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#ifndef _SPEL_BAYES_FACTOR_VAR_H_
#define _SPEL_BAYES_FACTOR_VAR_H_
#include "pedigree.h"
struct bn_message_type {
typedef std::map<genotype_comb_type::key_list, double>::iterator iterator;
typedef std::map<genotype_comb_type::key_list, double>::const_iterator const_iterator;
bn_message_type() : m_map(), m_default_val(0) {}
bn_message_type(double default_val) : m_map(), m_default_val(default_val) {}
/*double&*/
/*operator [] (const genotype_comb_type::key_list& keys) { return m_map[keys]; }*/
void
set(const genotype_comb_type::key_list& keys, double d) { if (d != m_default_val) { m_map[keys] = d; } }
void
accumulate(const genotype_comb_type::key_list& keys, double d)
{
auto it = m_map.find(keys);
if (it == m_map.end()) {
if (d == 0) {
return;
} else {
m_map.emplace(keys, d);
}
}
it->second += d;
}
double
operator [] (const genotype_comb_type::key_list& keys) const
{
auto it = m_map.find(keys);
if (it == m_map.end()) {
return m_default_val;
}
return it->second;
}
double
default_val() const { return m_default_val; }
void
default_val(double p) { m_default_val = p; }
double
delta(const bn_message_type& other) const
{
/*MSG_DEBUG_INDENT_EXPR("[delta] ");*/
double accum = 0;
for (const auto& kv: m_map) {
accum += fabs(kv.second - other[kv.first]);
/*MSG_DEBUG("on " << kv.first << ", " << kv.second << "; other[" << kv.first << "] = " << other[kv.first] << "; accum = " << accum);*/
}
for (const auto& kv: other.m_map) {
if (m_map.find(kv.first) == m_map.end()) {
accum += fabs(default_val() - kv.second);
/*MSG_DEBUG("on " << kv.first << ", " << kv.second << "; accum = " << accum);*/
}
/*MSG_DEBUG("delta(" << (*this) << ", " << other << ") = " << accum);*/
/*MSG_DEBUG_DEDENT;*/
return accum;
}
iterator begin() { return m_map.begin(); }
iterator end() { return m_map.end(); }
const_iterator begin() const { return m_map.begin(); }
const_iterator end() const { return m_map.end(); }
const_iterator cbegin() const { return m_map.cbegin(); }
const_iterator cend() const { return m_map.cend(); }
void
extract_variable(size_t var, const std::vector<bn_label_type>& domain, bn_message_type& output) const
{
std::map<bn_label_type, bool> visited;
for (const auto& kv: m_map) {
for (const auto& key: kv.first) {
if (key.parent == var) {
genotype_comb_type::key_list kl(key);
output.m_map[kl] += kv.second;
visited[key.state] = true;
break;
} else if (key.parent > var) {
break;
}
}
}
for (const bn_label_type& label: domain) {
if (!visited[label]) {
genotype_comb_type::key_list kl({var, label});
output.m_map[kl] = default_val();
}
}
}
void
clear() { m_map.clear(); }
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friend
std::ostream&
operator << (std::ostream& os, const bn_message_type& msg)
{
os << '{';
for (const auto& kv: msg) {
os << kv.first << '=' << kv.second << ' ';
}
return os << "default=" << msg.default_val() << '}';
}
private:
std::map<genotype_comb_type::key_list, double> m_map;
double m_default_val;
};
struct bn_factor_type;
struct bn_factor_interface_type;
struct bn_factor_interface_type {
bn_factor_interface_type(
const std::vector<size_t>& variables,
std::shared_ptr<bn_factor_type> f1,
std::shared_ptr<bn_factor_type> f2)
: m_variables(variables)
, m_f1(f1), m_f2(f2)
, m_msg_to_f1({1., 1.}), m_msg_to_f2({1., 1.})
{}
double
delta() const
{
return m_msg_to_f1[0].delta(m_msg_to_f1[1]) + m_msg_to_f2[0].delta(m_msg_to_f2[1]);
}
const bn_factor_type&
get_target_from(const bn_factor_type* source) const
{
return source == m_f1.get() ? *m_f2 : *m_f1;
}
const bn_message_type&
get_message_to(const bn_factor_type* dest, size_t buffer_index) const
{
