402 lines
14 KiB
C
402 lines
14 KiB
C
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/** Methods computing or estimating the second moment of the Ising model given
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* the natural parameters of the p.m.f. in exponential family form. That is
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* f(x) = p0(params) exp(vech(x x')' params)
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* where `params` are the natural parameters. The scaling constant `p0(params)`
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* is also the zero event `x = (0, ..., 0)` probability.
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*
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* Three different version are provided.
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* - exact: Exact method computing the true second moment `E[X X']` given the
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* parameters `params`. This method has a runtime of `O(2^dim)` where
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* `dim` is the dimension of the random variable `X`. This means it is
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* infeasible for bigger (like 25 and above) values if `dim`
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* - MC: Monte-Carlo method used in case the exact method is not feasible.
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* - MC Thrd: Multi-Threaded Monte-Carlo method.
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*
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* The natural parameters `params` of the Ising model is a `dim (dim + 1) / 2`
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* dimensional numeric vector containing the log-odds. The indexing schema into
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* the parameters corresponding to the log-odds of single or two way interactions
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* with indicex `i, j` are according to the half-vectorization schema
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*
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* i = 4'th row => Symmetry => Half-Vectorized Storage
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*
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* [ * * * * * * ] [ * * * * * * ] [ * * * 15 * * ]
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* [ * * * * * * ] [ * * * * * * ] [ * * 12 16 * ]
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* [ * * * * * * ] [ * * * * * * ] [ * 8 * 17 ]
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* [ 3 8 12 15 16 17 ] [ 3 8 12 15 * * ] [ 3 * * ]
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* [ * * * * * * ] [ * * * 16 * * ] [ * * ]
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* [ * * * * * * ] [ * * * 17 * * ] [ * ]
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*
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*/
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#include "R_api.h"
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#include "bit_utils.h"
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#include "int_utils.h"
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#include "ising_MCMC.h"
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#ifndef __STDC_NO_THREADS__
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#include <threads.h>
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#endif
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////////////////////////////////////////////////////////////////////////////////
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// TODO: read //
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// https://developer.r-project.org/Blog/public/2019/04/18/common-protect-errors/
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// and
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// https://developer.r-project.org/Blog/public/2018/12/10/unprotecting-by-value/index.html
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// as well as do the following PROPERLLY
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// TODO: make specialized version using the parameters in given sym mat form //
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// similar to `ising_sample()` //
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////////////////////////////////////////////////////////////////////////////////
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// void ising_m2_exact_mat(
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// const size_t dim, const size_t ldA, const double* A,
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// double* M2
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// ) {
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// double sum_0 = 1.0;
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// const uint32_t max_event = (uint32_t)1 << dim;
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// (void)memset(M2, 0, dim * dim * sizeof(double));
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// for (uint32_t X = 1; X < max_event; ++X) {
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// // Evaluate quadratic form `X' A X` using symmetry of `A`
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// double XtAX = 0.0;
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// for (uint32_t Y = X; Y; Y &= Y - 1) {
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// const int i = bitScanLS32(Y);
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// XtAX += A[i * (ldA + 1)];
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// for (uint32_t Z = Y & (Y - 1); Z; Z &= Z - 1) {
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// XtAX += 2 * A[i * ldA + bitScanLS32(Z)];
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// }
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// }
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// const double prob_X = exp(XtAX);
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// sum_0 += prob_X;
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// for (uint32_t Y = X; Y; Y &= Y - 1) {
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// const int i = bitScanLS32(Y);
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// for (uint32_t Z = Y; Z; Z &= Z - 1) {
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// M2[i * dim + bitScanLS32(Z)] += prob_X;
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// }
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// }
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// }
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// const double prob_0 = 1.0 / sum_0;
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// for (size_t j = 0; j < dim; ++j) {
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// for (size_t i = 0; i < j; ++i) {
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// M2[j * dim + i] = M2[i * dim + j];
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// }
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// for (size_t i = j; i < dim; ++i) {
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// M2[i * dim + j] *= prob_0;
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// }
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// }
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// }
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double ising_m2_exact(const size_t dim, const double* params, double* M2) {
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// Accumulator of sum of all (unscaled) probabilities
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double sum_0 = 1.0;
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// max event (actually upper bound)
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const uint32_t max_event = (uint32_t)1 << dim;
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// Length of parameters
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const size_t len = dim * (dim + 1) / 2;
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// Initialize M2 to zero
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(void)memset(M2, 0, len * sizeof(double));
