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Meet Covid-19 Data Superstar

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Spring 2020 brought with it the arrival of the celebrity statistical model. As the public tried to gauge how big a deal the covid-19 might be in March and April, it was pointed again and again to two forecasting systems: one built by Imperial College London, the other by the Institute for Health Metrics and Evaluation, or IHME, based in Seattle.

But the models yielded wildly divergent predictions. Imperial warned that the U.S. might see as many as 2 million Covid-19 deaths by the summer, while the IHME forecast was far more conservative, predicting about 60,000 deaths by August.

Neither, it turned out, was very close. The U.S. ultimately reached about 160,000 deaths by the start of August. The huge discrepancy in the forecasting figures that spring caught the attention of a then 26-year-old data scientist named Youyang Gu.

The young man had a master’s degree in electrical engineering and computer science from the Massachusetts Institute of Technology and another degree in mathematics, but no formal training in a pandemic-related area such as medicine or epidemiology. Still, he thought his background dealing with data models could prove useful during the pandemic.

In mid-April, while he was living with his parents in Santa Clara, Calif., Gu spent a week building his own Covid death predictor and a website to display the morbid information.

Before long, his model started producing more accurate results than those cooked up by institutions with hundreds of millions of dollars in funding and decades of experience.

“His model was the only one that seemed sane,” says Jeremy Howard, a renowned data expert and research scientist at the University of San Francisco. “The other models were shown to be nonsense time and again, and yet there was no introspection from the people publishing the forecasts or the journalists reporting on them.

Peoples’ lives were depending on these things, and Youyang was the one person actually looking at the data and doing it properly.” The forecasting model that Gu built was, in some ways, simple.

He had first considered examining the relationship among Covid tests, hospitalizations, and other factors but found that such data was being reported inconsistently by states and the federal government.

The most reliable figures appeared to be the daily death counts. “Other models used more data sources, but I decided to rely on past deaths to predict future deaths,” Gu says. “Having that as the only input helped filter the signal from the noise.”

The novel, sophisticated twist of Gu’s model came from his use of machine learning algorithms to hone his figures. After MIT, Gu spent a couple years working in the financial industry writing algorithms for high-frequency trading systems in which his forecasts had to be accurate if he wanted to keep his job.

When it came to Covid, Gu kept comparing his predictions to the eventual reported death totals and constantly tuned his machine learning software so that it would lead to ever more precise prognostications. Even though the work required the same hours as a demanding full-time job, Gu volunteered his time and lived off his savings.

He wanted his data to be seen as free of any conflicts of interest or political bias. While certainly not perfect, Gu’s model performed well from the outset. In late April he predicted the U.S. would see 80,000 deaths by May 9. The actual death toll was 79,926.

A similar late-April forecast from IHME predicted that the U.S. would not surpass 80,000 deaths through all of 2020. Gu also predicted 90,000 deaths on May 18 and 100,000 deaths on May 27, and once again got the numbers right.

Where IHME expected the virus to fade away as a result of social distancing and other policies, Gu predicted there would be a second, large wave of infections and deaths as many states reopened from lockdowns. relates to The 27-Year-Old Who Became a Covid-19 Data Superstar “Other models used more data sources, but I decided to rely on past deaths to predict future deaths,” Gu says. “Having that as the only input helped filter the signal from the noise.”

PHOTOGRAPHER: JUSTIN WEE FOR BLOOMBERG BUSINESSWEEK IHME faced some criticism in March and April, when its numbers didn’t match what was happening.

 Still, the prestigious center, based at the University of Washington and bolstered by more than $500 million in funding from the Bill & Melinda Gates Foundation, was cited on an almost daily basis during briefings by members of President Donald Trump’s Administration.

In April, U.S. infectious-disease chief Anthony Fauci told an interviewer that Covid’s death toll “looks more like 60,000 than the 100,000 to 200,000” once expected—a prediction that reflected IHME forecasts.

And on April 19, the same day Gu cautioned about a second wave, Trump pointed to IHME’s 60,000-death forecast as an indicator that the fight against the virus would soon be over. IHME officials also actively promoted their numbers.

