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Add skyglide in benchmark and improve C++ wrappers
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4ment committed Jan 30, 2024
1 parent 9c94f57 commit 6ebfb68
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Showing 4 changed files with 240 additions and 55 deletions.
166 changes: 127 additions & 39 deletions examples/benchmarking.c
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@

#include "phyc/datatype.h"
#include "phyc/demographicmodels.h"
#include "phyc/gradient.h"
#include "phyc/parameters.h"
#include "phyc/sequenceio.h"
#include "phyc/sitepattern.h"
Expand All @@ -14,7 +15,8 @@
#include "phyc/treetransform.h"

double mseconds(struct timespec start, struct timespec end) {
return (end.tv_sec - start.tv_sec) * 1000. + (end.tv_nsec - start.tv_nsec) / 1000000.;
return (end.tv_sec - start.tv_sec) * 1000. +
(end.tv_nsec - start.tv_nsec) / 1000000.;
}

char* json_jc69_strict =
Expand Down Expand Up @@ -111,9 +113,10 @@ char* json_gtr_unrooted =
\"tree\": \"&tree\" \
}";

// Calculate the log of the determinant of the Jacobian for the node height transform.
// Derivatives are wrt ratio/root height parameters.
void test_height_transform_jacobian(size_t iter, const char* newick, int reparameterization, FILE* csv, bool debug) {
// Calculate the log of the determinant of the Jacobian for the node height
// transform. Derivatives are wrt ratio/root height parameters.
void test_height_transform_jacobian(size_t iter, const char* newick,
int reparameterization, FILE* csv, bool debug) {
struct timespec start, end;

Tree* tree = new_Tree(newick, true);
Expand All @@ -132,12 +135,14 @@ void test_height_transform_jacobian(size_t iter, const char* newick, int reparam
double logP;
clock_gettime(CLOCK_MONOTONIC_RAW, &start);
for (size_t i = 0; i < iter; i++) {
logP = mtt->logP(mtt);
logP = tt->log_jacobian(tt);
}
clock_gettime(CLOCK_MONOTONIC_RAW, &end);
printf(" %zu evaluations: %f ms (%f)\n", iter, mseconds(start, end), logP);
if (csv != NULL)
fprintf(csv, "ratio_transform_jacobian%s,evaluation,off,%f,%f\n", (reparameterization == TREE_TRANSFORM_RATIO_NAIVE ? "2" : ""), mseconds(start, end) / 1000., logP);
fprintf(csv, "ratio_transform_jacobian%s,evaluation,off,%f,%f\n",
(reparameterization == TREE_TRANSFORM_RATIO_NAIVE ? "2" : ""),
mseconds(start, end) / 1000., logP);

if (debug) {
printf("logP %f\n", logP);
Expand All @@ -153,7 +158,9 @@ void test_height_transform_jacobian(size_t iter, const char* newick, int reparam
clock_gettime(CLOCK_MONOTONIC_RAW, &end);
printf(" %zu gradient evaluations: %f ms\n", iter, mseconds(start, end));
if (csv != NULL)
fprintf(csv, "ratio_transform_jacobian%s,gradient,off,%f,\n", (reparameterization == TREE_TRANSFORM_RATIO_NAIVE ? "2" : ""), mseconds(start, end) / 1000.);
fprintf(csv, "ratio_transform_jacobian%s,gradient,off,%f,\n",
(reparameterization == TREE_TRANSFORM_RATIO_NAIVE ? "2" : ""),
mseconds(start, end) / 1000.);

if (debug) {
for (int j = 0; j < Parameters_count(reparams); j++) {
Expand All @@ -167,8 +174,10 @@ void test_height_transform_jacobian(size_t iter, const char* newick, int reparam

// Transform node ratios to node height.
// Derivatives are wrt ratio/root height parameters.
// At each iteration, node heights are updated from the ratios/root height parameters.
void test_height_transform(size_t iter, const char* newick, int reparameterization, FILE* csv, bool debug) {
// At each iteration, node heights are updated from the ratios/root height
// parameters.
void test_height_transform(size_t iter, const char* newick, int reparameterization,
FILE* csv, bool debug) {
struct timespec start, end;