return dest == m_f1.get() ? m_msg_to_f1[buffer_index] : m_msg_to_f2[buffer_index];
}
void
update_messages(const bn_message_type& observations, size_t buffer_index);
const std::vector<size_t>&
variables() const { return m_variables; }
bool
operator < (const bn_factor_interface_type& other) const
{
return m_variables < other.m_variables;
}
void clear()
{
for (size_t i = 0; i < 2; ++i) {
m_msg_to_f1[i].clear();
m_msg_to_f2[i].clear();
}
}
const bn_factor_type* f1() const { return m_f1.get(); }
const bn_factor_type* f2() const { return m_f2.get(); }
operator << (std::ostream& os, const bn_factor_interface_type& interf);
private:
std::vector<size_t> m_variables;
std::shared_ptr<bn_factor_type> m_f1, m_f2;
bn_message_type m_msg_to_f1[2], m_msg_to_f2[2];
};
inline
std::ostream&
operator << (std::ostream& os, const std::pair<genotype_comb_type::key_list, double>& kd)
{
return os << kd.first << ':' << kd.second;
}
bn_factor_type() : m_variables(), m_joint_prob_table(), m_interfaces(), m_leaves() {}
bn_factor_type(const genotype_comb_type& joint)
: m_variables(), m_joint_prob_table(joint), m_interfaces(), m_leaves()
{
m_variables = get_parents(m_joint_prob_table);
}
bn_factor_type(const bn_factor_type& other)
: m_variables(other.m_variables), m_joint_prob_table(other.m_joint_prob_table), m_interfaces(other.m_interfaces), m_leaves(other.m_leaves)
{}
bn_factor_type(bn_factor_type&& other)
: m_variables(std::move(other.m_variables)), m_joint_prob_table(std::move(other.m_joint_prob_table)),
m_interfaces(std::move(other.m_interfaces)), m_leaves(std::move(other.m_leaves))
{}
bn_factor_type(genotype_comb_type&& joint)
: m_variables(), m_joint_prob_table(std::move(joint)), m_interfaces(), m_leaves()
{
m_variables = get_parents(m_joint_prob_table);
}
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void
compute_leaves(const pedigree_tree_type& T)
{
m_leaves.reserve(m_variables.size() - 1);
for (size_t v: m_variables) {
auto anc = T.count_ancestors(v);
bool add = true;
for (const auto& kv: anc) {
if (std::find(m_variables.begin(), m_variables.end(), kv.first) != m_variables.end()) {
add = false;
break;
}
}
if (add) {
m_leaves.push_back(v);
}
}
}
genotype_comb_type
project(const std::vector<size_t>& project_variables)
{
if (project_variables == m_variables) {
return m_joint_prob_table;
}
std::vector<size_t> norm_variables(m_leaves.size());
auto it = std::set_difference(m_leaves.begin(), m_leaves.end(),
project_variables.begin(), project_variables.end(),
norm_variables.begin());
norm_variables.resize(it - norm_variables.begin());
return ::project(m_joint_prob_table, project_variables, norm_variables);
}
bn_message_type
compute_norm_factors(const std::vector<size_t>& targets)
{
bn_message_type norm(1.);
#if 1
/*size_t debug_i = m_joint_prob_table.size();*/
auto i = m_joint_prob_table.begin(), j = m_joint_prob_table.end();
/*for (; i != j && debug_i != 0; ++i, --debug_i) {*/
for (; i != j; ++i) {
/*MSG_DEBUG("normalizing " << (++debug_i) << "...");*/
/*MSG_QUEUE_FLUSH();*/
/*MSG_DEBUG("normalizing on element " << (*i));*/
/*MSG_QUEUE_FLUSH();*/
auto ke = i->extract(targets);
norm.accumulate(ke.second.keys, ke.second.coef);
/*norm.accumulate(ke.first, ke.second.coef);*/
}
MSG_DEBUG("norm factors " << norm);
for (auto& kv: norm) {
kv.second = 1. / kv.second;
}
#endif
return norm;
}
bn_message_type
compute_message_for(const bn_factor_interface_type* interface, const bn_message_type& observations, size_t buffer_index)
{
double accum = 0;
bn_message_type ret;
bn_message_type norm = compute_norm_factors(interface->variables());
std::vector<std::pair<genotype_comb_type::key_list, double>> debug;
MSG_DEBUG("joint_prob_table.size=" << m_joint_prob_table.size());
