Exploring convolutional neural networks and spatial video for on-the-ground mapping in informal settlements.

BACKGROUND: The health burden in developing world informal settlements often coincides with a lack of spatial data that could be used to guide intervention strategies. Spatial video (SV) has proven to be a useful tool to collect environmental and social data at a granular scale, though the effort required to turn these spatially encoded video frames into maps limits sustainability and scalability. In this paper we explore the use of convolution neural networks (CNN) to solve this problem by automatically identifying disease related environmental risks in a series of SV collected from Haiti. Our objective is to determine the potential of machine learning in health risk mapping for these environments by assessing the challenges faced in adequately training the required classification models. RESULTS: We show that SV can be a suitable source for automatically identifying and extracting health risk features using machine learning. While well-defined objects such as drains, buckets, tires and animals can be efficiently classified, more amorphous masses such as trash or standing water are difficult to classify. Our results further show that variations in the number of image frames selected, the image resolution, and combinations of these can be used to improve the overall model performance. CONCLUSION: Machine learning in combination with spatial video can be used to automatically identify environmental risks associated with common health problems in informal settlements, though there are likely to be variations in the type of data needed for training based on location. Success based on the risk type being identified are also likely to vary geographically. However, we are confident in identifying a series of best practices for data collection, model training and performance in these settings. We also discuss the next step of testing these findings in other environments, and how adding in the simultaneously collected geographic data could be used to create an automatic health risk mapping tool.

The Use of Spatial Video to Map Dynamic and Challenging Environments: A Case Study of Cholera Risk in the Mujoga Relief Camp, D.R.C.

In this paper, we provide an overview of how spatial video data collection enriched with contextual mapping can be used as a universal tool to investigate sub-neighborhood scale health risks, including cholera, in challenging environments. To illustrate the method's flexibility, we consider the life cycle of the Mujoga relief camp set up after the Nyiragongo volcanic eruption in the Democratic Republic of Congo on 22 May 2021. More specifically we investigate how these methods have captured the deteriorating conditions in a camp which is also experiencing lab-confirmed cholera cases. Spatial video data are collected every month from June 2021 to March 2022. These coordinate-tagged images are used to make monthly camp maps, which are then returned to the field teams for added contextual insights. At the same time, a zoom-based geonarrative is used to discuss the camp's changes, including the cessation of free water supplies and the visible deterioration of toilet facilities. The paper concludes by highlighting the next data science advances to be made with SV mapping, including machine learning to automatically identify and map risks, and how these are already being applied in Mujoga.

Spatial Patterns of COVID-19 Vaccination Coverage by Social Vulnerability Index and Designated COVID-19 Vaccine Sites in Texas.

Equitable access to the COVID-19 vaccine remains a public health priority. This study explores the association between ZIP Code−Tabulation Area level Social Vulnerability Indices (SVI) and COVID-19 vaccine coverage in Texas. A mixed-effects, multivariable, random-intercept negative binomial model was used to explore the association between ZIP Code−Tabulation Area level SVI and COVID-19 vaccination coverage stratified by the availability of a designated vaccine access site. Lower COVID-19 vaccine coverage was observed in ZIP codes with the highest overall SVIs (adjusted mean difference (aMD) = −13, 95% CI, −23.8 to −2.1, p < 0.01), socioeconomic characteristics theme (aMD = −16.6, 95% CI, −27.3 to −5.7, p = 0.01) and housing and transportation theme (aMD = −18.3, 95% CI, −29.6 to −7.1, p < 0.01) compared with the ZIP codes with the lowest SVI scores. The vaccine coverage was lower in ZIP Code−Tabulation Areas with higher median percentages of Hispanics (aMD = −3.3, 95% CI, −6.5 to −0.1, p = 0.04) and Blacks (aMD = −3.7, 95% CI, −6.4 to −1, p = 0.01). SVI negatively impacted COVID-19 vaccine coverage in Texas. Access to vaccine sites did not address disparities related to vaccine coverage among minority populations. These findings are relevant to guide the distribution of COVID-19 vaccines in regions with similar demographic and geospatial characteristics.

Spatial Video and EpiExplorer: A Field Strategy to Contextualize Enteric Disease Risk in Slum Environments.

Disease risk associated with contaminated water, poor sanitation, and hygiene in informal settlement environments is conceptually well understood. From an analytical perspective, collecting data at a suitably fine scale spatial and temporal granularity is challenging. Novel mobile methodologies, such as spatial video (SV), can complement more traditional epidemiological field work to address this gap. However, this work then poses additional challenges in terms of analytical visualizations that can be used to both understand sub-neighborhood patterns of risk, and even provide an early warning system. In this paper, we use bespoke spatial programming to create a framework for flexible, fine-scale exploratory investigations of simultaneously-collected water quality and environmental surveys in three different informal settlements of Port-au-Prince, Haiti. We dynamically mine these spatio-temporal epidemiological and environmental data to provide insights not easily achievable using more traditional spatial software, such as Geographic Information System (GIS). The results include sub-neighborhood maps of localized risk that vary monthly. Most interestingly, some of these epidemiological variations might have previously been erroneously explained because of proximate environmental factors and/or meteorological conditions.

Fine Scale Replicable Risk Mapping in an Informal Settlement: A Case Study of Mathare, Nairobi.

