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fionntan

Coronavirus Models Are Nearing Consensus, but Reopening Could Throw Them Off Again - 0 views

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    The researchers say that they are getting better at understanding the dynamics of the pandemic as Americans largely shelter in place, and that improved knowledge may explain the growing consensus of the models. The near-term future of the pandemic is also a little easier to imagine, with deaths flattening instead of growing rapidly. There may be some peer pressure, too. Nicholas Reich, a biostatistician at the University of Massachusetts who has led a project to standardize and compare model outputs, said he worried about the temptation to "herd" outputs. "Probably no one wants to have the really super-outlying low model or the super-outlying high model," he said.
Ben Snaith

Which Covid-19 Data Can You Trust? - 2 views

  • In a crisis situation like the one we are in, data can be an essential tool for crafting responses, allocating resources, measuring the effectiveness of interventions, such as social distancing, and telling us when we might reopen economies. However, incomplete or incorrect data can also muddy the waters, obscuring important nuances within communities, ignoring important factors such as socioeconomic realities, and creating false senses of panic or safety, not to mention other harms such as needlessly exposing private information.
  • Unfortunately, many of these technological solutions — however well intended — do not provide the clear picture they purport to. In many cases, there is insufficient engagement with subject-matter experts, such as epidemiologists who specialize in modeling the spread of infectious diseases or front-line clinicians who can help prioritize needs. But because technology and telecom companies have greater access to mobile device data, enormous financial resources, and larger teams of data scientists, than academic researchers do, their data products are being rolled out at a higher volume than high quality studies.
  • To some extent, all data risk breaching the privacy of individual or group identities, but publishing scorecards for specific neighborhoods risks shaming or punishing communities, while ignoring the socioeconomic realities of people’s lives that make it difficult for them to stay home.
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  • Even more granular examples, such as footfalls at identifiable business locations, risks de-identifying religious groups; patients visiting cancer hospitals, HIV clinics, or reproductive health clinics; or those seeking public assistance. The medical and public health communities long ago deemed the un-masking of such information without consent unacceptable, but companies have recently been releasing it on publicly available dashboards.
  • Until we know more about how these changing movement patterns impact epidemiological aspects of the disease, we should use these data with caution.
  • Simply presenting them, or interpreting them without a proper contextual understanding, could inadvertently lead to imposing or relaxing restrictions on lives and livelihoods, based on incomplete information.
  • In the absence of a tightly coupled testing and treatment plan, however, these apps risk either providing false reassurance to communities where infectious but asymptomatic individuals can continue to spread disease, or requiring an unreasonably large number of people to quarantine. The behavioral response of the population to these apps is therefore unknown and likely to vary significantly across societies.
  • Some contact-tracing apps follow black-box algorithms, which preclude the global community of scientists from refining them or adopting them elsewhere. These non-transparent, un-validated interventions — which are now being rolled out (or rolled back) in countries such as China, India, Israel and Vietnam — are in direct contravention to the open cross-border collaboration that scientists have adopted to address the Covid-19 pandemic.
  • pidemiological models that can help predict the burden and pattern of spread of Covid-19 rely on a number of parameters that are, as yet, wildly uncertain. We still lack many of the basic facts about this disease, including how many people have symptoms, whether people who have been infected are immune to reinfection, and — crucially — how many people have been infected so far. In the absence of reliable virological testing data, we cannot fit models accurately, or know confidently what the future of this epidemic will look like for all these reasons, and yet numbers are being presented to governments and the public with the appearance of certainty
  • Telenor, the Norwegian telco giant has led the way in responsible use of aggregated mobility data from cell phone tower records. Its data have been used, in close collaboration with scientists and local practitioners, to model, predict, and respond to outbreaks around the world. Telenor has openly published its methods and provided technological guidance on how telco data can be used in public health emergencies in a responsible, anonymized format that does not risk de-identification.
  • The Covid-19 Mobility Data Network, of which we are part, comprises a voluntary collaboration of epidemiologists from around the world analyzes aggregated data from technology companies to provide daily insights to city and state officials from California to Dhaka, Bangladesh.
fionntan

Coronavirus exposes the problems and pitfalls of modelling | Science | The Guardian - 1 views

