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u/GroundBeautiful2015

r/comp_chem r/molecularbiology r/genomics r/alphaandbetausers r/bioinformatics
▲ 1 r/genomics

Feedback Request for an miRNA therapeutic design model

Hey r/genomics,
My name is Joshua Haigler, and I am looking for feedback on my custom GatV2 GNN model I call CPOP, the catalytic precision oligonucleotide platform. Specifically, I’m looking for feedback on the viability of the strategy it tries to use to reduce dosages and resulting toxicity.

Basically what it does is it designs an enzyme that is specific to a certain species of miRNA and destroys that species catalytically. It’s effectively taking the best of an ASO and an RNAzyme and combining it in a sort of hybrid therapeutic. I’ve gotten really good LOOCV numbers (since the dataset is pretty small at n=2000+, including transfer learning), but I’d like an expert who’s already deep in this or a similar field to take a look at it and give me their opinion and feedback on its viability. Just as a clarification, I’m not asking for any kind of collab, commitment, funding, or anything else, just a 5 minute visit to my site and to give me your thoughts on its potential.

I’ve attached a public website that contains the model demo and information on how it works, so any feedback at all on its usefulness, viability, hidden limitations, etc would be greatly appreciated.

Thanks for taking the time to read this and for any feedback you may provide!
Sincerely,
Joshua Haigler
UNC Charlotte
jshaigler07@gmail.com

Here’s the demo: cpop-website.vercel.app

reddit.com
u/GroundBeautiful2015 — 6 days ago
▲ 0 r/molecularbiology

Feedback request for a new catalytic RNA therapeutic design model

Hey r/molecularbiology,
My name is Joshua Haigler, and I am looking for feedback on my custom GatV2 GNN model I call CPOP, the catalytic precision oligonucleotide platform. Specifically, I’m looking for feedback on the viability of the strategy it tries to use to reduce dosages.

Basically what it does is it designs an enzyme that is specific to a certain species of miRNA and destroys that species catalytically. It’s effectively taking the best of an ASO and an RNAzyme and combining it in a sort of hybrid therapeutic. I’ve gotten really good LOOCV numbers (since the dataset is pretty small at n=2000+, including transfer learning), but I’d like an expert who’s already deep in this or a similar field to take a look at it and give me their opinion and feedback on its viability. Just as a clarification, I’m not asking for any kind of collab, commitment, funding, or anything else, just a 5 minute visit to my site and to give me your thoughts on its potential.

I’ve attached a public website that contains the model demo and information on how it works, so any feedback at all on its usefulness, viability, hidden limitations, etc would be greatly appreciated.

Thanks for taking the time to read this and for any feedback you may provide!
Sincerely,
Joshua Haigler
UNC Charlotte
jshaigler07@gmail.com

Here’s the demo: cpop-website.vercel.app

reddit.com
u/GroundBeautiful2015 — 7 days ago
▲ 2 r/comp_chem

Expert feedback request for a GATV2-GNN based RNA design tool

Hey r/comp-chem,
My name is Joshua Haigler, and I am looking for feedback on my custom GatV2 GNN model I call CPOP, the catalytic precision oligonucleotide platform.

Basically what it does is it designs an enzyme that is specific to a certain species of miRNA and destroys that species catalytically. It’s effectively taking the best of an ASO and an RNAzyme and combining it in a sort of hybrid therapeutic. I’ve gotten really good LOOCV numbers (since the dataset is pretty small at n=2000+, including transfer learning), but I’d like an expert who’s already deep in this or a similar field to take a look at it and give me their opinion and feedback on its viability. Just as a clarification, I’m not asking for any kind of collab, commitment, funding, or anything else, just a 5 minute visit to my site and to give me your thoughts on it.

I’ve attached a public website that contains the model demo and information on how it works, so any feedback at all on its usefulness, viability, hidden limitations, etc would be greatly appreciated.

