def optimize(self, formula, model):
"""
Try to optimize the solution with a MaxSAT solver.
"""
MaxSAT = RC2Stratified if self.options.weighted else RC2
formula_new = WCNF()
formula_new.extend(formula.hard)
# hardening the soft clauses based on the model
for j in range(1, self.nof_terms + 1):
formula_new.append([model[self.unused(j)]])
for lb in self.labels:
for q in self.samps[lb]:
formula_new.append([model[self.miss(q + 1)]])
for j in range(1, self.nof_terms + 1):
for r in range(1, self.nof_feats + 1):
formula_new.append([-self.dvar1(j, r)], weight=1)
formula_new.append([-self.dvar0(j, r)], weight=1)
with MaxSAT(
formula_new,
solver=self.options.solver,
adapt=self.options.am1,
exhaust=self.options.exhaust,
minz=self.options.minz,
trim=self.options.trim,
) as rc2:
model = rc2.compute()
return model
def get_MCS(KBa_s, KBa_h, q, seed, clauses_dict):
# Compute minimal hitting set
wcnf = WCNF()
for c in KBa_s:
if c not in seed: # don't add to the soft clauses those in the seed
wcnf.append(c, weight=1)
for c in KBa_h:
wcnf.append(c)
for c in seed: # add clauses in the seed as hard
if any(isinstance(el, list) for el in c):
for cs in c:
wcnf.append(cs)
else:
wcnf.append(c)
wcnf.extend(q.negate().clauses)
lbx = LBX(wcnf, use_cld=True, solver_name='g3')
# Compute mcs and return the clauses indexes
mcs = lbx.compute()
# Current mcs is computed w.r.t. the soft clauses excluding the seed. Below we find the corresponding indexes of these clauses in KBa_s
temp_cl_lookup = create_clauses_lookup(wcnf.soft)
clauses = get_clauses_from_index(mcs, temp_cl_lookup)
mcs = get_index_from_clauses(clauses, clauses_dict)
return mcs
def MUSExtraction(self, C):
wcnf = WCNF()
wcnf.extend(self.cnf.clauses)
wcnf.extend([[l] for l in C], [1] * len(C))
with MUSX(wcnf, verbosity=0) as musx:
mus = musx.compute()
# gives back positions of the clauses !!
return set(C[i - 1] for i in mus)
def __createWncf(self, initialisationFormulas, distanceFormula, artefactForMinimization):
'''
This method creates the wncf formulas with the weighted variables depending on the distance and artefact.
:param initialisationFormulas: @see __artefactsInitialisation
:param distanceFormula: @see __compute_distance
:param artefactForMinimization: MULTI_ALIGNMENT or ANTI_ALIGNMENT or EXACT_ALIGNMENT
:return:
'''
formulas = initialisationFormulas + distanceFormula + self.__sup_to_minimize(artefactForMinimization)
full_formula = And([], [], formulas)
cnf = full_formula.operatorToCnf(self.__vars.iterator)
wcnf = WCNF()
wcnf.extend(cnf)
wcnf = self.__createWeights(wcnf,artefactForMinimization)
self.__formula_time = time.time()
return wcnf
def get_MUS(KB, e, q):
# Compute minimal unsatisfiable set
wcnf2 = WCNF()
for k in e:
if any(isinstance(el, list) for el in k):
for ks in k:
wcnf2.append(ks, weight=1)
else:
wcnf2.append(k, weight=1)
if KB:
for c in KB.clauses:
wcnf2.append(c, weight=1)
wcnf2.extend((q.negate().clauses))
mmusx = MUSX(wcnf2, verbosity=0)
mus = mmusx.compute()
return [list(wcnf2.soft[m - 1]) for m in mus]
def grow_maxsat(self, f, A, HS):
remaining, weights = None, None
wcnf = WCNF()
# HARD clauses
wcnf.extend(self.cnf.clauses)
wcnf.extend([[l] for l in HS])
# SOFT clauses to grow
if self.params.interpretation is Interpretation.INITIAL:
remaining = list(self.I0 - HS)
elif self.params.interpretation is Interpretation.ACTUAL:
remaining = list(self.I - HS)
elif self.params.interpretation is Interpretation.FULL:
remaining = list(self.Iend - HS)
elif self.params.interpretation is Interpretation.FINAL:
remaining = list(A - HS)
remaining_clauses = [[l] for l in remaining]
if self.params.maxsat_weighing is Weighing.POSITIVE:
weights = [f(l) for l in remaining]
elif self.params.maxsat_weighing is Weighing.INVERSE:
max_weight = max(f(l) for l in remaining) + 1
weights = [max_weight - f(l) for l in remaining]
elif self.params.maxsat_weighing is Weighing.UNIFORM:
weights = [1] * len(remaining)
# cost is associated for assigning a truth value to literal not in
# contrary to A.
wcnf.extend(clauses=remaining_clauses, weights=weights)
# solve the MAXSAT problem
with RC2(wcnf) as s:
if self.params.maxsat_polarity and hasattr(s, 'oracle'):
s.oracle.set_phases(literals=list(self.Iend))
t_model = s.compute()
return set(t_model)
def encode(self, label, nof_terms=1):
"""
Encode the problem of computing a DS of size nof_terms.
