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covid-19 modeling, Youyang Gu, machine learning, data science

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covid-19 modeling, Youyang Gu, machine learning, data science


“It became clear that we’re not going to reach herd immunity in 2021, at least definitely not across the whole country,” he says. “And I think it’s important, especially if you’re trying to instill confidence, that we make sensible paths to when we can go back to normal. We shouldn’t be pegging that on an unrealistic goal like reaching herd immunity. I’m still cautiously optimistic that my original forecast in February, for a return to normal in the summer, will be valid.”

In early March, he packed up shop entirely—he figured he’d made what contribution he could. “I wanted to step back and let the other modelers and experts do their work,” he says. “I don’t want to muddle the space.”

He’s still keeping an eye on the data, doing research and analysis—on the variants, the vaccine rollout, and the fourth wave. “If I see anything that’s particularly troubling or worrisome that I think people aren’t talking about, I’ll definitely post it,” he says. But for the time being he is focusing on other projects, such as “YOLO Stocks,” a stock ticker analytics platform. His main pandemic work is as a member of the World Health Organization’s technical advisory group on covid-19 mortality assessment, where he shares his outsider’s expertise.

“I’ve definitely learned a lot this past year,” Gu says. “It was very eye-opening.”

Lesson #1: Focus on fundamentals

“From the data science perspective, my models have shown the importance of simplicity, which is often undervalued,” says Gu. His death forecasting model was simple in not only its design—the SEIR component with a machine-learning layer—but also its very pared-down, “bottom-up” approach regarding input data. Bottom-up means “start from the bare-bones minimum and add complexity as needed,” he says. “My model only uses past deaths to predict future deaths. It doesn’t use any other real data source.”

Gu noticed that other models drew on an eclectic variety data about cases, hospitalizations, testing, mobility, mask use, comorbidities, age distribution, demographics, pneumonia seasonality, annual pneumonia death rate, population density, air pollution, altitude, smoking data, self-reported contacts, airline passenger traffic, point of care, smart thermometers, Facebook posts, Google searches, and more.

“There is this belief that if you add more data to the model, or make it more sophisticated, then the model will do better,” he says. “But in real-word situations like the pandemic, where data is so noisy, you want to keep things as simple as possible.”

“I decided early on that past deaths are the best predictor of future deaths. It’s very simple: input, output. Adding more data sources will just make it more difficult to extract the signal from the noise.”

Lesson #2: Minimize assumptions

Gu considers that he had an advantage in approaching the problem with a blank slate. “My goal was to just follow the data on covid to learn about covid,” he says. “That’s one of the main benefits of an outsider’s perspective.”

But not being an epidemiologist, Gu also had to be sure that he wasn’t making incorrect or inaccurate assumptions. “My role is to design the model such that it can learn the assumptions for me,” he says.

“When new data comes along that goes against our beliefs, sometimes we tend to overlook that new data or ignore it, and that can cause repercussions down the road,” he notes. “I certainly found myself falling victim to that, and I know that lots of other people have as well.”

“So being aware of the potential bias that we have and recognizing it, and being able to adjust our priors—adjusting our beliefs if new data disproves them—is really important, especially in a fast-moving environment like what we’ve seen with covid.”

Lesson #3: Test the hypothesis

“What I’ve seen over the last few months is that anyone can make claims or manipulate data to fit the narrative of what they want to believe in,” Gu says. This highlights the importance of simply making testable hypotheses.

“For me, that is the whole basis of my projections and forecasts. I have a set of assumptions, and if those assumptions are true, then this is what we predict will happen in the future,” he says. “And if the assumptions end up being wrong, then of course we have to admit that the assumptions we make are not true and adjust accordingly. If you don’t make testable hypotheses, then there is no way to show whether you are actually right or wrong.”

Lesson #4: Learn from mistakes

“Not all the projections that I made were correct,” Gu says. In May 2020, he projected 180,000 deaths in the US by August. “That is much higher than we saw,” he recalls. His testable hypothesis proved incorrect—“and that forced me to adjust my assumptions.”

At the time, Gu was using a fixed infection fatality rate of approximately 1% as a constant in the SEIR simulator. When in the summer he lowered the infection fatality rate to about 0.4% (and later to about 0.7%), his projections returned to a more realistic range. 