  • The model, based on 13-year-old code for a long-feared influenza pandemic, assumed that the demand for intensive care units would be the same for both infections. Data from China soon showed this to be dangerously wrong, but the model was only updated when more data poured out of Italy, where intensive care was swiftly overwhelmed and deaths shot up.
  • It did not consider the impact of widespread rapid testing, contact tracing and isolation, which can be used in the early stages of an epidemic or in lockdown conditions to keep infections down to such an extent that when restrictions are lifted the virus should not rebound.
Ben Snaith

Improbable's simulation tech could help us build better pandemic models | WIRED UK - 1 views

  • “Agent-based models are particularly good in situations where you need to explicitly model the interactions and the behaviour of the individual components of a system,” says Nick Malleson, a professor of spatial science at the University of Leeds, who has worked with Improbable to study crime patterns. “I think the reason that they've become popular for [studying] disease spread is that very often in a disease spread, you might need to look at how people are interacting – when they come into contact in shops, how the social networks affect how people move, how they behave, how they interact, all these kinds of things.”
Ben Snaith

Mobile phone data for informing public health actions across the COVID-19 pandemic life... - 0 views

  • Decision-making and evaluation or such interventions during all stages of the pandemic life cycle require specific, reliable, and timely data not only about infections but also about human behavior, especially mobility and physical copresence. We argue that mobile phone data, when used properly and carefully, represents a critical arsenal of tools for supporting public health actions across early-, middle-, and late-stage phases of the COVID-19 pandemic.
  • Seminal work on human mobility has shown that aggregate and (pseudo-)anonymized mobile phone data can assist the modeling of the geographical spread of epidemics (7–11).
  • Although ad hoc mechanisms leveraging mobile phone data can be effectively (but not easily) developed at the local or national level, regional or even global collaborations seem to be much more difficult given the number of actors, the range of interests and priorities, the variety of legislations concerned, and the need to protect civil liberties. The global scale and spread of the COVID-19 pandemic highlight the need for a more harmonized or coordinated approach.
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  • Government and public health authorities broadly raise questions in at least four critical areas of inquiries for which the use of mobile phone data is relevant. First, situational awareness questions seek to develop an understanding of the dynamic environment of the pandemic. Mobile phone data can provide access to previously unavailable population estimates and mobility information to enable stakeholders across sectors better understand COVID-19 trends and geographic distribution. Second, cause-and-effect questions seek to help identify the key mechanisms and consequences of implementing different measures to contain the spread of COVID-19. They aim to establish which variables make a difference for a problem and whether further issues might be caused. Third, predictive analysis seeks to identify the likelihood of future outcomes and could, for example, leverage real-time population counts and mobility data to enable predictive capabilities and allow stakeholders to assess future risks, needs, and opportunities. Finally, impact assessments aim to determine which, whether, and how various interventions affect the spread of COVID-19 and require data to identify the obstacles hampering the achievement of certain objectives or the success of particular interventions.
  • During the acceleration phase, when community transmission reaches exponential levels, the focus is on interventions for containment, which typically involve social contact and mobility restrictions. At this stage, aggregated mobile phone data are valuable to assess the efficacy of implemented policies through the monitoring of mobility between and within affected municipalities. Mobility information also contributes to the building of more accurate epidemiological models that can explain and anticipate the spread of the disease, as shown for H1N1 flu outbreaks (29). These models, in turn, can inform the mobilization of resources (e.g., respirators and intensive care units).
  • Continued situational monitoring will be important as the COVID-19 pandemic is expected to come in waves (4, 31). Near real-time data on mobility and hotspots will be important to understand how lifting and reestablishing various measures translate into behavior, especially to find the optimal combination of measures at the right time (e.g., general mobility restrictions, school closures, and banning of large gatherings), and to balance these restrictions with aspects of economic vitality.
  • After the pandemic has subsided, mobile data will be helpful for post hoc analysis of the impact of different interventions on the progression of the disease and cost-benefit analysis of mobility restrictions. During this phase, digital contact-tracing technologies might be deployed, such as the Korean smartphone app Corona 100m (32) and the Singaporean smartphone app TraceTogether (33), that aim at minimizing the spread of a disease as mobility restrictions are lifted.
  • Origin-destination (OD) matrices are especially useful in the first epidemiological phases, where the focus is to assess the mobility of the population. The number of people moving between two different areas daily can be computed from the mobile network data, and it can be considered a proxy of human mobility.
  • Amount of time spent at home, at work, or other locations are estimates of the individual percentage of time spent at home/work/other locations (e.g., public parks, malls, and shops), which can be useful to assess the local compliance with countermeasures adopted by governments. The home and work locations need to be computed in a period of time before the deployment of mobility restrictions measures.
  • The use of mobile phone data for tackling the COVID-19 pandemic has gained attention but remains relatively scarce.
  • First, governments and public authorities frequently are unaware and/or lack a “digital mindset” and capacity needed for both for processing information that often is complex and requires multidisciplinary expertise (e.g., mixing location and health data and specialized modeling) and for establishing the necessary interdisciplinary teams and collaborations. Many government units are understaffed and sometimes also lack technological equipment.
  • Second, despite substantial efforts, access to data remains a challenge. Most companies, including mobile network operators, tend to be very reluctant to make data available—even aggregated and anonymized—to researchers and/or governments. Apart from data protection issues, such data are also seen and used as commercial assets, thus limiting the potential use for humanitarian goals if there are no sustainable models to support operational systems. One should also be aware that not all mobile network operators in the world are equal in terms of data maturity. Some are actively sharing data as a business, while others have hardly started to collect and use data.
  • Third, the use of mobile phone data raises legitimate public concerns about privacy, data protection, and civil liberties.
  • Control of the pandemic requires control of people—including their mobility and other behaviors. A key concern is that the pandemic is used to create and legitimize surveillance tools used by government and technology companies that are likely to persist beyond the emergency. Such tools and enhanced access to data may be used for purposes such as law enforcement by the government or hypertargeting by the private sector. Such an increase in government and industry power and the absence of checks and balance is harmful in any democratic state. The consequences may be even more devastating in less democratic states that routinely target and oppress minorities, vulnerable groups, and other populations of concern.
  • Fourth, researchers and technologists frequently fail to articulate their findings in clear, actionable terms that respond to practical political and technical questions. Researchers and domain experts tend to define the scope and direction of analytical problems from their perspective and not necessarily from the perspective of governments’ needs. Critical decisions have to be taken, while key results are often published in scientific journals and in jargon that are not easily accessible to outsiders, including government workers and policy makers.
  • Last, there is little political will and resources invested to support preparedness for immediate and rapid action. On country levels, there are too few latent and standing mixed teams, composed of (i) representatives of governments and public authorities, (ii) mobile network operators and technology companies, and (iii) different topic experts (virologists, epidemiologists, and data analysts); and there are no procedures and protocols predefined. None of these challenges are insurmountable, but they require a clear call for action.
  • To effectively build the best, most up-to-date, relevant, and actionable knowledge, we call on governments, mobile network operators, and technology companies (e.g. Google, Facebook, and Apple), and researchers to form mixed teams.
  • For later stages of the pandemic, and for the future, stakeholders should aim for a minimum level of “preparedness” for immediate and rapid action.
Ben Snaith