 “You had the IHME on all these news shows trying to tell people that deaths would go to zero by July,” Gu says. “Anyone with common sense could see we would be at 1,000 to 1,500 daily deaths for a while. I thought it was very disingenuous for them to do that.” Christopher Murray, the director of IHME, says that once the organization got a better handle on the virus after April, its forecasts radically improved. But that spring, week by week, more people started to pay attention to Gu’s work.

He flagged his model to reporters on Twitter and e-mailed epidemiologists, asking them to check his numbers.

Toward the end of April, the prominent University of Washington biologist Carl Bergstrom tweeted about Gu’s model, and not long after that the U.S. Centers for Disease Control and Prevention included Gu’s numbers on its Covid forecasting website.

As the pandemic progressed, Gu, a Chinese immigrant who grew up in Illinois and California, found himself taking part in regular meetings with the CDC and teams of professional modelers and epidemiologists, as everyone tried to improve their forecasts. Traffic to Gu’s website exploded, with millions of people checking in daily to see what was happening in their states and the U.S. overall. More often than not, his predicted figures ended up hugging the line of actual death figures when they arrived a few weeks later.

With such intense interest around these forecasts, more models began to appear through the spring and summer of 2020. Nicholas Reich, an associate professor in the biostatistics and epidemiology department at the University of Massachusetts, Amherst, collected the 50 or so models and measured their accuracy over many months at the Covid-19 Forecast Hub.

“Youyang’s model was consistently among the top,” Reich says. In November, Gu decided to wind down his death forecast operation. Reich had been blending the various forecasts and found that the most accurate predictions came from the this “ensemble model,” or combined data.

“Youyang stepped back with a remarkable sense of humility,” Reich says. “He saw the other models were doing well and his work here was done.” A month before stopping the project, Gu had predicted that the U.S. would record 231,000 deaths on Nov. 1. When Nov. 1 arrived, the U.S. reported 230,995 deaths.

The IHME’s Murray has his own take on Gu’s exit. He says Gu’s model would not have picked up on the seasonal nature of the coronavirus and would have missed the winter surge in cases and deaths.

“He had the epidemic going away in the winter, and we had picked up that there was seasonality as early as May,” Murray says. The machine learning methods used by Gu work well at short-range predictions, Murray says, but “are not very good at understanding what is going on” in the bigger picture.

The algorithms, based on the past, can’t account for virus variants and how well vaccines may or may not work against them, according to Murray.

For its part, IHME called the early peak of the virus correctly, then erred when it came to predicting a steep decline in deaths until it adjusted its model to better reflect reality.

“We got it wrong the first of April,” Murray says. “Since then we are the only group that has gotten it right consistently.” Reich, who compiles the list of the major models, said that the organization’s predictions later in the pandemic were passable.

“Early on, IHME’s model didn’t do what it advertised,” Reich says. “More recently, it has been a reasonable model. I would not say it is one of the best, but it is reasonable.” Gu declined to address Murray’s remarks about his model.

Instead, he offers a data scientist’s version of a backhanded compliment. “I’m very appreciative of Dr. Chris Murray and his team for the work they did,” Gu says. “Without them, I would not be in the position I am today.”

To the extent that we can learn from this data story, Reich asks that people not rush to place too much faith in early individual models the next time a pandemic arrives. He also questions whether forecasts beyond six to eight weeks out will ever be very accurate.

 Ideally, the CDC and others will be quicker to combine models and distribute the blended data in the future. “I hope we will invest the time, energy, and money into setting up a system that is more ready to respond with a wider array of models closer to the get-go,” Reich says.

“We have to have people ready, instead of going around and knocking on peoples’ doors.” After taking a bit of a break, Gu, now 27 and living in a New York apartment, did get back into the modeling game.

This time, he’s creating figures related to how many people in the U.S. have been infected by Covid-19, how quickly vaccines are being rolled out, and when, if ever, the country might reach herd immunity.

His forecasts suggest that about 61% of the population should have some form of immunity—either from the vaccine or past infection—by June.

Before the pandemic, Gu hoped to start a new venture, possibly in sports analytics. Now he’s considering sticking to public health.

