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courses:bin:tutorials:tutorial12 [2019/05/13 11:05]
barvijac [TreeLiker instructions for tutorial]
courses:bin:tutorials:tutorial12 [2019/05/13 11:10] (current)
barvijac [TreeLiker instructions for tutorial]
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-===== TreeLiker instructions for tutorial =====+ ===== TreeLiker instructions for tutorial =====
 The dataset we are going to use is a dataset of peptide structures along with the information whether or not they exhibit antimicrobial activity. Determining such properties is important in the development of novel antibiotics. ​ The dataset we are going to use is a dataset of peptide structures along with the information whether or not they exhibit antimicrobial activity. Determining such properties is important in the development of novel antibiotics. ​
  
   - Load project. Navigate to ''​examples_treelikergui/​peptides''​. Open directory. ​   - Load project. Navigate to ''​examples_treelikergui/​peptides''​. Open directory. ​
-  - Click "Add New Dataset"​. Check if there is correct path in "Data directory field"​. Keep format on "​pseudo-prolog with class label"​. +  - Click "Add New Dataset"​. Check if there is correct path in "Data directory field" ​-- it should be ''​examples_treelikergui/​peptides/​dataset''​. Keep format on "​pseudo-prolog with class label"​. 
-  - Navigate to the "​Template"​ tab. Make sure you have an understanding of what the template means, otherwise you can keep it. You are later encouraged to tweak it and observe what happens.+  - Navigate to the "​Template"​ tab. Make sure you have an understanding of what the template means, otherwise you can keep it. You are later encouraged to tweak it and observe what happens. ​The template should be ''​residue[1](+a0,​!aaType),​residue(-a0,#​aa),​ next[1](+a0,​-a1),​ dist(+a0, !aa, -a1, !aa, #dist), residue[1](+a1,#​aa) ''​
   - Navigate to "​Pattern Search"​ tab. Select RelF algorithm. Run "​Search!"​. ​ Wait for the computation to finish, it may take several minutes.   - Navigate to "​Pattern Search"​ tab. Select RelF algorithm. Run "​Search!"​. ​ Wait for the computation to finish, it may take several minutes.
   - Navigate to the "Found Patterns"​ tab. Look at the discovered patterns. Can you see how they were generated from the template? How do you interpret the Chi^2 and Information Gain values?   - Navigate to the "Found Patterns"​ tab. Look at the discovered patterns. Can you see how they were generated from the template? How do you interpret the Chi^2 and Information Gain values?
courses/bin/tutorials/tutorial12.txt · Last modified: 2019/05/13 11:10 by barvijac