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A Java based Neuron Modeling framework
package model.MARK_II;
/**
* A data structure that partly represents the connection strength from a
* Segment to an Cell. Each Synapse has an Cell and has a permanenceValue. A
* Synapse with permanenceValue Greater than or equal to 0.2 means that it is connected to an Cell.
* This creates a binary connection from a Synapse to an Cell. For example a
* permanenceValue of 0.19 means a Synapse is not connected to an Cell whereas a
* permanenceValue of 0.205 does. Furthermore, A permanceValue of 0.9 will only
* be considered by the algorithm to be connected. The idea is that the
* connection is now very "permanent" and not easy to forget. This
* permanenceValue implementation strategy was done to make the learning
* algorithms involving Synapses more efficient and minimally reduces the
* learning algorithms performance.
*
* There are 2 types of synapses in the brain. The MARK I Synapse data structure
* models the chemical synapse and not the electrical synapse using the
* following neuroscience ideas: 1) synaptic plasticity(also known as Hebbian
* plasticity) = If neuron A repeatedly takes part in firing neuron B, then the
* synapses from A to B are strengthened. 2) longterm potentiation/depression =
* Experimentally observed increase/decrease in synaptic strength that lasts for
* hours or days.
*
* NOTE: When getting the activeState or previousActiveState of a Synapse make
* sure to check that the Synapse is connected to it's Cell by calling
* synapse.getConnectedState()
*
* Input of Synapse: activity state of Cell.
*
* Output of Synapse: whether this Synapse is connected or not to the Cell.
*
* @param A synapse can be connected to either a SensorCell or a Neuron.
* @author Quinn Liu ([email protected])
* @author Michael Cogswell ([email protected])
* @version June 8, 2013
*/
public class Synapse {
/**
* When a Synapse's Cell is active, the Synapse will create excitatory
* post-synaptic potential (EPSPs). However, when a Synapse's Cell is not
* active it will not contribute to the spiking of the post-synaptic Neuron
* which is not inhibitory like an inhibitory post synaptic potential
* (IPSPs).
*/
private Cell cell;
private double permanenceValue;
private int cellColumn;
private int cellRow;
// class level variables that can be changed for all synapses
/**
* Amount permanenceValue is increased during one iteration of learning.
*/
public static double PERMANENCE_INCREASE = 0.02;
/**
* Amount permanenceValue is decreased during one iteration of learning.
*/
public static double PERMANENCE_DECREASE = 0.005;
/**
* Minimal permanenceValue needed for a Synapse to be connected.
*/
public static double MINIMAL_CONNECTED_PERMANENCE = 0.2;
public static double INITIAL_PERMANENCE = 0.3;
/**
* Create a new Synapse object with an Cell object and INITIAL_PERMANENCE
* value.
*/
public Synapse(Cell cell, int cellColumn, int cellRow) {
if (cell == null) {
throw new IllegalArgumentException(
"cell in Synapse class constructor cannot be null");
} else if (cellColumn < 0 || cellRow < 0) {
throw new IllegalArgumentException(
"cellColumn and cellRow in Synapse class constructor must be > 0");
}
this.cell = cell;
this.permanenceValue = INITIAL_PERMANENCE;
this.cellColumn = cellColumn;
this.cellRow = cellRow;
}
/**
* Create a new synapse object with an Cell object and given permanence
* value.
*/
public Synapse(Cell cell, double initialPermanence, int cellColumn,
int cellRow) {
this(cell, cellColumn, cellRow);
if (initialPermanence < 0.0 || initialPermanence > 1.0) {
throw new IllegalArgumentException(
"initialPermanence in Synapse class constructor must be between 0 and 1");
}
this.permanenceValue = initialPermanence;
}
/**
* @return This Synapse's Cell if it is connected. Otherwise return null.
*/
public Cell getConnectedCell() {
if (this.isConnected()) {
return this.cell;
} else {
return null;
}
}
public Cell getCell() {
return this.cell;
}
/**
* @return true if this Synapses' permanenceValue is greater than the
* MINIMAL_CONNECTED_PERMANCE represented the Synapse and Cell are
* connected.
*/
public boolean isConnected() {
return (this.permanenceValue >= MINIMAL_CONNECTED_PERMANENCE);
}
/**
* Increase the permanenceValue of a Synapse object by PERMANENCE_INCREASE
* while forcing permanenceValue to always be less than 1.0.
*
* Simulates longterm potentiation in a real Synapse.
*/
public void increasePermanence() {
this.permanenceValue = Math.min(1.0, this.permanenceValue
+ PERMANENCE_INCREASE);
}
/**
* Decrease the permanenceValue of a Synapse object by PERMANENCE_DECREASE
* while forcing permanenceValue to always be greater than 0.0.
*
* Simulates longterm depression in a real Synapse.
*/
public void decreasePermanence() {
this.permanenceValue = Math.max(0.0, this.permanenceValue
- PERMANENCE_DECREASE);
}
public int getCellColumn() {
return this.cellColumn;
}
public int getCellRow() {
return this.cellRow;
}
@Override
public String toString() {
StringBuilder stringBuilder = new StringBuilder();
Cell cell = this.getConnectedCell();
stringBuilder.append("\n===========================");
stringBuilder.append("\n----Synapse Information----");
stringBuilder.append("\n Connected to a: ");
stringBuilder.append(this.cell.toString());
stringBuilder.append("\n Located at (row, column): ");
stringBuilder.append("(" + this.cellRow + ", ");
stringBuilder.append(this.cellColumn + ")");
stringBuilder.append("\npermanenceValue: ");
stringBuilder.append(this.permanenceValue);
stringBuilder.append("\n isConnected: ");
if (this.getConnectedCell() == null) {
stringBuilder.append("false");
} else {
stringBuilder.append("true");
}
;
stringBuilder.append("\n===========================");
String synapseInformation = stringBuilder.toString();
return synapseInformation;
}
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result + cellColumn;
result = prime * result + cellRow;
return result;
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
Synapse other = (Synapse) obj;
if (cellColumn != other.cellColumn)
return false;
if (cellRow != other.cellRow)
return false;
if (Double.doubleToLongBits(permanenceValue) != Double
.doubleToLongBits(other.permanenceValue))
return false;
if (!this.cell.equals(other.cell)) {
return false;
}
return true;
}
public double getPermanenceValue() {
return this.permanenceValue;
}
public void setPermanenceValue(double permanenceValue) {
this.permanenceValue = permanenceValue;
}
}