MSG_QUEUE_FLUSH();
for (const auto& e: m_joint_prob_table) {
debug.clear();
/*genotype_comb_type::key_list output_key = e.keys % interface->variables();*/
genotype_comb_type::key_list output_key;
genotype_comb_type::element_type sub_element;
std::tie(output_key, sub_element) = e.extract(interface->variables());
/*double prob = e.coef * norm[sub_element.keys];*/
/*double prob = e.coef * norm[output_key];*/
/*norm.accumulate(output_key, prob);*/
/*MSG_DEBUG("initial coef: " << prob);*/
for (const auto& key: e.keys) { /* FIXME: all keys or all keys BUT the output ones? */
prob *= observations[key];
debug.emplace_back(key, observations[key]);
/*MSG_DEBUG("(obs) prob: " << prob << " obs[" << key << "]=" << observations[key]);*/
}
for (const auto& i: m_interfaces) {
/*MSG_DEBUG("using interface " << (*i));*/
if (i.get() == interface || i->variables() == interface->variables()) {
continue;
}
genotype_comb_type::key_list interface_key = e.keys % i->variables();
prob *= i->get_message_to(this, buffer_index)[interface_key];
debug.emplace_back(interface_key, i->get_message_to(this, buffer_index)[interface_key]);
/*MSG_DEBUG("(itf) prob: " << prob << " itf[" << interface_key << "]=" << i->get_message_to(this, buffer_index)[interface_key]);*/
}
ret.accumulate(output_key, prob);
accum += prob;
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MSG_DEBUG("output_key=" << output_key << " coef=" << e.coef << " probs { " << debug << " } result=" << prob);
}
MSG_DEBUG("RAW MESSAGE: " << ret);
/*for (auto& kv: ret) {*/
/*kv.second /= norm[kv.first];*/
/*}*/
if (accum != 0) {
accum = 1. / accum;
for (auto& kv: ret) {
kv.second *= accum;
}
}
/*MSG_DEBUG("NORMALIZED MESSAGE: " << ret);*/
return ret;
}
bn_message_type
compute_state(const bn_message_type& observations, size_t buffer_index)
{
bn_message_type ret;
double accum = 0;
for (const auto& e: m_joint_prob_table) {
double prob = e.coef;
for (const auto& key: e.keys) { /* FIXME: all keys or all keys BUT the output ones? */
prob *= observations[key];
}
for (const auto& i: m_interfaces) {
genotype_comb_type::key_list interface_key = e.keys % i->variables();
prob *= i->get_message_to(this, buffer_index)[interface_key];
}
ret.set(e.keys, prob);
accum += prob;
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}
if (accum != 0) {
accum = 1. / accum;
for (auto& kv: ret) {
kv.second *= accum;
}
}
return ret;
}
std::vector<size_t>
common_variables(const bn_factor_type& other) const
{
std::vector<size_t> ret(std::min(m_variables.size(), other.m_variables.size()));
auto end = std::set_intersection(m_variables.begin(), m_variables.end(), other.m_variables.begin(), other.m_variables.end(), ret.begin());
ret.resize(end - ret.begin());
return ret;
}
friend
std::ostream&
operator << (std::ostream& os, const bn_factor_type& factor)
{
os << "FACTOR @" << (&factor) << " on variables {" << factor.m_variables << '}' << std::endl;
os << "joint prob. table: " << factor.m_joint_prob_table << std::endl;
os << "interfaces:" << std::endl;
for (const auto& i: factor.interfaces()) {
os << (*i) << std::endl;
}
return os;
}
friend
std::ostream&
operator << (std::ostream& os, std::shared_ptr<bn_factor_type> factor)
{
return os << '{' << factor->variables() << '}';
}
const std::vector<size_t>&
variables() const { return m_variables; }
const std::vector<std::shared_ptr<bn_factor_interface_type>>&
interfaces() const { return m_interfaces; }
void
add_interface(std::shared_ptr<bn_factor_interface_type> interf)
{
m_interfaces.emplace_back(interf);
}
const genotype_comb_type&
table() const { return m_joint_prob_table; }
private:
std::vector<size_t> m_variables;
