Edit costs for graphs contained in Protein dataset. More...
#include <protein.hpp>
Inheritance diagram for ged::Protein< UserNodeLabel, UserEdgeLabel >:
Public Member Functions | |
| Protein (double node_ins_del_cost=11, double edge_ins_del_cost=1, double alpha=0.75) | |
| Constructor. More... | |
| virtual double | node_ins_cost_fun (const UserNodeLabel &node_label) const final |
| Node insertions cost function. More... | |
| virtual double | node_del_cost_fun (const UserNodeLabel &node_label) const final |
| Node deletion cost function. More... | |
| virtual double | node_rel_cost_fun (const UserNodeLabel &node_label_1, const UserNodeLabel &node_label_2) const final |
| Node relabeling cost function. More... | |
| virtual double | edge_ins_cost_fun (const UserEdgeLabel &edge_label) const final |
| Edge insertion cost function. More... | |
| virtual double | edge_del_cost_fun (const UserEdgeLabel &edge_label) const final |
| Edge deletion cost function. More... | |
| virtual double | edge_rel_cost_fun (const UserEdgeLabel &edge_label_1, const UserEdgeLabel &edge_label_2) const final |
| Edge relabeling cost function. More... | |
 Public Member Functions inherited from ged::EditCosts< UserNodeLabel, UserEdgeLabel > | |
| virtual | ~EditCosts ()=0 |
| Virtual destructor. More... | |
| EditCosts () | |
| Constructor. | |
| virtual void | vectorize_node_label (const UserNodeLabel &node_label, std::vector< double > &vector_representation) const |
| Computes a node label's representation as a real-valued vector. More... | |
| virtual void | vectorize_edge_label (const UserEdgeLabel &edge_label, std::vector< double > &vector_representation) const |
| Computes an edge label's representation as a real-valued vector. More... | |
Detailed Description
template<class UserNodeLabel, class UserEdgeLabel>
class ged::Protein< UserNodeLabel, UserEdgeLabel >
Edit costs for graphs contained in Protein dataset.
The graphs contained in the Protein dataset represent proteins from the BRENDA enzyme database. Nodes are attributed with their type (named "type") and their amino acid sequence (named "sequence"). Edges are attributed with their frequency (named "frequency"), their types (named "type<frequency>") and their distances (named "distance<frequency>"). The Protein dataset is contained in the IAM graph database repository which can be downloaded from http://www.fki.inf.unibe.ch/databases/iam-graph-database:
- K. Riesen, H. Bunke: “IAM graph database repository for graph based pattern recognition and machine learning”, https://doi.org/10.1007/978-3-540-89689-0_33
Implements the edit costs suggested in:
- Z. Abu-Aisheh, R. Raveaux, J.-Y. Ramel: “A graph database repository and performance evaluation metrics for graph edit distance”, https://doi.org/10.1007/978-3-319-18224-7_14
- K. Riesen, H. Bunke: “Graph data”, in: Graph Classification and Clustering Based on Vector Space Embedding, https://doi.org/10.1142/9789814304726_0004
Definition at line 54 of file protein.hpp.
Constructor & Destructor Documentation
◆ Protein()
template<class UserNodeLabel , class UserEdgeLabel >
| ged::Protein< UserNodeLabel, UserEdgeLabel >::Protein | ( | double | node_ins_del_cost = 11, |
| double | edge_ins_del_cost = 1, |
||
| double | alpha = 0.75 |
||
| ) |
Constructor.
- Parameters
-
[in] node_ins_del_cost Cost for deleting or inserting nodes. [in] edge_ins_del_cost Cost for deleting or inserting edges. [in] alpha Importance of node edit operations vs. importance of edge edit operations.
- Note
- Calling the constructor with the default arguments constructs the edit costs suggested in https://doi.org/10.1007/978-3-319-18224-7_14.
Member Function Documentation
◆ edge_del_cost_fun()
template<class UserNodeLabel , class UserEdgeLabel >
|
finalvirtual |
Edge deletion cost function.
- Parameters
-
[in] edge_label An edge label.
- Returns
- The cost of deleting an edge with label
edge_label.
- Note
- Must be implemented by derived classes of ged::EditCosts.
Reimplemented from ged::EditCosts< UserNodeLabel, UserEdgeLabel >.
◆ edge_ins_cost_fun()
template<class UserNodeLabel , class UserEdgeLabel >
|
finalvirtual |
Edge insertion cost function.
- Parameters
-
[in] edge_label An edge label.
- Returns
- The cost of inserting an edge with label
edge_label.
- Note
- Must be implemented by derived classes of ged::EditCosts.
Reimplemented from ged::EditCosts< UserNodeLabel, UserEdgeLabel >.
◆ edge_rel_cost_fun()
template<class UserNodeLabel , class UserEdgeLabel >
|
finalvirtual |
Edge relabeling cost function.
- Parameters
-
[in] edge_label_1 An edge label. [in] edge_label_2 An edge label.
- Returns
- The cost of changing an edge's label from
edge_label_1toedge_label_2.
- Note
- Must be implemented by derived classes of ged::EditCosts.
Reimplemented from ged::EditCosts< UserNodeLabel, UserEdgeLabel >.
◆ node_del_cost_fun()
template<class UserNodeLabel , class UserEdgeLabel >
|
finalvirtual |
Node deletion cost function.
- Parameters
-
[in] node_label A node label.
- Returns
- The cost of deleting a node with label
node_label.
- Note
- Must be implemented by derived classes of ged::EditCosts.
Reimplemented from ged::EditCosts< UserNodeLabel, UserEdgeLabel >.
◆ node_ins_cost_fun()
template<class UserNodeLabel , class UserEdgeLabel >
|
finalvirtual |
Node insertions cost function.
- Parameters
-
[in] node_label A node label.
- Returns
- The cost of inserting a node with label
node_label.
- Note
- Must be implemented by derived classes of ged::EditCosts.
Reimplemented from ged::EditCosts< UserNodeLabel, UserEdgeLabel >.
◆ node_rel_cost_fun()
template<class UserNodeLabel , class UserEdgeLabel >
|
finalvirtual |
Node relabeling cost function.
- Parameters
-
[in] node_label_1 A node label. [in] node_label_2 A node label.
- Returns
- The cost of changing a node's label from
node_label_1tonode_label_2.
- Note
- Must be implemented by derived classes of ged::EditCosts.
Reimplemented from ged::EditCosts< UserNodeLabel, UserEdgeLabel >.
The documentation for this class was generated from the following files:
- src/edit_costs/protein.hpp
- src/edit_costs/protein.ipp
