Leash Belka — small molecule–protein binding with GNNs
Leash Belka — small molecule–protein binding with GNNsPredicts which drug-like molecules stick to which proteins. That's normally lab work.Models checked against a real answer
The model learns from molecules drawn as dots and links, then trains on graphics chips rented by the hour.
My first attempt at using AI assistance for coding, and a really fun one. It was the Leash Belka Kaggle competition — predicting small molecule–protein binding. The goal was to take my understanding of graph neural networks, learn PyTorch Geometric, and apply it to the competition dataset. AI's role was narrow and honest: I used ChatGPT and Gemini to learn the framework, and autocomplete inside Visual Studio while I wrote. Not code generation. It took four and a half months, and it was a great learning experience.
What it taught me How to build and train these models properly. I rented time on powerful machines to train the final ones, and what I learned there I used again on two later projects.
What AI actually did AI carried the domain encoding well — getting raw molecular data into a form the model could eat was where it helped most. It could argue the architecture about half the way. Beyond that it did nothing: I hadn't started using models for debugging at this point, and nothing about evaluation or keeping the repo honest involved AI at all.
It ran longer than anything else here, and it is the project where AI did the least.