 He wants to find a job where he can have a large impact while avoiding politics, bias, and the baggage that sometimes comes with large institutions.

“There are a lot of shortcomings in the field that could be improved by people with my background,” he says. “But I still don’t know quite how I would fit in.”

Bloomberg

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Person of the week

NASA Astronaut Who Piloted Apollo 11’s Mission to Moon Dies

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The American Space Agency NASA is mourning the loss of retired Air Force general Michael Collins that went down in history for piloting  Apollo 11’s mission to the moon.

According to family sources, Michael Collins at the age of 90 years, died early Wednesday.

Collins launched from Kennedy Space Center with crewmates Neil Armstrong and Buzz Aldrin on July 16, 1969, kicking off an eight-day mission that culminated in a successful landing on the moon.

He was tasked with piloting the Columbia command module while Armstrong and Aldrin descended to the surface in the Eagle lunar module.

“We regret to share that our beloved father and grandfather passed away today after a valiant battle with cancer,” his family said in a statement posted to his official Twitter account. “He spent his final days peacefully with family by his side.”

NASA posted a tribute video for Collins on Twitter, calling the former astronaut an “advocate for exploration” that “inspired generations.”

“Today the nation lost a true pioneer,” said acting NASA Administrator Steve Jurczyk in a release. “As pilot of the Apollo 11 command module – some called him ‘the loneliest man in history’ – while his colleagues walked on the Moon for the first time, he helped our nation achieve a defining milestone.”

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Health

Prof Happi Proposes Covid-19 Vaccine Made in Africa For Africa

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Professor Christian Tientcha Happi is a Professor of Molecular Biology and Genomics in the Department of Biological Sciences, and the Director African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University.

He holds a BSc in Biochemistry, MSc and PhD in Molecular Parasitology from the University of Ibadan in 1993, 1995 and 2000 respectively.

He did his post-doctoral research in Molecular Biology and Genomics at Harvard University, School of Public Health, Boston, MA, USA (2000-2003, ).

He is currently the Director, Directorate of Research Innovations and Partnerships (DRIPs), Redeemer’s University.

He has carried out research focus on Human Genomics, Molecular Biology and Genomics of Infectious Diseases, especially Malaria, Viral Haemorrhagic Fevers (Lassa fever, Ebola Virus Disease, and HIV among others.

His laboratory confirmed the first case of Ebola Virus Disease in Nigeria in the 2014 Ebola outbreak, and work with Nigerian Health Officials for the successful containment of the Ebola outbreak in Nigeria.

In this interview, he talked about how they developed the rapid diagnostic test kit for covid, which can give result within 10 minutes to 15 minutes.

He also talked about the need to encourage Nigerians to be vaccinated because the COVID-19 vaccine is efficacious and that it has been demonstrated all over the world that people that take the vaccine, protect themselves against the virus infection.

Here is an excerpt from the interview.

Current Research Interest

My research focus is on Human Genomics, Molecular Biology and Genomics of Infectious Diseases, especially Malaria, Viral Haemorrhagic Fevers (Lassa fever, Ebola Virus Disease, and others), and HIV.

My current research activities consist of using innovative approaches that combine patient care, fieldwork, laboratory, molecular biology and genomics methods for discoveries that have shifted the paradigm in clinical research and applications in parasites and viral diagnosis, parasites biology and genomics, Pharmacogenomics, and human genomics.

Also, I am passionate about building research capacity and human resource through training and mentoring activities.

Through my research, we have been able to identify molecular markers of antimalarial drug resistance in Plasmodium falciparum, the agent of malaria.

We recently discovered new viruses (EKV-1 and EKV-2 and developed new rapid diagnoses for Ebola virus disease (EVD), and Lassa fever virus.

My laboratory confirmed the first case of Ebola Virus Disease in Nigeria in the 2014 Ebola outbreak, and work with Nigerian Health Officials for the successful containment of the Ebola outbreak in Nigeria.

Research work in my laboratory contributed significantly to the establishment of the global reference for human genetic variation.

Our research work has also resulted in the identification of new genes associated with human resistance to infection to the Lassa fever virus.