Lesson #5: Engage critics

“Not everyone will agree with my ideas, and I welcome that,” says Gu, who used Twitter to post his projections and analysis. “I try to respond to people as much as I can, and defend my position, and debate with people. It forces you to think about what your assumptions are and why you think they are correct.”

“It goes back to confirmation bias,” he says. “If I am not able to properly defend my position, then is it really the right claim, and should I be making these claims? It helps me understand, by engaging with other people, how to think about these problems. When other people present evidence that counters my positions, I have to be able to acknowledge when I may be incorrect in some of my assumptions. And that has actually helped me tremendously in improving my model.”

Lesson #6: Exercise healthy skepticism

“I am now much more skeptical of science—and it’s not a bad thing,” Gu says. “I think it’s important to always question results, but in a healthy way. It’s a fine line. Because a lot of people just flat-out reject science, and that’s not the way to go about it either.”

“But I think it’s also important to not just blindly trust science,” he continues. “Scientists aren’t perfect.” It is appropriate, he says, if something doesn’t seem right, to ask questions and find explanations. “It’s important to have different perspectives. If there is anything we’ve learned over the past year, it’s that no one is 100% right all the time.”

“I can’t speak for all scientists, but my job is to cut through all the noise and get to the truth,” he says. “I’m not saying I’ve been perfect over this past year. I’ve been wrong many times. But I think we can all learn to approach science as a method of finding the truth, rather than the truth itself.”

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The hunter-gatherer groups at the heart of a microbiome gold rush

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The hunter-gatherer groups at the heart of a microbiome gold rush


The first step to finding out is to catalogue what microbes we might have lost. To get as close to ancient microbiomes as possible, microbiologists have begun studying multiple Indigenous groups. Two have received the most attention: the Yanomami of the Amazon rainforest and the Hadza, in northern Tanzania. 

Researchers have made some startling discoveries already. A study by Sonnenburg and his colleagues, published in July, found that the gut microbiomes of the Hadza appear to include bugs that aren’t seen elsewhere—around 20% of the microbe genomes identified had not been recorded in a global catalogue of over 200,000 such genomes. The researchers found 8.4 million protein families in the guts of the 167 Hadza people they studied. Over half of them had not previously been identified in the human gut.

Plenty of other studies published in the last decade or so have helped build a picture of how the diets and lifestyles of hunter-gatherer societies influence the microbiome, and scientists have speculated on what this means for those living in more industrialized societies. But these revelations have come at a price.

A changing way of life

The Hadza people hunt wild animals and forage for fruit and honey. “We still live the ancient way of life, with arrows and old knives,” says Mangola, who works with the Olanakwe Community Fund to support education and economic projects for the Hadza. Hunters seek out food in the bush, which might include baboons, vervet monkeys, guinea fowl, kudu, porcupines, or dik-dik. Gatherers collect fruits, vegetables, and honey.

Mangola, who has met with multiple scientists over the years and participated in many research projects, has witnessed firsthand the impact of such research on his community. Much of it has been positive. But not all researchers act thoughtfully and ethically, he says, and some have exploited or harmed the community.

One enduring problem, says Mangola, is that scientists have tended to come and study the Hadza without properly explaining their research or their results. They arrive from Europe or the US, accompanied by guides, and collect feces, blood, hair, and other biological samples. Often, the people giving up these samples don’t know what they will be used for, says Mangola. Scientists get their results and publish them without returning to share them. “You tell the world [what you’ve discovered]—why can’t you come back to Tanzania to tell the Hadza?” asks Mangola. “It would bring meaning and excitement to the community,” he says.

Some scientists have talked about the Hadza as if they were living fossils, says Alyssa Crittenden, a nutritional anthropologist and biologist at the University of Nevada in Las Vegas, who has been studying and working with the Hadza for the last two decades.

The Hadza have been described as being “locked in time,” she adds, but characterizations like that don’t reflect reality. She has made many trips to Tanzania and seen for herself how life has changed. Tourists flock to the region. Roads have been built. Charities have helped the Hadza secure land rights. Mangola went abroad for his education: he has a law degree and a master’s from the Indigenous Peoples Law and Policy program at the University of Arizona.