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// Iterate all `2^dim` binary vectors `X`
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for (uint32_t X = 1; X < max_event; ++X) {
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// Dot product `<vech(X X'), params>`
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double dot_X = 0.0;
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// all bits in `X`
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for (uint32_t Y = X; Y; Y &= Y - 1) {
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const int i = bitScanLS32(Y);
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const int I = (i * (2 * dim - 1 - i)) / 2;
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// add single and two way interaction log odds
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for (uint32_t Z = Y; Z; Z &= Z - 1) {
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dot_X += params[I + bitScanLS32(Z)];
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}
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}
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// (unscaled) probability of current event `X`
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const double prob_X = exp(dot_X);
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sum_0 += prob_X;
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// Accumulate set bits probability for the first end second moment `E[X X']`
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for (uint32_t Y = X; Y; Y &= Y - 1) {
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const int i = bitScanLS32(Y);
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const int I = (i * (2 * dim - 1 - i)) / 2;
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for (uint32_t Z = Y; Z; Z &= Z - 1) {
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M2[I + bitScanLS32(Z)] += prob_X;
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}
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}
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}
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// Finish by scaling with zero event probability (Ising p.m.f. scaling constant)
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const double prob_0 = 1.0 / sum_0;
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for (size_t i = 0; i < len; ++i) {
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M2[i] *= prob_0;
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}
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return prob_0;
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}
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// Monte-Carlo method using Gibbs sampling for the second moment
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double ising_m2_MC(
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/* options */ const size_t nr_samples, const size_t warmup,
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/* dimension */ const size_t dim,
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/* vectors */ const double* params, double* M2
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) {
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// Length of `params` and `M2`
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const size_t len = (dim * (dim + 1)) / 2;
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// Dirty trick (reuse output memory for precise counting)
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_Static_assert(sizeof(uint64_t) == sizeof(double), "Dirty trick fails!");
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uint64_t* counts = (uint64_t*)M2;
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// Initialize counts to zero
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(void)memset(counts, 0, len * sizeof(uint64_t));
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// Allocate memory to store Markov-Chain value
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int* X = (int*)R_alloc(dim, sizeof(int));
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// Create/Update R's internal PRGN state
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GetRNGstate();
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// Spawn chains
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for (size_t sample = 0; sample < nr_samples; ++sample) {
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// Draw random sample `X ~ Ising(params)`
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ising_mcmc_vech(warmup, dim, params, X);
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// Accumulate component counts
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uint64_t* count = counts;
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for (size_t i = 0; i < dim; ++i) {
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for (size_t j = i; j < dim; ++j) {
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*(count++) += X[i] & X[j];
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}
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}
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}
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// Write R's internal PRNG state back (if needed)
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PutRNGstate();
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// Compute means from counts
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for (size_t i = 0; i < len; ++i) {
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M2[i] = (double)counts[i] / (double)(nr_samples);
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}
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return -1.0; // TODO: also compute prob_0
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}
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// in case the compile supports standard C threads
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#ifndef __STDC_NO_THREADS__
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// Worker thread to calling thread communication struct
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typedef struct thrd_data {
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rng_seed_t seed; // Pseudo-Random-Number-Generator seed/state value
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size_t nr_samples; // Nr. of samples this worker handles
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size_t warmup; // Monte-Carlo Chain burne-in length
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size_t dim; // Random variable dimension
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const double* params; // Ising model parameters
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int* X; // Working memory to store current binary sample
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uint32_t* counts; // (output) count of single and two way interactions
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double prob_0; // (output) zero event probability estimate
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} thrd_data_t;
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// Worker thread function
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int thrd_worker(thrd_data_t* data) {
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// Extract data as thread local variables (for convenience)
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const size_t dim = data->dim;
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int* X = data->X;
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// Initialize counts to zero
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(void)memset(data->counts, 0, (dim * (dim + 1) / 2) * sizeof(uint32_t));
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// Spawn Monte-Carlo Chains (one foe every sample)
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for (size_t sample = 0; sample < data->nr_samples; ++sample) {
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// Draw random sample `X ~ Ising(params)`
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ising_mcmc_vech_thrd(data->warmup, dim, data->params, X, data->seed);
