def rij(self, x_df, ntop):
x, labs_list, m, n = self.prepare(x_df)
if ntop == None:
ntop = int(st.mCn(n, 2))
rij_ar = st.rij(x)
rij_list = []
for i in range(int(st.mCn(n, 2))):
lab1 = labs_list[int(rij_ar[i, 0])]
lab2 = labs_list[int(rij_ar[i, 1])]
val = rij_ar[i, 2]
val2 = rij_ar[i, 3]
rij_list.append([lab1, lab2, val, val2])
rij_df = pd.DataFrame(rij_list, columns=["i", "j", "rij", "rij2"])
print(rij_df[:ntop])
def gij(self, x_df, ntop):
x, labs_list, m, n = self.prepare(x_df)
self.mc_check(x)
if ntop == None:
ntop = int(st.mCn(n, 2))
gij_ar = st.gij(x)
gij_list = []
for i in range(int(st.mCn(n, 2))):
lab1 = labs_list[int(gij_ar[i, 0])]
lab2 = labs_list[int(gij_ar[i, 1])]
val = gij_ar[i, 2]
val2 = gij_ar[i, 3]
gij_list.append([lab1, lab2, val, val2])
gij_df = pd.DataFrame(gij_list, columns=["i", "j", "gij", "gij2"])
print(gij_df[:ntop])
def __init__(self, x_df, y_se, n_len, n_one, score, n_ktop,
n_gen, nmax_pop, n_tou, p_gap, p_crs, p_mut, n_mut):
self.labs = x_df.columns.tolist()
self.x = x_df.values.copy()
self.y = y_se.values.copy()
self.n_len = n_len # the length of gene
self.n_one = n_one # the numper of "1" in the gene
#self.func = func # score calculator
self.max_flag = False # maximum search problem or not
#self.sw_size = sw_size # scale window size (for fitness calculation)
self.score = score
self.n_ktop = n_ktop # keep top (in the global ranking) size
# --- ga parameters ---
self.n_gen = n_gen # the number of generations
self.nmax_pop = nmax_pop # the maximum number of popurations in each generations
self.n_tou = n_tou # tournament size for selection (large: strong selection)
self.p_gap = p_gap # generation gap: (1-p_gap)*nmax_pop is the number of eliets
self.p_crs = p_crs # crossover ratio
self.p_mut = p_mut # mutation ratio
self.n_mut = n_mut # strength of the mutation (the number of swapping)
if score == "e2":
self.r_or_q = "R2"
else:
self.r_or_q = "Q2"
ncomb = int(st.mCn(self.n_len,self.n_one))
print(f"Genetic Algorithm for {self.n_one} descriptors: {self.n_len}C{self.n_one} = {ncomb}")
def hypervolume_comb(df,defined_list,candidate_list,k,ntop):
if ntop == None:
m = len(candidate_list)
ntop = int(st.mCn(m,k))
def_df = make_sub_df(df,defined_list)
can_df = make_sub_df(df,candidate_list)
use_list,unuse_list = make_comb_list(candidate_list,k)
ncomb = len(use_list)
vol_list = []
for i in range(ncomb):
use_df = make_sub_df(df,use_list[i])
base_df = pd.concat([def_df,use_df],axis=1)
base = base_df.values.copy()
vol = hypervolume(base)
vol_list.append([use_list[i],unuse_list[i],vol])
vol_df = pd.DataFrame(vol_list,columns=["Used","Unused","Volume"])
sorted_vol_df = vol_df.sort_values(by="Volume",ascending=False).reset_index()
print(sorted_vol_df[:ntop],"\n")
def exhaustive_search(x_df,y_se,k,ntop,const):
labs_list = x_df.columns.tolist()
n = len(labs_list)
x = x_df.values.copy()
y = y_se.values.copy()
syy = np.sum((y-np.mean(y))**2)
if const:
k = k-1
n = n-1
print("Caution!:")
print(" Constant term is always included in the search.")
print(" The number of descriptors contained in each combination is k.")
print(" (constant term is also regarded as a descriptor.)")
print(" The total number of combinations should be searched is now (n-1)C(k-1).")
print(" (constant term should be in the first column of span.)")