genotype_comb_type m_joint_prob_table;
std::vector<std::shared_ptr<bn_factor_interface_type>> m_interfaces;
};
void
bn_factor_interface_type::update_messages(const bn_message_type& observations, size_t buffer_index)
{
MSG_DEBUG("buffer_index=" << buffer_index);
MSG_QUEUE_FLUSH();
MSG_DEBUG_INDENT_EXPR("[to_f2] ");
m_msg_to_f2[!buffer_index] = m_f1->compute_message_for(this, observations, buffer_index);
MSG_DEBUG_DEDENT;
MSG_DEBUG_INDENT_EXPR("[to_f1] ");
m_msg_to_f1[!buffer_index] = m_f2->compute_message_for(this, observations, buffer_index);
inline
std::ostream&
operator << (std::ostream& os, const bn_factor_interface_type& interf)
{
return os << "[@" << interf.m_f1
<< " (" << interf.m_msg_to_f1[0] << ", " << interf.m_msg_to_f1[1]
<< ") <--(" << interf.variables() << ")--> ("
<< interf.m_msg_to_f2[0] << ", " << interf.m_msg_to_f2[1]
<< ") @" << interf.m_f2 << ']';
}
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struct compute_labels {
bn_label_type
find_label(size_t n, const genotype_comb_type::element_type& labels)
{
auto it
= std::find_if(labels.keys.begin(), labels.keys.end(),
[=] (const genotype_comb_type::key_type& k) { return k.parent == n; }
);
if (it == labels.keys.end()) {
MSG_ERROR("COULDN'T FIND LABEL FOR " << n << " IN " << labels, "");
MSG_QUEUE_FLUSH();
return {};
}
return it->state;
}
bn_label_type
operator () (const pedigree_tree_type& tree, size_t n, const genotype_comb_type::element_type& labels, const std::vector<bool>& recompute)
{
if (tree.get_p2(n) == NONE) {
/* gamete or ancestor */
if (tree.get_p1(n) == NONE) {
/* ancestor */
return find_label(n, labels);
} else {
auto gl = find_label(n, labels);
auto sub = operator () (tree, tree.get_p1(n), labels, recompute);
if (gl.first == GAMETE_L) {
return {sub.first, 0, sub.first_allele, 0};
} else {
return {sub.second, 0, sub.second_allele, 0};
}
}
} else if (recompute[n]) {
auto subl = operator () (tree, tree.get_p1(n), labels, recompute);
auto subr = operator () (tree, tree.get_p2(n), labels, recompute);
return {subl.first, subr.first, subl.first_allele, subr.first_allele};
} else {
return find_label(n, labels);
}
}
std::vector<bn_label_type>
operator () (const pedigree_tree_type& tree, size_t n, const genotype_comb_type& comb, const std::vector<bool>& recompute)
{
std::vector<bn_label_type> ret;
ret.reserve(comb.m_combination.size());
for (const auto& e: comb) {
ret.emplace_back(operator () (tree, n, e, recompute));
}
return ret;
}
/*static*/
/*genotype_comb_type*/
/*make_comb(const pedigree_tree_type& tree, size_t n, const genotype_comb_type& comb)*/
/*{*/
/*return state_to_combination(n, compute_labels()(tree, n, comb));*/
/*}*/
/*static*/
/*genotype_comb_type*/
/*add_labels(const pedigree_tree_type& tree, size_t n, const genotype_comb_type& comb)*/
/*{*/
/*auto labcomb = make_comb(tree, n, comb);*/
/*return hadamard(labcomb, comb);*/
/*}*/
};
struct factor_graph {
std::map<size_t, std::vector<bn_label_type>> m_variable_domains;
std::vector<std::shared_ptr<bn_factor_type>> m_factors;
std::vector<std::shared_ptr<bn_factor_interface_type>> m_interfaces;
bn_message_type m_observations;
size_t m_buffer_index;
factor_graph(const pedigree_type& ped)
: m_variable_domains(), m_factors(), m_interfaces(), m_observations(1.), m_buffer_index(0)
/*compute_factors_and_domains(ped);*/
/*compute_interfaces();*/
build_factors(ped);
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#if 0
std::vector<size_t>
get_joint_ancestry(const pedigree_tree_type& T, size_t p_node, const std::vector<size_t>& ancestors_to_join)
{
auto anc = T.count_ancestors(p_node);
std::vector<size_t> ret;
ret.reserve(ancestors_to_join.size() + 1);
