public Matrix createVector(BitVector selector) {
int rows = selector != null ? selector.countOnBits() : frame.size();
Matrix m = new Matrix(rows, 1);
for (int i = 0, j = 0; j < frame.size(); j++) {
if (selector == null || selector.isOn(j)) {
M rowValue = frame.object(j);
try {
Number numValue = (Number) numericField.get(rowValue);
m.set(i, 0, numValue.doubleValue());
} catch (IllegalAccessException e) {
e.printStackTrace();
throw new IllegalStateException(
String.format(
"Couldn't access field %s: %s", numericField.getName(), e.getMessage()));
}
i++;
}
}
return m;
}
public Matrix matrixAbjoint() { // 求伴随矩阵
int i, j;
Matrix matrix = new Matrix();
matrix = Matrix.matrixCopy(this);
matrix = matrix.matrixReverse().matrixNumMultiply(matrix.determinantValue());
return matrix;
}
public Matrix matrixNumMultiply(double x) { // 矩阵乘以一个数
int i, j;
Matrix matrix = new Matrix(this);
for (i = 0; i < matrix.getLine(); i++)
for (j = 0; j < matrix.getRow(); j++) matrix.setElement(i, j, x * matrix.getElement(i, j));
return matrix;
}
static void calculateEigenvector(String file, String chr, int binsize) throws IOException {
if (!file.endsWith("hic")) {
System.err.println("Only 'hic' files are supported");
System.exit(-1);
}
// Load the expected density function, if it exists.
Map<Integer, DensityFunction> zoomToDensityMap = null;
String densityFile = file + ".densities";
if (FileUtils.resourceExists(densityFile)) {
InputStream is = null;
try {
is = ParsingUtils.openInputStream(densityFile);
zoomToDensityMap = DensityUtil.readDensities(is);
} finally {
if (is != null) is.close();
}
} else {
System.err.println("Densities file doesn't exist");
System.exit(-1);
}
SeekableStream ss = IGVSeekableStreamFactory.getStreamFor(file);
Dataset dataset = (new DatasetReader(ss)).read();
Chromosome[] tmp = dataset.getChromosomes();
Map<String, Chromosome> chromosomeMap = new HashMap<String, Chromosome>();
for (Chromosome c : tmp) {
chromosomeMap.put(c.getName(), c);
}
if (!chromosomeMap.containsKey(chr)) {
System.err.println("Unknown chromosome: " + chr);
System.exit(-1);
}
int zoomIdx = 0;
boolean found = false;
for (; zoomIdx < HiCGlobals.zoomBinSizes.length; zoomIdx++) {
if (HiCGlobals.zoomBinSizes[zoomIdx] == binsize) {
found = true;
break;
}
}
if (!found) {
System.err.println("Unknown bin size: " + binsize);
System.exit(-1);
}
Matrix matrix = dataset.getMatrix(chromosomeMap.get(chr), chromosomeMap.get(chr));
MatrixZoomData zd = matrix.getObservedMatrix(zoomIdx);
final DensityFunction df = zoomToDensityMap.get(zd.getZoom());
double[] eigenvector = zd.computeEigenvector(df, 0);
for (double ev : eigenvector) System.out.print(ev + " ");
System.out.println();
}
public static Matrix panelToMatrix(JTextField[] jtfMatrix, int line, int row, double accuracy) {
int i, j;
Matrix matrix = new Matrix(line, row, accuracy);
for (i = 0; i < line; i++)
for (j = 0; j < row; j++) {
if (jtfMatrix[i * row + j].getText().equals("")) return null;
matrix.setElement(i, j, Double.parseDouble(jtfMatrix[i * row + j].getText()));
}
return matrix;
}
public static void matrixToPanel(JTextField[] jtfMatrix, Matrix matrix) {
int i, j;
DecimalFormat df = new DecimalFormat(String.valueOf(matrix.getAccuracy()).replace('1', '0'));
for (i = 0; i < matrix.getLine(); i++)
for (j = 0; j < matrix.getRow(); j++) {
jtfMatrix[i * matrix.getRow() + j].setText(
String.valueOf(df.format(matrix.getElement(i, j))));
}
}
public double[][] Eigenvectors(Matrix m) {
EigenvalueDecomposition decomposition = m.eig();
Matrix eigenVectorsMatrix = decomposition.getV();
double[][] eigenvectors = eigenVectorsMatrix.getArray();
// System.out.println("eigenvectors matrix");
// eigenVectorsMatrix.print(2,2);
return eigenvectors;
}
private void getnegphase() {
/*
* It does the negative phase of unsupervised RBM training algorithm
*
* For details, please refer to Dr. Hinton's paper:
* Reducing the dimensionality of data with neural networks. Science, Vol. 313. no. 5786, pp. 504 - 507, 28 July 2006.