Tree* tree = new_Tree(newick, true);
Expand All @@ -191,7 +200,8 @@ void test_height_transform(size_t iter, const char* newick, int reparameterizati
printf(" %zu evaluations: %f ms\n", iter, mseconds(start, end));
if (csv != NULL)
fprintf(csv, "ratio_transform%s,evaluation,off,%f,\n",
(reparameterization == TREE_TRANSFORM_RATIO_NAIVE ? "2" : ""), mseconds(start, end) / 1000.);
(reparameterization == TREE_TRANSFORM_RATIO_NAIVE ? "2" : ""),
mseconds(start, end) / 1000.);

double* gradient = malloc((Tree_tip_count(tree) - 1) * sizeof(double));
double* height_gradient = malloc((Tree_tip_count(tree) - 1) * sizeof(double));
Expand All @@ -208,7 +218,8 @@ void test_height_transform(size_t iter, const char* newick, int reparameterizati
printf(" %zu gradient evaluations: %f ms\n", iter, mseconds(start, end));
if (csv != NULL)
fprintf(csv, "ratio_transform%s,gradient,off,%f,\n",
(reparameterization == TREE_TRANSFORM_RATIO_NAIVE ? "2" : ""), mseconds(start, end) / 1000.);
(reparameterization == TREE_TRANSFORM_RATIO_NAIVE ? "2" : ""),
mseconds(start, end) / 1000.);

free(gradient);
free(height_gradient);
Expand Down Expand Up @@ -244,23 +255,15 @@ void test_constant(size_t iter, const char* newick, FILE* csv, bool debug) {
clock_gettime(CLOCK_MONOTONIC_RAW, &end);
printf(" %zu evaluations: %f ms (%f)\n", iter, mseconds(start, end), logP);
if (csv != NULL)
fprintf(csv, "coalescent,evaluation,off,%f,%f\n", mseconds(start, end) / 1000., logP);
fprintf(csv, "coalescent,evaluation,off,%f,%f\n", mseconds(start, end) / 1000.,
logP);

if (debug) {
printf("logP %f\n", logP);
}

Parameters* ps = new_Parameters(1);
Parameters_add(ps, N);
Parameter_set_value(N, value);
Node** nodes = Tree_nodes(tree);
for (int i = 0; i < Tree_node_count(tree); i++) {
if (!Node_isleaf(nodes[i])) {
Parameters_add(ps, nodes[i]->height);
}
}

model->prepare_gradient(model, ps);
size_t gradient_size = Coalescent_initialize_gradient(
model, GRADIENT_FLAG_COALESCENT_THETA | GRADIENT_FLAG_TREE_HEIGHTS);

clock_gettime(CLOCK_MONOTONIC_RAW, &start);
for (size_t i = 0; i < iter; i++) {
Expand All @@ -275,14 +278,75 @@ void test_constant(size_t iter, const char* newick, FILE* csv, bool debug) {
model->free(model);
mtree->free(mtree);
free_Parameter(N);
free_Parameters(ps);
}

// Calculate the log tree likelihood of a time tree (log det Jacbian term is included).
// Derivatives are wrt branch ratios/node height parameters.
// At each iteration, the probability matrices are updated and the whole tree likelihood
// Calculate the constant size coalescent log likelihood.
// The derivatives are wrt population size and the node height parameters
void test_skyglide(size_t iter, const char* newick, FILE* csv, bool debug,
int intervals, double cutoff) {
struct timespec start, end;

Tree* tree = new_Tree(newick, true);
parse_dates(tree);

init_leaf_heights_from_times(tree);

init_heights_from_distances(tree);

Model* mtree = new_TreeModel("letree", tree);

double value = 1.0;
Parameters* popSizes = new_Parameters(intervals);
for (size_t i = 0; i < intervals; i++) {
Parameter* N = new_Parameter("theta", i + 5.0, new_Constraint(0, INFINITY));
Parameters_move(popSizes, N);
value++;
}
Coalescent* coal = new_PiecewiseLinearGridCoalescent(tree, popSizes, intervals,
cutoff, COALESCENT_THETA);
free_Parameters(popSizes);

