| Package | Description |
|---|---|
| org.kramerlab.bmad.algorithms |
Contains many different implementations of essential parts of a
boolean matrix decomposition algorithm, that is: candidate generators,
basis selectors, and row combinators.
|
| org.kramerlab.bmad.matrix |
Contains implementations of elementary data structures, required to
perform boolean matrix decompositions: matrices.
|
| Modifier and Type | Method and Description |
|---|---|
BooleanMatrix |
Combinator.combineMatrix(BooleanMatrix a,
BooleanMatrix previousCombination,
BooleanMatrix basis,
double onesWeight)
Calculates the combination matrix C, that describes, how each row of the
original matrix A can be expressed as boolean combination of basis
patterns from basis matrix B.
|
protected BooleanMatrix |
CombinatorPipeline.combineRow(BooleanMatrix row,
BooleanMatrix previousCombination,
BooleanMatrix basis,
double onesWeight) |
protected BooleanMatrix |
Iter.combineRow(BooleanMatrix row,
BooleanMatrix previousCombination,
BooleanMatrix basis,
double onesWeight) |
BooleanMatrix |
GreedyCombinator.combineRow(BooleanMatrix row,
BooleanMatrix _,
BooleanMatrix basis,
double onesWeight) |
protected abstract BooleanMatrix |
Combinator.combineRow(BooleanMatrix row,
BooleanMatrix previousCombination,
BooleanMatrix basis,
double onesWeight)
Describes a row of the original matrix as combination of basis rows from
the basis matrix.
|
protected BooleanMatrix |
IdentityCombinator.combineRow(BooleanMatrix row,
BooleanMatrix previousCombination,
BooleanMatrix basis,
double onesWeight) |
BooleanMatrix |
CandidateGenerator.generateCandidates(BooleanMatrix a,
int dimension)
Generates candidates from the original matrix
|
BooleanMatrix |
RestrictedIntersectionGenerator.generateCandidates(BooleanMatrix a,
int dimension) |
BooleanMatrix |
IntersectionGenerator.generateCandidates(BooleanMatrix a,
int dimension) |
BooleanMatrix |
IdentityGenerator.generateCandidates(BooleanMatrix a,
int dimension) |
BooleanMatrix |
AssociationGenerator.generateCandidates(BooleanMatrix a,
int dimension) |
BooleanMatrix |
Cover.toBooleanMatrix()
transforms this cover to a boolean matrix
|
| Modifier and Type | Method and Description |
|---|---|
Tuple<BooleanMatrix,BooleanMatrix> |
BooleanMatrixDecomposition.decompose(BooleanMatrix a,
int dimension)
Decomposes matrix into two factor matrices.
|
Tuple<BooleanMatrix,BooleanMatrix> |
BooleanMatrixDecomposition.decompose(BooleanMatrix a,
int dimension)
Decomposes matrix into two factor matrices.
|
Tuple<BooleanMatrix,BooleanMatrix> |
BasisSelector.selectBasis(BooleanMatrix candidates,
BooleanMatrix a,
int dimension,
double onesWeight)
Calculates a boolean basis matrix B (second factor), and (optionally) a
coarse approximation of the combination matrix C (first factor).
|
Tuple<BooleanMatrix,BooleanMatrix> |
BasisSelector.selectBasis(BooleanMatrix candidates,
BooleanMatrix a,
int dimension,
double onesWeight)
Calculates a boolean basis matrix B (second factor), and (optionally) a
coarse approximation of the combination matrix C (first factor).
|
Tuple<BooleanMatrix,BooleanMatrix> |
GreedySelector.selectBasis(BooleanMatrix candidates,
BooleanMatrix a,
int dimension,
double onesWeight) |
Tuple<BooleanMatrix,BooleanMatrix> |
GreedySelector.selectBasis(BooleanMatrix candidates,
BooleanMatrix a,
int dimension,
double onesWeight) |
Tuple<BooleanMatrix,BooleanMatrix> |
FastLoc.selectBasis(BooleanMatrix candidates,
BooleanMatrix a,
int dimension,
double onesWeight) |
Tuple<BooleanMatrix,BooleanMatrix> |
FastLoc.selectBasis(BooleanMatrix candidates,
BooleanMatrix a,
int dimension,
double onesWeight) |
| Modifier and Type | Method and Description |
|---|---|
BooleanMatrix |
Combinator.combineMatrix(BooleanMatrix a,
BooleanMatrix previousCombination,
BooleanMatrix basis,
double onesWeight)
Calculates the combination matrix C, that describes, how each row of the
original matrix A can be expressed as boolean combination of basis
patterns from basis matrix B.
|
protected BooleanMatrix |
CombinatorPipeline.combineRow(BooleanMatrix row,
BooleanMatrix previousCombination,
BooleanMatrix basis,
double onesWeight) |
protected BooleanMatrix |
Iter.combineRow(BooleanMatrix row,
BooleanMatrix previousCombination,
BooleanMatrix basis,
double onesWeight) |
BooleanMatrix |
GreedyCombinator.combineRow(BooleanMatrix row,
BooleanMatrix _,
BooleanMatrix basis,
double onesWeight) |
protected abstract BooleanMatrix |
Combinator.combineRow(BooleanMatrix row,
BooleanMatrix previousCombination,
BooleanMatrix basis,
double onesWeight)
Describes a row of the original matrix as combination of basis rows from
the basis matrix.