*/
// start calculate the negative phase
// calculate the curved value of v1,h1
// find the vector of v1
Matrix negdata = poshidstates.times(vishid.transpose());
// (1 * numhid) * (numhid * numdims) = (1 * numdims)
negdata.plusEquals(visbiases);
// poshidstates*vishid' + visbiases
double[][] tmp1 = negdata.getArray();
int i1 = 0;
while (i1 < numdims) {
tmp1[0][i1] = 1 / (1 + Math.exp(-tmp1[0][i1]));
i1++;
}
// find the vector of h1
neghidprobs = negdata.times(vishid);
// (1 * numdims) * (numdims * numhid) = (1 * numhid)
neghidprobs.plusEquals(hidbiases);
double[][] tmp2 = neghidprobs.getArray();
int i2 = 0;
while (i2 < numhid) {
tmp2[0][i2] = 1 / (1 + Math.exp(-tmp2[0][i2]));
i2++;
}
negprods = negdata.transpose().times(neghidprobs);
// (numdims * 1) *(1 * numhid) = (numdims * numhid)
}
public Matrix matrixTranspose() { // 矩阵转置
int i, j;
Matrix trans_matrix = new Matrix();
for (i = 0; i < getLine(); i++)
for (j = 0; j < getRow(); j++) trans_matrix.setElement(j, i, this.getElement(i, j));
trans_matrix.setLine(getLine());
trans_matrix.setRow(getRow());
trans_matrix.setAccuracy(getAccuracy());
return trans_matrix;
}
private void prepareMatrices(String statusMatrixFile) {
wrs = new WeightedRandomSelection<Id<Zone>>();
Matrix avestatus = MatrixUtils.readMatrices(statusMatrixFile).getMatrix("avg");
for (Map.Entry<String, ArrayList<Entry>> fromLOR : avestatus.getFromLocations().entrySet()) {
if (BerlinZoneUtils.isInBerlin(fromLOR.getKey())) {
wrs.add(
Id.create(fromLOR.getKey(), Zone.class),
MatrixUtils.calculateTotalValue(fromLOR.getValue()));
}
}
}
public int matrixRank() // 矩阵的秩
{
int rank = 0, i, j;
Matrix matrix = new Matrix();
matrix = matrixLineSimplify();
for (i = 0; i < matrix.getLine(); i++)
for (j = 0; j < matrix.getRow(); j++)
if (Math.abs(matrix.getElement(i, j)) > matrix.getAccuracy()) {
rank++;
break;
}
return rank;
}
public void map(
LongWritable key,
Text value,
OutputCollector<IntWritable, DoubleWritable> output,
Reporter reporter)
throws IOException {
/*
* It implements the mapper. It outputs the numbers of weight and updated weights.
*
* Note that the format of intermediate output is <IntWritable, DoubleWritable>,
* because the key is the number of weight (an integer), and the value is the weight's value (double)
*/
inputData = value.toString();
// go through the process
initialize();
getposphase();
getnegphase();
update();
// output the intermediate data
// The <key, value> pairs are <weightID, weightUpdate>
double[][] vishidinc_array = vishidinc.getArray();
for (int i = 0; i < numdims; i++) {
for (int j = 0; j < numhid; j++) {
weightPos.set(i * numhid + j);
weightValue.set(vishidinc_array[i][j]);
output.collect(weightPos, weightValue);
}
}
}
long[][] initMatrix(int n, int start) {
long[][] m = Matrix.unit(n);
for (int i = 0; i < start; i++) {
m[i][start] = 1;
}
return m;
}
public Matrix(double[][] matrixArray, int line, int row, double accuracy, String name) {
this.matrixArray = Matrix.matrixArrayCopy(matrixArray);
this.line = line;
this.row = row;
this.accuracy = accuracy;
this.name = name;
}
public Matrix matrixPower(int n) { // 矩阵的幂
int i;
Matrix matrix = new Matrix(this);
for (i = 2; i <= n; i++) matrix = Matrix.matrixMultiply(matrix, this);
return matrix;
}
private void prop2nextLayer() {
/*
* It computes the forward propagation algorithm.
