All Publications


  • Routine asymptomatic testing strategies for airline travel during the COVID-19 pandemic: a simulation study. The Lancet. Infectious diseases Kiang, M. V., Chin, E. T., Huynh, B. Q., Chapman, L. A., Rodriguez-Barraquer, I., Greenhouse, B., Rutherford, G. W., Bibbins-Domingo, K., Havlir, D., Basu, S., Lo, N. C. 2021

    Abstract

    BACKGROUND: Routine viral testing strategies for SARS-CoV-2 infection might facilitate safe airline travel during the COVID-19 pandemic and mitigate global spread of the virus. However, the effectiveness of these test-and-travel strategies to reduce passenger risk of SARS-CoV-2 infection and population-level transmission remains unknown.METHODS: In this simulation study, we developed a microsimulation of SARS-CoV-2 transmission in a cohort of 100000 US domestic airline travellers using publicly available data on COVID-19 clinical cases and published natural history parameters to assign individuals one of five health states of susceptible to infection, latent period, early infection, late infection, or recovered. We estimated a per-day risk of infection with SARS-CoV-2 corresponding to a daily incidence of 150 infections per 100000 people. We assessed five testing strategies: (1) anterior nasal PCR test within 3 days of departure, (2) PCR within 3 days of departure and 5 days after arrival, (3) rapid antigen test on the day of travel (assuming 90% of the sensitivity of PCR during active infection), (4) rapid antigen test on the day of travel and PCR test 5 days after arrival, and (5) PCR test 5 days after arrival. Strategies 2 and 4 included a 5-day quarantine after arrival. The travel period was defined as 3 days before travel to 2 weeks after travel. Under each scenario, individuals who tested positive before travel were not permitted to travel. The primary study outcome was cumulative number of infectious days in the cohort over the travel period without isolation or quarantine (population-level transmission risk), and the key secondary outcome was the number of infectious people detected on the day of travel (passenger risk of infection).FINDINGS: We estimated that in a cohort of 100000 airline travellers, in a scenario with no testing or screening, there would be 8357 (95% uncertainty interval 6144-12831) infectious days with 649 (505-950) actively infectious passengers on the day of travel. The pre-travel PCR test reduced the number of infectious days from 8357 to 5401 (3917-8677), a reduction of 36% (29-41) compared with the base case, and identified 569 (88% [76-92]) of 649 actively infectious travellers on the day of flight; the addition of post-travel quarantine and PCR reduced the number of infectious days to 2520 days (1849-4158), a reduction of 70% (64-75) compared with the base case. The rapid antigen test on the day of travel reduced the number of infectious days to 5674 (4126-9081), a reduction of 32% (26-38) compared with the base case, and identified 560 (86% [83-89]) actively infectious travellers; the addition of post-travel quarantine and PCR reduced the number of infectious days to 3124 (2356-495), a reduction of 63% (58-66) compared with the base case. The post-travel PCR alone reduced the number of infectious days to 4851 (3714-7679), a reduction of 42% (35-49) compared with the base case.INTERPRETATION: Routine asymptomatic testing for SARS-CoV-2 before travel can be an effective strategy to reduce passenger risk of infection during travel, although abbreviated quarantine with post-travel testing is probably needed to reduce population-level transmission due to importation of infection when travelling from a high to low incidence setting.FUNDING: University of California, San Francisco.

    View details for DOI 10.1016/S1473-3099(21)00134-1

    View details for PubMedID 33765417

  • Frequency of Routine Testing for Coronavirus Disease 2019 (COVID-19) in High-risk Healthcare Environments to Reduce Outbreaks. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America Chin, E. T., Huynh, B. Q., Chapman, L. A., Murrill, M., Basu, S., Lo, N. C. 2020

    Abstract

    Routine asymptomatic testing strategies for COVID-19 have been proposed to prevent outbreaks in high-risk healthcare environments. We used simulation modeling to evaluate the optimal frequency of viral testing. We found that routine testing substantially reduces risk of outbreaks, but may need to be as frequent as twice weekly.