Model* model = new_CoalescentModel("", coal, mtree);

double logP;
clock_gettime(CLOCK_MONOTONIC_RAW, &start);
for (size_t i = 0; i < iter; i++) {
coal->need_update_intervals = true;
logP = model->logP(model);
}
clock_gettime(CLOCK_MONOTONIC_RAW, &end);
printf(" %zu evaluations: %f ms (%f)\n", iter, mseconds(start, end), logP);
if (csv != NULL)
fprintf(csv, "skyglide,evaluation,off,%f,%f\n", mseconds(start, end) / 1000.,
logP);

if (debug) {
printf("logP %f\n", logP);
}

size_t gradient_size = Coalescent_initialize_gradient(
model, GRADIENT_FLAG_COALESCENT_THETA | GRADIENT_FLAG_TREE_HEIGHTS);

clock_gettime(CLOCK_MONOTONIC_RAW, &start);
for (size_t i = 0; i < iter; i++) {
coal->need_update_intervals = true;
Coalescent_gradient(model);
}
clock_gettime(CLOCK_MONOTONIC_RAW, &end);
printf(" %zu skyglide evaluations: %f ms\n", iter, mseconds(start, end));
if (csv != NULL)
fprintf(csv, "skyglide,gradient,off,%f,\n", mseconds(start, end) / 1000.);

model->free(model);
mtree->free(mtree);
}

// Calculate the log tree likelihood of a time tree (log det Jacbian term is
// included). Derivatives are wrt branch ratios/node height parameters. At each
// iteration, the probability matrices are updated and the whole tree likelihood
// is calculated.
void test_tree_likelihood_time(size_t iter, char* fasta_file, const char* newick, int reparameterization, FILE* csv, bool debug) {
void test_tree_likelihood_time(size_t iter, char* fasta_file, const char* newick,
int reparameterization, FILE* csv, bool debug) {
struct timespec start, end;

Hashtable* hash2 = new_Hashtable_string(100);
Expand Down Expand Up @@ -316,7 +380,8 @@ void test_tree_likelihood_time(size_t iter, char* fasta_file, const char* newick

clock_gettime(CLOCK_MONOTONIC_RAW, &start);
for (size_t i = 0; i < iter; i++) {
mtt->update(mtt, NULL, 0); // force recalculation of node heights from ratios
mtt->update(mtt, NULL,
0); // force recalculation of node heights from ratios
logP = mlike->logP(mlike);
}
clock_gettime(CLOCK_MONOTONIC_RAW, &end);
Expand Down Expand Up @@ -360,9 +425,11 @@ void test_tree_likelihood_time(size_t iter, char* fasta_file, const char* newick

// Calculate the log tree likelihood of an unrooted tree.
// Derivatives are wrt branch lengths.
// At each iteration, the probability matrices are updated and the whole tree likelihood
// is calculated.
void test_tree_likelihood_unrooted(size_t iter, const char* json_model, const char* fasta_file, const char* newick, double scaler, FILE* csv, bool debug) {
// At each iteration, the probability matrices are updated and the whole tree
// likelihood is calculated.
void test_tree_likelihood_unrooted(size_t iter, const char* json_model,
const char* fasta_file, const char* newick,
double scaler, FILE* csv, bool debug) {
struct timespec start, end;

Hashtable* hash2 = new_Hashtable_string(100);
Expand Down Expand Up @@ -405,8 +472,11 @@ void test_tree_likelihood_unrooted(size_t iter, const char* json_model, const ch
clock_gettime(CLOCK_MONOTONIC_RAW, &end);
printf(" %zu evaluations: %f ms (%f)\n", iter, mseconds(start, end), logP);
if (csv != NULL)
fprintf(csv, "treelikelihood%s,evaluation,off,%f,%f\n", (tlk->m->modeltype == GTR ? "GTR" : "JC69"), mseconds(start, end) / 1000., logP);
// logP does not match tree time value because it does not include log det Jacobian
fprintf(csv, "treelikelihood%s,evaluation,off,%f,%f\n",
(tlk->m->modeltype == GTR ? "GTR" : "JC69"),
mseconds(start, end) / 1000., logP);
// logP does not match tree time value because it does not include log det
// Jacobian