Thanks for taking the time to read this and for any feedback you may provide!
Sincerely,
Joshua Haigler
UNC Charlotte
jshaigler07@gmail.com

Here’s the demo: cpop-website.vercel.app

reddit.com
u/GroundBeautiful2015 — 7 days ago
▲ 1 r/alphaandbetausers

Feedback request for the catalytic precision oligonucleotide platform, CPOP, an RNA drug design model

Hey r/alphaandbetausers,
I’m looking for feedback for my catalytic ASO designing model. Basically what it does is it takes an miRNA sequence and designs a molecule that has the specificity of an ASO and the catalytic knockdown of an RNAzyme that will catalytically target a single species of miRNA to reduce its affect on the disease at hand (cancer metastasis, chronic inflammation, etc).

If anybody has the chance to take a look at my demo and informational website and offer any advice/feedback on the viability of this model in a real world ASO designing scenario, I would greatly appreciate it!

I’m not asking for any sort of funding, commitment, etc, just a 5 minute visit to the site to give me your thoughts on its usefulness.

Here’s the site: https://cpop-website.vercel.app/

reddit.com
u/GroundBeautiful2015 — 7 days ago
▲ 0 r/bioinformatics

Seeking Feedback for CPOP V2, A GNN & Ensemble Platform for Catalytic miRNase Design

Hosted Demo: https://cpop-v2-designer-txmbwpw7qifbcuvcatby2m.streamlit.app/?token=cpop_vip

Feedback Form (Pharma/Biotech): https://forms.gle/qDi1JSoTr3c582VF9

Feedback Form (Academic): https://forms.gle/PS84eW3Hn7GVGwKN7

Hey r/bioinformatics,

My name is Joshua Haigler and I’m looking for technical feedback on CPOP V2, a revised computational platform for the precision design of artificial miRNases. The goal of this model is to speed up the lead optimization process of miRNA-based therapeutics that catalyitcally act on mRNA molecules to influence diseases like neurological disorders and cancers at significantly lower dosages than is currently possible.

The Evolution from V1 to V2
My initial version suffered from a small dataset of n=72, which was partially compensated for using LOOCV. CPOP V2 addresses this through a significantly expanded dataset that utilizes transfer learning.

Key Innovations in V2
Expanded Dataset (N=2,114): The dataset moved from 72 to 2,114 records using a three-tier strategy involving literature mining, surrogate transfer from ribozyme/DNAzyme assays, and physics-augmented data generated via NUPACK-driven thermodynamic simulations.

Dual-Architecture Approach: The system now utilizes a GATv2 Graph Neural Network (GNN) to encode molecular designs as graphs, capturing structural nuances that flat feature vectors miss. This is paired with a four-model ML ensemble (Random Forest, XGBoost, Gradient Boosting, and MLP) for performance prediction.

Uncertainty Quantification: A Gaussian Process (GP) head provides calibrated confidence intervals, flagging designs in underexplored chemical spaces.

Current Performance Metrics
Validation of the ensemble model using a 5-fold cross-validation protocol shows significant improvements over the baseline:

Metric
CPOP V1 (N=50) vs CPOP V2 (N=2,114)

Accuracy (R²)
0.72 vs 0.842

MAE
12.4% vs 7.15%

Reliability
Low (Overfit) vs High (Generalizable)

Call to Action
I would greatly appreciate the community's eyes on my methodology and performance. You can interact with the current model state and provide feedback through the links at the top of this post.
Specific Questions for the Community
Methodology: Does the transition to a GATv2 GNN backbone effectively address the limitations of V1’s small dataset in drug design, or are there alternative architectures (e.g., Transformer-based) that might better capture the 3D interaction geometry of oligo-peptide conjugates?

Pareto Optimization: My current Pareto Front balances target cleavage against the 2,656 human miRNAs in miRBase v22. Are there additional biological "noise" factors or off-target repositories you would recommend integrating?

 Symmetry Index Predictions: I am modeling the relationship between bilateral symmetry and catalytic rate as a sigmoid response curve. Based on your experience with enzyme kinetics, does this plateauing effect at high symmetry align with biological expectations, or should I consider a different functional form?

Regardless of the outcome, thank you for your time and expertise.

Joshua Haigler
UNC Charlotte

u/GroundBeautiful2015 — 21 days ago