MST graph comparing the top-10 ranking overlap between many commonly used fingerprint types and variants.

Four UMAP visualizations of chemical space based on 700k fingerprints on the biostructures dataset using various molecular fingerprint types.

Just updated our preprint on benchmarking molecular fingerprints!
--> www.biorxiv.org/content/10.1...

Some key points
- Count fingerprints should be the default (not binary!)
- Unfolded fingerprints are often worth it.
- Larger radius Morgan or FCFP fingerprints are good first bets.

Work done with @julianpollmann.bsky.social at @zdd-hsd.bsky.social

Code:
- Central functionalities are now pip installable --> github.com/matchms/chemap
- Notebooks for experiments --> github.com/florian-huber/molecular_fingerprint_comparisons

#openscience #opensource #cheminformatics #python

Haftbefehl shows that Germany loves art born from alienation – just not the people who create it A hit Netflix documentary about Germany’s favourite rapper demonstrates how popular the aesthetics of migrant life are – just as politicians debate how to remove it from inner cities

Haftbefehl shows that Germany loves art born from alienation – just not the people who create it

New #matchms release (0.31)🚀

With functionalities that were on our TODO list for a looooong time: Flash Entropy and BLINK scores! The new "FlashSimilarity" allows computing modified cosine, spectral entropy etc., about 100x faster (or more if you use Linux).

#Python #opensource #massspec

Chemical Space Visualizations using UMAP and various molecular fingerprints.

4/4
We also highlight options for count fingerprints, such as log-counts and IDF weighted counts. The latter can be used to adjust the bit importance to a dataset of your choice.

An example use-case are chemical space visualizations.

Preprint: www.biorxiv.org/content/10.1...

3/4
A huge issue is bit collisions.
Fingerprints with a high bit occupation (RDKit, MAP4) often lead to (1) arbitrary misinterpretations, (2) shifts to high Tanimoto scores, (3) very different handling of small and large molecules.

--> Consider using sparse fingerprints!
--> Morgan >> MAP4 / RDKit

Benchmarking plot on fingerprint duplications.

2/4
We focused on weaknesses of the fingerprints.
Many show frequent duplicates, so same fingerprint for different compounds. Most problematic: this can include *very* different compounds ending up with identical fingerprints.

- MAP4 >> Morgan-type >> daylight
- count >> binary

#cheminformatics

Sketch of count/binary fingerprints and weighing options.

New preprint out!
1/4

@julianpollmann.bsky.social and I went down several rabbit holes to assess some commonly used molecular fingerprints.

Bottom line: For large datasets, make an effort to select suitable settings. "We used Tanimoto" is not good enough.

--> www.biorxiv.org/content/10.1...

Motivational quotes like "If you can dream it, you can do it." will help to relax in such environment.

Libertäre kennen • den Preis von allem • den Wert von gar nichts • das Schutzalter in jeder Juristiktion

was @tante.cc sagt

Wir dachten, KI würde uns irgendwann durch Terminator-Roboter versklaven. Aber wir werden durch Bequemlichkeit versklavt.

Hello @pyconde.bsky.social
Curious to listen to some interesting Talks and meet new people 😀

First draft online version of The RLHF Book is DONE. Recently I've been creating the advanced discussion chapters on everything from Constitutional AI to evaluation and character training, but I also sneak in consistent improvements to the RL specific chapter.

rlhfbook.com

„Bei der #SPD haben noch die Mitglieder die Chance, die Notbremse zu ziehen und den Abbau wichtiger Grundrechte zu verhindern. Wir appellieren daher an die Sozialdemokraten: Stimmt dieser Überwachungsliste nicht zu!“ 🤝👏 @ccc.de

Einige Hochschulen ziehen bereits Einstellungsstopps für Professor:innen und Mitarbeiter:innen in Betracht und haben die Zahl der Hilfskräfte reduziert. #IchBinHanna #BildungKostet 2/2