if (debug) {
printf("logP %f\n", logP);
Expand Down Expand Up @@ -434,7 +504,9 @@ void test_tree_likelihood_unrooted(size_t iter, const char* json_model, const ch
clock_gettime(CLOCK_MONOTONIC_RAW, &end);
printf(" %zu gradient evaluations: %f ms\n", iter, mseconds(start, end));
if (csv != NULL)
fprintf(csv, "treelikelihood%s,gradient,off,%f,\n", (tlk->m->modeltype == GTR ? "GTR" : "JC69"), mseconds(start, end) / 1000.);
fprintf(csv, "treelikelihood%s,gradient,off,%f,\n",
(tlk->m->modeltype == GTR ? "GTR" : "JC69"),
mseconds(start, end) / 1000.);

if (debug) {
double dlogP;
Expand All @@ -454,7 +526,9 @@ void test_tree_likelihood_unrooted(size_t iter, const char* json_model, const ch

int main(int argc, char* argv[]) {
if (argc == 1) {
printf("USAGE: benchmarking -r iterations -i alignment-file-name -t tree-file-name\n\n");
printf(
"USAGE: benchmarking -r iterations -i alignment-file-name -t "
"tree-file-name\n\n");
printf("positional arguments:\n");
printf(" -r iterations number of iterations\n");
printf(" -i alignment-file-name alignment file\n");
Expand All @@ -467,6 +541,8 @@ int main(int argc, char* argv[]) {
char* newick = NULL;
bool debug = false;
double scaler = 1.0;
int intervals = -1;
double cutoff = INFINITY;
FILE* csv = NULL;

for (int i = 1; i < argc; i++) {
Expand All @@ -481,14 +557,19 @@ int main(int argc, char* argv[]) {
fprintf(csv, "function,mode,JIT,time,logprob\n");
} else if (strcmp(argv[i], "-s") == 0) {
scaler = atof(argv[++i]);
} else if (strcmp(argv[i], "--cutoff") == 0) {
cutoff = atof(argv[++i]);
} else if (strcmp(argv[i], "--intervals") == 0) {
intervals = atoi(argv[++i]);
} else if (strcmp(argv[i], "--debug") == 0) {
debug = true;
}
}

printf("Height transform log det Jacobian:\n");
printf("naive:\n");
test_height_transform_jacobian(iter, newick, TREE_TRANSFORM_RATIO_NAIVE, csv, debug);
test_height_transform_jacobian(iter, newick, TREE_TRANSFORM_RATIO_NAIVE, csv,
debug);
printf("efficient:\n");
test_height_transform_jacobian(iter, newick, TREE_TRANSFORM_RATIO, csv, debug);

Expand All @@ -501,9 +582,16 @@ int main(int argc, char* argv[]) {
printf("Constant coalescent:\n");
test_constant(iter, newick, csv, debug);

if (intervals > 0 && !isinf(cutoff)) {
printf("Piecewise linear coalescent:\n");
test_skyglide(iter, newick, csv, debug, intervals, cutoff);
}

printf("Tree likelihood unrooted:\n");
test_tree_likelihood_unrooted(iter, json_jc69_unrooted, fasta_file, newick, scaler, csv, debug);
test_tree_likelihood_unrooted(iter, json_gtr_unrooted, fasta_file, newick, scaler, csv, debug);
test_tree_likelihood_unrooted(iter, json_jc69_unrooted, fasta_file, newick, scaler,
csv, debug);
test_tree_likelihood_unrooted(iter, json_gtr_unrooted, fasta_file, newick, scaler,
csv, debug);

