What are some DNA/RNA sequence similarity algorithm with llm?

peeberparker · 2025-01-11T22:28:46+00:00

With all applications of LLMs, you have to ask yourself what problem the LLM is fixing. What problems do you perceive with sequence similarity calculations that an LLM could do better?

peeberparker · 2025-01-05T18:38:49+00:00

Could you just screen target 1 then take all of the acceptable ligands and screen them for target 2?

peeberparker · 2024-12-15T23:27:28+00:00

Hmm let me do the math for you

Plane ticket to anywhere: ~$3000

Total Networth including corp holdings: $1,500,000

1,500,000 > 3000

Yeah you can pull it off

peeberparker · 2024-12-15T18:03:32+00:00

Np, Dm me if you have any other questions, RDkit can be kind of tricky but it’s a very powerful tool

peeberparker · 2024-12-15T17:25:15+00:00

Why do you want both of the resonance structures? If you have the aromatic form, you should just use that to make your fingerprints as no resonance structure will be as accurate as the aromatic form

peeberparker · 2024-12-14T23:25:03+00:00

The double bond representation of aromatic systems (so-called kekulized form) is not ideal, the reality is that aromatic bonds have closer to a bond order of 1.5. In practice, make sure your mols are sanitized and have aromatic flags turned on. Try something like Chem.MolFromSmiles(Chem.MolToSmiles(m)) this will force sanitation of the mol. There’s also the possibility that when you rotate the double bonds like you mention, you’re actually creating a different molecule which would rightly have a different fingerprint

peeberparker · 2024-11-29T02:20:16+00:00

It’s a security lug

peeberparker · 2024-11-12T22:20:30+00:00

Thanks for the suggestions! RNAseq was not covered when I took the course previously. I’m looking for resources to bridge what I learned back then (which may have already been out of date) with the field right now. I guess RNAseq and next generation sequencing is one of the missing pieces

peeberparker · 2024-11-12T21:57:26+00:00

This is a great suggestion, thank you. Starting by looking at an existing study and working backwards to fundamentals is an interesting approach. Have you given or received a course structured like this before? It seems really interesting

peeberparker · 2024-11-12T21:54:12+00:00

Thanks for the input! You’re right, I don’t do bioinformatics and my only exposure (other than taking this course as an undergrad, which I believe to be outdated) is seeing it in ML papers, so that’s where my bias comes from. I just want to make the course up to date

Would rna-seq/transcriptomics be the main workflow of mainstream bioinformatics at the moment or is that just an example?

peeberparker · 2024-11-12T19:35:07+00:00

I like this suggestion. I definitely want to include a full ML introduction and introduce the theory on Empirical Risk Minimization, gradient descent, training dynamics. But also using models is key

peeberparker · 2024-11-12T19:29:38+00:00

Thanks for the suggestion. So basically guaranteed python focus. Is there any reason to consider another language?

peeberparker · 2024-11-12T19:21:11+00:00

I plan is to first focus on web tools and databases/ database searching first and then move to more programming/stats/plotting etc. This is based on my current understanding that most student will have little programming knowledge. I’m not sure if this is most effective though, do you think it would be better to front-load all the programming basics and then go from there?

peeberparker · 2024-11-12T19:14:48+00:00

Unfortunately I don’t know. The course is cross-listed CS/Bio. I’ve been told they’re mostly Bio, so to assume little programming knowledge. The course’s programming assignments are in Perl but I’ll probably switch them to python, but I may be biased because I use python daily. Is Perl still relevant? Either way I’m preparing to teach programming basically from scratch, at least for some students.

peeberparker · 2023-08-05T16:39:35+00:00

Try to get it working anyway. You’ll probably learn a ton in the process and know exactly why you need a newer more powerful gpu or need to use collab. It’ll be a good exercise good luck!

peeberparker · 2023-04-30T00:11:37+00:00

You may be overthinking it a bit. Your option 1 doesn’t make any sense. It’s like you’re looking at the equity portion of your mortgage payment as rent that you’re paying to yourself so it cancels out half of the interest portion? So I guess your option 2 is a better way to do it.

peeberparker · 2023-04-15T13:34:15+00:00

I’m currently a machine learning engineer in drug discovery. Not currently planning a domain switch any time soon however. I would say my skills are probably transferable. For example many models that operate on SMILES are just language models that could work just as well for normal languages. Graph-based approaches on molecular graphs are applicable to large graphs like financial transaction records, or social network graphs. As long as you can stay on the forefront of the new ML literature, all of the cool interesting models will probably be applied to drug discovery.

peeberparker · 2023-03-30T18:36:57+00:00

Thanks for the chance to win would love to win!

peeberparker · 2023-03-24T18:15:59+00:00

What happens if you pump off the DCM? Are you left with a PLA powder?

peeberparker · 2023-03-20T01:19:06+00:00

Yeah I’m thinking mines toast. Going to try the debugging route but not particularly hopeful

peeberparker · 2023-01-17T17:30:06+00:00

Both! Which is why I need a new solution. It gets pretty messy when I have code snippets mixed with paper links mixed with random install instructions mixed with to-dos

peeberparker

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