Comments (1)
Hi @odannis,
sorry for the long wait - I have been busy lately. Generally speaking the two-state MRF is a special case of the standard 20 state mrf, where all the singleton potentials corresponding to the 18 "forbidden" states are set to -infinity.
By default training should make the singleton potentials small, given that there's no prior on the singletons. You need to be careful with pseudocounts, though! I would not add any, just to be sure.
If the "forbidden" amino acids still pop up during simulation, you could also modify the parameters manually and set the singleton potentials corresponding to the unwanted states to a large negative number.
from ccmgen.
Related Issues (8)
- Interpretation of compared output HOT 1
- AttributeError: 'str' object has no attribute 'decode' (scipy1.7)
- nmut approximation via rounded expectation can be inaccurate in edge cases.
- Pseudo-likelihood optimization does not take pseudo-counts into account
- Error with CCMgen --tree-newick HOT 3
- when gaps included in x_single, there is an error in sampling
- How to use --seq0-file option ? HOT 1
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 ccmgen.