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The Download: a microbiome gold rush, and Eric Schmidt’s election misinformation plan

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The Download: a microbiome gold rush, and Eric Schmidt’s election misinformation plan


Over the last couple of decades, scientists have come to realize just how important the microbes that crawl all over us are to our health. But some believe our microbiomes are in crisis—casualties of an increasingly sanitized way of life. Disturbances in the collections of microbes we host have been associated with a whole host of diseases, ranging from arthritis to Alzheimer’s.

Some might not be completely gone, though. Scientists believe many might still be hiding inside the intestines of people who don’t live in the polluted, processed environment that most of the rest of us share. They’ve been studying the feces of people like the Yanomami, an Indigenous group in the Amazon, who appear to still have some of the microbes that other people have lost. 

But there is a major catch: we don’t know whether those in hunter-gatherer societies really do have “healthier” microbiomes—and if they do, whether the benefits could be shared with others. At the same time, members of the communities being studied are concerned about the risk of what’s called biopiracy—taking natural resources from poorer countries for the benefit of wealthier ones. Read the full story.

—Jessica Hamzelou

Eric Schmidt has a 6-point plan for fighting election misinformation

—by Eric Schmidt, formerly the CEO of Google, and current cofounder of philanthropic initiative Schmidt Futures

The coming year will be one of seismic political shifts. Over 4 billion people will head to the polls in countries including the United States, Taiwan, India, and Indonesia, making 2024 the biggest election year in history.

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Navigating a shifting customer-engagement landscape with generative AI

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Navigating a shifting customer-engagement landscape with generative AI


A strategic imperative

Generative AI’s ability to harness customer data in a highly sophisticated manner means enterprises are accelerating plans to invest in and leverage the technology’s capabilities. In a study titled “The Future of Enterprise Data & AI,” Corinium Intelligence and WNS Triange surveyed 100 global C-suite leaders and decision-makers specializing in AI, analytics, and data. Seventy-six percent of the respondents said that their organizations are already using or planning to use generative AI.

According to McKinsey, while generative AI will affect most business functions, “four of them will likely account for 75% of the total annual value it can deliver.” Among these are marketing and sales and customer operations. Yet, despite the technology’s benefits, many leaders are unsure about the right approach to take and mindful of the risks associated with large investments.

Mapping out a generative AI pathway

One of the first challenges organizations need to overcome is senior leadership alignment. “You need the necessary strategy; you need the ability to have the necessary buy-in of people,” says Ayer. “You need to make sure that you’ve got the right use case and business case for each one of them.” In other words, a clearly defined roadmap and precise business objectives are as crucial as understanding whether a process is amenable to the use of generative AI.

The implementation of a generative AI strategy can take time. According to Ayer, business leaders should maintain a realistic perspective on the duration required for formulating a strategy, conduct necessary training across various teams and functions, and identify the areas of value addition. And for any generative AI deployment to work seamlessly, the right data ecosystems must be in place.

Ayer cites WNS Triange’s collaboration with an insurer to create a claims process by leveraging generative AI. Thanks to the new technology, the insurer can immediately assess the severity of a vehicle’s damage from an accident and make a claims recommendation based on the unstructured data provided by the client. “Because this can be immediately assessed by a surveyor and they can reach a recommendation quickly, this instantly improves the insurer’s ability to satisfy their policyholders and reduce the claims processing time,” Ayer explains.

All that, however, would not be possible without data on past claims history, repair costs, transaction data, and other necessary data sets to extract clear value from generative AI analysis. “Be very clear about data sufficiency. Don’t jump into a program where eventually you realize you don’t have the necessary data,” Ayer says.

The benefits of third-party experience

Enterprises are increasingly aware that they must embrace generative AI, but knowing where to begin is another thing. “You start off wanting to make sure you don’t repeat mistakes other people have made,” says Ayer. An external provider can help organizations avoid those mistakes and leverage best practices and frameworks for testing and defining explainability and benchmarks for return on investment (ROI).

Using pre-built solutions by external partners can expedite time to market and increase a generative AI program’s value. These solutions can harness pre-built industry-specific generative AI platforms to accelerate deployment. “Generative AI programs can be extremely complicated,” Ayer points out. “There are a lot of infrastructure requirements, touch points with customers, and internal regulations. Organizations will also have to consider using pre-built solutions to accelerate speed to value. Third-party service providers bring the expertise of having an integrated approach to all these elements.”

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