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Implement Model6 #172

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merged 15 commits into from
Aug 21, 2024
Merged

Implement Model6 #172

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6ac409c
Add --only_final_emissions
ThomasColthurst Aug 7, 2024
86fc810
Fix merge conflicts
ThomasColthurst Aug 15, 2024
f49bb5f
Initial commit of Model 6
ThomasColthurst Aug 15, 2024
f7b84ba
fix some build errors
ThomasColthurst Aug 15, 2024
989fa31
Finish prefix_path computation
ThomasColthurst Aug 16, 2024
3d5a438
Fix remaining build errors
ThomasColthurst Aug 16, 2024
8acf4b7
Fix tests; add tests
ThomasColthurst Aug 16, 2024
ca24eaf
Fix transition_hyperparameter bugs
ThomasColthurst Aug 16, 2024
e4782f8
Respond to reviewer comments
ThomasColthurst Aug 19, 2024
a8778c3
Fix build errors
ThomasColthurst Aug 19, 2024
6d7008a
Fix test errors
ThomasColthurst Aug 19, 2024
dba9466
Add tests for record_class_is_clean
ThomasColthurst Aug 19, 2024
37fed68
Added assert(false) when all hyperparameters give nanas
ThomasColthurst Aug 20, 2024
0d2df82
include cassert
ThomasColthurst Aug 20, 2024
7c01bd6
Fix integration tests
ThomasColthurst Aug 20, 2024
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11 changes: 8 additions & 3 deletions cxx/distributions/beta_bernoulli.cc
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Expand Up @@ -49,7 +49,12 @@ void BetaBernoulli::transition_hyperparameters(std::mt19937* prng) {
}
}
}
int i = sample_from_logps(logps, prng);
alpha = hypers[i].first;
beta = hypers[i].second;
if (logps.empty()) {
printf("Warning! All hyperparameters for BetaBernoulli give nans!\n");
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I guess practically inference gets stuck, because the hyperparameters don't move, but there might be some hope for other parameters to move and get unstuck? My thinking is these should be asserts since it would be hard to get out of here (you need the observations to change, so the cluster assignments to change) and highlights some suboptimality of inference that should be fixed somewhere else (either numerical stability, bad preconditioning of some sort, etc).

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Done.

assert(false);
} else {
int i = sample_from_logps(logps, prng);
alpha = hypers[i].first;
beta = hypers[i].second;
}
}
9 changes: 7 additions & 2 deletions cxx/distributions/bigram.cc
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Expand Up @@ -118,6 +118,11 @@ void Bigram::transition_hyperparameters(std::mt19937* prng) {
alphas.push_back(alphat);
}
}
int i = sample_from_logps(logps, prng);
set_alpha(alphas[i]);
if (logps.empty()) {
printf("Warning! All hyperparameters for Bigram give nans!\n");
assert(false);
} else {
int i = sample_from_logps(logps, prng);
set_alpha(alphas[i]);
}
}
9 changes: 7 additions & 2 deletions cxx/distributions/dirichlet_categorical.cc
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Expand Up @@ -51,6 +51,11 @@ void DirichletCategorical::transition_hyperparameters(std::mt19937* prng) {
alphas.push_back(alpha);
}
}
int i = sample_from_logps(logps, prng);
alpha = alphas[i];
if (alphas.empty()) {
printf("Warning: all Dirichlet hyperparameters give nans!\n");
assert(false);
} else {
int i = sample_from_logps(logps, prng);
alpha = alphas[i];
}
}
16 changes: 11 additions & 5 deletions cxx/distributions/normal.cc
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Expand Up @@ -3,6 +3,7 @@

#include "normal.hh"