The problem of modelling: Public policy and the coronavirus - 0 views

  • The current epidemic is a classic application of what economists call “radical uncertainty” (most recently explored by John Kay and Mervyn King in their brilliant book of that title, which came out last month): in a world that has inevitably become too complex to be adequately captured in models, a world of both “known unknowns” and “unknown unknowns”, the most sensible response to the question “what should we do?” is “I don’t know”. At the onset of this crisis, we could not put probabilities on which forms of social distancing would best limit its spread because we’d never done it before. We didn’t know how people would alter their behaviour in response to the appeal to “save the NHS”. We didn’t even know whether reducing the spread was desirable: perhaps fewer deaths now would come at the cost of more next winter. And these were just the known unknowns. With a disruption as big as this, unknown unknowns are also lurking. We have no experience of the material and economic repercussions from shutdowns of this nature and their aftermath in a modern economy, and no meaningful way of assigning probabilities; nor of how people’s behaviour will evolve.
  • What the modellers should have said, right from the beginning, was that it was vital to establish two fundamental parameters: the incidence and the rate of contagion, both of which require mass testing, and without which mortality rates are impossible to decipher and hence sensible policy impossible to implement. It is frankly astounding that four months into this new virus such tests are only now being instigated.
  • . Shifting responsibilities down the system not only enables rapid scale-up, it has a further huge advantage: the power of decision is closer to the coalface of practitioner experience. We learn not just from accumulating and analysing codifiable knowledge – the domain of the expert. We learn by doing, or by trying to do things that we can’t do and that force us to experiment. A decentralized system learns from a litany of failed experiments running in parallel, and so it learns fast: teams copy other teams that have hit on something that works well enough to get the job done.
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  • The political herd immunity to which governments are prone is that it is much safer to fail with a policy that others are following than to fail with a distinctive policy, even if, ex ante, the chances of failure are higher with the former.
fionntan

