Accurate virus identification with interpretable Raman signatures by machine learning.

Rapid identification of newly emerging or circulating viruses is an important first step toward managing the public health response to potential outbreaks. A portable virus capture device, coupled with label-free Raman spectroscopy, holds the promise of fast detection by rapidly obtaining the Raman signature of a virus followed by a machine learning (ML) approach applied to recognize the virus based on its Raman spectrum, which is used as a fingerprint. We present such an ML approach for analyzing Raman spectra of human and avian viruses. A convolutional neural network (CNN) classifier specifically designed for spectral data achieves very high accuracy for a variety of virus type or subtype identification tasks. In particular, it achieves 99% accuracy for classifying influenza virus type A versus type B, 96% accuracy for classifying four subtypes of influenza A, 95% accuracy for differentiating enveloped and nonenveloped viruses, and 99% accuracy for differentiating avian coronavirus (infectious bronchitis virus [IBV]) from other avian viruses. Furthermore, interpretation of neural net responses in the trained CNN model using a full-gradient algorithm highlights Raman spectral ranges that are most important to virus identification. By correlating ML-selected salient Raman ranges with the signature ranges of known biomolecules and chemical functional groups­for example, amide, amino acid, and carboxylic acid­we verify that our ML model effectively recognizes the Raman signatures of proteins, lipids, and other vital functional groups present in different viruses and uses a weighted combination of these signatures to identify viruses.

Prediction of histologic grade and type of small (< 4 cm) papillary renal cell carcinomas using texture and neural network analysis: a feasibility study.

OBJECTIVE: To predict the histologic grade and type of small papillary renal cell carcinomas (pRCCs) using texture analysis and machine learning algorithms. METHODS: This was a retrospective HIPAA-compliant study. 24 noncontrast (NC), 22 corticomedullary (CM) phase, and 24 nephrographic (NG) phase CTs of small (< 4 cm) surgically resected pRCCs were identified. Surgical pathology classified the tumors as low- or high-Fuhrman histologic grade and type 1 or 2. The axial image with the largest cross-sectional tumor area was exported and segmented. Six histogram and 31 texture (20 gray-level co-occurrences and 11 gray-level run-lengths) features were calculated for each tumor in each phase. Feature values in low- versus high-grade and type 1 versus 2 pRCCs were compared. Area under the receiver operating curve (AUC) was calculated for each feature to assess prediction of histologic grade and type of pRCCs in each phase. Histogram, texture, and combined histogram and texture feature sets were used to train and test three classification algorithms (support vector machine (SVM), random forest, and histogram-based gradient boosting decision tree (HGBDT)) with stratified shuffle splits and threefold cross-validation; AUCs were calculated for each algorithm in each phase to assess prediction of histologic grade and type of pRCCs. RESULTS: Individual histogram and texture features did not have statistically significant differences between low- and high-grade or type 1 and type 2 pRCCs across all phases. Individual features had low predictive power for tumor grade or type in all phases (AUC < 0.70). HGBDT was highly accurate at predicting pRCC histologic grade and type using histogram, texture or combined histogram and texture feature data from the CM phase (AUCs = 0.97-1.0). All algorithms had highest AUCs using CM phase feature data sets; AUCs decreased using feature sets from NC or NG phases. CONCLUSIONS: The histologic grade and type of small pRCCs can be predicted with classification algorithms using CM histogram and texture features, which outperform NC and NG phase image data. The accurate prediction of pRCC histologic grade and type may be able to further guide management of patients with small (< 4 cm) pRCCs being considered for active surveillance.