Patrick Walters

cheminformatics, machine learning, drug discovery, opinions

[Patrick Walters @wpwalters]

M6 Mac Mini as the prize in the @marimo Cheminformatics notebook competition

[marimo @marimo_io]

For our cheminformatics competition, you can now win an @Apple Mac Mini M6. You have 1 month left to take a dataset and build a marimo notebook that brings cheminformatics to life. Competition details below.

[Patrick Walters @wpwalters]

A great opportunity to showcase your marimo skills and compete for some solid prizes. Looking forward to seeing what the community builds.

[marimo @marimo_io]

33 days to win a mac mini.

the challenge: pick a cheminformatics dataset and build a marimo notebook that answers a question you want the answer to.
we're judging based on creativity, not on model accuracy. co-hosted with @wpwalters.

we'll see you in our submissions 👀

[Patrick Walters @wpwalters]

Excited to team up with @marimo to explore new relationships between chemical structures and biological data.

Bring your creativity, push the boundaries of reactive notebooks, and compete for prizes! Details below 👇

[marimo @marimo_io]

We're running a cheminformatics notebook competition with @wpwalters and OpenADMET. Take a dataset & bring cheminformatics to life.

Mac Mini + $2.5K in prizes, deadline Oct 4 👀

[Patrick Walters @wpwalters]

@srikosuri @adic_9 The training data and code will be released on Monday.

[Patrick Walters @wpwalters]

@adic_9 @srikosuri The underlying methods are pretty simple; it's just a bunch of SMARTS matches and enrichment calculations.

[Patrick Walters @wpwalters]

@adic_9 @srikosuri Not sure how you're making this statement. I conceived the study, ran the experiments, and wrote the initial draft. Claude, Gemini, and Grammarly helped me to clean up the text. Claude audited and reformatted my code. It also improved the figures. Gemini made the cartoon.

[Patrick Walters @wpwalters]

@dextrodexter @srikosuri Here's my last sentence. "We don't need better rules of thumb. We need more datasets like this one, and the models we can build on top of them." I'm not sure what you wanted to hear.

[Patrick Walters @wpwalters]

@dextrodexter @srikosuri However, that's not what we're doing. We generate large, consistent datasets and make them publicly available.

[Patrick Walters @wpwalters]

@dextrodexter @srikosuri I agree that it's tough to pull a signal from ChEMBL data. The data comes from dozens, or even hundreds, of experiments that weren't conducted under the same conditions.

[Patrick Walters @wpwalters]

@dextrodexter @srikosuri Synthetic data is an interesting idea, but I haven't seen it work in chemistry. Do you have any references?

[Patrick Walters @wpwalters]

@anthonygitter @srikosuri 10K from the Enamine diversity set and 1K FDA drugs. I didn't look at the breakdown of the hits. I'll check that out.

[Patrick Walters @wpwalters]

An interesting piece about Axiom Bio's work combining cell painting and machine learning to predict toxicity

[Alex Kesin @alexkesin]

For a decade, techbio optimized the drug discovery "paper mill": more molecules, faster. But the hard part - knowing which ones will work safely in humans - hardly moved at all.

Late last year, I spent time with Axiom Bio, a company built around the idea that the real bottleneck is predicting clinical activity in molecules, *not* merely discovering them.

[Patrick Walters @wpwalters]

@andrewwhite01 Nice, you should ask kosmos to submit to the OpenADMET/ExpansionRx blind challenge.

[Patrick Walters @wpwalters]

@ddale8 @jaketapper Zz

[Patrick Walters @wpwalters]

New Practical Cheminformatics post, "Three Papers Demonstrating That Co-folding Still Has a Ways to Go”.
https://t.co/uTtjdcRuHC

[Patrick Walters @wpwalters]

@davidlmobley My favorite paper this year!

[Patrick Walters @wpwalters]

New Practical Cheminformatics Post, "Useful RDKit Utils - A Mötley Collection of Helpful Routines"
https://t.co/MaP7vjkQ39

[Patrick Walters @wpwalters]

The latest Practical Cheminformatics post, “The Trouble With Tautomers,” emerged from a discussion about the impact of tautomers on machine learning model predictions.

https://t.co/nylhStlG42

[pen(Taka) @iwatobipen]

Integration Chembl REST API and Claude with MCP #cheminformatics #mcp #ai https://t.co/TbPQ2j0Z81

[Patrick Walters @wpwalters]

The latest addition (#33) to the Practical Cheminformatics Tutorials series explores Bayesian optimization of reaction conditions.
https://t.co/NEii9bKEaN