I have been working in the space of infectious diseases in the past 22 years, across west Africa Lassa fever, ebola, monkeypox, yellow fever and covid.

The genomic works that I have been doing over the past 12 years hemorrhagic fever is mainly to understand the nature of the virus and leverage those information and translate it to tools like a point of care diagnostic, also things like a vaccine.

We are also very much involved in capacity building, so we set up one of the best genomic platforms where we are training what we call a critical mass of young Africans so Africa Centre of Excellence for Genomic infectious diseases that I am the founder and director, is to create what we call academic and research environment that transcend national boundaries, where young Africans can actually use that platform to express their God-given talent and then use such platform to do genomics for public health, development of the continent so in so doing, we are basically focusing on training what we refer to as critical mass African scientists that can annex the knowledge and skill, tools of genomics to address problem of infectious disease and specifically control and elimination, eradication of infectious disease.

In addition to that, we are building a new genomic curriculum that applies to infectious disease. Also, we are engaging the public health community in education.

That is what we have been doing in the past decade; overall our goal is basically to build the next generation of what is called African pathogen hunters, doing this in Africa, with Africa in collaboration with friends, colleague and partners outside so that we can stop playing what I call orphans instead of defence.

Because what we see today, is that anytime there is an outbreak or epidemic of diseases somewhere the world start battling, but I think now we need to start thinking of how we can use the skill and knowledge that we have to start uncovering those viruses and develop countermeasures before they come to us.

That is the countermeasure we are taking now and we are going to be leveraging on platform and skill, the talent we are grooming.

Fast track test kit for covid-19?

We can develop one of the fastest rapid diagnostic test kits for covid-19 in the world, before that we did something five days or within a week after the first case of covid was announced in Nigeria, we can come up with e-sub-screening test tools in Nigeria and link that up with other local government and Yaba Hospital.

Then we went on to develop the rapid diagnostic test kit for covid, how did we do that?

We did that because we were the lab that reconfirmed the very first case in Lagos that was tested by PCR, NCDC sent the sample to us and we can confirm it.

We did that speedily. We set up the record that nobody is ever able to beat in the world, from sample collection to releasing data on the international genomic platform call G-SET, it took us 72 hours.

This process usually takes weeks but we did it in 72 hours. And it is base on that particular sequence and other sequences that follow that we went on to develop diagnose test kit.

This test kit is faster and cheaper, in which within 10 minutes to 15 minutes you will have the result.

You don’t need to collect a blood sample, just saliva and you don’t need a specialized laboratory.

It is the test that is mostly adopted for Africa because you don’t need a highly specialized lab. It is just like a pregnancy test, another thing is that it targets the virus RNA and it is very precise and specific.

Research funding in Africa?

I don’t think African countries see any value in research, African leaders promised that they are going to dedicate 2 per cent of their GDP to support research but they are not doing it only a few countries like Rwanda are dedicating about 0.5% towards research.

So that is a problem, you cannot make progress, as a nation if you do not fund education and research and that is the reason Africa is over-dependent on other countries for everything.

It’s evident even during this covid-19 when we over-dependent on international communities for everything from PPE, to Vaccine, we are depending on international communities.

Africa’s independence will only come when they invest in research and take responsibility for their problem and when they start to look inward in finding a solution to their problems.

It is obvious that we are at the mercy of different countries we do not produce anything, we are consumers, not producers, which puts us in a weak and vulnerable position.

That is the fact we can’t shy away from. The truth of the matter is, as long as Africa does not invest in research and develop her capacity and addresses her problems, we will continue to be weak and exploited and at the back of the queue.

Research and innovation in addressing our developmental challenges in Africa?

The only way to do that is investment through the private sector and government establishment.

Funding research is not only the responsibility of the government, but the private sector also need to be involved but unfortunately in Africa, private sector investment is nothing on research.

What you see in Africa people that can invest in research refuse to do so, what they do is to go to Harvard or Cambridge to donate, to an institution where their money will not make any impact.

They ignore where they should put their money and go elsewhere because they have an inferiority complex.