*/
poshidprobs = data.times(vishid);
// (1 * numdims) * (numdims * numhid)
poshidprobs.plusEquals(hidbiases);
// data*vishid + hidbiases
double[][] product_tmp2 = poshidprobs.getArray();
for (int i2 = 0; i2 < numhid; i2++) {
/*
* compute the updated input, and write them to newinput
*/
product_tmp2[0][i2] = 1 / (1 + Math.exp(-product_tmp2[0][i2]));
newinput[i2] = (int) (product_tmp2[0][i2] * 255.0);
}
}
/** toy example */
public static void test2() {
int N = 500;
double[][] m1 = new double[N][N];
double[][] m2 = new double[N][N];
double[][] m3 = new double[N][N];
// init
Random rand = new Random();
for (int i = 0; i < N; i++)
for (int j = 0; j < N; j++) {
m1[i][j] = 10 * (rand.nextDouble() - 0.2);
m2[i][j] = 20 * (rand.nextDouble() - 0.8);
}
// inverse
System.out.println("Start");
Matrix mat1 = new Matrix(m1);
Matrix mat2 = mat1.inverse();
Matrix mat3 = mat1.times(mat2);
double[][] m4 = mat3.getArray();
/*
for (int i = 0; i < m4.length; i++) {
int ss = 10;
for (int j = 0; j < ss; j++) {
System.out.printf("%f ", m4[i][j]);
}
System.out.print("\n");
}
*/
System.out.println("Done");
/*
// matrix *
System.out.println("Start");
for (int i = 0; i < N; i++) for (int j = 0; j < N; j++) {
double cell = 0;
for (int k = 0; k < N; k++)
cell += m1[i][k] * m2[k][j];
// System.out.printf("%f ", cell);
m3[i][j] = cell;
}
System.out.println("Done");
*/
}
public Matrix createVector() {
int rows = frame.size();
Matrix m = new Matrix(rows, 1);
for (int i = 0; i < rows; i++) {
M rowValue = frame.object(i);
try {
Number numValue = (Number) numericField.get(rowValue);
m.set(i, 0, numValue.doubleValue());
} catch (IllegalAccessException e) {
e.printStackTrace();
throw new IllegalStateException(
String.format("Couldn't access field %s: %s", numericField.getName(), e.getMessage()));
}
}
return m;
}
public double[] Eigenvalues(Matrix m) {
EigenvalueDecomposition decomposition = m.eig();
double[] eigenvalues = decomposition.getRealEigenvalues();
// System.out.println("eigenvalues: ");
// for(int i=0;i<eigenvalues.length;i++)
// System.out.println(""+eigenvalues[i]);
return eigenvalues;
}
private void getposphase() {
/*
* It does the positive phase of unsupervised RBM training algorithm
*
* For details, please refer to Dr. Hinton's paper:
* Reducing the dimensionality of data with neural networks. Science, Vol. 313. no. 5786, pp. 504 - 507, 28 July 2006.
*/
// Start calculate the positive phase
// calculate the cured value of h0
poshidprobs = data.times(vishid);
// (1 * numdims) * (numdims * numhid)
poshidprobs.plusEquals(hidbiases);
// data*vishid + hidbiases
double[][] product_tmp2 = poshidprobs.getArray();
int i2 = 0;
while (i2 < numhid) {
product_tmp2[0][i2] = 1 / (1 + Math.exp(-product_tmp2[0][i2]));
i2++;
}
posprods = data.transpose().times(poshidprobs);
// (numdims * 1) * (1 * numhid)
// end of the positive phase calculation, find the binary presentation of h0
int i3 = 0;
double[][] tmp1 = poshidprobs.getArray();
double[][] tmp2 = new double[1][numhid];
Random randomgenerator = new Random();
while (i3 < numhid) {
/*
* a sampling according to possiblity given by poshidprobs
*/
if (tmp1[0][i3] > randomgenerator.nextDouble()) tmp2[0][i3] = 1;
else tmp2[0][i3] = 0;
i3++;
}
// poshidstates is a binary sampling according to possiblity given by poshidprobs
poshidstates = new Matrix(tmp2);
}
/**
* Transition function. Currently, we only get the list of probabilities of each item.
