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r_plambda_pitheta_full.py
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import argparse
import time
from datetime import datetime
import os
import sqlite3
import random
from random import shuffle
import math
from tqdm import tqdm
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from torch.autograd import Variable
import pandas as pd
from fuzzysearch import find_near_matches
from tensorboardX import SummaryWriter
parser = argparse.ArgumentParser(description='PyTorch LSTM Language Model')
parser.add_argument('--epochs', type=int, default=100, help='maximum number of epochs')
parser.add_argument('--ds_size', type=int, default=1000, help='training set size')
parser.add_argument('--distill_size', type=int, default=20000, help='training set size')
parser.add_argument('--motif', type=int, default=2, help='=1= short motif, =4= long motif')
parser.add_argument('--nmotifs', type=int, default=1, help='number of motifs that define the process')
parser.add_argument('--mtype', type=str, default='m', help='m, mam, m1m2, mult')
parser.add_argument('--n', type=int, default=30, help='string size')
parser.add_argument('--p', type=float, default=0.5, help='probability of flipping a coin')
parser.add_argument('--print_softm', type=str, default='', help='train or print')
parser.add_argument('--job', type=int, default=0, help='slurm job id')
#parser.add_argument('--feat', type=str, default='111', help='features for motifs with -.- separator; 0 or 1 at i-th position adds 0 to motif')
#parser.add_argument('--feat', type=str, default='1101000', help='features for motifs with -.- separator; (motif, supermotif, submotif, 1st bit==0, 10101, 1001001, 00110011)')
parser.add_argument('--feat', type=str, default='1001111', help='features for motifs with -.- separator; (motif, supermotif, submotif__2, 1st bit==0, 10101_len_m, 1001001_le_m_2, 00110011_len_m__2)')
parser.add_argument('--train', type=str, default='rs', help='=rs= rejection sampling, =snis_mix= snis mixture, =snis_r= snis r')
parser.add_argument('--restore', type=str, default='', help='checkpoint to restore model from')
parser.add_argument('--theta_fixed', action='store_false', help='train theta with lambda (log-linear model) or only lambda')
parser.add_argument('--test_run', action='store_true', help='if False - testing run, do not store accuracies')
parser.add_argument('--train2', type=str, default='distill', help='=distill=, =pg=, =dpg=, =cyclic_1=, =cyclic_r=')
parser.add_argument('--optim', type=str, default='adam', help='=adam=, =manual_lr=')
parser.add_argument('--debug_opt', type=str, default='no_motif', help='=no_motif=, =fix_length=')
parser.add_argument('--logdir', type=str, default='/tmp-network/user/tparshak')
parser.add_argument('--wandb', action='store_true')
parser.add_argument('--tensorboard', action='store_true')
parser.add_argument('--expect_len', type=float, default=30, help='expected length of strings in PFSA')
# hype parameters
parser.add_argument('--rl_lr', type=float, default=0.01, help='reinforcement learning learning rate')
parser.add_argument('--rl_scale_iter', type=float, default=100, help='reinforcement learning scaled number of iterations in one epoch')
parser.add_argument('--rl_target_kl', type=float, default=0.01, help='early stopping in ppo')
parser.add_argument('--rl_clip_param', type=float, default=0.2, help='in ppo')
parser.add_argument('--rl_value_loss_coeff', type=float, default=0.2, help='coefficient for critic loss')
parser.add_argument('--rl_seed', type=int, default=-999, help='for fair comparison')
parser.add_argument('--rl_patience', type=int, default=10, help='early stopping')
parser.add_argument('--rl_mini_batch', type=int, default=500, help='in rl setting')
parser.add_argument('--rl_plan_depth', type=int, default=1, help='plannign in AC D-PG')
"""
train2 combinations:
[dpg || pg || ppo] + [crit, wn]
[dpg || ac_dpg] + [stable_q]
[ppo_fl] + [crit]
[dpg] + [stable_q_fix]
"""
args = parser.parse_args()
if 'M' or 'v' in args.feat:
args.max_len = 100
else:
args.max_len = args.n*5
torch.set_printoptions(precision=15)
torch.backends.cudnn.deterministic = True
torch.backends.cudnn.benchmark = False
if args.rl_seed != -999:
np.random.seed(args.rl_seed)
torch.manual_seed(args.rl_seed)
torch.cuda.manual_seed(args.rl_seed)
random.seed(args.rl_seed)
torch.cuda.manual_seed_all(args.rl_seed)
# W&B configuration
if args.wandb:
import wandb
wandb.init(project=args.train2, name=str(args.job))
wandb.config.update(args)
args.nmotifs = 1
s = "\nParameters:\n"
for k in sorted(args.__dict__):
s += "{} = {} \n".format(k.lower(), args.__dict__[k])
print(s)
# input vocabulary size
ntoken = 5
batch_size = 500
nhid = 200
# one hot input vector embeddings size
ninp = 3
nlayers = 2
dropout = 0.2 # prob to be zeroed
loss_scale = 1
log_interval = 10
clip = 0.25
nsamples = 10
start_symbol = torch.tensor([[3]*10000]).cuda()
PAD = 4
timestamp = datetime.now().strftime("%mm%dd_%H%M_") + str(args.job)
