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Amy D Willis

@amydwillis.bsky.social
625 followers 134 following 99 posts

Biodiversity-loving, error bar-needing statistics nerd; Associate Professor @UWBiostat. Methods & software for #microbiome & #biodiversity data. She/her.

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Reposted by Amy D Willis
Carl T. Bergstrom @carlbergstrom.com · 21/07/2026
13. Hence our dismal conclusion: rather than finding that LLMs free us to do a better job of what we were doing before they came along, they shift scientific incentives (and the playing field of academic competition) in ways that compel us to do more and more, faster and faster, less and less well.
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Amy D Willis @amydwillis.bsky.social · 22/07/2026
Understood -- thanks for sharing, @erikvannimwegen.bsky.social !! That's a helpful perspective.
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Amy D Willis @amydwillis.bsky.social · 22/07/2026
Awesome, thanks Mike!!! 😽😽
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Amy D Willis @amydwillis.bsky.social · 22/07/2026
Thanks so much for sharing, @dutchscientist.bsky.social !! Much appreciated.
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Amy D Willis @amydwillis.bsky.social · 22/07/2026
Super helpful to know -- thanks!! I appreciate you taking the time, Alex!! @acritschristoph.bsky.social
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Amy D Willis @amydwillis.bsky.social · 20/07/2026
Many thanks to all for sharing, and feel free to email/DM me if you don't want to answer publicly. These chats really help me understand what you all need in terms of methods. So, thank you 🙏🏻🙏🏻 ❤️, Amy 7/
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Amy D Willis @amydwillis.bsky.social · 20/07/2026
Without exaggeration, uncertainty quantification is my livelihood -- I'm a statistician, that's what we do. So, I know what these numbers mean to me... but what do they mean to you all, dear bacteria/microbiome friends, when you produce and read numbers that imply such confidence? 6/
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Amy D Willis @amydwillis.bsky.social · 20/07/2026
(And yes, I am familiar with the debate about this paper and the Author Correction.) 5/
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Amy D Willis @amydwillis.bsky.social · 20/07/2026
and almost all of these splits have >99% posterior probability (Fig 2 of the same paper) 4/
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Amy D Willis @amydwillis.bsky.social · 20/07/2026
Here's what I'm talking about: Almost all of these splits have >90% bootstrap support (Fig 1 of www.nature.com/articles/s41...) 3/
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Amy D Willis @amydwillis.bsky.social · 20/07/2026
Almost all of these numbers are >90%, >95%, >99%... That level of confidence may makes sense for more recent evolution, but the same confident numbers appear when we are talking divergences from billions and billions of years ago. 2/
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Amy D Willis @amydwillis.bsky.social · 20/07/2026
Genuine question for folx who look at bacterial phylogenies: How do you interpret the bootstrap support and posterior probabilities that you get on your tree estimates? Do you take them seriously? Do you think: "Wow, all 99%, that must be a reliable tree!"? 1/
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Amy D Willis @amydwillis.bsky.social · 25/06/2026
I'm hiring a #postdoc 🥳 and applications are open 🤩 Candidates with interests in EITHER statistical methodology or microbial ecology / microbiome are welcome to apply. The position / projects will be tailored to the candidate 🌟📈🎤 Thank you for sharing widely! apply.interfolio.com/188571
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Amy D Willis @amydwillis.bsky.social · 16/06/2026
I'm hiring a #postdoc!! 🥳 Official ad is making its way through HR but If you have interests in statistical methodology OR microbial bioinformatics, please reach out via my UW email. I'll share the description with you when it's available. 🔥😻
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Amy D Willis @amydwillis.bsky.social · 18/05/2026
This isn't a full-picture benchmark against all other methods BUT I am rather pleased and thought I would share 🥳 A great argument for radEmu's robust-centering approach to identifiability 🔥 and valid error rate control 😻 Those score tests ran overnight, but were definitely worth waiting for 🎤
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Amy D Willis @amydwillis.bsky.social · 18/05/2026
radEmu took the cake today. I'm looking at a dataset where the truth is known (a complex spike-in, spiked-in at varying intensities). All taxa should be unchanging in abundance except for the spike-ins... True "positives": 6 / 1505 radEmu score tests identifies 7 CLR + linear model identifies 517
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Amy D Willis @amydwillis.bsky.social · 20/03/2026
