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  1. Abstract The rapid spread of the COVID-19 pandemic has resulted in an unprecedented amount of sequence data of the SARS-CoV-2 genome—millions of sequences and counting. This amount of data, while being orders of magnitude beyond the capacity of traditional approaches to understanding the diversity, dynamics, and evolution of viruses, is nonetheless a rich resource for machine learning (ML) approaches as alternatives for extracting such important information from these data. It is of hence utmost importance to design a framework for testing and benchmarking the robustness of these ML models. This paper makes the first effort (to our knowledge) to benchmark the robustness of ML models by simulating biological sequences with errors. In this paper, we introduce several ways to perturb SARS-CoV-2 genome sequences to mimic the error profiles of common sequencing platforms such as Illumina and PacBio. We show from experiments on a wide array of ML models that some simulation-based approaches with different perturbation budgets are more robust (and accurate) than others for specific embedding methods to certain noise simulations on the input sequences. Our benchmarking framework may assist researchers in properly assessing different ML models and help them understand the behavior of the SARS-CoV-2 virus or avoid possible future pandemics. 
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    Free, publicly-accessible full text available December 1, 2024
  2. Free, publicly-accessible full text available July 1, 2024
  3. The emergence of third-generation single-molecule sequencing (TGS) technology has revolutionized the generation of long reads, which are essential for genome assembly and have been widely employed in sequencing the SARS-CoV-2 virus during the COVID-19 pandemic. Although long-read sequencing has been crucial in understanding the evolution and transmission of the virus, the high error rate associated with these reads can lead to inadequate genome assembly and downstream biological interpretation. In this study, we evaluate the accuracy and robustness of machine learning (ML) models using six different embedding techniques on SARS-CoV-2 error-incorporated genome sequences. Our analysis includes two types of error-incorporated genome sequences: those generated using simulation tools to emulate error profiles of long-read sequencing platforms and those generated by introducing random errors. We show that the spaced k-mers embedding method achieves high accuracy in classifying error-free SARS-CoV-2 genome sequences, and the spaced k-mers and weighted k-mers embedding methods are highly accurate in predicting error-incorporated sequences. The fixed-length vectors generated by these methods contribute to the high accuracy achieved. Our study provides valuable insights for researchers to effectively evaluate ML models and gain a better understanding of the approach for accurate identification of critical SARS-CoV-2 genome sequences. 
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    Free, publicly-accessible full text available June 1, 2024
  4. Free, publicly-accessible full text available December 1, 2023
  5. Voting is used widely to identify a collective decision for a group of agents, based on their preferences. In this paper, we focus on evaluating and designing voting rules that support both the privacy of the voting agents and a notion of fairness over such agents. To do this, we introduce a novel notion of group fairness and adopt the existing notion of local differential privacy. We then evaluate the level of group fairness in several existing voting rules, as well as the trade-offs between fairness and privacy, showing that it is not possible to always obtain maximal economic efficiency with high fairness or high privacy levels. Then, we present both a machine learning and a constrained optimization approach to design new voting rules that are fair while maintaining a high level of economic efficiency. Finally, we empirically examine the effect of adding noise to create local differentially private voting rules and discuss the three-way trade-off between economic efficiency, fairness, and privacy.This paper appears in the special track on AI & Society. 
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