Using transfer learning and dimensionality reduction techniques to improve generalisability of machine-learning predictions of mosquito ages from mid-infrared spectra

• Published in: BMC bioinformatics Vol. 24; no. 1; pp. 11 - 15
• Main Authors: Mwanga, Emmanuel P., Siria, Doreen J., Mitton, Joshua, Mshani, Issa H., González-Jiménez, Mario, Selvaraj, Prashanth, Wynne, Klaas, Baldini, Francesco, Okumu, Fredros O., Babayan, Simon A.
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 09.01.2023; BioMed Central; BMC
• Subjects: Adult; Analysis; Animals; Anopheles; Anopheles arabiensis; Convolutional neural network; Dimensionality reduction; Disease transmission; Female; Generalisability; Humans; Machine Learning; Malaria; Mosquito Vectors; Prevention; Standard machine learning; Transfer learning; South Africa; Dimensionality reduction; Anopheles arabiensis; Generalisability; Transfer learning; Convolutional neural network; Standard machine learning
• DOI: 10.1186/s12859-022-05128-5
• ISSN: 1471-2105

Old mosquitoes are more likely to transmit malaria than young ones. Therefore, accurate prediction of mosquito population age can drastically improve the evaluation of mosquito-targeted interventions. However, standard methods for age-grading mosquitoes are laborious and costly. We have shown that Mid-infrared spectroscopy (MIRS) can be used to detect age-specific patterns in mosquito cuticles and thus can be used to train age-grading machine learning models. However, these models tend to transfer poorly across populations. Here, we investigate whether applying dimensionality reduction and transfer learning to MIRS data can improve the transferability of MIRS-based predictions for mosquito ages. We reared adults of the malaria vector Anopheles arabiensis in two insectaries. The heads and thoraces of female mosquitoes were scanned using an attenuated total reflection-Fourier transform infrared spectrometer, which were grouped into two different age classes. The dimensionality of the spectra data was reduced using unsupervised principal component analysis or t-distributed stochastic neighbour embedding, and then used to train deep learning and standard machine learning classifiers. Transfer learning was also evaluated to improve transferability of the models when predicting mosquito age classes from new populations. Model accuracies for predicting the age of mosquitoes from the same population as the training samples reached 99% for deep learning and 92% for standard machine learning. However, these models did not generalise to a different population, achieving only 46% and 48% accuracy for deep learning and standard machine learning, respectively. Dimensionality reduction did not improve model generalizability but reduced computational time. Transfer learning by updating pre-trained models with 2% of mosquitoes from the alternate population improved performance to ~ 98% accuracy for predicting mosquito age classes in the alternative population. Combining dimensionality reduction and transfer learning can reduce computational costs and improve the transferability of both deep learning and standard machine learning models for predicting the age of mosquitoes. Future studies should investigate the optimal quantities and diversity of training data necessary for transfer learning and the implications for broader generalisability to unseen datasets.