|
protected BooleanMatrix |
IdentityCombinator.combineRow(BooleanMatrix row,
BooleanMatrix previousCombination,
BooleanMatrix basis,
double onesWeight) |
double |
Cover.coverChangeDensityOnInclusion(BooleanMatrix coveredRow,
BooleanMatrix basisRow)
weighted cover change (indicating "direction" of the change), divided by
the weighted number of changed entries (indicating "magnitude" of the
change)
|
double |
Cover.coverChangeOnExclusion(BooleanMatrix coveredRow,
BooleanMatrix basisRow)
analogous to coverChangeOnInclusion
|
double |
Cover.coverChangeOnInclusion(BooleanMatrix coveredRow,
BooleanMatrix basisRow)
weighted sum of the results returned by coveredOnesAndZerosOnInclusion
|
Tuple<Integer,Integer> |
Cover.coveredOnesAndZerosOnInclusion(BooleanMatrix coveredRow,
BooleanMatrix basisRow)
Predicts the number of covered ones and zeros, given the row that is
being covered, and the basis row that could be included into this cover.
|
Tuple<BooleanMatrix,BooleanMatrix> |
BooleanMatrixDecomposition.decompose(BooleanMatrix a,
int dimension)
Decomposes matrix into two factor matrices.
|
void |
Cover.exclude(BooleanMatrix basisRow)
Excludes a basis row from this cover
|
BooleanMatrix |
CandidateGenerator.generateCandidates(BooleanMatrix a,
int dimension)
Generates candidates from the original matrix
|
BooleanMatrix |
RestrictedIntersectionGenerator.generateCandidates(BooleanMatrix a,
int dimension) |
BooleanMatrix |
IntersectionGenerator.generateCandidates(BooleanMatrix a,
int dimension) |
BooleanMatrix |
IdentityGenerator.generateCandidates(BooleanMatrix a,
int dimension) |
BooleanMatrix |
AssociationGenerator.generateCandidates(BooleanMatrix a,
int dimension) |
void |
Cover.include(BooleanMatrix basisRow)
Includes a basis row into this cover
|
Tuple<BooleanMatrix,BooleanMatrix> |
BasisSelector.selectBasis(BooleanMatrix candidates,
BooleanMatrix a,
int dimension,
double onesWeight)
Calculates a boolean basis matrix B (second factor), and (optionally) a
coarse approximation of the combination matrix C (first factor).
|
Tuple<BooleanMatrix,BooleanMatrix> |
GreedySelector.selectBasis(BooleanMatrix candidates,
BooleanMatrix a,
int dimension,
double onesWeight) |
Tuple<BooleanMatrix,BooleanMatrix> |
FastLoc.selectBasis(BooleanMatrix candidates,
BooleanMatrix a,
int dimension,
double onesWeight) |
Tuple<Integer,Integer> |
Cover.uncoveredOnesAndZerosOnExclusion(BooleanMatrix coveredRow,
BooleanMatrix basisRow)
analogous to coveredOnesAndZerosOnInclusion
|
protected double |
DensityGreedyCombinator.usefulness(Cover cover,
BooleanMatrix row,
BooleanMatrix basisRow) |
protected abstract double |
GreedyCombinator.usefulness(Cover cover,
BooleanMatrix row,
BooleanMatrix basisRow) |
protected double |
CoverGreedyCombinator.usefulness(Cover cover,
BooleanMatrix row,
BooleanMatrix basisRow) |
| Modifier and Type | Method and Description |
|---|---|
BooleanMatrix |
BooleanMatrix.booleanProduct(BooleanMatrix other)
Calculates the boolean product with the other matrix.
|
BooleanMatrix |
BooleanMatrix.getRow(int r)
Extracts single row as separate matrix.
|
BooleanMatrix |
BooleanMatrix.getRows(List<Integer> indices) |
BooleanMatrix |
BooleanMatrix.mapBoolean(Function<Byte,Byte> function)
Map-method, restricted to boolean matrices as output.
|
| Modifier and Type | Method and Description |
|---|---|
void |
BooleanMatrix.baxoy(byte alpha,
BooleanMatrix x)
In-place operation on two row vectors, corresponding to SAXPY in
linear algebra
|
BooleanMatrix |
BooleanMatrix.booleanProduct(BooleanMatrix other)
Calculates the boolean product with the other matrix.
|
double |
BooleanMatrix.reconstructionError(BooleanMatrix reconstruction,
double onesWeight)
Calculates the reconstruction error between this matrix and the
reconstruction.
|
Tuple<Double,Double> |
BooleanMatrix.relativeOneZeroZeroOneReconstructionError(BooleanMatrix reconstruction,
double onesWeight)
Calculates the relative
1->0 and 0->1
reconstruction error, that is, the total error divided by total
maximum possible error. |
double |
BooleanMatrix.relativeReconstructionError(BooleanMatrix reconstruction,
double onesWeight)
Calculates the relative error
(error divided by the maximum possible error).
|
void |
BooleanMatrix.setRow(int r,
BooleanMatrix row)
Analogous to get row: no values are copied
|
| Constructor and Description |
|---|
BooleanMatrix(BooleanMatrix b)
Creates a deep copy of another matrix
|
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