    View details for DOI 10.1093/cid/ciaa1383

    View details for PubMedID 33570097

  • Projected geographic disparities in healthcare worker absenteeism from COVID-19 school closures and the economic feasibility of child care subsidies: a simulation study. BMC medicine Chin, E. T., Huynh, B. Q., Lo, N. C., Hastie, T., Basu, S. 2020; 18 (1): 218

    Abstract

    BACKGROUND: School closures have been enacted as a measure of mitigation during the ongoing coronavirus disease 2019 (COVID-19) pandemic. It has been shown that school closures could cause absenteeism among healthcare workers with dependent children, but there remains a need for spatially granular analyses of the relationship between school closures and healthcare worker absenteeism to inform local community preparedness.METHODS: We provide national- and county-level simulations of school closures and unmet child care needs across the USA. We develop individual simulations using county-level demographic and occupational data, and model school closure effectiveness with age-structured compartmental models. We perform multivariate quasi-Poisson ecological regressions to find associations between unmet child care needs and COVID-19 vulnerability factors.RESULTS: At the national level, we estimate the projected rate of unmet child care needs for healthcare worker households to range from 7.4 to 8.7%, and the effectiveness of school closures as a 7.6% and 8.4% reduction in fewer hospital and intensive care unit (ICU) beds, respectively, at peak demand when varying across initial reproduction number estimates by state. At the county level, we find substantial variations of projected unmet child care needs and school closure effects, 9.5% (interquartile range (IQR) 8.2-10.9%) of healthcare worker households and 5.2% (IQR 4.1-6.5%) and 6.8% (IQR 4.8-8.8%) reduction in fewer hospital and ICU beds, respectively, at peak demand. We find significant positive associations between estimated levels of unmet child care needs and diabetes prevalence, county rurality, and race (p<0.05). We estimate costs of absenteeism and child care and observe from our models that an estimated 76.3 to 96.8% of counties would find it less expensive to provide child care to all healthcare workers with children than to bear the costs of healthcare worker absenteeism during school closures.CONCLUSIONS: School closures are projected to reduce peak ICU and hospital demand, but could disrupt healthcare systems through absenteeism, especially in counties that are already particularly vulnerable to COVID-19. Child care subsidies could help circumvent the ostensible trade-off between school closures and healthcare worker absenteeism.

    View details for DOI 10.1186/s12916-020-01692-w

    View details for PubMedID 32664927

  • Projected geographic disparities in healthcare worker absenteeism from COVID-19 school closures and the economic feasibility of child care subsidies: a simulation study. medRxiv : the preprint server for health sciences Chin, E. T., Huynh, B. Q., Lo, N. C., Hastie, T. n., Basu, S. n. 2020

    Abstract

    School closures have been enacted as a measure of mitigation during the ongoing COVID-19 pandemic. It has been shown that school closures could cause absenteeism amongst healthcare workers with dependent children, but there remains a need for spatially granular analyses of the relationship between school closures and healthcare worker absenteeism to inform local community preparedness.We provide national- and county-level simulations of school closures and unmet child care needs across the United States. We develop individual simulations using county-level demographic and occupational data, and model school closure effectiveness with age-structured compartmental models. We perform multivariate quasi-Poisson ecological regressions to find associations between unmet child care needs and COVID-19 vulnerability factors.At the national level, we estimate the projected rate of unmet child care needs for healthcare worker households to range from 7.5% to 8.6%, and the effectiveness of school closures to range from 3.2% (R0 = 4) to 7.2% (R0 = 2) reduction in fewer ICU beds at peak demand. At the county-level, we find substantial variations of projected unmet child care needs and school closure effects, ranging from 1.9% to 18.3% of healthcare worker households and 5.7% to 8.8% reduction in fewer ICU beds at peak demand (R0 = 2). We find significant positive associations between estimated levels of unmet child care needs and diabetes prevalence, county rurality, and race (p < 0.05). We estimate costs of absenteeism and child care and observe from our models that an estimated 71.1% to 98.8% of counties would find it less expensive to provide child care to all healthcare workers with children than to bear the costs of healthcare worker absenteeism during school closures.School closures are projected to reduce peak ICU bed demand, but could disrupt healthcare systems through absenteeism, especially in counties that are already particularly vulnerable to COVID-19. Child care subsidies could help circumvent the ostensible tradeoff between school closures and healthcare worker absenteeism.