Are you doing prediction using microbial community data as input? Please report accuracy as *average percentage error* of the prediction relative to the measurement. I'm not interested in their correlation -- I want to know how many orders magnitude you're off by. Thx! #microbiome #deeplearning
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Amy D Willis @amydwillis.bsky.social · 16/12/2025
We really appreciate your support, Kendra!!
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Amy D Willis @amydwillis.bsky.social · 16/12/2025
Thx for checking! Co-author Teichman joined the team after v1. Here's what I'll be using: David S Clausen, Sarah V Teichman, & Amy D Willis. 2025+. "Estimating Ratios of Means of Multicategory Data Observed with Sample and Category Perturbations." Biometrika, In Press. arxiv.org/abs/2402.05231.
arxiv.org
Estimating Fold Changes from Partially Observed Outcomes with Applications in Microbial Metagenomics
We consider the problem of estimating fold-changes in the expected value of a multivariate outcome observed with unknown sample-specific and category-specific perturbations. This challenge arises in h...
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Amy D Willis @amydwillis.bsky.social · 16/12/2025
Documentation: statdivlab.github.io/radEmu/ Blog post: statdivlab.github.io/blog/article... 4/4
statdivlab.github.io
Using Relative Abundance Data to Estimate of Multiplicative Differences in Mean Absolute Abundance
A differential abundance method for the analysis of microbiome data. radEmu estimates fold-differences in the abundance of taxa across samples relative to "typical" fold-differences. Notably, it does ...
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Amy D Willis @amydwillis.bsky.social · 16/12/2025
Feel guilty about replacing your zeroes with pseudocounts? Fed up with checking robustness to said pseudocount? Not sure what it means biologically to have a difference of 0.34 in averages of CLR-transformed data?* radEmu 🕶️🦤 3/ *Spoiler: It means nothing. It's inherently not interpretable.
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Amy D Willis @amydwillis.bsky.social · 16/12/2025
Oh yeah, ICYMI... radEmu is a method for differential abundance (or differential expression). It's especially well-suited to genomics and microbiome studies.
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Amy D Willis @amydwillis.bsky.social · 16/12/2025
Also, we made some common cases superdooper fast last week, so pull changes ⚡🏎️ Happy holidays, y'all! ❤️🦤❤️🦤❤️🦤❤️🦤❤️🦤❤️🦤❤️ 2/
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Amy D Willis @amydwillis.bsky.social · 16/12/2025
I am delighted to share that the radEmu manuscript was accepted today to Biometrika 🥳 Sending gratitude to our users and reviewers for their enthusiasm and support!! Huge congrats to @davidandacat.bsky.social and Sarah Teichman on all their hard work and brilliance 😻❗ 1/
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Amy D Willis @amydwillis.bsky.social · 08/12/2025
With many thanks to @svteichman for bringing this to my attention and making these figures
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Reposted by Amy D Willis
Amy D Willis @amydwillis.bsky.social · 08/12/2025
Thanks for corroborating!! We've seen again and again that ALDEx2's p-values can be either very conservative (= underpowered) or very anticonservative (= wrong), but this points to something more problematic, such as a mistake in how they're being calculated.
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Amy D Willis @amydwillis.bsky.social · 08/12/2025
Thanks for corroborating!! We've seen again and again that ALDEx2's p-values can be either very conservative (= underpowered) or very anticonservative (= wrong), but this points to something more problematic, such as a mistake in how they're being calculated.
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Amy D Willis @amydwillis.bsky.social · 08/12/2025
ALDEx2's p-values are unusually strongly correlated with its effect sizes. Has anyone else noticed this? That... shouldn't happen. Data is actual shotgun coverages, ~8000 "taxa", 57 samples.
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Amy D Willis @amydwillis.bsky.social · 04/12/2025
Let's do better science together by using agreed-upon definitions! Woohoo! 4/4
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Amy D Willis @amydwillis.bsky.social · 04/12/2025
Same article but without the paywall (sorry, I didn't think they'd paywall it! duh Amy...) github.com/statdivlab/p... 3/
github.com
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Amy D Willis @amydwillis.bsky.social · 04/12/2025
There's some more info on confounders in microbiome studies (and how they differ from precision variables) in this perspective we wrote last year: www.nature.com/articles/s41... 2/
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Amy D Willis @amydwillis.bsky.social · 04/12/2025
I had this conversation again with someone today, so posting a screenshot of an old t**** for those who missed it the first time around -- or want a refresher! 1/n
A screenshot from a retweet dated March 2021. 