*
* @param current - The current state
* @param action - The action
* @param possible - The possible state
* @return The list of probabilities where each index refers to the probability of that item
*/
private List<Double> transition(State current, Action action, State possible) {
List<Double> probs = new ArrayList<Double>(); // Probabilities
Map<Integer, Integer> currentStock, purchase, possibleStock; // Maps
double currentProb; // The current probability
Matrix currentMatrix; // The current probability matrix
int row, column; // The row and column
for (int i = 0; i < current.getState().size(); ++i) {
currentProb = 0.0;
currentStock = current.getState();
purchase = action.getPurchases();
possibleStock = possible.getState();
row = currentStock.get(i) + purchase.get(i);
column = row - possible.getState().get(i);
currentMatrix = this.probabilities.get(i);
if (column < 0
|| column >= currentMatrix.getNumCols()
|| row >= currentMatrix.getNumRows()) { // Invalid state
probs.add(0.0);
continue;
}
if (possibleStock.get(i) > 0
|| (possibleStock.get(i) == 0 && column == 0)) { // Sufficiently provided
currentProb = currentMatrix.get(row, column);
} else if (possibleStock.get(i) == 0 && column > 0) {
// Range of probabilities because user could have eaten plenty
for (int j = column; j < currentMatrix.getNumCols(); ++j) {
currentProb += currentMatrix.get(row, j);
}
}
probs.add(currentProb);
}
return probs;
}
double calculateMSEOnValidationSet(Matrix featuresValidationSet, Matrix labelsValidationSet)
throws Exception {
double sumSquaredError = 0;
for (int instance = 0; instance < featuresValidationSet.rows(); instance++) {
double errorAcrossOutputNodes = 0;
double[] predictedLabel = labelsValidationSet.row(instance); // this is the target
predict(featuresValidationSet.row(instance), labelsValidationSet.row(instance));
for (int col = 0; col < globalStoredOutputNodeFNetValues.length; col++) {
errorAcrossOutputNodes +=
(globalStoredOutputNodeTargetValues[col] - globalStoredOutputNodeFNetValues[col]);
}
sumSquaredError += (errorAcrossOutputNodes * errorAcrossOutputNodes);
}
double MSE =
(sumSquaredError
/ (featuresValidationSet.rows() * globalStoredOutputNodeFNetValues.length));
return MSE;
}
public Matrix matrixAccuralize() { // 精确化矩阵
int i, j;
Matrix matrix = new Matrix(this);
for (i = 0; i < matrix.getLine(); i++)
for (j = 0; j < matrix.getRow(); j++)
if (Math.abs(matrix.getElement(i, j)) <= matrix.getAccuracy()) matrix.setElement(i, j, 0.0);
return matrix;
}
public static Matrix scanMatrix() { // 输入矩阵
int i, j;
Matrix matrix = new Matrix();
Scanner scanner = new Scanner(System.in);
matrix.setLine(scanner.nextInt());
matrix.setRow(scanner.nextInt());
matrix.setAccuracy(scanner.nextDouble());
for (i = 0; i < matrix.getLine(); i++) {
for (j = 0; j < matrix.getRow(); j++) matrix.setElement(i, j, scanner.nextDouble());
}
return matrix;
}
// update the weights and biases
// This serves as a reducer
private void update() {
/*
* It computes the update of weights using previous results and parameters
*
* For details, please refer to Dr. Hinton's paper:
* Reducing the dimensionality of data with neural networks. Science, Vol. 313. no. 5786, pp. 504 - 507, 28 July 2006.