    View details for DOI 10.1101/2020.03.19.20039404

    View details for PubMedID 32511455

    View details for PubMedCentralID PMC7239083

  • Frequency of routine testing for SARS-CoV-2 to reduce transmission among workers. medRxiv : the preprint server for health sciences Chin, E. T., Lo, N. C., Huynh, B. Q., Murrill, M. n., Basu, S. n. 2020

    Abstract

    Shelter-in-place policies have been considered effective in mitigating the transmission of the virus SARS-CoV-2. To end such policies, routine testing and self-quarantine of those testing positive for active infection have been proposed, yet it remains unclear how often routine testing would need to be performed among workers returning to workplaces, and how effective this strategy would be to meaningfully prevent continued transmission of the virus. We simulated SARS-CoV-2 polymerase chain reaction testing to estimate the frequency of testing needed to avert continued epidemic propagation as shelter-in-place orders are relaxed. We find that testing strategies less frequent than twice weekly (e.g. weekly testing or testing once prior to returning to work) are unlikely to prevent workforce outbreaks. Even given unlimited testing capacity, the impact of frequent testing may not be sufficient to reliably relax shelter-in-place policies without risking continued epidemic propagation, unless other measures are instituted to complement testing and self-isolation.

    View details for DOI 10.1101/2020.04.30.20087015

    View details for PubMedID 32511523

    View details for PubMedCentralID PMC7273291

  • Forecasting Internally Displaced Population Migration Patterns in Syria and Yemen. Disaster medicine and public health preparedness Huynh, B. Q., Basu, S. 2019: 1–6

    Abstract

    OBJECTIVES: Armed conflict has contributed to an unprecedented number of internally displaced persons (IDPs), individuals who are forced out of their homes but remain within their country. IDPs often urgently require shelter, food, and healthcare, yet prediction of when IDPs will migrate to an area remains a major challenge for aid delivery organizations. We sought to develop an IDP migration forecasting framework that could empower humanitarian aid groups to more effectively allocate resources during conflicts.METHODS: We modeled monthly IDP migration between provinces within Syria and within Yemen using data on food prices, fuel prices, wages, location, time, and conflict reports. We compared machine learning methods with baseline persistence methods of forecasting.RESULTS: We found a machine learning approach that more accurately forecast migration trends than baseline persistence methods. A random forest model outperformed the best persistence model in terms of root mean square error of log migration by 26% and 17% for the Syria and Yemen datasets, respectively.CONCLUSIONS: Integrating diverse data sources into a machine learning model appears to improve IDP migration prediction. Further work should examine whether implementation of such models can enable proactive aid allocation for IDPs in anticipation of forecast arrivals.

    View details for DOI 10.1017/dmp.2019.73

    View details for PubMedID 31452495

  • Breast lesion classification based on dynamic contrast-enhanced magnetic resonance images sequences with long short-term memory networks. Journal of medical imaging (Bellingham, Wash.) Antropova, N., Huynh, B., Li, H., Giger, M. L. 2019; 6 (1): 011002

    Abstract

    We present a breast lesion classification methodology, based on four-dimensional (4-D) dynamic contrast-enhanced magnetic resonance images (DCE-MRI), using recurrent neural networks in combination with a pretrained convolutional neural network (CNN). The method enables to capture not only the two-dimensional image features but also the temporal enhancement patterns presented in DCE-MRI. We train a long short-term memory (LSTM) network on temporal sequences of feature vectors extracted from the dynamic MRI sequences. To capture the local changes in lesion enhancement, the feature vectors are obtained from various levels of a pretrained CNN. We compare the LSTM method's performance to that of a CNN fine-tuned on "RGB" MRIs, formed by precontrast, first, and second postcontrast MRIs. LSTM significantly outperformed the fine-tuned CNN, resulting in AUC LSTM = 0.88 and AUC fine - tuned = 0.84 , p = 0.00085 , in the task of distinguishing benign and malignant lesions. Our method captures clinically useful information carried by the full 4-D dynamic MRI sequence and outperforms the standard fine-tuning method.

    View details for PubMedID 30840721

  • Recurrent Neural Networks for Breast Lesion Classification based on DCE-MRIs Antropova, N., Huynh, B., Giger, M., Petrick, N., Mori, K. SPIE-INT SOC OPTICAL ENGINEERING. 2018

    View details for DOI 10.1117/12.2293265

    View details for Web of Science ID 000432546900091

  • Deep learning in breast cancer risk assessment: evaluation of convolutional neural networks on a clinical dataset of full-field digital mammograms. Journal of medical imaging (Bellingham, Wash.) Li, H. n., Giger, M. L., Huynh, B. Q., Antropova, N. O. 2017; 4 (4): 041304