#include <cassert>
#include <cmath>
#include <numbers>

Expand Down Expand Up @@ -91,9 +92,14 @@ void Normal::transition_hyperparameters(std::mt19937* prng) {
}
}

int i = sample_from_logps(logps, prng);
r = std::get<0>(hypers[i]);
v = std::get<1>(hypers[i]);
m = std::get<2>(hypers[i]);
s = std::get<3>(hypers[i]);
if (logps.empty()) {
printf("Warning! All hyperparameters for Normal give nans!\n");
assert(false);
} else {
int i = sample_from_logps(logps, prng);
r = std::get<0>(hypers[i]);
v = std::get<1>(hypers[i]);
m = std::get<2>(hypers[i]);
s = std::get<3>(hypers[i]);
}
}
16 changes: 11 additions & 5 deletions cxx/distributions/skellam.cc
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Expand Up @@ -38,11 +38,17 @@ void Skellam::transition_hyperparameters(std::mt19937* prng) {
}
}
}
int i = sample_from_logps(logps, prng);
mean1 = std::get<0>(hypers[i]);
stddev1 = std::get<1>(hypers[i]);
mean2 = std::get<2>(hypers[i]);
stddev2 = std::get<3>(hypers[i]);

if (logps.empty()) {
printf("Warning! All hyperparameters for Skellam gave nans!\n");
assert(false);
} else {
int i = sample_from_logps(logps, prng);
mean1 = std::get<0>(hypers[i]);
stddev1 = std::get<1>(hypers[i]);
mean2 = std::get<2>(hypers[i]);
stddev2 = std::get<3>(hypers[i]);
}
}

void Skellam::init_theta(std::mt19937* prng) {
Expand Down
12 changes: 9 additions & 3 deletions cxx/distributions/zero_mean_normal.cc
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Expand Up @@ -3,6 +3,7 @@

#include "zero_mean_normal.hh"

#include <cassert>
#include <cmath>
#include <numbers>

Expand Down Expand Up @@ -73,7 +74,12 @@ void ZeroMeanNormal::transition_hyperparameters(std::mt19937* prng) {
}
}

int i = sample_from_logps(logps, prng);
alpha = std::get<0>(hypers[i]);
beta = std::get<1>(hypers[i]);
if (logps.empty()) {
printf("Warning! All hyperparameters for ZeroMeanNormal gave nans!\n");
assert(false);
} else {
int i = sample_from_logps(logps, prng);
alpha = std::get<0>(hypers[i]);
beta = std::get<1>(hypers[i]);
}
}
4 changes: 2 additions & 2 deletions cxx/integration_tests.sh
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Expand Up @@ -20,8 +20,8 @@ startt2=$(date +%s)
endt2=$(date +%s)
startt3=$(date +%s)
./bazel-bin/pclean/pclean --schema=assets/flights.schema --obs=assets/flights_dirty.10.csv --iters=5
./bazel-bin/pclean/pclean --schema=assets/hospitals.schema --obs=assets/hospital_dirty.10.csv --iters=5
./bazel-bin/pclean/pclean --schema=assets/rents.schema --obs=assets/rents_dirty.10.csv --iters=5
./bazel-bin/pclean/pclean --schema=assets/hospitals.schema --obs=assets/hospital_dirty.10.csv --iters=5 --only_final_emissions
./bazel-bin/pclean/pclean --schema=assets/rents.schema --obs=assets/rents_dirty.10.csv --iters=5 --record_class_is_clean
endt3=$(date +%s)
echo "Integration tests in /tests ran in $(($endt1-$startt1)) seconds"
echo "hirm integration tests ran in $(($endt2-$startt2)) seconds"
Expand Down
4 changes: 2 additions & 2 deletions cxx/pclean/io.cc
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Expand Up @@ -98,7 +98,7 @@ bool read_class(std::istream& is, PCleanClass* pclass) {
return false;
}

pclass->vars.push_back(v);
pclass->vars[v.name] = v;
}
return true;
}
Expand Down Expand Up @@ -204,7 +204,7 @@ bool read_schema(std::istream& is, PCleanSchema* schema) {
if (!success) {
return false;
}
schema->classes.push_back(pcc);
schema->classes[pcc.name] = pcc;
continue;
}

