Dispatches

Interactive visualizations with Plotly

For the last couple of years, I’ve been using Plotly to create visually appealing interactive plots. You can create an account at plot.ly and then create and edit your plots from their online platform (they also have a premium option with extra features), but I prefer using Plotly offline, just ...

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New apper out in PLOS Biology on Why potentially important genes are ignored

We just published a new paper performing a large-scale investigation of the reasons why potentially important genes are ignored.

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New paper in Nature Human Behaviour on Personality Types

We just published a new paper investigating personality types in four large datasets (>1.5M respondents) finding robust support for at least four personality types.

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New paper in Science Advances combining topic models and complex networks

Topic models are a popular way to extract information from text data, but its most popular flavours (based on Dirichlet priors, such as LDA) make unreasonable assumptions about the data which severely limit its applicability. Martin Gerlach, member of the Amaral-lab, and co-authors explore an alternative way of doing topic modelling, based on stochastic block models (SBM), thus exploiting a mathematical connection with finding community structure in networks. A network approach to topic models Science Advances 4, eaaq1360 (2018)

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The Importance of Computational Social Science

A new discipline for the digital age.

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Alumni consulting company acquired by Ideo

Ideo is a San Francisco Bay Area consulting firm that helps companies design new products and services. It has 52 employees in Chicago and will add 16 more, including 15 data scientists, with the acquisition of Datascope Analytics. Datascope, founded by two Northwestern University and Amaral Lab alumni, has partnered ...

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New paper linking fractal dynamics of worms to aging and stress

Luiz G. A. Alves, Peter B. Winter, Leonardo N. Ferreira, Renée M. Brielmann, Richard I. Morimoto, and Luís A. N. Amaral: Long-range correlations and fractal dynamics in C. elegans: Changes with aging and stress Physical Review E 96, 022417 (2017)

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Shootings in U.S. schools are linked to increased unemployment

By Megan Fellman EVANSTON – A rigorous Northwestern University study of a quarter-century of data has found that economic insecurity is related to the rate of gun violence at K-12 and postsecondary schools in the United States. When it becomes more difficult for people coming out of school to find ...

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New paper out in Open biology

How do bacteria tune translation efficiency?

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New paper out in G3:Genes|Genomes|Genetics!

The recent work of Chuyue Yang, a talent undergraduate (now recently graduated!), and graduate student Adam Hockenberry is now online. This work is a part of a multi-year collaboration with Professor Michael Jewett investigating the mechanisms by which the sequence of messenger-RNA can influence its translation. In this particular work, ...

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Unintended effects of data privacy in healthcare

I would like to draw attention to an instance where I believe the pendulum has swung too far: the Healthcare Insurance Portability and Accountability Act (HIPAA)

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R v Python: Dawn of Analytics

A fresh yet slightly biased perspective on the recent data science language war.

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The ultimate book about folktales

I’d like to use my first blog post to advertise the ultimate story book – which also happens to be one of the most successful works of information-based science: the Aarne-Thompson index. Briefly, this index tries nothing less than to identify and categorize every folklore tale. Although the first version of the index is more than a hundred years old, it has stayed as a useful tool for folklore research ever since. Parts of the success of the Aarne-Thompson index seem to stem from time-less design decisions for organizing data.

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Toward a Social Contract in Data Journalism

In the ongoing saga of American politics, we the voters have seen some pretty improbable things this election cycle. But to many, the starkest instance of the improbable has been Donald Trump’s rise to presumptive nominee for the GOP. But I won’t be talking about the situation in question – instead I want to discuss the state of data journalism in the wake of this campaign season.

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Computational research, no longer a red-headed stepchild!

This week I had the, almost obscene, pleasure of participating in Northwestern’s Computational Research Day as a chairperson and poster judge.I typically cringe at the thought of attending conferences and symposia, since I am mainly a homebody (I love my desk, computer, research, and daily schedule), but at the symposium ...

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Dataclysm: The very best of

I recently read Dataclysm by Christian Rudder. These are some of my favorite stories from this book.

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Building trustworthy Big Data algorithms

By Emily Ayshford Much of our reams of data sit in large databases of unstructured text. Finding insights among emails, text documents, and websites is extremely difficult unless we can search, characterize, and classify their text data in a meaningful way. One of the leading big data algorithms for finding ...

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'Friending' your way thin

By Erin White EVANSTON, Ill. —- If you want to lose pounds using an online weight management program, don’t be a wallflower. A new Northwestern University study shows that online dieters with high social embeddedness — who logged in regularly, recorded their weigh-ins and ‘friended’ other members — lost more ...

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Data analysis trumps critics, wisdom of crowds and number of awards

EVANSTON, Ill. —- Don’t rely on the Academy Awards next month if you are seeking to know whether the movies deemed great today will survive the test of time. According to a new Northwestern University study, the best predictor of a movie’s significance is how often a movie is referenced ...

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Mounting a remote folder on OS X over SSH (Yosemite)

This is an update of my previous post. The current project I am working on needs to access to a folder on a remote server. It seems like a simple task, but there is one issue: I am a Mac user. Mounting a server folder is very useful if you have a lot of data to share with your colleagues. It is insane to copy it to your hard drive every time that it changes or manage large amounts of data with version control since it will slow down the repository. The best solution we found in the lab is using SSH and mounting folders using sshfs. It works really well in Linux and we don’t want to use a different system for other operating systems.

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