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// Accumulate component counts
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uint32_t* count = data->counts;
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for (size_t i = 0; i < dim; ++i) {
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for (size_t j = i; j < dim; ++j) {
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*(count++) += X[i] & X[j];
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}
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}
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}
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return 0;
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}
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double ising_m2_MC_thrd(
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/* options */ const size_t nr_samples, const size_t warmup,
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const size_t nr_threads,
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/* dimension */ const size_t dim,
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/* vectors */ const double* params, double* M2
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) {
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// Length of `params` and `M2`
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const size_t len = (dim * (dim + 1)) / 2;
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// Allocate working and self memory for worker threads
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int* Xs = (int*)R_alloc(dim * nr_threads, sizeof(int));
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uint32_t* counts = (uint32_t*)R_alloc(len * nr_threads, sizeof(uint32_t));
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thrd_t* threads = (thrd_t*)R_alloc(nr_threads, sizeof(thrd_data_t));
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thrd_data_t* threads_data = (thrd_data_t*)R_alloc(nr_threads, sizeof(thrd_data_t));
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// Provide instruction wor worker and dispatch them
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for (size_t tid = 0; tid < nr_threads; ++tid) {
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// Every thread needs its own PRNG seed!
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init_seed(threads_data[tid].seed);
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// divide work among workers (more or less) equaly with the first worker
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// (tid = 0) having the additional remainder of divided work (`nr_samples`)
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threads_data[tid].nr_samples = nr_samples / nr_threads + (
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tid ? 0 : nr_samples % nr_threads
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);
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threads_data[tid].warmup = warmup;
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threads_data[tid].dim = dim;
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threads_data[tid].params = params;
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// Every worker gets its disjint working memory
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threads_data[tid].X = &Xs[dim * tid];
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threads_data[tid].counts = &counts[len * tid];
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// dispatch the worker
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thrd_create(&threads[tid], (thrd_start_t)thrd_worker, (void*)&threads_data[tid]);
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}
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// Join (Wait for) all worker
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for (size_t tid = 0; tid < nr_threads; ++tid) {
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thrd_join(threads[tid], NULL);
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}
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// Accumulate worker results into first (tid = 0) worker counts result
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for (size_t tid = 1; tid < nr_threads; ++tid) {
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for (size_t i = 0; i < len; ++i) {
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counts[i] += counts[tid * len + i];
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}
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}
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// convert discreat counts into means
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for (size_t i = 0; i < len; ++i) {
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M2[i] = (double)counts[i] / (double)nr_samples;
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}
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return -2.0; // TODO: also compute prob_0
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}
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#endif /* !__STDC_NO_THREADS__ */
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/* Implementation of `.Call` entry point */
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////////////////////////////////////////////////////////////////////////////////
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// TODO: make specialized version using the parameters in given sym mat form //
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// similar to `ising_sample()` //
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////////////////////////////////////////////////////////////////////////////////
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extern SEXP R_ising_m2(
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SEXP _params, SEXP _use_MC, SEXP _nr_samples, SEXP _warmup, SEXP _nr_threads
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) {
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// Extract and validate arguments
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size_t protect_count = 0;
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if (!Rf_isReal(_params)) {
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_params = PROTECT(Rf_coerceVector(_params, REALSXP));
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protect_count++;
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}
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// Depending on parameters given in symmetric matrix form or natural
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// or natrual parameters in the half-vectorized memory layout
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size_t dim;
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double* params;
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if (Rf_isMatrix(_params)) {
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if (Rf_nrows(_params) != Rf_ncols(_params)) {
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Rf_error("Invalid 'params' value, exected square matrix");
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}
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// Convert to natural parameters
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dim = Rf_nrows(_params);
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params = (double*)R_alloc(dim * (dim + 1) / 2, sizeof(double));
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double* A = REAL(_params);
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for (size_t j = 0, I = 0; j < dim; ++j) {
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for (size_t i = j; i < dim; ++i, ++I) {
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params[I] = (1 + (i != j)) * A[i + j * dim];
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}
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}
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} else {
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// Get Ising random variable dimension `dim` from "half-vectorized" parameters
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// vector. That is, compute `dim` from `length(params) = dim (dim + 1) / 2`.