Herzlichen Glückwunsch zum Spatenstich für das neue Gebäude! Es bleibt zu hoffen, dass die von Ina Brandes geplanten Kürzungen der Grundfinanzierung der Hochschulen in Höhe von 255Mio EUR in #NRW nicht zu einem Mangel an Wissenschaftler:innen führen. #IchBinHanna #BildungKostet 1/2

I think this is an important point that we missed the last 10y. We need to call out fiction as fiction and fighting for reality (can be boring, but it’s real).
Reality is, there is no AGI, just language models. If you think they are giving you some truth, the stupidity is on you, not the LLM.

Enabling the Next Generation in AI & Open Source: Free Remote Tickets for Students at PyCon DE & PyData Join PyCon DE & PyData 2025 in Darmstadt (Frankfurt), April 23-25! Germany’s largest Python and Data Science conference with talks, workshops, and community events like DjangoGirls and sprints. Be…

👨‍🏫 Can you help spread the word? Our community supports future #AI professionals like engineers and data analysts. With backing from PySV and Pioneers Hub, we provide students free virtual passes to Germany's top AI conference. Learn more at 2025.pycon.de/blog/free-re....

Nice keynote by @tante.cc for the opening of @zdd-hsd.bsky.social #HSD

ZDD Foyer bereit für die feierliche Eröffnung

Die Vorbereitungen für die Einweihung des #ZDD laufen auf Hochtouren!

Wir freuen uns auf morgen.

An Open-Source AI Agent for Doing Tasks on the Web | Stanford HAI NNetNav learns how to navigate websites by mimicking childhood learning through exploration.

Stanford scholars introduced an open-source AI agent that learns how to navigate websites by mimicking childhood learning – an approach that could lead to more efficient, transparent, and privacy-conscious AI: hai.stanford.edu/news/an-open...

@chrmanning.bsky.social @shikharmurty.bsky.social

#IchBinHanna & der 🐘 senden 1 Botschaft in die Koalitionsverhandlungen!

#WissZeitVG

@drkeichhorn.bsky.social @kubon.bsky.social

Interesting paper on Human Cognition in the Age of #AI or how not to brainrot arxiv.org/html/2502.12...

Die amerikanische Forschung ist auch für Deutschland wichtig. Das ist ja kein Wettbewerb, den wir gewinnen wollen. Wenn es anderen schlechter geht, wirkt sich das auch auf uns und unseren gesellschaftlichen Fortschritt aus.

It is super weird how little reception David Golumbia's last book "Cyberlibertarianism" has had. I mean I know why, he dropped a bunch of uncomfortable truth bombs there but it's still weird how little that book is talked about. It is probably the most important book about tech in the last decade.

I helped build a government AI system. DOGE fired me, rolled the AI out to the whole agency, and implied the AI can do my job and the jobs of the others they've fired.

It can't. But, what DOGE accidentally revealed about themselves in the process is fascinating. 🧵

A friend pointed out that the quasi-religious way so many tech guys talk about AI is in part because they don't want to grapple with the guilt of what they do; AI is a God, AI will fix it. No need to be responsible for what you put in the world.

I can't stop thinking about that.

Heftig. Laut Datenbank sind alle meine 4 Bücher - 3 davon zusammen mit @pialamberty.bsky.social verfasst - im Datensatz enthalten.

📢 #ACL2025NLP Student Research Workshop CFP is out 🙌
👉 2025.aclweb.org/calls/studen...
Send your paper by ⏰ May 18th, 2025 🚀 #nlproc

Just as an update ... 🚀 Call for Papers – CVPR 3rd Workshop on Multi-Modal Foundation Models (MMFM)
@cvprconference.bsky.social ! 🚀

🌐 sites.google.com/view/mmfm3rd...
📅 Deadline: Apr 1, 2025 (non-proceedings)
📝 Submission: cmt3.research.microsoft.com/MMFM2025