Prediction models for diagnosis and prognosis of covid-19 infection: systematic review ... - 1 views

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    This review indicates that proposed models are poorly reported, at high risk of bias, and their reported performance is probably optimistic. Immediate sharing of well documented individual participant data from covid-19 studies is needed for collaborative efforts to develop more rigorous prediction models and validate existing ones. The predictors identified in included studies could be considered as candidate predictors for new models.
olivierthereaux

CovidJSON | Standards based GeoJSON data model for infection data - 0 views

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    A proposed data standard (GeoJSON data model) for exchanging data for viral infection tests, contact events used for contact tracing and regional infection statistics. The model is based on OGC/ISO Observations & measurements Standard (OGC O&M, ISO 19156) concepts. Created specifically for recording and exchanging data on SARS-CoV-2 infection tests, but likely applicable also to describing test data for detecting other infectious diseases too.
fionntan

How can coronavirus models get it so wrong? - 0 views

  • One moment the prime minister, Boris Johnson, was asking people with symptoms to stay home for seven days; a few days later, he had ordered a lockdown. What changed was data from Italy’s experience of the pandemic, in which more people were critically ill than anticipated, and from the NHS about its inability to cope if the same should happen in the UK.
Ben Snaith

Covid-19 Project - 1 views

For discussion of the Covid-19 project

Coronavirus Data Contact-Tracing Data-Access Models

started by Ben Snaith on 23 Apr 20 no follow-up yet
Ben Snaith

Corona Positive Deviance - 0 views

  • Positive Deviants are individuals, groups, cities, regions etc. who outperform their peers in a comparable context thanks to creative and highly adaptive solutions they have come up with.
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    We want to contribute to this effort and have come together as individuals from diverse backgrounds and professions to join forces in analyzing the data available and identifying what we call the "positive deviants".
Ben Snaith

NHS tracing app in question as experts assess Google-Apple model | Financial Times - 0 views

  • Health chiefs in the UK have tasked a team of software developers to “investigate” switching its unique contact-tracing app to the global standard proposed by Apple and Google, signalling a potential about-turn just days after the NHS launched its new coronavirus app. 
fionntan

Publishing with purpose? Reflections on designing with standards and locating user enga... - 0 views

  • Purpose should govern the choice of dataset to focus on Standards should be the primary guide to the design of the datasets User engagement should influence engagement activities ‘on top of’ published data to secure prioritised outcomes New user needs should feed into standard extension and development User engagement should shape the initiatives built on top of data
  • The call for ‘raw data now‘ was not without purpose: but it was about the purpose of particular groups of actors: not least semantic web reseachers looking for a large corpus of data to test their methods on. This call configured open data towards the needs and preferences of a particular set of (technical) actors, based on the theory that they would then act as intermediaries, creating a range of products and platforms that would serve the purpose of other groups. That theory hasn’t delivered in practice
  • They describe a process that started with a purpose (“get better bids on contract opportunities”), and then engaged with vendors to discuss and test out datasets that were useful to them.
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  • But in seeking to be generally usable, standard are generally not tailored to particular combinations of local capacity and need. (This pairing is important: if resource and capacity were no object, and each of the requirements of a standard were relevant to at least one user need, then there would be a case to just implement the complete standard. This resource unconstrained world is not one we often find ourselves in.)
  • The Open Contracting Partnership, which has encouraged governments to purposely prioritise publication of procurement data for a number of years now,
    • fionntan
       
      how does the open contracting partnership relate to models?
  • The Open Contracting Partnership, which has encouraged governments to purposely prioritise publication of procurement data for a number of years now,
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