for (size_t ja: ancestors_to_join) {
if (anc.find(ja) != anc.end()) {
ret.push_back(ja);
}
}
ret.push_back(p_node);
return ret;
}
#endif
struct factor_creation_list_type {
struct factor_creation_op {
std::vector<size_t> variables;
std::vector<size_t> f1_vars, f2_vars;
size_t progeny;
void
cross(const pedigree_tree_type& T, factor_creation_list_type& fcl, std::vector<std::shared_ptr<bn_factor_type>>& factors) const
{
static std::vector<bn_label_type> label_g = {{GAMETE_L, 0, 0, 0}, {GAMETE_R, 0, 0, 0}};
genotype_comb_type
G1 = state_to_combination((size_t) T.get_p1(progeny), label_g) * .5;
genotype_comb_type
G2 = state_to_combination((size_t) T.get_p2(progeny), label_g)
* (T.get_p1(progeny) != T.get_p2(progeny) ? .5 : 1);
genotype_comb_type p1, parents;
if (f1_vars.size() == 1 && T[f1_vars.front()].is_ancestor()) {
size_t n1 = f1_vars.front();
p1 = state_to_combination(n1, fcl.get_domain(n1));
} else {
size_t comp_fac = fcl.find_compatible_factor(f1_vars);
MSG_DEBUG("finding factor that provides {" << f1_vars << "} => " << comp_fac << " (array size is " << factors.size() << ')');
MSG_QUEUE_FLUSH();
p1 = factors[comp_fac]->project(f1_vars);
MSG_DEBUG("resulting table: " << p1);
MSG_QUEUE_FLUSH();
}
if (f2_vars.size() == 1 && T[f2_vars.front()].is_ancestor()) {
size_t n2 = f2_vars.front();
parents = kronecker(p1, state_to_combination(n2, fcl.get_domain(n2)));
} else if (f2_vars.size() > 0) {
size_t comp_fac = fcl.find_compatible_factor(f2_vars);
MSG_DEBUG("finding factor that provides {" << f2_vars << "} => " << comp_fac << " (array size is " << factors.size() << ')');
MSG_QUEUE_FLUSH();
parents = kronecker(p1, factors[comp_fac]->project(f2_vars));
MSG_DEBUG("resulting table: " << parents);
MSG_QUEUE_FLUSH();
} else {
parents = p1;
}
if (progeny != (size_t) -1) {
genotype_comb_type
unmarked_cross = kronecker(parents, kronecker(G1, G2));
MSG_DEBUG("unmarked_cross " << unmarked_cross);
MSG_QUEUE_FLUSH();
std::vector<bool> recompute(progeny + 1, false);
recompute.back() = true;
auto label_per_state = compute_labels()(T, progeny, unmarked_cross, recompute);
auto new_jp_table
= fold(sum_over(hadamard(unmarked_cross, state_to_combination(progeny, label_per_state)),
{(size_t) T.get_p1(progeny), (size_t) T.get_p2(progeny)}));
factors.emplace_back(std::make_shared<bn_factor_type>(new_jp_table));
fcl.add_ind_domain(progeny, label_per_state);
} else {
factors.emplace_back(std::make_shared<bn_factor_type>(parents));
}
factors.back()->compute_leaves(T);
}
friend
std::ostream&
operator << (std::ostream& os, const factor_creation_op& op)
{
if (op.progeny != (size_t) -1) {
return os << '{' << op.variables << "}: " << op.progeny << " = {" << op.f1_vars << "} ⨝ {" << op.f2_vars << '}';
} else {
return os << '{' << op.variables << "}: {" << op.f1_vars << "} ⨝ {" << op.f2_vars << '}';
}
}
};
const std::vector<bn_label_type>&
get_domain(size_t n) const
{
static std::vector<bn_label_type> empty;
auto it = variable_domains.find(n);
return it == variable_domains.end() ? empty : it->second;
}
size_t
find_compatible_factor(const std::vector<size_t>& interface) const
{
auto
ret = std::find_if(operations.begin(), operations.end(),
[&] (const factor_creation_op& fco)
{
return std::includes(fco.variables.begin(), fco.variables.end(),
interface.begin(), interface.end());
});
if (ret == operations.end()) {
return (size_t) -1;
}
return ret - operations.begin();
}
std::vector<size_t>
joint_ancestors(const pedigree_tree_type& T, size_t node, const std::vector<size_t>& reent) const
{
auto p_anc = T.count_ancestors(node);
std::vector<size_t> joint_reent;
joint_reent.reserve(reent.size());
for (size_t r: reent) {
if (p_anc.find(r) != p_anc.end()) {
