Data Science newsletter – April 8, 2020

GROUP CURATION: N/A

Often considered desolate, remote, unalterable places, the high seas are, in fact, hotbeds of activity for both people and wildlife. Technology has enabled more human activity in areas once difficult to reach, and that in turn has brought a growing presence of industries such as fishing, mining and transportation in international waters — the ocean beyond 200 nautical miles from any coast.

This increase is cause for concern to people like UC Santa Barbara researchers Douglas McCauley, Morgan Visalli and Benjamin Best, who are interested in the health and biodiversity of the oceans. That no nation has jurisdiction over international waters has, at least historically, made regulation very difficult and puts sensitive and essential ocean habitats and resources at risk.

CU Boulder researcher Daniel Larremore has never held a nasal swab and doesn’t wear scrubs. Instead, he relies on math to track the spread of human diseases.

This week, Larremore and several colleagues from Colorado joined a nationwide study that seeks to use social media data to better understand how coronavirus cases might grow and travel in the coming weeks.

The COVID-19 Mobility Data Network will draw on huge volumes of anonymized location information supplied by Facebook to follow how groups of people move from spot to spot over time. That will allow researchers like Larremore, an assistant professor in the Department of Computer Science and in the BioFrontiers Institute, to build maps that show where people are still traveling in the age of social distancing.

It’s totally anonymous and designed with privacy as a top priority, he said.

“You can’t tell anything about individual mobility since Facebook gives us only anonymized and aggregated data,” said Larremore. “But we will be able to see, for example, how many people went from Jefferson County to Boulder County last week and compare it to how many people made the same trip several weeks ago.”

It’s official: The University of Oregon is preparing the next generation of leaders in data science. With all reviews completed and final approvals in hand, the data science degree program will begin this fall.

Developed by the Presidential Initiative in Data Science, the new undergraduate degree was granted final approval by the UO’s accrediting body, the Northwest Commission on Colleges and Universities, in February.

“I am thrilled that the UO is launching a degree in data science,” said UO President Michael H. Schill. “This approval reflects awareness of the increasingly central role of data science in higher education and society, its impact for our state and national economies and its vital usefulness in helping to solve some of the greatest challenges now facing our world. Especially given the role date science is playing globally in tracking and responding to the COVID-19 health emergency, I am proud to note that the UO’s program will place a strong emphasis on building ethical frameworks for working with and learning from big data.”

Scientists, scholars and medical professionals say false and misleading information and a lack of preparedness for the coronavirus has made a bad situation worse. But does the world’s lack of preparation for the outbreak have a silver lining? Naomi Oreskes, professor of the history of science at Harvard University and author of “Why Trust Science?” joins Hari Sreenivasan for more. [video, 5:11]

Earlier this year, the chair of Harvard’s chemistry department was arrested and charged with lying to federal law-enforcement officials about secretly working for the Chinese government. While the story of nanotechnology pioneer Charles Lieber is shocking and dramatic, it is indicative of a broader challenge facing America’s leading scientific research institutions. We must secure the research we conduct on our campuses from foreign interference while at the same time protecting the openness and free flow of scientific knowledge that has made American universities the world’s leaders in research and higher education.

Fortunately, there are practical steps that America’s research universities and institutions are taking to ensure that we secure and protect the intellectual capital that U.S. universities generate through taxpayer-supported federal research.

Instead of socializing around tables, participants were alone in their homes. But they were joking around and yelling “Bingo!” as they normally would. Hitchcock was the DJ for the night, haphazardly streaming Spotify from a separate laptop and taking requests from the audience via Zoom chat. The whole event cost about $300.

“People laugh and say it’s just bingo,” [Theresa] Hitchcock said. But she knows how much her students miss their friends and their campus, and how much uncertainty the pandemic has caused. She’s afraid some students will drop out and never come back.

“I sent the FDA an email saying that we’re going live with the test, and I listed the instruments we used and reagents,” Landry says. “Then I had a 15-day grace period before submitting our extensive validation studies for review.” This was done on March 24 and approval was granted on April 1.

Beginning on March 13, she and her team began testing samples from patients already hospitalized at Yale New Haven Hospital (YNHH), followed by other network hospitals, including those in Greenwich, Bridgeport, and New London and turned results around in 6 hours. Five days later, after additional virology staff were trained, her lab was set up to handle health care worker testing. A third shift to the lab was added and testing ramped up quickly.

The state of Connecticut then approved testing by Yale’s pathology lab, further increasing Yale’s on-site testing capability which, combined, is capable of providing up to 800 tests per day, depending on the available supply of reagents, which has turned out to be sporadic.

Anyway, clear that a vast underclass of America’s workers is left no choice but to put their health and the health of their families on the line every day. The choice is exposure or starvation/bankruptcy [thread]

COVID-19 continues to spread across the country and around the world. The current strategy for managing the spread of COVID-19 is social distancing, and a new white paper from Georgia Tech applies the use of an interactive Artificial Intelligence (AI) tool to conceptualize the impact of social distancing on the spread of COVID-19.

Funded with a South Big Data Hub SPOKE grant, the Virtual Ecological Research Assistant (VERA) is web application that enables users to construct conceptual models of ecological systems, and run interactive simulations of these models.

The Borderlands series has long offered players a chaotic loot scramble of explosive cel-shaded cartoon violence and intricately tuned shooting that leaves anything that isn’t the fun part on the cutting room floor. It’s like the gaming equivalent of a very large, very rich dessert — and what if, by eating dessert, you could also make the world better? Imagine.

