Comments (3)
At first thanks for your interesting work and framework. I run its CNN-CNN case and it's constructive for me. Now I want to run S-W and Pubchem-Sim case instead of CNN-CNN case. for this purpose I replace build_baseline function in run_regression function and run the code but I receive untrackable errors. Maybe the required data for this is not in your default database? or other settings (like TensorFlow version and etc.) that I must observe in my run? I ran code in google colab. Could I have your advice on this?
an error occurs when using build_baseline function with input_shape equal to drug_count and target_count for each input.
isn't required to set problem_type to another value to run S-W and Pubchem-Sim? what does this parameter show?
@hkmztrk
from deepdta.
Hi @SAkbari93, you can modify/use the example functions build_single_drug or build_single_prot functions if you want to run the model with S-W and Pubchem similarity matrices (the following files for corresponding datasets).
kiba_drug_sim.txt
kiba_target_sim.txt
drug-drug_similarities_2D.txt
target-target_similarities_WS.txt
from deepdta.
kiba_target_sim.txt
Hi @hkmztrk Thanks for your response. I try to do this but I can't find lines that these files included in the code. can you help me to use them in the code? It seems there isn't a function to parse them, isn't?
from deepdta.
Related Issues (20)
- Prediction of binding affinity using DeepDTA interpretation HOT 3
- Complete Code HOT 1
- the question about the two datasets. HOT 2
- Question about KIBA score HOT 4
- MSE for davis dataset is very high than that is mentioned in the paper HOT 5
- some questions HOT 1
- Could the pre-trained model be made available? HOT 2
- Help with retraining the combined model with a different dataset HOT 2
- new datas HOT 9
- Reimplementation of DeepDTA with Pytorch HOT 2
- I have some questions, can you help me!!! HOT 1
- Help with installation HOT 3
- Question about implementation HOT 4
- During implementation on my own dataset, I got weird results HOT 4
- Regarding data leakage caused by amino acid sequences in the data set HOT 1
- A question about Davis dataset HOT 1
- Install tensorflow=1.x needs python>=3.5 HOT 1
- Issue regarding the datasets HOT 3
- when use DeepDTA error
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 deepdta.