"""
self.nof_terms = nof_terms
enc = WCNF()
# all the hard clauses
#
# constraint 6 (relaxed with the unused variable)
for j in range(1, self.nof_terms + 1):
for r in range(1, self.nof_feats + 1):
enc.append([-self.unused(j), self.svar(j, r)])
enc.append(
[self.unused(j)] +
[-self.svar(j, r) for r in range(1, self.nof_feats + 1)])
# sort unused rules
for j in range(1, self.nof_terms):
enc.append([-self.unused(j), self.unused(j + 1)])
# constraint 7
for j in range(1, self.nof_terms + 1):
for r in range(1, self.nof_feats + 1):
d0 = self.dvar0(j, r)
p0 = [-self.svar(j, r), self.lvar(j, r)]
enc.append([d0, -p0[0], -p0[1]])
enc.append([-d0, p0[0]])
enc.append([-d0, p0[1]])
d1 = self.dvar1(j, r)
p1 = [-self.svar(j, r), -self.lvar(j, r)]
enc.append([d1, -p1[0], -p1[1]])
enc.append([-d1, p1[0]])
enc.append([-d1, p1[1]])
# constraint 8
if len(self.labels) == 1: # distinguish one class from all the others
other_labels = set(self.samps.keys())
else: # distinguish the classes under question only
other_labels = set(self.labels)
other_labels.remove(label)
other_labels = sorted(other_labels)
for j in range(1, self.nof_terms + 1):
for lb in other_labels:
for q in self.samps[lb]:
cl = [self.unused(j),
self.miss(q + 1)] # the clause is relaxed
shift = 0
for r in range(1, self.nof_feats + 1):
if r - 1 in self.data.vmiss[q]:
# this feature is missing in q'th sample
cl.append(-self.svar(j, r))
shift += 1
elif self.data.samps[q][r - 1 - shift] > 0:
cl.append(self.dvar1(j, r))
else:
cl.append(self.dvar0(j, r))
enc.append(cl)
# constraint 9
for j in range(1, self.nof_terms + 1):
for q in self.samps[label]:
cr = self.crvar(j, q + 1)
cl = [self.unused(j)]
shift = 0
for r in range(1, self.nof_feats + 1):
if r - 1 in self.data.vmiss[q]:
# this feature is missing in q'th sample
cl.append(-self.svar(j, r))
shift += 1
elif self.data.samps[q][r - 1 - shift] > 0:
cl.append(self.dvar1(j, r))
else:
cl.append(self.dvar0(j, r))
enc.append([cr] + cl)
for l in cl:
enc.append([-cr, -l])
# constraint 10
for q in self.samps[label]:
enc.append(
[self.miss(q + 1)] +
[self.crvar(j, q + 1) for j in range(1, self.nof_terms + 1)])
# at most one value can be chosen for a feature
for feats in six.itervalues(self.ffmap.dir):
if len(feats) > 2:
for j in range(1, self.nof_terms + 1):
lits = [self.dvar0(j, r + 1)
for r in feats] # atmost1 can be true
onev = CardEnc.atmost(lits,
top_id=enc.nv,
encoding=self.options.enc)
enc.extend(onev.clauses)
# soft clauses
# minimizing the number of literals used
for j in range(1, self.nof_terms + 1):
enc.append([self.unused(j)], weight=self.lambda_)
# minimizing the number of missclassifications
for lb in self.labels:
for q in self.samps[lb]:
enc.append([-self.miss(q + 1)], weight=self.data.wghts[q])
# there should be at least one rule for this class
enc.append([-self.unused(1)])
# saving comments
for j in range(1, self.nof_terms + 1):
for r in range(1, self.nof_feats + 1):
enc.comments.append('c s({0}, {1}) => v{2}'.format(
j, r, self.svar(j, r)))
enc.comments.append('c l({0}, {1}) => v{2}'.format(
j, r, self.lvar(j, r)))
enc.comments.append('c d0({0}, {1}) => v{2}'.format(
j, r, self.dvar0(j, r)))
enc.comments.append('c d1({0}, {1}) => v{2}'.format(
j, r, self.dvar1(j, r)))
for q in range(len(self.data.samps)):
enc.comments.append('c cr({0}, {1}) => v{2}'.format(
j, q + 1, self.crvar(j, q + 1)))
for j in range(1, self.nof_terms + 1):
enc.comments.append('c u({0}) => v{1}'.format(j, self.unused(j)))
for lb in self.labels:
for q in self.samps[lb]:
enc.comments.append('c m({0}) => v{1}'.format(
q + 1, self.miss(q + 1)))
for n, f in zip(self.data.names[:-1], self.data.feats[:-1]):
for v in f:
if self.data.fvmap.dir[(n, v)] > 0:
enc.comments.append('c {0} = {1} => positive'.format(n, v))
else:
enc.comments.append('c {0} = {1} => negative'.format(n, v))
return enc
def encode(self, label, nof_lits=1):
"""
Encode the problem of computing a DS of size nof_lits.