Slums and informal settlements continue to pose considerable health challenges, mostly associated with the unavailability of basic amenities and proper waste management. While mapping where risks occur, such as the location of features associated with disease is obviously beneficial, the spatial data required is frequently not available, especially on a continuous basis. In this paper, we employ a robust, cost-effective, and efficient means of monitoring for these types of environments, using the Mathare SIS in Kenya as an illustration. We show how spatial videos can be used to capture microenvironments around homes or other key features such as toilets and water points, to show localized environmental risks such as standing water and mud. We also show the utility of this approach to capture longitudinal change. The objective of this paper is to illustrate how this method can map changes in the spatial variability of health risks in a challenging environment.

Appreciating the complexity of localized malaria risk in Ghana: Spatial data challenges and solutions.

Various factors have been associated with the ongoing high prevalence of malaria in Ghana. Among these are poor sanitation, low socioeconomic status (SES), building construction and other proximate micro environmental risks, and individual behaviors. What makes the curbing of malaria more challenging, is that for many of the most impacted areas there is little data for modeling or predictions, which are needed, as risk is not homogenous at the sub-neighborhood scale. In this study we use available local surveillance data combined with novel on-the-ground fine scale environmental data collection, to gain an initial understanding of malaria risk for the Teshie township of Accra, Ghana. Mapped environmental risk factors include open drains, stagnant water and trash. Overlaid onto these were clinical data of reported malaria cases collected between 2012 and 2016 at LEKMA hospital. We then enrich these maps with local context using a new method for malaria research, spatial video geonarratives (SVGs). These SVGs provide insights into the underlying spatial-social patterns of risks, to reveal where traditional data collection is lacking, and how and where to develop local intervention strategies.

Multidrug-resistant Staphylococcus aureus Colonization in Healthy Adults Is more Common in Bhutanese Refugees in Nepal than Those Resettled in Ohio.

Although studies have shown that human migration is one of the risk factors for the spread of drug-resistant organisms such as methicillin-resistant Staphylococcus aureus (MRSA), surveillance studies examining MRSA among refugee populations in the US are lacking. This study aimed to assess the prevalence and molecular characteristics of S. aureus among Bhutanese refugees living in Nepal and resettled in Northeast Ohio (NEO). One hundred adult Bhutanese refugees from each geographic location were enrolled between August 2015 and January 2016. The participants were interviewed to collect demographic information and potential risk factors for carriage. Nasal and throat swabs were collected for bacterial isolation. All S. aureus isolates were characterized by spa typing and tested for the presence of Panton-Valentine leukocidin (PVL) and mecA genes; selected isolates were tested by multilocus sequence typing (MLST). The overall prevalence of S. aureus was 66.0% and 44.0% in NEO and Nepal, respectively. In Nepal, 5.8% (3/52) of isolates were MRSA and 1.1% (1/88) in NEO. Twenty-one isolates in NEO (23.9%) were multidrug-resistant S. aureus (MDRSA), while 23 (44.2%) in Nepal were MDRSA. In NEO, 41 spa types were detected from 88 S. aureus isolates. In Nepal, 32 spa types were detected from 52 S. aureus isolates. spa types t1818 and t345 were most common in NEO and Nepal, respectively. The overall prevalence of PVL-positive isolates among S. aureus in Nepal and NEO was 25.0% and 10.2%. ST5 was the most common sequence type in both locations. Bhutanese refugees living in Nepal and resettled in NEO had high prevalence of S. aureus and MDRSA. The findings suggest a potential need for CA-MRSA surveillance among the immigrant population in the U S and among people living in Nepal, and a potential need to devise appropriate public health measures to mitigate the risk imposed by community-associated strains of S. aureus and MRSA.

Micro-Space Complexity and Context in the Space-Time Variation in Enteric Disease Risk for Three Informal Settlements of Port au Prince, Haiti.

Diffusion of cholera and other diarrheal diseases in an informal settlement is a product of multiple behavioral, environmental and spatial risk factors. One of the most important components is the spatial interconnections among water points, drainage ditches, toilets and the intervening environment. This risk is also longitudinal and variable as water points fluctuate in relation to bacterial contamination. In this paper we consider part of this micro space complexity for three informal settlements in Port au Prince, Haiti. We expand on more typical epidemiological analysis of fecal coliforms at water points, drainage ditches and ocean sites by considering the importance of single point location fluctuation coupled with recording micro-space environmental conditions around each sample site. Results show that spatial variation in enteric disease risk occurs within neighborhoods, and that while certain trends are evident, the degree of individual site fluctuation should question the utility of both cross-sectional and more aggregate analysis. Various factors increase the counts of fecal coliform present, including the type of water point, how water was stored at that water point, and the proximity of the water point to local drainage. Some locations fluctuated considerably between being safe and unsafe on a monthly basis. Next steps to form a more comprehensive contextualized understanding of enteric disease risk in these environments should include the addition of behavioral factors and local insight.

Spatial Video Health Risk Mapping in Informal Settlements: Correcting GPS Error.

Informal settlements pose a continuing health concern. While spatial methodologies have proven to be valuable tools to support health interventions, several factors limit their widespread use in these challenging environments. One such technology, spatial video, has been used for fine-scale contextualized mapping. In this paper, we address one of the limitations of the technique: the global positioning system (GPS) coordinate error. More specifically, we show how spatial video coordinate streams can be corrected and synced back to the original video to facilitate risk mapping. Past spatial video collections for the Mathare informal settlement of Kenya are used as an illustration as these data had been previously discarded because of excessive GPS error. This paper will describe the bespoke software that makes these corrections possible, and then will go on to investigate patterns in the coordinate error.