joint_reent.push_back(r);
}
}
return joint_reent;
}
std::vector<size_t>
unite(size_t n, const std::vector<size_t>& v1, const std::vector<size_t>& v2) const
{
std::set<size_t> tmp;
if (n != (size_t) -1) {
tmp.insert(n);
}
tmp.insert(v1.begin(), v1.end());
tmp.insert(v2.begin(), v2.end());
return {tmp.begin(), tmp.end()};
}
/* returns interface */
std::vector<size_t>
ensure_factor(const pedigree_tree_type& T, size_t p_node, const std::vector<size_t>& reent)
{
MSG_DEBUG("... ensure_factor(" << p_node << ", " << reent << ')');
auto joint_anc = joint_ancestors(T, p_node, reent);
std::vector<size_t> interface = joint_anc;
interface.push_back(p_node);
size_t f = find_compatible_factor(interface);
if (f != (size_t) -1) {
/* factor exists, OK. */
MSG_DEBUG("... ... factor exists " << operations[f]);
return interface;
}
operations.emplace_back();
auto& new_op = operations.back();
new_op.f1_vars = ensure_factor(T, T.get_p1(T.get_p1(p_node)), joint_anc);
new_op.f2_vars = ensure_factor(T, T.get_p1(T.get_p2(p_node)), joint_anc);
/* create cross {p_node} U itf1 U itf2 */
new_op.progeny = (size_t) -1;
new_op.variables = unite(new_op.progeny, new_op.f1_vars, new_op.f2_vars);
MSG_DEBUG("... ... created new factor " << new_op);
return interface;
}
void
add_ind_domain(size_t ind_node, const std::vector<bn_label_type>& table)
{
std::set<bn_label_type> uniq(table.begin(), table.end());
variable_domains[ind_node].assign(uniq.begin(), uniq.end());
}
void
add_ind(const pedigree_type& ped, size_t ind_node)
{
if (ped.tree[ind_node].is_ancestor()) {
MSG_DEBUG("add_ind(" << ind_node << ')');
MSG_DEBUG("... is ancestor");
std::vector<bn_label_type> labels;
char letter = ped.ancestor_letters.find(ind_node)->second;
for (size_t i = 0; i < ped.n_alleles; ++i) {
labels.emplace_back(letter, letter, i, i);
}
variable_domains[ind_node] = labels;
} else {
auto reent = ped.tree.cleanup_reentrants(ind_node);
genotype_comb_type result;
std::vector<size_t> itf1, itf2;
size_t p1 = (size_t) ped.tree.get_p1(ped.tree.get_p1(ind_node));
size_t p2 = (size_t) ped.tree.get_p1(ped.tree.get_p2(ind_node));
MSG_DEBUG("add_ind(" << ind_node << ", " << p1 << ", " << p2 << ')');
if (reent.size()) {
MSG_DEBUG("... has reentrants");
std::vector<size_t> R;
R.reserve(reent.size());
for (const auto& kv: reent) { R.push_back(kv.first); }
itf1 = ensure_factor(ped.tree, p1, R);
itf2 = ensure_factor(ped.tree, p2, R);
if (find_compatible_factor({p1, p2}) == (size_t) -1) {
operations.emplace_back();
auto& op = operations.back();
op.progeny = (size_t) -1;
op.variables = unite(op.progeny, itf1, itf2);
op.f1_vars = itf1;
op.f2_vars = itf2;
MSG_DEBUG("... joint parents for #" << ind_node << ": " << op);
}
{
operations.emplace_back();
auto& op = operations.back();
op.variables = {p1 > p2 ? p2 : p1, p1 > p2 ? p1 : p2, ind_node};
op.progeny = ind_node;
op.f1_vars = {p1 > p2 ? p2 : p1, p1 > p2 ? p1 : p2};
op.f2_vars = {};
MSG_DEBUG("... result for #" << ind_node << ": " << op);
}
} else {
MSG_DEBUG("... simple cross");
operations.emplace_back();
auto& op = operations.back();
op.variables = {p1 < p2 ? p1 : p2, p1 < p2 ? p2 : p1, ind_node};
op.f1_vars = {p1};
op.f2_vars = {p2};
op.progeny = ind_node;
MSG_DEBUG("... result for #" << ind_node << ": " << op);
}
}
}
void
add_all(const pedigree_type& ped)
{
for (size_t ind: ped.tree.m_ind_number_to_node_number) {
if (ind == (size_t) NONE) {
continue;
}
add_ind(ped, ind);
}
for (const auto& op: operations) {
MSG_DEBUG("[OP] " << op);
}
}
void
cleanup()
{
std::vector<bool> included(operations.size(), false);
size_t total = operations.size();
for (size_t i1 = 0; i1 < operations.size(); ++i1) {
