Comments (5)
Hi,
You should be able to train it using train_openfold.py. It's set up to do fine-tuning by initialising the network with the original weights: https://github.com/lhatsk/AlphaLink/blob/main/train_openfold.py#L135
from alphalink.
Thank you for reply my issue.
By the way, than how to set the initial dataset?
In the paper, you said that 'fine the network on 13,000 proteins from the trRosetta38 training set with simulated photo-AA crosslinking data.'.
And I already downloaded the trRosetta training set, but it consisted with 15,000 proteins which didn't match 13,000. Furthermore, how can I preprocess it with AA-crosslinking data?
Additionally, I want to ask how to consist of the data with crop size!
Thank you for reading.
from alphalink.
I don't quite remember why I didn't take the full set. There are two possibilities that come to mind: I think I originally had a train/ validation split on the trRosetta training data from a previous project and only used the training split. Another possibility is that I didn't have crosslinks for all the targets. Just take as much as you can. You would need to simulate the photoAA crosslinking data. I did it on the fly during training.
Additionally, I want to ask how to consist of the data with crop size!
I used the default crop size for fine-tuning which is 384AA.
from alphalink.
thank you for explaining for my question.
Additionally, I have some more questions.
I used the default crop size for fine-tuning which is 384AA.
- In this case, I want to know the way to crop methodolgy.
Did you choose overlap strategy for cropping AA? or using consequent cropping AA?
from alphalink.
I didn't alter the cropping strategy. It's a random crop of size 384AA.
from alphalink.
Related Issues (18)
- Over-weight of crosslinking data HOT 4
- Wrong array shape when using single crosslink record HOT 1
- problem with model loading HOT 12
- CUDA stub file missing for cpu-only build HOT 1
- No MSA output - precomputed alignments called automatically HOT 3
- Request for an example folder HOT 1
- Problem with Crosslinking data input HOT 12
- Inter-subunit crosslinking data HOT 2
- Run "python preprocessing_distributions.py --infile restraints.csv" but get an error HOT 4
- Running "predict_with_crosslinks.py" with "restraints.csv --distograms" gives the error HOT 6
- Alphalink install failed HOT 3
- Installation unclear HOT 1
- crosslinks need to be provided as comma separated, not space HOT 1
- FDR Description in Arg parse is potentially wrong HOT 3
- Issue with multimer HOT 3
- Save pkl files HOT 1
- hands-on protocol for contacts_to_distograms HOT 34
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 alphalink.