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Accurate prediction of the transmission fitness of emerging SARS-CoV-2 variants is vital for timely public health responses. In this study, we present a deep learning framework that predicts variant fitness from raw genomic sequences using a convolutional neural network (CNN) trained to regress Differential Population Growth Rate (DPGR) values. Our approach achieves high predictive accuracy R-square value of 0.92 on genomic sequences sampled from the USA and Europe. To interpret the model’s predictions, we apply SHapley Additive exPlanations (SHAP) to identify nucleotide-level contributions to predicted fitness. Our analysis highlights key mutations in ORF9 (nucleocapsid), ORF2 (spike), ORF5 (membrane), and ORF8 that either enhance or reduce predicted DPGR. Notably, we identify amino acid–altering mutations such as D3L, E484K, N501Y, and V97I as strong positive contributors to fitness, while synonymous or non-coding mutations had more subtle or regulatory effects. These findings validate the potential of sequence-based modeling and interpretable AI to support early detection and prioritization of high-risk variants. 

High-throughput microfluidics-based assays can potentially increase the speed and quality of yeast replicative lifespan measurements. One major challenge is to efficiently convert large volumes of time-lapse images into quantitative measurements of cellular lifespans. Here, we address this challenge by prototyping an algorithm that can track cellular division events through family trees of cells. We generated a null distribution using single cells inside microfluidic traps. Based on this null distribution, we prototyped a maximum likelihood algorithm for cell tracking between images at different time-points. We inferred cell family trees through a likelihood based trace-back method. The branching patterns of the cell family trees are then used to infer replicative lifespan of the yeast mother cells. The longest branch of a cell family tree represents the full trajectory of a yeast mother cell. The replicative lifespan of this mother cell can be counted as the number of bifurcating branches of this family tree. In addition, we prototyped a different approach based on summing cells area which improved the replicative lifespan estimation significantly. These generic methods have the potential to accelerate the efficiency and expand the range of quantitative measurement of yeast replicative aging experiments.