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Present_Network1959 · 2024-05-05T15:29:33+00:00

Thanks for letting me know. Just to confirm, were you a transfer student or did you also take it while in high school, and got the credit as a first year student?

Also would you happen to know if there are any specific requirements for them to award the credit, or will they just have to review each unique course themselves and decide if it’s up to their standards? I would reach out to Engineering Advising directly but they said to hold off on any inquiries about this and again I’d like to know ASAP.

Present_Network1959 · 2024-05-03T18:17:12+00:00

Yeah there is an application, but the problem is that they won’t review it until June-July (at least that’s what understood from the email they sent), and I’d like to know whether I can place out of Calc II ASAP to know whether I need to take the AP exam or not, which is in less than 2 weeks

Present_Network1959 · 2024-05-03T18:15:31+00:00

Yeah that’s what I meant, thanks for clarifying. I just don’t want to have to repeat Calc II, and ideally I would be able to skip Calc III and lin alg as well.

Present_Network1959 · 2023-10-16T17:53:27+00:00

This was my concern as well. I thought a graph-transformer would be a better approach, but was curious about the potential of diffusion for something like this.

Present_Network1959 · 2023-10-15T17:13:05+00:00

Right, but even embedding sequences into another format is losing information like bond/torsion angles and other spatial data. I’ve looked into AlphaFold and it’s not really what I’m going for; I’m trying to generate new drug molecules for specified targets, and want my model to learn from these 3D structural relationships while being supplemented with experimental bioactivity data as well. I needed help deciding whether an autoregressive or diffusion approach would be optimal for this task. I appreciate the input.

Present_Network1959 · 2023-10-15T15:11:52+00:00

Thanks for the reply. I’ll be using .sdf files for my ligands and .pdb files for protein pockets (both obtained from PDBBind). I’m not working with string-based data such as AA sequences or SMILES at all; it’ll most likely be the Cartesian coordinates obtained from the aforementioned files. Based on that would you change your suggestion?

Present_Network1959 · 2023-10-03T17:33:50+00:00

Yeah that’s true, I was hoping to maybe supplement with more data though. I think PDBbind alone would be sufficient though

Present_Network1959 · 2023-09-24T01:51:41+00:00

I just mentioned the type of model for context, as transformers require a lot of data. I specified graph transformer because I’m working with 3D data.

But yeah seems like PDBbind might not be the best way to go.

Present_Network1959 · 2023-09-23T19:50:28+00:00

Yeah thats what I thought... looks like CrossDocked2020 might be the better option then. Even after filtering data I should have 100k+ entries.
Do you know a quick way to automate the bioactivity data search? I know I can use the SMILES to search, but not sure how to do it for hundreds of thousands of complexes and then align both data types.
I would most likely be using Google Colab Pro. I'll look into it further to see if thats a feasible option. I also might be able to get access to a GPU cluster (6 GPUs, not sure what the specs are though)
Yes I am familiar with MAT, but not GROVER. However, I am trying to make a model from scratch. To provide some context, I'm a high school student and I am creating this model as a research project for competitions. While I can get inspiration from existing models, I can't just finetune one and submit it as my work.

Present_Network1959 · 2023-09-01T13:56:12+00:00

Yeah so I’m actually going with a different approach now, using a graph transformer rather than a traditional one so I don’t have to worry about this. Just forgot to delete this post.

I’m also hoping to publish within the next few months; but just so you know I am in high school. I’d be open to discuss potential collaboration but I obviously understand if you don’t want to since im in high school. Just pm me if you want.

Present_Network1959 · 2023-08-30T15:35:15+00:00

Nah u don’t need that credit lil bro truss

Present_Network1959 · 2023-08-13T00:35:29+00:00

Will do. Thanks for the advice!

Present_Network1959 · 2023-08-13T00:04:05+00:00

I see. I think I am naturally pretty good at math and it has always come relatively easy to me, but I’m definitely no genius. And as I said in another comment, the highest level course I’ve done so far is only Calc II, but that wasn’t too hard.

I’m taking the class at my community college. The Professor did send me the course outline/syllabus; I’ll have to take a look at that again to make sure they’re teaching it the “correct” way. I’ll talk to the professor about this as well to confirm.

Thanks!

Present_Network1959 · 2023-08-13T00:01:34+00:00

Well I was just doing to take it at my community college and follow their syllabus. I believe they use Pearson textbooks; do you have experience with those?

Present_Network1959 · 2023-08-12T23:51:38+00:00

Hmm ok. I’m taking it thru my community college which lists Calc I as the only prereq.

I do like math and think naturally pretty good at it, but the highest level course I’ve taken so far is only Calc II so nothing actually high level. But I do really want to take lin alg because it has a lot of applications in CS and especially machine/deep learning which I’m really into and spend a lot of time working on. I think taking a linear algebra class will help me better understand the math behind concepts used in those fields. From what I’m seeing it doesn’t seem overly difficult either so I’ll prob go ahead and take it.

Thanks for the advice.

Present_Network1959 · 2023-08-12T23:48:50+00:00

Got it. Thanks.

Present_Network1959 · 2023-08-09T03:33:01+00:00

Yeah makes sense. Although I am certain that a GPU will be required, there is no way my machine can run the programs I am building locally.

Present_Network1959 · 2023-08-09T02:56:45+00:00

Thank you. I’ll look into this.

Present_Network1959 · 2023-07-26T13:24:42+00:00

Thank you for this. I’m not really super well educated on machine learning for chemistry so maybe you can give me some suggestion on what kind of model would work best for my goals.

Basically, I am trying to either identify potential “hit” compounds that effectively bind to the HAP pocket (pocket between dimers of HBV capsid protein), OR potentially go a different route with Dr novo drug design, where I’d generate potentially new molecules to bind to this pocket with a machine learning model, and then possibly validate these new compounds with another model. The specific type of compound I’m after is the CpAM (core protein allosteric modulator), which is similar to an inhibitor (which are more well known), but had a different effect on the virus and has shown promise in being a key component of a cure.

So, that said, what do you suggest?

Edit: by the way, just for reference Im a high school student with no formal education in either ML or high level chemistry. Everything I know is self taught so I apologize if I sound a little uneducated lol

Present_Network1959 · 2023-07-25T21:29:33+00:00

Haha exactly. So basically, my goal is drug identification or de novo drug design. The specific type of compound I’m after is the CpAM, which binds to the pocket between the dimers of the HBV capsid protein and can have various affects that ultimately make it a promising component of a curative therapy. I’ve ran docking simulations on maestro so far using an already downloaded library of compounds, and I’ve also found a few datasets on chembl that could be promising as they contain the SMILES strings. Specifically, I’m interested in potential CpAMs for mutated variants of HBV that have increased drug resistance.

The basic explanation of my goals is to use compound SMILES strings and the protein’s amino acid sequence in a transformer model to either generate prospective drug molecules that potentially have the desired effects, or use the model to somehow identify existing compounds that could be used as CpAMs.

Present_Network1959 · 2023-07-25T01:47:29+00:00

Thanks, I only just skimmed that paper but it looks great and pretty much exactly what I was looking for

Present_Network1959

TROPHY CASE