*/
double momentum;
// if (epoch > 5)
// momentum = finalmomentum;
// else
// momentum = initialmomentum;
// vishidinc = momentum*vishidinc + epsilonw*( (posprods-negprods)/numcases -
// weightcost*vishid);
// vishidinc.timesEquals(momentum);
Matrix temp1 = posprods.minus(negprods);
Matrix temp2 = vishid.times(weightcost);
temp1.minusEquals(temp2);
temp1.timesEquals(epsilonw);
// the final updates of weights are written in vishidinc
vishidinc.plusEquals(temp1);
}
public int solve(long coins_sum, long[] values) {
int n = values.length;
long[][][] step = new long[n][][];
step[0] = Matrix.unit(n);
for (int i = 1; i < n; i++) {
long div = values[i] / values[i - 1];
step[i] = Matrix.mul(initMatrix(n, i), Matrix.pow(step[i - 1], div, MOD), MOD);
}
long[][] total = Matrix.unit(n);
for (int i = n - 1; i >= 0; i--) {
long length = coins_sum / values[i];
coins_sum %= values[i];
total = Matrix.mul(Matrix.pow(step[i], length, MOD), total, MOD);
}
long res = 0;
for (int i = 0; i < n; i++) {
res += total[0][i];
}
return (int) (res % MOD);
}
public static void main(String[] args) {
Scanner scanner = new Scanner(System.in);
Matrix o = Matrix.load(scanner);
System.out.println(o.solve());
}
public void initFrame(double time) { // add animation here!!!!!!
boolean rotate = false;
rotate = true;
// fundation
m.identity();
if (rotate) m.rotateY(time * speed);
m.translate(0, foundPosition, 0);
m.scale(foundW, foundH, foundW);
m.rotateX(-Math.PI / 2);
m.transform(g[0], t[0]);
// largest ball
m.identity();
if (rotate) m.rotateY(time * speed);
m.translate(ballLX, ballLPosition, ballLZ);
m.scale(ballLR, ballLR, ballLR);
m.rotateX(Math.PI / 2);
m.transform(g[1], t[1]);
// middle ball
m.identity();
if (rotate) m.rotateY(time * speed);
m.translate(ballLX, ballMPosition, ballLZ);
m.scale(ballMR, ballMR, ballMR);
m.rotateX(Math.PI / 2);
m.transform(g[2], t[2]);
// head ball
m.identity();
if (rotate) m.rotateY(time * speed);
m.translate(ballLX, ballHPosition, ballLZ);
m.scale(ballHR, ballHR, ballHR);
m.rotateX(Math.PI / 2);
m.transform(g[3], t[3]);
// hat
m.identity();
if (rotate) m.rotateY(time * speed);
m.translate(ballLX, ballHPosition, ballLZ);
m.rotateZ(-Math.PI / 18);
m.translate(0, hatPosition - ballHPosition, 0);
m.scale(hatR, hatR, hatR);
m.rotateX(Math.PI / 2);
m.transform(g[4], t[4]);
// hat bottom
m.identity();
if (rotate) m.rotateY(time * speed);
m.translate(ballLX, ballHPosition, ballLZ);
m.rotateZ(-Math.PI / 18);
m.translate(0, hatBPosition - ballHPosition, 0);
m.scale(hatBR, hatBH, hatBR);
m.rotateX(Math.PI / 2);
m.transform(g[5], t[5]);
// eye
m.identity();
if (rotate) m.rotateY(time * speed);
m.translate(eyeX, eyeY, Math.sqrt(Math.pow(ballHR, 2) - Math.pow(eyeX, 2) - Math.pow(eyeY, 2)));
m.translate(ballLX, ballHPosition, ballLZ);
m.scale(eyeW, eyeH, eyeT);
m.rotateZ(Math.PI / 18);
m.rotateX(Math.PI / 2);
m.transform(g[6], t[6]);
// eye
m.identity();
if (rotate) m.rotateY(time * speed);
m.translate(
-eyeX, eyeY, Math.sqrt(Math.pow(ballHR, 2) - Math.pow(eyeX, 2) - Math.pow(eyeY, 2)));
m.translate(ballLX, ballHPosition, ballLZ);
m.scale(eyeW, eyeH, eyeT);
m.rotateZ(-Math.PI / 18);
m.rotateX(Math.PI / 2);
m.transform(g[7], t[7]);
// nose
m.identity();
if (rotate) m.rotateY(time * speed);
m.translate(ballLX, ballHPosition, ballLZ + ballHR);
m.scale(noseR, noseR, noseL);
m.transform(g[8], t[8]);
// botton 1
m.identity();
if (rotate) m.rotateY(time * speed);
m.translate(0, bottonY, Math.sqrt(Math.pow(ballMR, 2) - Math.pow(bottonY, 2)));