printf("Tree likelihood time tree:\n");
test_tree_likelihood_time(iter, fasta_file, newick, 0, csv, debug);
Expand Down
10 changes: 5 additions & 5 deletions src/phyc/treelikelihood.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -188,7 +188,7 @@ void _model_prepare_gradient(Model* self, const Parameters* ps){
Parameter* p = Parameters_at(ps, i);
if ((p->model == MODEL_TREE || p->model == MODEL_TREE_TRANSFORM) && !prepare_tree) {
prepare_tree = true;
tlk->prepared_gradient |= TREELIKELIHOOD_FLAG_TREE;
tlk->prepared_gradient |= TREELIKELIHOOD_FLAG_TREE_MODEL;
if(!Tree_is_time_mode(tlk->tree)){
gradient_length += Tree_node_count(tlk->tree);
}
Expand Down Expand Up @@ -236,7 +236,7 @@ size_t TreeLikelihood_initialize_gradient(Model *self, int flags){
size_t gradient_length = 0;
tlk->include_root_freqs = true;

int prepare_tree = tlk->prepared_gradient & TREELIKELIHOOD_FLAG_TREE;
int prepare_tree = tlk->prepared_gradient & TREELIKELIHOOD_FLAG_TREE_MODEL;
int prepare_site_model = tlk->prepared_gradient & TREELIKELIHOOD_FLAG_SITE_MODEL;
int prepare_branch_model = tlk->prepared_gradient & TREELIKELIHOOD_FLAG_BRANCH_MODEL;
int prepare_substitution_model_unconstrained = tlk->prepared_gradient & TREELIKELIHOOD_FLAG_SUBSTITUTION_MODEL_UNCONSTRAINED;
Expand All @@ -253,7 +253,7 @@ size_t TreeLikelihood_initialize_gradient(Model *self, int flags){
prepare_site_model = tlk->sm->proportions != NULL || Parameters_count(tlk->sm->rates) > 0 || tlk->sm->mu != NULL;
prepare_branch_model = tlk->bm!= NULL;
prepare_substitution_model = tlk->m->dPdp != NULL;
tlk->prepared_gradient |= TREELIKELIHOOD_FLAG_TREE;
tlk->prepared_gradient |= TREELIKELIHOOD_FLAG_TREE_MODEL;
if(prepare_site_model){
tlk->prepared_gradient |= TREELIKELIHOOD_FLAG_SITE_MODEL;
}
Expand Down Expand Up @@ -355,7 +355,7 @@ double _singleTreeLikelihood_dlogP_prepared(Model *self, const Parameter* p){
tlk->update_upper = false;
}

int prepare_tree = tlk->prepared_gradient & TREELIKELIHOOD_FLAG_TREE;
int prepare_tree = tlk->prepared_gradient & TREELIKELIHOOD_FLAG_TREE_MODEL;
int prepare_site_model = tlk->prepared_gradient & TREELIKELIHOOD_FLAG_SITE_MODEL;
int prepare_branch_model = tlk->prepared_gradient & TREELIKELIHOOD_FLAG_BRANCH_MODEL;
int prepare_substitution_model = tlk->prepared_gradient & TREELIKELIHOOD_FLAG_SUBSTITUTION_MODEL_UNCONSTRAINED;
Expand Down Expand Up @@ -3205,7 +3205,7 @@ void TreeLikelihood_calculate_gradient( Model *model, double* grads ){
pattern_likelihoods[i] = exp(tlk->pattern_lk[i]);
}

bool prepare_tree = tlk->prepared_gradient & TREELIKELIHOOD_FLAG_TREE;
bool prepare_tree = tlk->prepared_gradient & TREELIKELIHOOD_FLAG_TREE_MODEL;
bool prepare_site_model = tlk->prepared_gradient & TREELIKELIHOOD_FLAG_SITE_MODEL;
bool prepare_branch_model = tlk->prepared_gradient & TREELIKELIHOOD_FLAG_BRANCH_MODEL;
bool prepare_substitution_model = tlk->prepared_gradient & TREELIKELIHOOD_FLAG_SUBSTITUTION_MODEL_UNCONSTRAINED || tlk->prepared_gradient & TREELIKELIHOOD_FLAG_SUBSTITUTION_MODEL;
Expand Down
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