Massive molecular testing for COVID-19 has been pointed out as fundamental to moderate the spread of the pandemic. Pooling methods can enhance testing efficiency, but they are viable only at low incidences of the disease. We propose Smart Pooling, a machine learning method that uses clinical and sociodemographic data from patients to increase the efficiency of informed Dorfman testing for COVID-19 by arranging samples into all-negative pools. To do this, we ran an automated method to train numerous machine learning models on a retrospective dataset from more than 8000 patients tested for SARS-CoV-2 from April to July 2020 in Bogotá, Colombia. We estimated the efficiency gains of using the predictor to support Dorfman testing by simulating the outcome of tests. We also computed the attainable efficiency gains of non-adaptive pooling schemes mathematically. Moreover, we measured the false-negative error rates in detecting the ORF1ab and N genes of the virus in RT-qPCR dilutions. Finally, we presented the efficiency gains of using our proposed pooling scheme on proof-of-concept pooled tests. We believe Smart Pooling will be efficient for optimizing massive testing of SARS-CoV-2.
Massive molecular testing for COVID-19 has been pointed as fundamental to moderate the spread of the disease. Pooling methods can enhance testing efficiency, but they are viable only at very low prevalences of the disease. We propose Smart Pooling, a machine learning method that uses sociodemographic data from patients to increase the efficiency of pooled molecular testing for COVID-19 by arranging samples into all-negative pools. We show efficiency gains of 42% with respect to individual testing at disease prevalence of up to 25%, a regime in which two-step pooling offers marginal efficiency gains. Additionally, we calculate the possible efficiency gains of one- and two-dimensional two-step pooling strategies and present the optimal strategies for disease prevalences up to 25%. We discuss practical limitations to conduct pooling in the laboratory.
This paper addresses the challenge of generating Counterfactual Explanations (CEs), involving the identification and modification of the fewest necessary features to alter a classifier's prediction for a given image. Our proposed method, Text-to-Image Models for Counterfactual Explanations (TIME), is a black-box counterfactual technique based on distillation. Unlike previous methods, this approach requires solely the image and its prediction, omitting the need for the classifier's structure, parameters, or gradients. Before generating the counterfactuals, TIME introduces two distinct biases into Stable Diffusion in the form of textual embeddings: the context bias, associated with the image's structure, and the class bias, linked to class-specific features learned by the target classifier. After learning these biases, we find the optimal latent code applying the classifier's predicted class token and regenerate the image using the target embedding as conditioning, producing the counterfactual explanation. Extensive empirical studies validate that TIME can generate explanations of comparable effectiveness even when operating within a black-box setting.
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