m.translate(ballLX, ballMPosition, ballLZ);
m.scale(bottonR, bottonR, bottonT);
m.rotateX(Math.PI / 2);
m.transform(g[9], t[9]);
// botton 2
m.identity();
if (rotate) m.rotateY(time * speed);
m.translate(0, -bottonY / 2, Math.sqrt(Math.pow(ballMR, 2) - Math.pow(bottonY / 2, 2)));
m.translate(ballLX, ballMPosition, ballLZ);
m.scale(bottonR, bottonR, bottonT);
m.rotateX(Math.PI / 2);
m.transform(g[10], t[10]);
// botton 3
m.identity();
if (rotate) m.rotateY(time * speed);
m.translate(0, bottonY, Math.sqrt(Math.pow(ballLR, 2) - Math.pow(bottonY, 2)));
m.translate(ballLX, ballLPosition, ballLZ);
m.scale(bottonR, bottonR, bottonT);
m.rotateX(Math.PI / 2);
m.transform(g[11], t[11]);
}
@Override
protected void applyModelviewTransform(DrawContext dc, SurfaceTileDrawContext sdc) {
// Apply the geographic to surface tile coordinate transform.
Matrix modelview = sdc.getModelviewMatrix();
dc.getGL().glMultMatrixd(modelview.toArray(new double[16], 0, false), 0);
}
protected int computeCartesianPolygon(
Globe globe,
List<? extends LatLon> locations,
List<Boolean> edgeFlags,
Vec4[] points,
Boolean[] edgeFlagArray,
Matrix[] transform) {
if (globe == null) {
String message = Logging.getMessage("nullValue.GlobeIsNull");
Logging.logger().severe(message);
throw new IllegalArgumentException(message);
}
if (locations == null) {
String message = "nullValue.LocationsIsNull";
Logging.logger().severe(message);
throw new IllegalArgumentException(message);
}
if (points == null) {
String message = "nullValue.LocationsIsNull";
Logging.logger().severe(message);
throw new IllegalArgumentException(message);
}
if (points.length < (1 + locations.size())) {
String message =
Logging.getMessage(
"generic.ArrayInvalidLength", "points.length < " + (1 + locations.size()));
Logging.logger().severe(message);
throw new IllegalArgumentException(message);
}
if (transform == null) {
String message = "nullValue.TransformIsNull";
Logging.logger().severe(message);
throw new IllegalArgumentException(message);
}
if (transform.length < 1) {
String message = Logging.getMessage("generic.ArrayInvalidLength", "transform.length < 1");
Logging.logger().severe(message);
throw new IllegalArgumentException(message);
}
// Allocate space to hold the list of locations and location vertices.
int locationCount = locations.size();
// Compute the cartesian points for each location.
for (int i = 0; i < locationCount; i++) {
LatLon ll = locations.get(i);
points[i] = globe.computePointFromPosition(ll.getLatitude(), ll.getLongitude(), 0.0);
if (edgeFlagArray != null) edgeFlagArray[i] = (edgeFlags != null) ? edgeFlags.get(i) : true;
}
// Compute the average of the cartesian points.
Vec4 centerPoint = Vec4.computeAveragePoint(Arrays.asList(points));
// Test whether the polygon is closed. If it is not closed, repeat the first vertex.
if (!points[0].equals(points[locationCount - 1])) {
points[locationCount] = points[0];
if (edgeFlagArray != null) edgeFlagArray[locationCount] = edgeFlagArray[0];
locationCount++;
}
// Compute a transform that will map the cartesian points to a local coordinate system centered
// at the average
// of the points and oriented with the globe surface.
Position centerPos = globe.computePositionFromPoint(centerPoint);
Matrix tx = globe.computeSurfaceOrientationAtPosition(centerPos);
Matrix txInv = tx.getInverse();
// Map the cartesian points to a local coordinate space.
for (int i = 0; i < locationCount; i++) {
points[i] = points[i].transformBy4(txInv);
}
transform[0] = tx;
return locationCount;
}
