Nicola Romanò @nicolaromano@qoto.org

There are some *beautiful* lessons on building ML-based classifiers in biology in the recent Gihawi et al. paper (Major data analysis errors invalidate cancer microbiome findings)

Classifiers will always look for weird things and then report way-too-good-accuracies. At first glance no classifier in biology should be highly accurate: by now that should be a red flag.

I wonder whether there's a fun 'signal' in studies including randomness: so many tutorials, notebooks, and repos use 42 as a random seed.
I wonder whether by now we have a weird bias because of that number somewhere :)

Today I'm seeing multiple posts alerting me to serious problems with an update to Zoom's terms of use (variously stated as dated last March or April) according to which
- They have the right to feed all your Zoom calls and associated data to an AI learning system
- They own this data forever
- There is no opt-out
- If you show anything copyrighted on a Zoom call and the copyright owner goes after Zoom for copyright infringement for using this data, then you are personally on the hook for all legal damages

For example see https://the.webm.ink/not-using-zoom, via https://news.ycombinator.com/item?id=37034145

Even if you are somehow ok with training AI to look like you and talk like you, I think the last point makes it no longer safe to use Zoom for any purpose. That's a big issue for online collaboration, conferencing, and online office hours with students (note high likelihood of incorporating copyrighted textbook material into those office hours).

There's a good discussion of alternatives at https://mathstodon.xyz/@MedievalMideast@hcommons.social/110838371676478198 and probably starting up at many other places as well.

Just discovered there is an extension of #Inkscape to quickly edit scientific figures (change axis ratio, font sizes, etc) 🤩

https://github.com/burghoff/Scientific-Inkscape

behind "hello world" on Linux https://jvns.ca/blog/2023/08/03/behind--hello-world/

"A developed country is not a place where the poor have cars. It's where the rich use public transportation."

'She had consented to be a part of our research project and was determined to contribute — she had told me that it wasn’t every day that a person had electrodes implanted in their brain, and what else was she doing while she waited to have seizures that the epileptologists could track?'

https://www.jci.org/articles/view/173352

#BookReview
#HistoryOfLogic #HistoryOfMathematics #HistoryOfComputing
https://thonyc.wordpress.com/2023/07/26/when-is-an-algorithm-not-an-algorithm/

What if we told you that you could run Fedora... on Android? 👀
#Fedora #Android #Linux #Termux

➡️ https://fedoramagazine.org/how-to-install-and-update-fedora-linux-on-android-using-termux/

First post of my summer blog series on image communication in (bio/med) publications!

Today: Many papers, many images, many problems (and some first solutions).

Why we should make sure our figure are understandable.

https://helenajamborwrites.netlify.app/posts/image_numbers/

The more I work with #rstats, the less I know about it!
Today I learned about the function utils::stack() to convert a named list to a data frame.

R-Ladies Remote is now on Mastodon 🎉

We are the only fully online chapter of R-Ladies, the global organization promoting gender diversity in the R community. Our chapter particularly welcomes people working remotely or living in places remote from other chapters.

Our main community is on Slack, where we sometimes hold organized sessions (coffee chats, reading groups) and we also hold occasional online talks/workshops.

#RLadies #RStats

The most disappointingly simplistic thinking in tech, to me personally, is when people think just because something is being deployed IN education, in a classroom, or in a school, that means it's an unquestionable public good.

Instead of seeing the many, many complex ways that we take advantage of schools, or indeed damage schools, with our technology.

I'm always amazed by the strength of this association for people who haven't worked directly in education.

@devezer

Underlying problem is that we literally have college courses in noise mining (we call them Stats 101) so millions of scientists are out there noise mining, and so we have a lot of papers that really do have low evidentiary value. It's not because they're not preregistered, it's because the people doing the analysis wouldn't know what a good analysis looked like, and in fact would likely fight a good analysis tooth and nail.

I wrote a script that takes as input a gene of interest:

```console
./script/plot_heatmap.sh -p 10 TP53
```

and generates a gene expression heatmap with genes that have correlated expression patterns.

Behind the scenes is a Bash script (calling `gget`) and a #Rstats script available at https://github.com/davetang/archs4_heatmap

One of my professors during PhD used to say “you can drive a truck through the holes in any given paper. so you look for what you *can* learn instead.” and being the smartass grad students we used to think driving that truck was fun. After so many years, I now appreciate her wisdom more than ever. All scholarly work has limitations but it’s refreshing when people critically evaluate what’s the actual value of the research. It's about humility, honesty, rigorous intellectual work.

New posting! This addresses the recent controversy at the 2023 Lindau Nobel Laureate meeting, where one of the speakers used his time to complain that he felt discriminated against as a white man.

To my mind, that isn't what's surprising and shocking about the episode.

The surprising thing is that on this occasion, a courageous young female scientist actually called him out on it.

The shocking thing is that despite such sexist, chauvinistic comments still being commonplace, such interventions basically never happen. And they should. #womeninstem

https://totalinternalreflectionblog.com/2023/07/16/speaking-up-speaking-out-the-2023-lindau-nobel-laureate-meeting-controversy/