Original tweet from David + Cat: "A confounder is a variable that has a causal effect on an outcome of interest and is associated with a (possibly causal) predictor of interest.

It is not any process/phenomenon/feature of reality that makes a study more difficult to conduct or interpret."

Comment on retweet from Amy: 

'Happy Definition Monday! “Confounder” is an overused term in microbial ecology & next-gen sequencing, often used to mean “something that makes science difficult”. Here’s what it actually means  — thanks for the great reminder, @davidandacat! 🙌🏻💯'
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Amy D Willis @amydwillis.bsky.social · 11/11/2025
With much gratitude to everyone who supported the wonderful #STAMPS summer course at the MBL, I share that STAMPS will not be offered in 2026. 💔😿
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Amy D Willis @amydwillis.bsky.social · 06/11/2025
pixi is awesome. That is all. @titus.idyll.org you're all over this, right?
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Amy D Willis @amydwillis.bsky.social · 04/11/2025
Are you looking for a #tenuretrack or #openrank job in #biostatistics or #statistics? @fredhutch.org is hiring! Seattle is a wonderful place to grow your career; the bio/stat & science scene here is world-class; and you will work w/ amazing UW Biostat students. Apply! apply.interfolio.com/176402
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Amy D Willis @amydwillis.bsky.social · 03/11/2025
dude you can just text me with this stuff ❤️ % of microbiome (& changes) aren't identifiable from HTS, but stacked barplots are helpful for generating clues esp if big shifts data snooping has implications for error rate control. there isn't a hypothesis you're interested in? good luck & enjoy xx
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Amy D Willis @amydwillis.bsky.social · 31/10/2025
In other news, I just had the great pleasure of teaching at #EBAME10 in Brittany 🇫🇷🥐. For this workshop, I made a tutorial showing how to use radEmu with the taxonomic profiling output of #anvio 😍😻 Workflow available for everyone on our blog: statdivlab.github.io/blog/article... ❤️❤️
A screenshot of the header for the tutorial linked in the post
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Amy D Willis @amydwillis.bsky.social · 31/10/2025
Happy Friday from the StatDivLab! We just made updates to radEmu to make it faster & more stable than ever. Thanks to all our users -- we're excited to keep supporting it. github.com/statdivlab/r... Interpretable and robust microbial differential abundance, woohoo!
github.com
GitHub - statdivlab/radEmu
Contribute to statdivlab/radEmu development by creating an account on GitHub.
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Amy D Willis @amydwillis.bsky.social · 18/10/2025
Thanks for your interest, @genomesevolve.bsky.social ! As a field, *on average*, I feel we have moved... 1. away from obsessing over alpha and beta diversity comparisons 2. towards comparisons that are less sensitive to rare/undetected species (than diversity) So 📈 🥳
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Amy D Willis @amydwillis.bsky.social · 23/07/2025
Wisdom from @titus.idyll.org on the final day of #STAMPS2025: "There's free as in beer, and there's free as in kittens. #Bioinformatics software is free as in kittens. You have to love and care for them or they... well... yeah."
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Amy D Willis @amydwillis.bsky.social · 22/07/2025
The question was "...*on the same sequencing run*?"
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Amy D Willis @amydwillis.bsky.social · 19/07/2025
Given that a Poisson regression with log link targets the same parameter as your NB regression, I'd be curious to see the coverage of robust Wald CI's. `rigr` wraps this, so does `raoBust`, so should be easy to add. (Sorry -- I'm at a workshop today or I'd do it myself)
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Amy D Willis @amydwillis.bsky.social · 19/07/2025
raoBust doesn't invert score tests @nlaroy.bsky.social, but it does implement (model-misspecification) robust score tests, which are amazing for inference. Feel free to open a feature request. We'll see what we can do. github.com/statdivlab/r...
github.com
GitHub - statdivlab/raoBust: Generalized Linear Models with robust and non-robust Wald and Rao (score) tests
Generalized Linear Models with robust and non-robust Wald and Rao (score) tests - statdivlab/raoBust
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Amy D Willis @amydwillis.bsky.social · 07/07/2025
The StatDivLab is getting excited for #STAMPS2025 and working on our lectures for 🤩 Stats Day 😻. We ran this think-pair-share activity last year and, wow, the ensuing discussion was *very* engaged 😹😅 Reach out if you'd like to attend! Woods Hole, MA, July 14-24 2025. #microbiome #dataanalysis
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Amy D Willis @amydwillis.bsky.social · 01/07/2025
Agreed that (eg) MAG assembly vs taxonomic estimation makes a huge difference to your answer. Also, please definitely read the Conflict of Interest statement for the shallow shotgun paper and note how much of its claims rely on bioinfomatic subsampling *and not actual shallow sequencing data*
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Reposted by Amy D Willis
Prof. Isabelle Laforest-Lapointe @ilafores.bsky.social · 30/06/2025
Best workshop you can ever follow
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Amy D Willis @amydwillis.bsky.social · 30/06/2025
That's wonderful to hear, Isabelle!! Thanks for sharing, too. Hope to see you there in 2026.
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Amy D Willis @amydwillis.bsky.social · 29/06/2025
We had a last minute cancellation for STAMPS -- a phenomenal course on microbiome data analysis. Woods Hole, MA, July 14-24 2025. If you or *anyone* you know is interested to attend, please email Titus &/or me... and we'll do what we can!!! Thx for sharing widely! 🤞❤️
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Amy D Willis @amydwillis.bsky.social · 21/05/2025
The StatDivLab is *fully* reliant on our NIGMS #MIRA R35 to bring you top-quality statistical methods for microbiome research. #NIH They are quietly taking MIRAs away from this year's applicants. It's sneaky and scary. Fight back! Call your reps and tell them to protect science!
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Reposted by Amy D Willis
Ethan White @ethanwhite.weecology.org · 21/05/2025
It only takes 2 minutes to help defend our amazing program officers (and many other federal employees) and allow them to keep serving all Americans instead of responding to the whims of a single person
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