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dim = invTriag(Rf_length(_params));
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if (!dim) {
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Rf_error("Expected parameter vector of length `p (p + 1) / 2` where"
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" `p` is the dimension of the random variable");
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}
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params = REAL(_params);
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}
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// Determin the method to use and validate if possible
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const int use_MC = Rf_asLogical(_use_MC);
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if (use_MC == NA_LOGICAL) {
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Rf_error("Invalid 'use_MC' value, expected ether TRUE or FALSE");
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}
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// Allocate result vector
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SEXP _M2 = PROTECT(Rf_allocVector(REALSXP, dim * (dim + 1) / 2));
|
||
|
|
++protect_count;
|
||
|
|
|
||
|
|
// asside computed zero event probability (inverse partition function), the
|
||
|
|
// scaling factor for the Ising model p.m.f.
|
||
|
|
double prob_0 = -1.0;
|
||
|
|
|
||
|
|
if (use_MC) {
|
||
|
|
// Convert and validate arguments for the Monte-Carlo methods
|
||
|
|
const size_t nr_samples = asUnsigned(_nr_samples);
|
||
|
|
if (nr_samples == 0 || nr_samples == NA_UNSIGNED) {
|
||
|
|
Rf_error("Invalid 'nr_samples' value, expected pos. integer");
|
||
|
|
}
|
||
|
|
const size_t warmup = asUnsigned(_warmup);
|
||
|
|
if (warmup == NA_UNSIGNED) {
|
||
|
|
Rf_error("Invalid 'warmup' value, expected non-negative integer");
|
||
|
|
}
|
||
|
|
const size_t nr_threads = asUnsigned(_nr_threads);
|
||
|
|
if (nr_threads == 0 || nr_threads > 256) {
|
||
|
|
Rf_error("Invalid 'nr_thread' value");
|
||
|
|
}
|
||
|
|
|
||
|
|
if (nr_threads == 1) {
|
||
|
|
// Single threaded Monte-Carlo method
|
||
|
|
prob_0 = ising_m2_MC(nr_samples, warmup, dim, params, REAL(_M2));
|
||
|
|
} else {
|
||
|
|
// Multi-Threaded Monte-Carlo method if provided, otherwise use
|
||
|
|
// the single threaded version with a warning
|
||
|
|
#ifdef __STDC_NO_THREADS__
|
||
|
|
Rf_warning("Multi-Threading NOT supported, using fallback.");
|
||
|
|
prob_0 = ising_m2_MC(nr_samples, warmup, dim, params, REAL(_M2));
|
||
|
|
#else
|
||
|
|
prob_0 = ising_m2_MC_thrd(
|
||
|
|
nr_samples, warmup, nr_threads,
|
||
|
|
dim, params, REAL(_M2)
|
||
|
|
);
|
||
|
|
#endif
|
||
|
|
}
|
||
|
|
} else {
|
||
|
|
// Exact method (ignore other arguments), only validate dimension
|
||
|
|
if (25 < dim) {
|
||
|
|
Rf_error("Dimension '%d' too big for exact method (max 24)", dim);
|
||
|
|
}
|
||
|
|
|
||
|
|
// and call the exact method
|
||
|
|
prob_0 = ising_m2_exact(dim, params, REAL(_M2));
|
||
|
|
}
|
||
|
|
|
||
|
|
// Set log-lokelihood as an attribute to the computed second moment
|
||
|
|
SEXP _prob_0 = PROTECT(Rf_ScalarReal(prob_0));
|
||
|
|
++protect_count;
|
||
|
|
Rf_setAttrib(_M2, Rf_install("prob_0"), _prob_0);
|
||
|
|
|
||
|
|
// release SEPXs to the garbage collector
|
||
|
|
UNPROTECT(protect_count);
|
||
|
|
|
||
|
|
return _M2;
|
||
|
|
}
|