Dataset Information

Raman spectroscopy and artificial intelligence to predict the Bayesian probability of breast cancer.

ABSTRACT: This study addresses the core issue facing a surgical team during breast cancer surgery: quantitative prediction of tumor likelihood including estimates of prediction error. We have previously reported that a molecular probe, Laser Raman spectroscopy (LRS), can distinguish healthy and tumor tissue. We now report that combining LRS with two machine learning algorithms, unsupervised k-means and stochastic nonlinear neural networks (NN), provides rapid, quantitative, probabilistic tumor assessment with real-time error analysis. NNs were first trained on Raman spectra using human expert histopathology diagnostics as gold standard (74 spectra, 5 patients). K-means predictions using spectral data when compared to histopathology produced clustering models with 93.2-94.6% accuracy, 89.8-91.8% sensitivity, and 100% specificity. NNs trained on k-means predictions generated probabilities of correctness for the autonomous classification. Finally, the autonomous system characterized an extended dataset (203 spectra, 8 patients). Our results show that an increase in DNA|RNA signal intensity in the fingerprint region (600-1800 cm^-1) and global loss of high wavenumber signal (2800-3200 cm^-1) are particularly sensitive LRS warning signs of tumor. The stochastic nature of NNs made it possible to rapidly generate multiple models of target tissue classification and calculate the inherent error in the probabilistic estimates for each target.

SUBMITTER: Kothari R

PROVIDER: S-EPMC7985361 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

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Raman spectroscopy and artificial intelligence to predict the Bayesian probability of breast cancer.

Kothari Ragini R Jones Veronica V Mena Dominique D Bermúdez Reyes Viviana V Shon Youkang Y Smith Jennifer P JP Schmolze Daniel D Cha Philip D PD Lai Lily L Fong Yuman Y Storrie-Lombardi Michael C MC

Scientific reports 20210322 1

This study addresses the core issue facing a surgical team during breast cancer surgery: quantitative prediction of tumor likelihood including estimates of prediction error. We have previously reported that a molecular probe, Laser Raman spectroscopy (LRS), can distinguish healthy and tumor tissue. We now report that combining LRS with two machine learning algorithms, unsupervised k-means and stochastic nonlinear neural networks (NN), provides rapid, quantitative, probabilistic tumor assessment ...[more]

PMID: 33753760

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Project description:Inflammatory bowel diseases (IBD) are chronic inflammatory disorders that can be categorized as ulcerative colitis (UC), Crohn’s disease (CD) and indeterminate colitis (IC). Deep remission has been shown to improve disease outcome. There may be a lack of concordance between endoscopic and histologic remission. IBD patients with long standing colitis are at risk of developing dysplasia and colorectal cancer (CRC). However, it can be challenging to diagnose dysplasia in IBD patients during colonoscopy, as dysplasia frequently manifests as non-pedunculated lesions that present with only subtle visible changes or are even invisible due to the surrounding inflammation, scarring, pseudopolyps, or hyperplasia. Although white light endoscopy and chromoendoscopy are the current standard modality of imaging, there is still a gap to be bridged, in terms of improving endoscopic diagnosis of dysplasia and improving concordance of endoscopic and histologic remission. Raman spectroscopy is an inelastic light scattering technique provide specific fingerprints of molecular compositions and structures of biological tissues. It may be able to provide additional diagnostic information over standard endoscopy. A second-generation Raman endoscope system for improving in vivo tissue characterization and diagnosis during colonoscopy has been developed (SPECTRA IMDx system). Preliminary data suggested its utility in the diagnosis of colorectal neoplasia during colonoscopy. There is currently a lack of data concerning the application of this novel technology in the context of IBD. Specifically, whether the spectral signals generated can be used to better classify disease remission, and thus achieve higher concordance with histology when compared to standard endoscopy. It is also unclear whether this technology can be used to differentiate dysplastic mucosa from non-dysplastic mucosal in IBD patients. Hypotheses 1. Raman spectroscopy based artificial intelligence system has the potential to be used to differentiate disease remission from active mucosal inflammation and hence improve concordance between endoscopic and histologic remission, with the potential to decrease the need for random biopsies real-time during colonoscopy. 2. Raman spectroscopy based artificial intelligence system has the potential to differentiate dysplastic mucosa in IBD patients (low grade and high grade dysplasia; colorectal cancer) from non-dysplastic mucosa. real-time during colonoscopy.