If there is any lesson to learn I think they would have seen through this pandemic that it is better to invest in your country than to go elsewhere because during the pandemic everybody was on lockdown and they couldn’t fly around with a private jet.

Investment in research in Africa academic will be very helpful because Africa needs to develop. Secondly, when you look at Africa, one of the reasons why Africa is stagnant is simply because there is no brain circulation in Africa. knowledge does not circulate in Africa.

The reason why I’m saying this is because it’s a shame in Africa that we can’t have Africa research circulating moving from one country to another sharing knowledge. It is easier for African to go abroad to share knowledge than to share with African counterpart.

What are your thoughts about the Covid-19 vaccine?

Firstly, the COVID-19 vaccine is efficacious. And it has been demonstrated all over the world that people that take the vaccine, protect themselves against the virus infection.

The AstraZeneca vaccine that is in Nigeria, we should encourage people to take it. I also understand the fears of the people because this vaccine is foreign so people are afraid.

If anything to go by and the Africa government are listening, is basically that people in Africa are telling them that they don’t have confidence in the vaccine that is coming from outside Africa. And the message is that fund vaccine that will emanate from Africa.

I can tell you that Africans will be more comfortable if they hear that the vaccine emanated from Africa. I hope our government will listen to the masses.

The people are telling our leaders that they are tired of using imported things. Imported vaccines among other things am not against the fact that they are good but the message is that we will trust vaccine made in Africa by our researchers more than what is coming from outside.

That is why you are seeing vaccine resistance and apathy. People want to see what is made by their people so that they will be very comfortable using it.

Misconception about COVID-19?

Covid-19 is real, people should take necessary precautions if we did not respect the safety rules it will be difficult to get rid of this disease even if the vaccine is given out.

Even with the availability of the vaccine, people should continue to protect themselves.

Adapted from Vanguard

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Business

Glimpse Into Soraya Deputy Governor Of Rwanda Central Bank

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Rwanda Central Bank has a new Deputy Governor in the person of Soraya Hakuziyaremye appointed to the post in a recent mini cabinet reshuffle.

Soraya as popularly known, officially got herself under the roof of the Central Bank on Monday after her new office files were handed to her.

“Thank you Governor John Rwangombwa and colleagues at Central Bank for the warmest welcome into the BNR family. Ready to build on the achievements and contribute fully to the mission and continued transformation of the Bank,” Soraya said on Monday.

On March 15, upon her appointment, Soraya thanked the appointing authority and said, ” Grateful to President Paul Kagame for the trust and incredible opportunity to serve at Central Bank. I will give it my utmost best. Thanking Trade Ministry team for the unwavering support at the Ministry and government for the unparalleled teamwork  and dedication.”

Soraya joins the central bank at a time Rwanda’s economic outlook has worsened due to effects of Covid-19 pandemic. At this point Rwanda will need more foreign aid contrally to views held by Soraya on foreign aid dependence.

Soraya also observed in a 2013 article that for Africa to re-grow, it must wean off donations and aid.

” In this time of age, African countries need to stop believing in Santa Claus and work hard to get off aid,” she said then.

According to her, no country has ever lifted itself from an-underdeveloped economy to a developed or an emerging economy by holding out its hands for donors’ money.

However, Rwanda’s economy has been severely impacted by the Covid-19 pandemic with weaker domestic demand losses of revenue, and a sharp decline in exports and remittances.

She picks Japan and South Korea, Argentina as  case studies that Africa could take lessons from; ”  if Africa does not draw on these examples fast enough and get off aid, well, we will be doomed not only to economic instability, but also to pressure from donors for more decades to come!”

In her views as captured from her previous articles published in local press, Soraya strongly supports elevation of women to boardrooms of global financial institutions.

For her, the lack of women in leadership positions in the banking industry is a serious issue. The Financial sector lags behind in progressing towards gender balance.

She noted too that low level of financial inclusion overall in Africa and the lack of access to financial services for women impedes the rise on the corporate ladder for African women.

“This demonstrates how daunting it is for an African woman to embrace an industry whose products nor services they have not been exposed to,” she wrote in a 2018 article.

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