Rapid identification of pathogenic bacteria using Raman spectroscopy and deep learning.

Raman optical spectroscopy promises label-free bacterial detection, identification, and antibiotic susceptibility testing in a single step. However, achieving clinically relevant speeds and accuracies remains challenging due to weak Raman signal from bacterial cells and numerous bacterial species and phenotypes. Here we generate an extensive dataset of bacterial Raman spectra and apply deep learning approaches to accurately identify 30 common bacterial pathogens. Even on low signal-to-noise spectra, we achieve average isolate-level accuracies exceeding 82% and antibiotic treatment identification accuracies of 97.0±0.3%. We also show that this approach distinguishes between methicillin-resistant and -susceptible isolates of Staphylococcus aureus (MRSA and MSSA) with 89±0.1% accuracy. We validate our results on clinical isolates from 50 patients. Using just 10 bacterial spectra from each patient isolate, we achieve treatment identification accuracies of 99.7%. Our approach has potential for culture-free pathogen identification and antibiotic susceptibility testing, and could be readily extended for diagnostics on blood, urine, and sputum.

Using machine learning to discover shape descriptors for predicting emulsion stability in a microfluidic channel.

In soft matter consisting of many deformable objects, object shapes often carry important information about local forces and their interactions with the local environment, and can be tightly coupled to the bulk properties and functions. In a concentrated emulsion, for example, the shapes of individual droplets are directly related to the local stress arising from interactions with neighboring drops, which in turn determine their stability and the resulting rheological properties. Shape descriptors used in prior work on single drops and dilute emulsions, where droplet-droplet interactions are largely negligible and the drop shapes are simple, are insufficient to fully capture the broad range of droplet shapes in a concentrated system. This paper describes the application of a machine learning method, specifically a convolutional autoencoder model, that learns to: (1) discover a low-dimensional code (8-dimensional) to describe droplet shapes within a concentrated emulsion, and (2) predict whether the drop will become unstable and undergo break-up. The input consists of images (N = 500 002) of two-dimensional droplet boundaries extracted from movies of a concentrated emulsion flowing through a confined microfluidic channel as a monolayer. The model is able to faithfully reconstruct droplet shapes, as well as to achieve a classification accuracy of 91.7% in the prediction of droplet break-up, compared with ∼60% using conventional scalar descriptors based on droplet elongation. It is observed that 4 out of the 8 dimensions of the code are interpretable, corresponding to drop skewness, elongation, throat size, and surface curvature, respectively. Furthermore, the results show that drop elongation, throat size, and surface curvature are dominant factors in predicting droplet break-up for the flow conditions tested. The method presented is expected to facilitate follow-on work to identify the relationship between drop shapes and the interactions with other drops, and to identify potentially new modes of break-up mechanisms in a concentrated system. Finally, the method developed here should also apply to other soft materials such as foams, gels, and cells and tissues.

Combining satellite imagery and machine learning to predict poverty.

Reliable data on economic livelihoods remain scarce in the developing world, hampering efforts to study these outcomes and to design policies that improve them. Here we demonstrate an accurate, inexpensive, and scalable method for estimating consumption expenditure and asset wealth from high-resolution satellite imagery. Using survey and satellite data from five African countries--Nigeria, Tanzania, Uganda, Malawi, and Rwanda--we show how a convolutional neural network can be trained to identify image features that can explain up to 75% of the variation in local-level economic outcomes. Our method, which requires only publicly available data, could transform efforts to track and target poverty in developing countries. It also demonstrates how powerful machine learning techniques can be applied in a setting with limited training data, suggesting broad potential application across many scientific domains.