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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Congratulations to June Lee on winning the lightning talk competition at @Northwestern Computational Research Day!

Several students from our lab participated this week in the Northwestern Computational Research Day, where they presented some of the interdisciplinary research currently being done here. PhD candidate Hyojun (June) Ada Lee won the lightning talk competition with her presentation on the use of a smartphone app to improve quality ...

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Looking for outstanding postdoctoral fellows

The Amaral Lab invites applications of recent graduates to new postdoctoral positions. The new hires will join an active group comprised of 1 research professor, 3 postdoctoral fellows, and 9 graduate students, many of whom are co-advised with collaborators. Currently, the Lab pursues projects in the modeling of microbial communities ...

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The Importance of Computational Social Science

A new discipline for the digital age.

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An outlook of the fight against climate change

According to the Paris Agreement (also known as the Paris climate accord), which was initialed in 2015 and signed by more than 190 countries all over the world, we all human beings are in a war against the global climate change and should work together to curb the greenhouse emissions. The Paris Agreement has a very specific goal to limit a global temperature rise within 2 Celsius degrees compared with the pre-industrial levels. Otherwise, the temperature rise will be irreversible and lead to sea level rising and more frequent extreme weather conditions threatening millions of lives.

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Artificial intelligence is the future, is it?

Many believe that, Artificial Intelligence (AI) has the potential to revolutionize the future. During the Cold War, then-Senate Majority Leader Lyndon Johnson believed that “whoever wins the space race would gain control over the Earth”. Today, AI development is the new space race. Recently, Russian President Putin said, “Whoever becomes the leader in this sphere will become the ruler of the world”. Despite the hyperbole in this statement, the importance of technology’s power should never be overlooked and artificial intelligence is truly today’s hot topic.

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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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Holiday Fashion

An introductory guide to personalized livery.

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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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Function wrapper and python decorator

When researchers translate their thoughts into codes, they usually have the needs to modify their existing functions to accommodate their new ideas, such as adding new arguments or a little more computations to the functions.

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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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Do it live!

Code at rest is a dreary thing. Worse, it’s often ignored. Distributing your lifeless code is nice and all, but running it for others can be even better.

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Effectively communicating scientific information

How do scientists make effective connections with the public?

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Thought about imperial units

As a European, I’ve never been interested in working with the imperial units. But today I want to talk about a good point I discovered in it.

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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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post hoc != propter hoc

Lest I scare you away immediately, let me clarify that the topic of this blog is only marginally about the ethics of animal research. Rather, it’s about making a cogent argument. And more specifically, about the sense of nausea I feel when reading terrible arguments from people who should know ...

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