Expand Down
21 changes: 10 additions & 11 deletions cxx/pclean/io_test.cc
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Expand Up @@ -54,16 +54,15 @@ observe
tt::per_element());

BOOST_TEST(schema.classes.size() == 5);
BOOST_TEST(schema.classes[0].name == "School");
BOOST_TEST(schema.classes[0].vars.size() == 2);
BOOST_TEST(schema.classes[0].vars[0].name == "name");
BOOST_TEST(std::get<ScalarVar>(schema.classes[0].vars[0].spec).joint_name == "bigram");
BOOST_TEST(schema.classes[0].vars[1].name == "degree_dist");
BOOST_TEST(std::get<ScalarVar>(schema.classes[0].vars[1].spec).joint_name == "categorical");
BOOST_TEST(std::get<ScalarVar>(schema.classes[0].vars[1].spec).params["num_classes"] == "100");
BOOST_TEST(schema.classes["School"].vars.size() == 2);
BOOST_TEST(schema.classes["School"].vars.contains("name"));
BOOST_TEST(std::get<ScalarVar>(schema.classes["School"].vars["name"].spec).joint_name == "bigram");
BOOST_TEST(schema.classes["School"].vars.contains("degree_dist"));
BOOST_TEST(std::get<ScalarVar>(schema.classes["School"].vars["degree_dist"].spec).joint_name == "categorical");
BOOST_TEST(std::get<ScalarVar>(schema.classes["School"].vars["degree_dist"].spec).params["num_classes"] == "100");

BOOST_TEST(schema.classes[1].name == "Physician");
BOOST_TEST(schema.classes[1].vars.size() == 3);
BOOST_TEST(schema.classes[1].vars[0].name == "school");
BOOST_TEST(std::get<ClassVar>(schema.classes[1].vars[0].spec).class_name == "School");
BOOST_TEST(schema.classes.contains("Physician"));
BOOST_TEST(schema.classes["Physician"].vars.size() == 3);
BOOST_TEST(schema.classes["Physician"].vars.contains("school"));
BOOST_TEST(std::get<ClassVar>(schema.classes["Physician"].vars["school"].spec).class_name == "School");
}
10 changes: 9 additions & 1 deletion cxx/pclean/pclean.cc
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Expand Up @@ -31,6 +31,11 @@ int main(int argc, char** argv) {
("i,iters", "Number of inference iterations",
cxxopts::value<int>()->default_value("10"))
("seed", "Random seed", cxxopts::value<int>()->default_value("10"))
("only_final_emissions", "Only create one layer of emissions",
cxxopts::value<bool>()->default_value("false"))
("record_class_is_clean",
"If false, model queries of the query class with emissions noise.",
cxxopts::value<bool>()->default_value("true"))
("t,timeout", "Timeout in seconds for inference",
cxxopts::value<int>()->default_value("0"))
("v,verbose", "Verbose output",
Expand Down Expand Up @@ -63,7 +68,10 @@ int main(int argc, char** argv) {

// Translate schema
std::cout << "Making schema helper ...\n";
PCleanSchemaHelper schema_helper(pclean_schema);
PCleanSchemaHelper schema_helper(
pclean_schema,
result["only_final_emissions"].as<bool>(),
result["record_class_is_clean"].as<bool>());
std::cout << "Translating schema ...\n";
T_schema hirm_schema = schema_helper.make_hirm_schema();

Expand Down
6 changes: 4 additions & 2 deletions cxx/pclean/schema.hh
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Expand Up @@ -26,7 +26,8 @@ struct PCleanVariable {

struct PCleanClass {
std::string name;
std::vector<PCleanVariable> vars;
// Map from variable name to variable.
std::map<std::string, PCleanVariable> vars;
// TODO(thomaswc): Figure out how to handle class level configurations.
};

Expand All @@ -43,6 +44,7 @@ struct PCleanQuery {
};

struct PCleanSchema {
std::vector<PCleanClass> classes;
// Map from class name to class.
std::map<std::string, PCleanClass> classes;
PCleanQuery query;
};
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