if (included[i1]) { continue; }
const auto& o1 = operations[i1];
for (size_t i2 = 0; i2 < operations.size(); ++i2) {
if (included[i2] || i1 == i2) { continue; }
const auto& o2 = operations[i2];
if (o1.variables == o2.variables) {
included[std::max(i1, i2)] = true;
continue;
}
if (std::includes(o2.variables.begin(), o2.variables.end(), o1.variables.begin(), o1.variables.end())) {
total -= !included[i1];
included[i1] = true;
}
}
}
std::vector<factor_creation_op> tmp;
tmp.reserve(total);
for (size_t i = 0; i < included.size(); ++i) {
if (!included[i]) {
tmp.emplace_back(operations[i]);
}
}
operations.swap(tmp);
for (const auto& op: operations) {
MSG_DEBUG("[POST CLEANUP OP] " << op);
}
}
void
compute_factors(const pedigree_type& ped, std::vector<std::shared_ptr<bn_factor_type>>& factors)
{
for (const auto& op: operations) {
op.cross(ped.tree, *this, factors);
}
}
private:
std::vector<factor_creation_op> operations;
std::map<size_t, std::vector<bn_label_type>> variable_domains;
};
factor_creation_list_type factor_creation_operations;
void
build_factors(const pedigree_type& ped)
{
factor_creation_operations.add_all(ped);
/*factor_creation_operations.cleanup();*/
factor_creation_operations.compute_factors(ped, m_factors);
cleanup_factor_list();
}
friend
std::ostream&
operator << (std::ostream& os, const factor_graph& fg)
{
os << "FACTOR GRAPH @" << (&fg) << std::endl;
os << "Variable domains:" << std::endl;
/*for (size_t i = 1; i < fg.m_variable_domains.size(); ++i) {*/
/*os << " - " << i << ": " << fg.m_variable_domains[i] << std::endl;*/
for (const auto& kv: fg.m_variable_domains) {
os << " - " << kv.first << ": " << kv.second << std::endl;
}
os << (*f) << std::endl;
}
os << "Ordered m_interfaces:" << std::endl;
for (const auto& i: fg.m_interfaces) {
os << (*i) << std::endl;
}
return os;
}
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#if 0
bn_factor_type
compute_factor2(const pedigree_type& ped, size_t n,
const std::vector<size_t>& reentrant_variables)
{
if (ped.tree[n].is_ancestor()) {
} else if (ped.tree[n].is_genotype()) {
std::vector<size_t> project_variables(3 + reentrant_variables.size());
size_t p1 = (size_t) ped.tree.get_p1(ped.tree.get_p1(n));
size_t p2 = (size_t) ped.tree.get_p1(ped.tree.get_p2(n));
std::vector<size_t> base_variables = {n, p1, p2};
auto it = std::set_union(base_variables.begin(), base_variables.end(),
reentrant_variables.begin(), reentrant_variables.end(),
project_variables.begin());
}
}
std::shared_ptr<bn_factor_type>
find_factor(const pedigree_type& ped, size_t n, const std::vector<size_t>& reentrant_variables)
{
std::vector<size_t> variables = reentrant_variables;
variables.push_back(n);
auto it = std::find_if(m_factors.begin(), m_factors.end(),
[&] (std::shared_ptr<bn_factor_type> fac)
{
const auto& fv = fac->variables();
return std::includes(fv.begin(), fv.end(), variables.begin(), variables.end());
});
if (it == m_factors.end()) {
m_factors.emplace_back(compute_factor2(ped, n, reentrant_variables));
return m_factors.back();
}
return *it;
}
#endif
genotype_comb_type
compute_factor_rec(const pedigree_type& ped, int n0, int n, const std::vector<bool>& recompute, std::vector<size_t>& gametes, std::vector<bool>& visited)
{
/*if (visited[n]) {*/
/*return {1.};*/
/*}*/
/*visited[n] = true;*/
if (ped.tree[n].is_ancestor()) {
std::vector<bn_label_type> labels;
/* FIXME allow heterozygous ancestors allele-wise? */
if (n == n0) {
char letter = ped.ancestor_letters.find(n)->second;
for (size_t i = 0; i < ped.n_alleles; ++i) {
labels.emplace_back(letter, letter, i, i);
}
return state_to_combination((size_t) n, m_variable_domains[n]);
} else if (ped.tree[n].is_gamete()) {