    Abstract

    To evaluate deep learning in the assessment of breast cancer risk in which convolutional neural networks (CNNs) with transfer learning are used to extract parenchymal characteristics directly from full-field digital mammographic (FFDM) images instead of using computerized radiographic texture analysis (RTA), 456 clinical FFDM cases were included: a "high-risk" BRCA1/2 gene-mutation carriers dataset (53 cases), a "high-risk" unilateral cancer patients dataset (75 cases), and a "low-risk dataset" (328 cases). Deep learning was compared to the use of features from RTA, as well as to a combination of both in the task of distinguishing between high- and low-risk subjects. Similar classification performances were obtained using CNN [area under the curve [Formula: see text]; standard error [Formula: see text]] and RTA ([Formula: see text]; [Formula: see text]) in distinguishing BRCA1/2 carriers and low-risk women. However, in distinguishing unilateral cancer patients and low-risk women, performance was significantly greater with CNN ([Formula: see text]; [Formula: see text]) compared to RTA ([Formula: see text]; [Formula: see text]). Fusion classifiers performed significantly better than the RTA-alone classifiers with AUC values of 0.86 and 0.84 in differentiating BRCA1/2 carriers from low-risk women and unilateral cancer patients from low-risk women, respectively. In conclusion, deep learning extracted parenchymal characteristics from FFDMs performed as well as, or better than, conventional texture analysis in the task of distinguishing between cancer risk populations.

    View details for PubMedID 28924576

    View details for PubMedCentralID PMC5596198

  • A deep feature fusion methodology for breast cancer diagnosis demonstrated on three imaging modality datasets. Medical physics Antropova, N. n., Huynh, B. Q., Giger, M. L. 2017

    Abstract

    Deep learning methods for radiomics/computer-aided diagnosis (CADx) are often prohibited by small datasets, long computation time, and the need for extensive image preprocessing.We aim to develop a breast CADx methodology that addresses the aforementioned issues by exploiting the efficiency of pre-trained convolutional neural networks (CNNs) and using pre-existing handcrafted CADx features.We present a methodology that extracts and pools low- to mid-level features using a pretrained CNN and fuses them with handcrafted radiomic features computed using conventional CADx methods. Our methodology is tested on three different clinical imaging modalities (dynamic contrast enhanced-MRI [690 cases], full-field digital mammography [245 cases], and ultrasound [1125 cases]).From ROC analysis, our fusion-based method demonstrates, on all three imaging modalities, statistically significant improvements in terms of AUC as compared to previous breast cancer CADx methods in the task of distinguishing between malignant and benign lesions. (DCE-MRI [AUC = 0.89 (se = 0.01)], FFDM [AUC = 0.86 (se = 0.01)], and ultrasound [AUC = 0.90 (se = 0.01)]).We proposed a novel breast CADx methodology that can be used to more effectively characterize breast lesions in comparison to existing methods. Furthermore, our proposed methodology is computationally efficient and circumvents the need for image preprocessing.

    View details for PubMedID 28681390

  • Digital mammographic tumor classification using transfer learning from deep convolutional neural networks. Journal of medical imaging (Bellingham, Wash.) Huynh, B. Q., Li, H., Giger, M. L. 2016; 3 (3): 034501-?

    Abstract

    Convolutional neural networks (CNNs) show potential for computer-aided diagnosis (CADx) by learning features directly from the image data instead of using analytically extracted features. However, CNNs are difficult to train from scratch for medical images due to small sample sizes and variations in tumor presentations. Instead, transfer learning can be used to extract tumor information from medical images via CNNs originally pretrained for nonmedical tasks, alleviating the need for large datasets. Our database includes 219 breast lesions (607 full-field digital mammographic images). We compared support vector machine classifiers based on the CNN-extracted image features and our prior computer-extracted tumor features in the task of distinguishing between benign and malignant breast lesions. Five-fold cross validation (by lesion) was conducted with the area under the receiver operating characteristic (ROC) curve as the performance metric. Results show that classifiers based on CNN-extracted features (with transfer learning) perform comparably to those using analytically extracted features [area under the ROC curve [Formula: see text]]. Further, the performance of ensemble classifiers based on both types was significantly better than that of either classifier type alone ([Formula: see text] versus 0.81, [Formula: see text]). We conclude that transfer learning can improve current CADx methods while also providing standalone classifiers without large datasets, facilitating machine-learning methods in radiomics and precision medicine.

    View details for DOI 10.1117/1.JMI.3.3.034501

    View details for PubMedID 27610399