Borderlands 3 publisher 2K and developer Gearbox Software is elevating the series’ latest game to lofty new ideals with a new in-game experience called Borderlands Science, a crowdsourced citizen science project that will leverage the hit game’s massive player base to conduct actual scientific research. In this case that’s mapping the gut microbiome — one of the most interesting frontiers in biological science right now. Scientists believe that microbes in the gut could play a role in everything from autism to allergies, though many of those mechanics remain mysterious and difficult to study given the massive breadth of microbes in the gut and the limits of computational power.

Washington University in St. Louis now offers a major in environmental analysis through the Environmental Studies program in Arts & Sciences. The interdisciplinary major is a response to global demand for environmental and sustainability experts who can think critically, communicate clearly and solve problems in collaboration with their communities.

“When you look at the big issues facing humanity, they are all touching on the environment — climate change, environmental justice, environmental health,” said David Fike, director of environmental studies, professor of earth and planetary sciences in Arts & Sciences and associate director of the International Center for Energy, Environment & Sustainability (InCEES). “The new environmental analysis major will provide students a foundation in the natural sciences, the social sciences and the humanities, and give them the skills to put that knowledge into an analysis-forward framework. It’s an interdisciplinary approach that reflects what’s happening in the real world.”

Artificial intelligence is helping us find novel, useful molecules. For the field to really take off, though, these tools will need to be accessible to the wider chemistry community

Activity from phony Twitter accounts established by the Russian Internet Research Agency (IRA) between 2015 and 2017 may have contributed to politicizing Americans’ position on the nature and efficacy of vaccines, a health care topic that has not historically fallen along party lines, according to new research published in the American Journal of Public Health.

The findings, based on machine learning analysis of nearly 3 million tweets from fake accounts, expose a general threat made startlingly more relevant in the face of the pandemic caused by the novel coronavirus, according to Yotam Ophir, assistant professor of communication, College of Arts and Sciences, who co-authored the study.

Beginning today, Facebook is assisting Carnegie Mellon University in gathering data about U.S. residents who are experiencing symptoms consistent with COVID-19 — information that is available from no other source and could help researchers in forecasting the spread of the pandemic.

Some Facebook users will now see a link at the top of their news feed that will lead them to an optional survey operated by Carnegie Mellon. Information from the survey will be used by CMU for its pandemic forecasting efforts and also will be shared with other collaborating universities. Aggregate information from the survey will be shared publicly.

“We’re hoping for millions of people to take the survey each week,” said Ryan Tibshirani, associate professor of statistics and machine learning. Obtaining the help of a company such as Facebook is crucial for this endeavor, he added.

Usually, if biomedical researchers want to publish in a high-quality journal, their research must first withstand review by several outside experts. These “peer reviewers” judge the quality of the research, ask questions and offer critiques.

When it comes to COVID-19 research, that conventional model has been upended.

The urgent need for immediate solutions to the COVID-19 pandemic has led biomedical researchers to favor a different form of publishing, called preprints – full articles made publicly available before passing the gauntlet of peer review.

“It’s a great way to get preliminary results out and shared with the wider community, which can encourage collaboration and speed up the science,” said Russ Altman.

In December when the disease that now is known as COVID-19 emerged in China, Ensheng Dong was studying the worrying spread of measles. A first-year graduate student in civil and systems engineering with a focus on disease epidemiology at Johns Hopkins University in Baltimore, Maryland, Dong began tracking the new disease.

On 22 January, he and his thesis advisor in civil and systems engineering Lauren Gardner, who is co-director of the Center for Systems Science and Engineering (CSSE) at Hopkins, released an online ‘dashboard’ documenting its spread.

That dashboard, like its subject, quickly went viral. It has become a familiar feature on news sites and on TV the world over, tracking the total number of confirmed COVID-19 cases, deaths, and recoveries globally. The site which Dong built in just a few hours receives more than a billion hits per day.

Online April 29-30. “Join us on Apr 29th or 30th (depending on your time zone) and watch a whole bunch of mappers share their knowledge live on the internet!”

Online May 5, starting at 8:45 a.m. EDT. “Learn how to detect, measure, and quantify emotion at scale — via machine learning, natural language processing, voice technologies, facial coding, behavioral analytics and more — for conversational interfaces, customer experience and consumer insights, healthcare, finance, and applications — and share your own experiences and challenges.” [$$$]

Those who stored up on toilet paper until summer are probably set, but I suspect a good number of people are starting to run low. When you go to restock, here’s a calculator to figure out how much you need to buy.

How can we improve the data efficiency and interpretability of the ML models?

We draw our inspiration from the human learning scenario. As a motivating example, consider a 3-year-old learning what a “car” is. By showing the baby a few pictures, he/she will be able to tell that “a car is something with wheels and windshields that people can drive”.

Typically, humans perceive the world as a set of discrete concepts, e.g. “car”, “person” and so on. And on top of it, we describe the world with natural languages that make use of these concepts and as well as their relations.

“The Academic Data Science Alliance is working with partners to pull together data and data science resources related to the COVID-19 pandemic. This is a living list of resources and we welcome additions, suggestions, and collaborations. Please send additions, corrections, comments, and suggestions to us using this feedback form.”

“Neuroimaging experiments result in complicated data that can be arranged in many different ways. So far there is no consensus how to organize and share data obtained in neuroimaging experiments. Even two researchers working in the same lab can opt to arrange their data in a different way. Lack of consensus (or a standard) leads to misunderstandings and time wasted on rearranging data or rewriting scripts expecting certain structure. With the Brain Imaging Data Structure (BIDS), we describe a simple and easy to adopt way of organizing neuroimaging and behavioral data.”