static std::vector<bn_label_type> label_g = {{GAMETE_L, 0, 0, 0}, {GAMETE_R, 0, 0, 0}};
genotype_comb_type G = state_to_combination((size_t) n, label_g) * .5;
gametes.push_back((size_t) n);
return kronecker(compute_factor_rec(ped, n0, ped.tree.get_p1(n), recompute, gametes, visited), G);
} else if (recompute[n]) {
auto tmp = kronecker(
compute_factor_rec(ped, n0, ped.tree.get_p1(n), recompute, gametes, visited),
compute_factor_rec(ped, n0, ped.tree.get_p2(n), recompute, gametes, visited));
auto label_per_state = compute_labels()(ped.tree, n, tmp, recompute);
if (n == n0) {
std::set<bn_label_type> uniq_sorted(label_per_state.begin(), label_per_state.end());
m_variable_domains[n].assign(uniq_sorted.begin(), uniq_sorted.end());
}
MSG_DEBUG("intermediary " << tmp);
auto labels = state_to_combination((size_t) n, label_per_state);
MSG_DEBUG("adding labels " << labels);
return hadamard(labels, tmp);
} else {
return state_to_combination((size_t) n, m_variable_domains[n]);
#if 1
genotype_comb_type
compute_joint_crossing(const pedigree_type& ped, const genotype_comb_type& p1p2, int n)
{
static std::vector<bn_label_type> label_g = {{GAMETE_L, 0, 0, 0}, {GAMETE_R, 0, 0, 0}};
size_t g1 = ped.tree.get_p1(n);
size_t g2 = ped.tree.get_p2(n);
genotype_comb_type cross = kronecker(kronecker(
p1p2, state_to_combination(g1, label_g)) * .5,
state_to_combination(g2, label_g) * .5);
std::vector<bool> recompute(n, false);
recompute[n] = recompute[g1] = recompute[g2] = true;
auto label_per_state = compute_labels()(ped.tree, n, cross, recompute);
return fold(sum_over(hadamard(cross, state_to_combination((size_t) n, label_per_state)), {g1, g2}));
}
#endif
genotype_comb_type
compute_raw_factor(const pedigree_type& ped, int n)
{
std::vector<size_t> gametes;
std::vector<bool> visited(n + 1, false);
auto raw_fac = compute_factor_rec(ped, n, n, ped.tree.m_must_recompute[n], gametes, visited);
std::sort(gametes.begin(), gametes.end());
MSG_DEBUG("raw factor " << raw_fac);
auto clean = fold(sum_over(raw_fac, gametes));
MSG_DEBUG("cleaned factor " << clean);
return clean;
}
void
compute_factors_and_domains(const pedigree_type& ped)
{
for (int ind_node: ped.tree.m_ind_number_to_node_number) {
MSG_DEBUG_INDENT_EXPR("[ind_node " << ind_node << "] ");
MSG_QUEUE_FLUSH();
if (ind_node == NONE) {
MSG_DEBUG("...not an individual...");
continue;
}
if (ped.tree[ind_node].is_ancestor()) {
MSG_DEBUG("...ancestor...");
(void) compute_raw_factor(ped, ind_node); /* to fill the variable domain */
continue;
}
auto raw_factor = compute_raw_factor(ped, ind_node);
if (!ped.tree[ind_node].is_ancestor()) {
const auto& recomp = ped.tree.m_must_recompute[ind_node];
size_t p1 = (size_t) ped.tree.get_p1(ped.tree.get_p1(ind_node));
size_t p2 = (size_t) ped.tree.get_p1(ped.tree.get_p2(ind_node));
if (recomp[p1] || recomp[p2]) {
/* create factor for joint probability of p1 and p2 */
m_factors.emplace_back(std::make_shared<bn_factor_type>(fold(sum_over(raw_factor, {(size_t) ind_node}))));
MSG_DEBUG("Joint parent probability:" << std::endl << (*m_factors.back()));
/* create factor for crossing */
/*std::vector<size_t> fold_vars;*/
/*for (size_t v: m_factors.back()->variables()) {*/
/*if (v != p1 && v != p2) {*/
/*fold_vars.push_back(v);*/
/*}*/
/*}*/
/*m_factors.emplace_back(std::make_shared<bn_factor_type>(fold(sum_over_dual(raw_factor, {(size_t) ind_node, (size_t) p1, (size_t) p2}))));*/
/*m_factors.emplace_back(std::make_shared<bn_factor_type>(fold(sum_over(raw_factor, fold_vars))));*/
std::set<genotype_comb_type::key_list> uniq_p1p2;
for (const auto& e: raw_factor) {
auto k = e.keys % std::vector<size_t>{p1, p2};
uniq_p1p2.insert(k);
}
genotype_comb_type p1p2;