"""
self.nof_lits = nof_lits
self.nof_samps = len(self.data.samps)
self.nof_labls = len(self.labels)
if len(self.labels) == 1: # distinguish one class from all the others
other_labels = set(self.samps.keys())
else: # distinguish the classes under question only
other_labels = set(self.labels)
other_labels.remove(label)
other_labels = sorted(other_labels)
for j in range(1, self.nof_lits + 1):
for r in range(1, self.nof_feats + 2):
self.feat(j, r)
for j in range(1, self.nof_lits + 1):
self.sign(j)
for j in range(1, self.nof_lits + 1):
self.leaf(j)
enc = WCNF()
# all the hard clauses
#
# exactly one feature per node (including class/label)
for j in range(1, self.nof_lits + 1):
feats = [self.feat(j, r) for r in range(1, self.nof_feats + 2)] + [self.unused(j)]
one = CardEnc.equals(lits=feats, vpool=self.idpool, encoding=self.options.enc)
enc.extend(one)
# at most one class/label per node
for j in range(1, self.nof_lits + 1):
labels = [self.label(j, z) for z in self.labels]
am1 = CardEnc.atmost(lits=labels, vpool=self.idpool, encoding=self.options.enc)
enc.extend(am1)
# the model is split,
# i.e. we currently target only rules for this concrete class
enc.append([self.label(j, label)])
# propagation of unused literals
for j in range(1, self.nof_lits):
enc.append([-self.unused(j), self.unused(j + 1)])
# leaf constraints
# this disallows empty (default) rules and thus is disabled
# enc.append([-self.leaf(1)]) # first node can't be a leaf
# last leaf
for j in range(1, self.nof_lits):
enc.append([-self.unused(j + 1), self.unused(j), self.leaf(j)])
enc.append([self.leaf(self.nof_lits), self.unused(self.nof_lits)])
# everything is reachable at node 1
for lb in self.labels:
for i in self.samps[lb]:
enc.append([self.reached(1, i + 1)])
# reachability propagation
for j in range(1, self.nof_lits):
for lb in self.labels:
for i in self.samps[lb]:
aij = self.agree(j, i + 1)
cl, shift = [], 0
for r in range(1, self.nof_feats + 1):
if r - 1 in self.data.vmiss[i]:
# this feature is missing in i'th sample
shift += 1
else:
# a = self.agree(j, i + 1, r) # node j agrees with sample i on feature r
f = self.feat(j, r) # feature r decided in node j
s = self.sign(j) # polarity of node j
if self.data.samps[i][r - 1 - shift] > 0:
a = self.sets1(j, r)
if a > enc.nv:
enc.extend([[-a, f], [-a, s], [a, -f, -s]])
else:
a = self.sets0(j, r)
if a > enc.nv:
enc.extend([[-a, f], [-a, -s], [a, -f, s]])
cl.append(a)
enc.append([-aij] + cl)
for l in cl:
enc.append([aij, -l])
cur = self.reached(j, i + 1) # node j is reachable for sample i
new = self.reached(j + 1, i + 1) # node j + 1 reachable for sample i
enc.append([-new, self.leaf(j), cur])
enc.append([-new, self.leaf(j), aij])
enc.append([ new, -self.leaf(j)])
enc.append([ new, -cur, -aij])
# correctness of leafs
for j in range(1, self.nof_lits + 1):
for lb in self.labels:
for i in self.samps[lb]:
enc.append([-self.leaf(j), -self.reached(j, i + 1),
self.label(j, lb), self.miss(i + 1)])
# coverage constraints
for i in self.samps[label]:
cl = [self.miss(i + 1)] # here the clause is relaxed
for j in range(1, self.nof_lits + 1):
cvar = self.covered(j, i + 1)
enc.append([-cvar, self.leaf(j)])
enc.append([-cvar, self.reached(j, i + 1)])
enc.append([cvar, -self.leaf(j), -self.reached(j, i + 1)])
cl.append(cvar)
enc.append(cl)
# soft clauses
# minimizing the number of literals used
for j in range(1, self.nof_lits + 1):
# enc.append([self.unused(j)], weight=self.lambdas[label])
enc.append([self.unused(j)], weight=self.lambda_)
# minimizing the number of missclassifications
for lb in self.labels:
for i in self.samps[lb]:
enc.append([-self.miss(i + 1)], weight=self.data.wghts[i])
# there should be at least two literals in the decision set
# since u_j variables are sorted, we know that they are u1 and u2
# enc.extend([[-self.unused(1)], [-self.unused(2)]])
# the previous constraints disallowed empty (default) rules
# and so this one looks better
enc.extend([[-self.unused(1)]])
# symmetry breaking
if self.options.bsymm:
self.add_bsymm(enc)
for v, o in self.idpool.id2obj.items():
enc.comments.append('c {0} <=> {1}'.format(o, v))
return enc