VMC: A Grammar for Visualizing Statistical Model Checks
Data Scientists check how well a statistical model fits observed data with numerical and graphical checks. Graphical checks have a huge range outside of the well knowns like Q-Q plots. Scientists are of course limited by their training and experience, and it’s not trivial to arrive at effective model checks. Both programmatic and visual plotting tools require significant effort to generate new plots increasing the friction to do proper checks.
Work out of Jessican Hullman‘s lab has created the VMC package (github) is a tool to easily access these methods and determine the quality of your model quickly. VMC is
a high-level declarative grammar for generating model check visualizations. VMC categorizes design choices in model check visualizations via four components: sampling specification, data transformation, visual representation(s), and comparative layout. VMC improves the state-of-the-art in graphical model check specification intwo ways:
(1) it allows users to explore a wide range of model checks through relatively small changes to a specification as opposed to more substantial code restructuring, and
(2) it simplifies the specification of model checks by defining a small number of semantically-meaningful design components tailored to model checking.
The work comes from a thoughtful place aiming not just to help out statisticians but to properly address and solve design considerations of a good tool, extending the wonderful familiy of tools that is ggplot2 built on the Grammar of Graphics.
Visualizations play a critical role in validating and improving statistical models. However, the design space of model check visualizations is not well understood, making it difficult for authors to explore and specify effective graphical model checks. VMC defines a model check visualization using four components:
1. samples of distributions of checkable quantities generated from the model, including predictive distributions for new data and distributions of model parameters;
2. transformations on observed data to facilitate comparison;
3. visual representations of distributions;
4. layouts to facilitate comparing model samples and observed data.
Pat Metheny: MoonDial
The central vibe here is one of resonant contemplation. This guitar allows me to go deep. Deep to a place that I maybe have never quite gotten to before. This is a dusk-to-sunrise record, hard-core mellow.
I have often found myself as a listener searching for music to fill those hours, and honestly, I find it challenging to find the kinds of things I like to hear. As much “mellow” music as there is out there, a lot of it just doesn’t do the thing for me.
This record might offer something to the insomniacs and all-night folks looking for the same sounds, harmonies, spirits, and melodies that I was in pursuit of during the late nights and early mornings that this music was recorded.
The above is from Pat’s website. I discovered Pat Metheny relatively recently and have grown to like his music. Last year he released MoonDial which I picked up last week. It’s nice.
Check it out:
While I know nothing about musical instruments, the man is a proper geek:
Some years back, I had asked Linda Manzer, one of the best luthiers on the planet and one of my major collaborators, to build me yet another acoustic Baritone guitar, but this time one with nylon strings as opposed to the steel string version that I had used on the records One Quiet Night and What’s It All About.
My deep dive into the world of Baritone guitar began when I remembered that as a kid in Missouri, a neighbor had shown me a unique way of stringing where the middle two strings are tuned up an octave while the general tuning of the Baritone instrument remains down a 4th or a 5th. This opened up a dimension of harmony that had been previously unavailable to me on any conventional guitar.
There were never really issues with Linda’s guitar itself, but finding nylon strings that could manage that tuning without a) breaking or b) sounding like a banjo – was difficult.
Just before we hit the road, I ran across a company in Argentina (Magma) that specialized in making a new kind of nylon string with a tension that allowed precisely the sound I needed to make Linda’s Baritone guitar viable in my special tuning.
Lake bacteria evolve like clockwork with the seasons
This article covers a pair of studies on bacteria and viruses in a lake.
researchers found that over the course of a year, most individual species of bacteria in Lake Mendota rapidly evolve, apparently in response to dramatically changing seasons.
Gene variants would rise and fall over generations, yet hundreds of separate species would return, almost fully, to near copies of what they had been genetically prior to a thousand or so generations of evolutionary pressures.
From the preprint of the virus paper:
In the evolutionary arms race between viruses and their hosts, “kill-the-winner” and other forms of dynamics frequently occur, causing fluctuations in the abundance of various viral strains55. Despite these fluctuations, certain viral species persist over extended periods and demonstrate high occurrence over time, indicating their evolutionary success in adapting to changing environmental conditions. These high occurrence viral species may represent a ‘royal family’ viral species in the model used to explain the “kill-the-winner” dynamics, where certain sub-populations with enhanced viral fitness have descendants that become dominant in subsequent “kill-the-winner” cycles. It is probable that these high occurrence viral species maintain a stable presence at the coarse diversity level while undergoing continuous genomic and physiological changes at the microdiversity level. The dynamics at the level of viral and host interactions play a pivotal role in driving viral evolution and maintaining the dominance of ‘royal family’ viral species.
Image credit: Sitting cat, from behind (1812) drawing in high resolution by Jean Bernard. Original from the Rijksmuseum. Digitally enhanced by rawpixel.
Aneesh Sathe 
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