Project description:ImportanceEarly breast cancer detection is associated with lower morbidity and mortality.ObjectiveTo examine whether a commercial artificial intelligence (AI) algorithm for breast cancer detection could estimate the development of future cancer.Design, setting, and participantsThis retrospective cohort study of 116 495 women aged 50 to 69 years with no prior history of breast cancer before they underwent at least 3 consecutive biennial screening examinations used scores from an AI algorithm (INSIGHT MMG, version 1.1.7.2; Lunit Inc; used September 28, 2022, to April 5, 2023) for breast cancer detection and screening data from multiple, consecutive rounds of mammography performed from September 13, 2004, to December 21, 2018, at 9 breast centers in Norway. The statistical analyses were performed from September 2023 to August 2024.ExposureArtificial intelligence algorithm score indicating suspicion for the presence of breast cancer. The algorithm provided a continuous cancer detection score for each examination ranging from 0 to 100, with increasing values indicating a higher likelihood of cancer being present on the current mammogram.Main outcomes and measuresMaximum AI algorithm score for cancer detection and absolute difference in score among breasts of women developing screening-detected cancer, women with interval cancer, and women who screened negative.ResultsThe mean (SD) age at the first study round was 58.5 (4.5) years for 1265 women with screening-detected cancer in the third round, 57.4 (4.6) years for 342 women with interval cancer after 3 negative screening rounds, and 56.4 (4.9) years for 116 495 women without breast cancer all 3 screening rounds. The mean (SD) absolute differences in AI scores among breasts of women developing screening-detected cancer were 21.3 (28.1) at the first study round, 30.7 (32.5) at the second study round, and 79.0 (28.9) at the third study round. The mean (SD) differences prior to interval cancer were 19.7 (27.0) at the first study round, 21.0 (27.7) at the second study round, and 34.0 (33.6) at the third study round. The mean (SD) differences among women who did not develop breast cancer were 9.9 (17.5) at the first study round, 9.6 (17.4) at the second study round, and 9.3 (17.3) at the third study round. Areas under the receiver operating characteristic curve for the absolute difference were 0.63 (95% CI, 0.61-0.65) at the first study round, 0.72 (95% CI, 0.71-0.74) at the second study round, and 0.96 (95% CI, 0.95-0.96) at the third study round for screening-detected cancer and 0.64 (95% CI, 0.61-0.67) at the first study round, 0.65 (95% CI, 0.62-0.68) at the second study round, and 0.77 (95% CI, 0.74-0.79) at the third study round for interval cancers.Conclusions and relevanceIn this retrospective cohort study of women undergoing screening mammography, mean absolute AI scores were higher for breasts developing vs not developing cancer 4 to 6 years before their eventual detection. These findings suggest that commercial AI algorithms developed for breast cancer detection may identify women at high risk of a future breast cancer, offering a pathway for personalized screening approaches that can lead to earlier cancer diagnosis.

Project description:The accurate analytical characterization of metastatic phenotype at primary tumor diagnosis and its evolution with time are critical for controlling metastatic progression of cancer. Here, we report a label-free optical strategy using Raman spectroscopy and machine learning to identify distinct metastatic phenotypes observed in tumors formed by isogenic murine breast cancer cell lines of progressively increasing metastatic propensities. Methods: We employed the 4T1 isogenic panel of murine breast cancer cells to grow tumors of varying metastatic potential and acquired label-free spectra using a fiber probe-based portable Raman spectroscopy system. We used MCR-ALS and random forests classifiers to identify putative spectral markers and predict metastatic phenotype of tumors based on their optical spectra. We also used tumors derived from 4T1 cells silenced for the expression of TWIST, FOXC2 and CXCR3 genes to assess their metastatic phenotype based on their Raman spectra. Results: The MCR-ALS spectral decomposition showed consistent differences in the contribution of components that resembled collagen and lipids between the non-metastatic 67NR tumors and the metastatic tumors formed by FARN, 4T07, and 4T1 cells. Our Raman spectra-based random forest analysis provided evidence that machine learning models built on spectral data can allow the accurate identification of metastatic phenotype of independent test tumors. By silencing genes critical for metastasis in highly metastatic cell lines, we showed that the random forest classifiers provided predictions consistent with the observed phenotypic switch of the resultant tumors towards lower metastatic potential. Furthermore, the spectral assessment of lipid and collagen content of these tumors was consistent with the observed phenotypic switch. Conclusion: Overall, our findings indicate that Raman spectroscopy may offer a novel strategy to evaluate metastatic risk during primary tumor biopsies in clinical patients.

Project description:PurposeThis study aimed to develop a machine learning model to retrospectively study and predict the recurrence risk of breast cancer patients after surgery by extracting the clinicopathological features of tumors from unstructured clinical electronic health record (EHR) data.MethodsThis retrospective cohort included 1,841 breast cancer patients who underwent surgical treatment. To extract the principal features associated with recurrence risk, the clinical notes and histopathology reports of patients were collected and feature engineering was used. Predictive models were next conducted based on this important information. All algorithms were implemented using Python software. The accuracy of prediction models was further verified in the test cohort. The area under the curve (AUC), precision, recall, and F1 score were adopted to evaluate the performance of each model.ResultsA training cohort with 1,289 patients and a test cohort with 552 patients were recruited. From 2011 to 2019, a total of 1,841 textual reports were included. For the prediction of recurrence risk, both LSTM, XGBoost, and SVM had favorable accuracies of 0.89, 0.86, and 0.78. The AUC values of the micro-average ROC curve corresponding to LSTM, XGBoost, and SVM were 0.98 ± 0.01, 0.97 ± 0.03, and 0.92 ± 0.06. Especially the LSTM model achieved superior execution than other models. The accuracy, F1 score, macro-avg F1 score (0.87), and weighted-avg F1 score (0.89) of the LSTM model produced higher values. All P values were statistically significant. Patients in the high-risk group predicted by our model performed more resistant to DNA damage and microtubule targeting drugs than those in the intermediate-risk group. The predicted low-risk patients were not statistically significant compared with intermediate- or high-risk patients due to the small sample size (188 low-risk patients were predicted via our model, and only two of them were administered chemotherapy alone after surgery). The prognosis of patients predicted by our model was consistent with the actual follow-up records.ConclusionsThe constructed model accurately predicted the recurrence risk of breast cancer patients from EHR data and certainly evaluated the chemoresistance and prognosis of patients. Therefore, our model can help clinicians to formulate the individualized management of breast cancer patients.

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Raman spectroscopy and artificial intelligence to predict the Bayesian probability of breast cancer.

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Raman spectroscopy and artificial intelligence to predict the Bayesian probability of breast cancer.

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