Author Archives: Antoine

Rise of the Machines

Recently, there’s been a lot of interesting activity in the field generative AI for science from large companies such as Google, Meta and Microsoft.
Creating new materials from scratch is difficult, since materials involve complex interactions that are difficult to simulate, or a fair amount of luck in experiments (serendipity is scientists’s most terrifying friend)
Thus most of these efforts aim to discover new material by accelerating simulations using machine learning. But recent advances (such as LLM, e.g., ChatGPT) have shown that you can use AI to make coherent sentences instead of a word soup. But the same way cooking is not just about putting ingredient together all at once but carefully preparing them, making a new material involves important intermediate steps.  And new approaches can be used create new materials.

The various steps of making a new material (from Szymanski et al.)

Last month, Google in collaboration with Berkeley Lab announced that their DeepMind’s Gnome project had discovered a lot of new structures: Google DeepMind Adds Nearly 400,000 New Compounds to Berkeley Lab’s Materials Project. They managed to actually make and analyze some of those new materials ; that is quite a tour de force, and while there’s some interesting pushback on the claims, it’s still pretty cool!
In September, I invited Meta’s Open Catalyst at Berkeley Lab (here’s the event description and the recording – accessible to lab employees only)

Zachary Ulissi (Meta/OpenCatalyst) and Jin Qian (Berkley Lab) at Lawrence Berkeley National Laboratory (September 2023)

Meanwhile, Microsoft is collaborating with Pacific Northwest National Laboratory on similar topics
Meanwhile, the research infrastructure has it gears moving; it seems that DeepMind’s AlphaFold is already routinely used at the lab to dream up new protein structures. I wonder where this will go!
Prediction is very difficult, especially if it’s about the future
– Niels Bohr
Thinkpieces blending chips and AI in full bloom:
We need a moonshot for computing – Brady Helwig and PJ Maykish,  Technology Review

The Shadow of Bell Labs

I want to resurface an interesting thread by my former colleague Ilan Gur:

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APS DPB newsletter

My piece for the American Physics Society Division of Physics of Beams Annual Newsletter  about the Advanced Light Source upgrade has been published!

Here it is for your own delight:

Antoine’s guide to Marseille

Because of the Paris Olympics, many friend ask me for advice about Paris, and I refer them to the my Insider’s guide to Paris. But there’s another French city I recommend visiting to people: Marseille. It is a city on the Mediterranean, with a very rich culture – the city was founded by settlers from Phocaea 26 centuries ago, with lots of great food, sights and people.
Actibus immensis urbs fulget masiliensis
“The city of Marseille shines through his great achievements”
So here’s a bunch of things not to miss in Marseille:
– Notre Dame de la Garde (“La Bonne Mere”, or the good mother), the cathedral that sits on top of the city. Unique architecture and history, you can see it from pretty much everywhere. Walking up there is doable, or you can take a bus. When you go down, there is path that brings you to Roucas Blanc (the fancy, low-key neighbourhood of Marseille), if you feel like wandering (ask around.)

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Rest in piece, Twitter

A lot has been said on the death of Twitter, a medium I enjoyed.

But Twitter was always more than a news source, or a conduit for information. It was a place where a sense of goofiness and comfort allowed communities to form—Weird Twitter, Philosophy Twitter, BTS Twitter. Such communities allowed users to find the platform endearing, even as they called it the “hellsite.”
What We Lost When Twitter Became X – Sheon Han, The New Yorker

You can now follow me on Threads, at @anto_nymous.

I’ve tested Mastodon and bluesky, but it never really did it for me. I’m try to communicate about science on LinkedIn, but is has the vibe of a hostage situation – except that it’s filled with humblebrags and emojis used as bullets to list platitudes.

The pi rule

These days things are getting pretty busy on my end – so many cool projects to engage with and only 24 hours a day.

And you end up doing more things that you can accomplish. The reason often lies in the unrealistic assessment of the time it would take to complete a task, and I came across the “pi” rule, initially posited by my mentor Ken, with a pretty neat explanation from my colleague Val:

If you estimate it will take one unit of time to complete a task, the task will effectively take 3.14 (≈π) times more than you initially anticipated.

