Comments (1)
Hi, Thank you for the amazing work! I am curious about the results in table 8. Why most models (other than GNN) perform dramatically worse in the 60% identity split than in the 30% identity split? Intuitively, the task with 60% split should be easier and achieve better performance as there is more similarity between protein sequences.
I agree with your theoretical guess. However, not only atom3d but also some other following studies show the similiar phenomenon. For instance, the table below is copied from Multi-Scale Representation Learning on Proteins
from atom3d.
Related Issues (20)
- Trouble reproducing GNN results on LBA using provided code HOT 11
- PSR dataset improvement
- `res` dataset source appears to be broken
- Questions on `chain` in LEP
- Benchmark for Atom3D HOT 2
- issue about tr.GraphTransform HOT 1
- Processing pdb data to get data for 3D CNN HOT 1
- da.load_dataset()加载数据
- Questions about the LEP dataset
- Severe contradiction over the LBA dataset at 60% identity
- ModuleNotFoundError HOT 3
- What does the edge feature stand for? HOT 1
- Clarifications in docs for data loading
- Missing `download_split_indices()`
- Request for data in h5 format
- No scripts for cnn3d and gnn for RES
- 'seq' value is ;[]', empty for the LBA dataset
- atom graph or residue graph for protein
- it cost long time for atom3d/examples/ppi/gnn /data.py
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from atom3d.