Ian Maurer's Avatar

Ian Maurer

@imaurer

Fighting cancer with code. Interests: Bioinformatics, Genomics, LLMs, Python, Rust, NLP. https://imaurer.com/ https://github.com/imaurer/

150
Followers
226
Following
45
Posts
25.10.2024
Joined
Posts Following

Latest posts by Ian Maurer @imaurer

I'm only here because @simonwillison.net posted about this on elon's plaything.

03.11.2025 19:47 πŸ‘ 0 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

Built on top of the powerful open access API services of the NIH:

- ClinicalTrials.gov

- MyVariant.info

- PubMed / Pubtator3
www.ncbi.nlm.nih.gov/research/pub...

08.04.2025 14:51 πŸ‘ 0 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0
Introduction to BioMCP
Introduction to BioMCP YouTube video by GenomOncology

Short video on YouTube:
www.youtube.com/watch?v=bKxO...

08.04.2025 14:51 πŸ‘ 0 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0
Post image

Proud to announce BioMCP, an open source Model Context Protocol (MCP) server for biomedical research AI assistants and agents. BioMCP searches and retrieves clinical trials, PubMed articles and genomic variants to provide up-to-date and relevant context to an LLM.

08.04.2025 14:51 πŸ‘ 2 πŸ” 0 πŸ’¬ 1 πŸ“Œ 1
Preview
GitHub - genomoncology/biomcp: BioMCP: Biomedical Model Context Protocol BioMCP: Biomedical Model Context Protocol. Contribute to genomoncology/biomcp development by creating an account on GitHub.

Github Repo (MIT License):
github.com/genomoncolog...

08.04.2025 14:51 πŸ‘ 0 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0

slick!

14.01.2025 21:12 πŸ‘ 1 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

Listening now... came here to say congrats. :)

14.01.2025 21:11 πŸ‘ 1 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0

I did finish it and listened to your podcast with @mkennedy.codes

Good stuff. Subscribed on overcast.

04.01.2025 13:23 πŸ‘ 1 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

Great article this morning. Got to the blog scroll link and… now I am here.

I hope I don’t get distracted too much longer. I want to finish it.

03.01.2025 12:52 πŸ‘ 0 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

Your line colors are messing with my mind.

01.01.2025 17:01 πŸ‘ 5 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

You can’t for-loop taste

22.12.2024 22:39 πŸ‘ 2 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

Just everything else with AI, you can get good results with low effort.

Then you can grind and keep eeking out gains.

This has add’l benefits:
- improvement on that task
- greater vision of what else you can do
- higher expectations on what good results are
- better first drafts the next time.

20.12.2024 02:17 πŸ‘ 3 πŸ” 1 πŸ’¬ 0 πŸ“Œ 0

Just everything else with AI, you can get good results with low effort.

Then you can grind and keep eeking out gains.

This has add’l benefits:
- improvement on that task
- greater vision of what else you can do
- higher expectations on what good results are
- better first drafts the next time.

20.12.2024 02:17 πŸ‘ 3 πŸ” 1 πŸ’¬ 0 πŸ“Œ 0

How are they going to get the sun to shine like that in winter?

19.12.2024 14:31 πŸ‘ 0 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

1. No
2. NaN

16.12.2024 01:42 πŸ‘ 0 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

PDF version

arxiv.org/pdf/2408.02442

14.12.2024 18:53 πŸ‘ 0 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0
Preview
Let Me Speak Freely? A Study on the Impact of Format Restrictions on Performance of Large Language Models Structured generation, the process of producing content in standardized formats like JSON and XML, is widely utilized in real-world applications to extract key output information from large language m...

Perplexity did find me this quote:

β€œUpon inspection, we found that 100% of GPT 3.5 Turbo JSON-mode responses placed the "answer" key before the "reason" key, resulting in zero-shot direct answering instead of zero-shot chain-of-thought reasoning.”

ar5iv.org/html/2408.02...

14.12.2024 18:47 πŸ‘ 0 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0

Any research on the impact of JSON key sort order on generating structured outputs?

For instance, I do something like this:

- analyze
- draft
- evaluate
- final

And then provide exemplars with errors to show self correction.

But I haven’t done extensive testing. Just seems like a good idea.

14.12.2024 18:47 πŸ‘ 0 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0

Congrats!

13.12.2024 01:46 πŸ‘ 1 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

Ugh. Sorry to hear this.

11.12.2024 17:27 πŸ‘ 2 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

Among Us lol.

10.12.2024 21:13 πŸ‘ 0 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

That's my favorite fun fact about SQLite. Seems to be a competitive advantage for them securing contracts from large organizations.

Which, good on them, I think it's a more than fair way to do OSS.

10.12.2024 19:48 πŸ‘ 19 πŸ” 0 πŸ’¬ 2 πŸ“Œ 0

That’d be sweet. Thank Claude for me.

08.12.2024 22:20 πŸ‘ 1 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

Bunny CDN still treating you alright?

08.12.2024 22:20 πŸ‘ 0 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0

Nice looking script.

08.12.2024 22:04 πŸ‘ 0 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

You are right bytes not tokens.

08.12.2024 22:03 πŸ‘ 1 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0
Preview
Git ingest Replace 'hub' with 'ingest' in any Github Url for a prompt-friendly text

Git ingest:
gitingest.com

08.12.2024 02:04 πŸ‘ 7 πŸ” 1 πŸ’¬ 1 πŸ“Œ 0
Post image

Chat with any open source repo easily. Gitingest (free online tool) turns any GitHub repository into a single markdown file for pasting. Claude artifacts makes this 300k token output pretty easy to work with.

08.12.2024 02:04 πŸ‘ 64 πŸ” 12 πŸ’¬ 4 πŸ“Œ 5

Makes sense. Thanks for the clarification.

I was wondering if it was a copyright thing which didn’t make much sense given the technology.

05.12.2024 17:02 πŸ‘ 0 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

Great thoughts.

AT protocol is interesting for the same reason podcasts are interesting. Love the open web.

Can you explain the legalities of why you can’t have a play button for some podcasts that have a public mp3 url?

05.12.2024 14:16 πŸ‘ 2 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0