The reason for the difference between dream and reality  is that we generally do not factor in:

  • (1) the time it takes to ease into the task (e.g. collecting documentation, emails) and
  • (2) the time requires to document the work done (reports, emails)

Taken together with the times its take to accomplish a task, you end up with roughly a factor three – and you end up feeling terrible during the week-ends trying to catch up what you were set to do during the week, but got busy doing (1) or (2)

A corollary of the pi rule is the “next up” rule: if you work on project with a relatively large team, it generally takes the next unit of time to complete it (e.g. one hour become one day; one day becomes a week; a week becomes a months), generally because of the friction at the interfaces. Reducing these frictions at the interfaces should therefore be a priority.

Engineering interfaces in big science collaborations

I recently learned that my colleague Bertrand Nicquevert has worked extensively on a model to describe interactions between various counterparts:

Modelling engineering interfaces in big science collaborations at CERN: an interaction-based model
https://cds.cern.ch/record/2808723?ln=fr

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Hotline bling

I was lucky to meet the President of the University of California Michael V. Drake, in my capacity of co-chair of the Berkeley Lab Global Employee Resource group (global.lbl.gov), dedicated to providing support to international employees at the national laboratory.

Berkeley Lab Employee Resource Groups meeting with UC president Michael Drake in November 2023

I made the point the re-building communities should be a priority after the pandemic, and particularly early career scientists, who do not have family or go to school where they could thread their social fabric. The participation of international scientist at Berkeley Lab is an important strength, because the national lab is de facto at the center of international research, and that gives it a competitive edge compared to other countries such as China or Saudi Arabia, where large research expenditure cannot compensate the lack of free flow of ideas.

I think my talking points were well received, and president Drake encouraged collaboration on these topics with the University of California, Berkeley

Ladder of causation

I’ve read an interesting piece on Twitter from the always excellent Kareem Carr on the ladder of causation. I found it very interesting, because it allows you to go beyond the mantra “corelation is not causation“, and links statistics to the concept of falsifiability that Thomas Kuhn puts as central to sciences.

The Ladder of Causation

The Ladder of Causation has three levels:

1. Association. This involves the prediction of outcomes as a passive observer of a system.

2. Intervention. This involves the prediction of the consequences of taking actions to alter the behavior of a system.

3. Counterfactuals. This involves prediction of the consequences of taking actions to alter the behavior of a system had circumstances been different.

I even read the book from which – “The Book of Why” [Full book on the Internet Archive] by Judea Pearl, a Turing prize recipient who worked on Bayesian network. The book quite illuminating, mentioning a bit too often  dark figures such as Galton, Pearson and Fisher (it seems statistician get really high on their own supply.)

This certainly begs the question – “Why not?”

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On Mentorship

This last month, I received two awards related to mentorship from Berkeley Lab. They both came as a surprise, since I consider myself more a student of mentorship than someone who has something to show for.

Berkeley Lab Outstanding Mentorship Award

Director’s award for For building the critical foundations of a complex mentoring ecosystem

I began to be interested in mentorship after I realized that mentorship plays a large role in the success of young scientist, (1) having experience myself the difference between having no mentorship and having appropriate mentorship (I’ll be forever grateful to my mentor/colleague/supervisor Ken Goldberg), (2) having had tepid internship supervision experience due to the lack of guidance, (3) realizing that academia is ill-equipped to provide the resources necessary for success.

While I was running Berkeley Lab Series X, I always asked the speakers (typically Nobel prize laureates, stellar scientists and directors of prominent research institutions) how they learned to manage a group, and they answer was generally: “on the spot, via trial and error”, what struck me as awfully wrong. If people don’t get the proper resources/training, many are likely to fail, and drag their own group down the abyss. In this post, I will try to share resources I gathered along the years, and what I learned about mentorship, and provide some resources I found useful. This is more descriptive of my experience than prescriptive, but I hope you find this useful.

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Dr. and Drs.

Last week, my partner and I got married, and we both decided to take the same surname.

I will now be known as Antoine İşlegen-Wojdyla – edit your contact info!

Golden Gate Bridge (credit: Jake Ricker)

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Lamaseries

It’s been a few months since the ChatGPT craze started, and we’re finally seeing some interesting courses and guidelines, particularly for coding, where I found the whole thing quite impressive.

https://static.tvtropes.org/pmwiki/pub/images/llama_loogie_tintin.jpg

Ad hoc use of LLaMa

Here’s a few that can be of interest, potentially growing over time (this is mostly a notes to self.)

Plus – things are getting really crazy: Large language models encode clinical knowledge (Nature, Google Research.)