Chris Smith Profile
Chris Smith

@chriscrsmith

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Postdoc in CIRES/NOAA. he/him

Boulder, CO
Joined August 2022
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@chriscrsmith
Chris Smith
1 year
@giliapatterson @petrelharp @pastramimachine and I just released our neural network that infers spatial maps of dispersal and population density using SNPs:.
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@chriscrsmith
Chris Smith
11 months
RT @molecology: Out in MER!.𝑚𝑎𝑝𝑁𝑁: a SNP-based inference tool for estimating geographic maps of population density and dispersal, by @chris….
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@chriscrsmith
Chris Smith
1 year
RT @min_jiseon: 1/ Individual-based simulations are a great way to model populations with less abstraction and more….
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@chriscrsmith
Chris Smith
1 year
We demonstrated mapNN on North American grey wolf data from Schweizer et al. Estimated dispersal distances increased with latitude, consistent with reports that wolf range size increases with latitude. Density was too high in Eastern Canada, likely due to reduced sampling there.
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@chriscrsmith
Chris Smith
1 year
Another selling point is mapNN uses SNPs, whereas MAPS (fourth column, above) requires IBD blocks so it doesn't work well with the 5,000 SNPs we gave it in this experiment.
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@chriscrsmith
Chris Smith
1 year
One selling point for mapNN is it tries to distinguish dispersal and density, whereas FEEMS (third column, above) estimates a single, "combined" map.
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@chriscrsmith
Chris Smith
1 year
mapNN (name of the program) trains on SLiMulations customized for the study species (geographic range, sample size, etc), and outputs pretty maps of demographic parameters. This figure shows ground truth maps in first column, and mapNN output in second column:
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@chriscrsmith
Chris Smith
2 years
RT @peter_innes1: Our paper on alternative splicing evolution in Great Sand Dunes sunflower ecotypes is now published in @HeredityJournal !….
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@chriscrsmith
Chris Smith
2 years
RT @Johri_Parul: Kavita Jain and I are organizing a symposium entitled "Genomic diversity in nonequilibrium populations" in the AsiaEvo Con….
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@chriscrsmith
Chris Smith
2 years
"Convolvulator" is credited to Nate Pope.
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@chriscrsmith
Chris Smith
2 years
The new program is available on PyPI:
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@chriscrsmith
Chris Smith
2 years
We're calling the new architecture a 'pairwise convolutional network' (aka, "the convolvulator").
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@chriscrsmith
Chris Smith
2 years
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@chriscrsmith
Chris Smith
2 years
The new model extracts summary information from pairs of genotypes at a time. And the geographic distance between a pair is also tacked onto the extracted features. All pairs are then combined to estimate the dispersal parameter. The new model is much more accurate.
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@chriscrsmith
Chris Smith
2 years
Our previous method, disperseNN, did not take advantage of available geographic information, but relied only on genetic variation for estimating dispersal.
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@chriscrsmith
Chris Smith
2 years
Check out my preprint with @pastramimachine, a brief update for our deep learning model that estimates dispersal rate from SNPs:
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@chriscrsmith
Chris Smith
2 years
RT @ramencult: i wrote a paper about using machine learning to identify patterns of co-dispersal in Anopheles and Plasmodium. https://t.co/….
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@chriscrsmith
Chris Smith
2 years
RT @drschield: Hello #JMIH23! I am recruiting PhD students to my new lab @uvabio starting Fall '24. I won't be at JMIH to meet in person, b….
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@chriscrsmith
Chris Smith
2 years
My #Evol2023 t-shirt is the smallest shirt I’ve ever tried to put on. Anyone want an XS (tag says medium)?.
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@chriscrsmith
Chris Smith
2 years
RT @evolauterbur: Very pleased to release FlexSweep and some new summary stats, designed for versatility in detecting selective sweeps of d….
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@chriscrsmith
Chris Smith
2 years
Beautiful location for EVO-WIBO conference: Fort Worden Historical State Park, WA
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