to pioneer a novel therapy for breast cancer based on bacteria, Tsinghua 2023 embraces the potential of software tools to enhance our research and development.
The iGEM Team Tsinghua 2023 Software Tool comprises two key components: the Promoter Promotion Model (PPM) and the Protein Engineering Diffusion Model (PEDM).
The first model, the Promoter Promotion Model (PPM), is a regression model designed to predict the strength of prokaryotic promoters, as characterized by the level of downstream gene expression. This model presents an enhancement of the software developed by the Tsinghua iGEM 2022 team, significantly reducing the memory footprint to just 1/20th of the original while simultaneously improving prediction accuracy by an impressive 22%.
The second model, the Protein Engineering Diffusion Model (PEDM), is a generative model that excels in proposing sequences while taking advantage of multiple oracle objectives. This model demonstrates remarkable efficiency in generating sequences with specific target features, providing support for a variety of differentiable oracle functions, offering a robust mathematical foundation, and avoiding the issue of mode collapse.