print()
ncomb = int(st.mCn(n,k))
print(f"Exhaustive search for {k} descriptors: {n}C{k} = {ncomb}")
di = 0.05*ncomb # display interval
cnt = 1
e_list = []
t0 = time.time()
if const:
for i,comb in enumerate(itertools.combinations(range(1,n+1),k), start=1): # for with const
comb = list(comb)
comb.insert(0,0)
q,r = np.linalg.qr(x[:,comb],mode="reduced")
qty = np.dot(q.T,y)
e = y - np.dot(q,qty)
q_adm = q*q
lev = np.sum(q_adm,axis=1) # leverage (diagonal part of hat matrix)
eq = e / (1. - lev)
e2 = np.dot(e,e)
eq2 = np.dot(eq,eq)
e_list.append([e2,eq2,comb])
if i >= di*cnt:
print(f"{int(i/ncomb*100): >4} % ({i}/{ncomb})")
cnt += 1
else:
for i,comb in enumerate(itertools.combinations(range(n),k), start=1):
q,r = np.linalg.qr(x[:,comb],mode="reduced")
qty = np.dot(q.T,y)
e = y - np.dot(q,qty)
q_adm = q*q
lev = np.sum(q_adm,axis=1) # leverage (diagonal part of hat matrix)
eq = e / (1. - lev)
e2 = np.dot(e,e)
eq2 = np.dot(eq,eq)
e_list.append([e2,eq2,comb])
if i >= di*cnt:
print(f"{int(i/ncomb*100): >4} % ({i}/{ncomb})")
cnt += 1
print()
print(f"Exhaustive search is finished.{int(i/ncomb*100): >4} % ({i}/{ncomb})")
print()
t1 = time.time()
print(f"Elapsed time for score calculatons")
print(f"time: {t1-t0} [s]")
print(f"time/{n}C{k} : {(t1-t0)/ncomb} [s/ncomb]")
print()
df = pd.DataFrame(e_list,columns=["e2","eq2","comb"])
# === e2 sort ===
t2 = time.time()
e_sort_df = df.sort_values(by="e2",ascending=True).reset_index()[:ntop]
t3 = time.time()
print(f"Elapsed time for sorting (by e2)")
print(f"time : {t3-t2} [s]")
print(f"time/{n}C{k} : {(t3-t2)/ncomb} [s/ncomb]")
print()
e_des_lis = []
r2_lis = []
q2_lis = []
print(f"Displayed only top {ntop} (sorted by e2)")
for i,(et,qt,cmb) in enumerate(zip(e_sort_df["e2"],e_sort_df["eq2"],e_sort_df["comb"])):
r2_lis.append(1.-et/syy)
q2_lis.append(1.-qt/syy)
e_des_lis.append([labs_list[j] for j in cmb])
e_sort_df["R2"] = r2_lis
e_sort_df["Q2"] = q2_lis
e_sort_df["Descriptors"] = e_des_lis
print(e_sort_df[["e2","R2","eq2","Q2","Descriptors"]])
pt.ex_plot(x,y,e_sort_df["comb"],"R2")
print()
# === q2 sort ===
t4 = time.time()
q_sort_df = df.sort_values(by="eq2",ascending=True).reset_index()[:ntop]
t5 = time.time()
print(f"Elapsed time for sorting (by eq2)")
print(f"time : {t5-t4} [s]")
print(f"time/{n}C{k} : {(t5-t4)/ncomb} [s/ncomb]")
print()
q_des_lis = []
r2_lis = []
q2_lis = []
print(f"Displayed only top {ntop} (sorted by eq2)")
for i,(et,qt,cmb) in enumerate(zip(q_sort_df["e2"],q_sort_df["eq2"],q_sort_df["comb"])):
r2_lis.append(1.-et/syy)
q2_lis.append(1.-qt/syy)
q_des_lis.append([labs_list[j] for j in cmb])
e_sort_df["R2"] = r2_lis
e_sort_df["Q2"] = q2_lis
e_sort_df["Descriptors"] = q_des_lis
print(e_sort_df[["e2","R2","eq2","Q2","Descriptors"]])
pt.ex_plot(x,y,q_sort_df["comb"],"Q2")
return e_des_lis,q_des_lis