print(timestamp)
if args.wandb:
wandb.log({'tstamp':timestamp})
# motif: ratio = 1: 1:50, 2: 1:100, 3: 1:500, 4: 1:1000
# choose 2,4,5,6,7
if args.mtype == 'm':
if args.motif == 1:
all_motifs = {10:'1111111', 30:'1000101111', 50:'10001010001'}
power_motifs = {30:21927961, 50:21571947468791}
elif args.motif == 2:
all_motifs = {30:'10001010001', 50:'100010100010'}
power_motifs = {30:10355564, 50:10547846544409}
elif args.motif == 3:
all_motifs = {30:'1000101000101', 50:'10011000111111', 100:'0111010000011101'}
power_motifs = {30:2334480, 50:2541261794559}
elif args.motif == 4:
all_motifs = {30:'10001011111000', 50:'100110001111111'}
power_motifs = {30:1113640, 50:1236662229247}
elif args.motif == 5:
all_motifs = {30:'01011101101'}
elif args.motif == 6:
all_motifs = {30:'001001100111'}
elif args.motif == 7:
all_motifs = {30:'1011100111001'}
elif args.mtype == 'mam':
if args.motif == 2:
all_motifs = {30:'100010100011.100010100011'}
power_motifs = {30:11787265}
elif args.motif == 3:
all_motifs = {30:'10001011111000.10001011111000'}
power_motifs = {30:3064058}
elif args.motif == 4:
all_motifs = {30:'1000101111100011.1000101111100011'}
power_motifs = {30:786542}
elif args.motif == 5:
all_motifs = {30:'01011101101.01011101101'}
elif args.motif == 6:
all_motifs = {30:'001001100111.001001100111'}
elif args.motif == 7:
all_motifs = {30:'1011100111001.1011100111001'}
elif args.mtype == 'mult':
if args.motif == 3:
all_motifs = {30:'multipl_3'}
elif args.motif == 17:
all_motifs = {30:'multipl_17'}
#wandb.config.update({'motif':all_motifs[args.n]})
entp_motifs_tm = {10:{'m.1111111':2.995732273553991/11}, 30:{'mult.multipl_3':19.62365305094772/31, 'mult.multipl_17':17.889051994558614/31, 'mam.100010100011':16.282530254126048/31, 'mam.1000101111100011':13.57540128031525/31,
'm.10001010001':16.15303451776991/31,'m.10001011111000':13.923144487457433/31,
'mam.10001011111000':14.935250784153713/31, 'm.01011101101':16.1633538708637/31,
'm.001001100111':15.420728378322668/31,'m.1011100111001':14.6736907/31, 'mam.01011101101':16.950563779/31,
'mam.001001100111':16.2827152768/31, 'mam.1011100111001':15.61062622/31, 'm.1000101000101':14.66329972621143/31}, 100:{'m.0111010000011101':62.665668876452344/101}}
z_motifs = {10:{'m.1111111':0.01953125}, 30:{'mult.multipl_3':0.3333333343343343, 'mult.multipl_17':0.05882352952952953, 'mam.100010100011':0.0046360, 'mam.1000101111100011':0.00022888,
'm.10001010001':0.00964437,'m.10001011111000':0.0010371580,
'mam.10001011111000':0.001037158, 'm.01011101101':0.0097444,
'm.001001100111':0.004637, 'm.1011100111001':0.002196863, 'mam.01011101101':0.00974440,
'mam.001001100111':0.004637, 'mam.1011100111001':0.002196863, 'm.1000101000101':0.0021741539239883423}, 100:{'m.0111010000011101':0.0012952530732785747}}
entp_motifs = {}
for ni, m in all_motifs.items():
if ni in entp_motifs_tm and ni == args.n:
entp_motifs[ni] = entp_motifs_tm[ni][args.mtype+'.'+m.split('.')[0]]
# get data
def get_batch(source_data, batch):
data = source_data[:-1,batch:batch+batch_size]
target = source_data[1:,batch:batch+batch_size].contiguous().view(-1)
return data, target
def get_batch_fsz(source_data, batch):
data = source_data[:-1,batch:batch+batch_size]
target = source_data[1:,batch:batch+batch_size].contiguous()
return data, target
def load_data_mult(n, sz, motif, ds_type):
ds = []
# input: <bos> binary string <eos>
# 3 {0,1}^n 2
data_file = os.path.join(os.path.join(args.logdir,'data'), 'multipl_%s'%(args.motif),"%s.txt"%ds_type)
max_len = 0
with open(data_file, "r") as file:
for line in file:
#assert motif in line
ds += [line.strip()]
max_len = max(max_len, len(line.strip()))
#print(line.strip())
if len(ds)>=sz:
break
n = max_len
args.n = max_len
original = ''
for l in ds:
original += ' '+ ''.join(c+' ' for c in l).strip()
original += ' 2 '+ ''.join(str(PAD)+' ' for _ in range(max_len-len(l))).strip()
original = original.strip()
print(len(original), max_len)
n += 1
original = np.fromstring(original, dtype=int, sep=' ')
original = original.reshape((original.shape[0]//n, n)).transpose()
for i in range(original.shape[1]):
res = ''.join([str(original[j,i]) for j in range(original.shape[0])])
#assert flag
dataset = (np.ones((n+1, original.shape[1]))).astype(int)
dataset[1:] = original
dataset[0] = dataset[0]*3
#dataset[-1] = dataset[-1]*2
print(dataset.shape, batch_size)
assert dataset.shape[1] >= sz
ds = dataset[:, :batch_size*int(1.0*dataset.shape[1]/batch_size)]
return torch.from_numpy(ds).cuda()
def load_data_motif(n, sz, motif, ds_type):
ds = ""
# input: <bos> binary string <eos>
# 3 {0,1}^n 2
if args.nmotifs == 1:
data_file = os.path.join(os.path.join(args.logdir,'data'), 'pfsa_%d_%s'%(n, motif),"%s.txt"%ds_type)
else:
data_file = os.path.join(os.path.join(args.logdir,'data'), 'pfsa_%d_%s'%(n-1, motif),"%s.txt"%ds_type)
with open(data_file, "r") as file:
for line in file:
#assert motif in line
ds += line.strip()
#print(line.strip())
if len(ds)>=sz*n:
break
original = ''.join(c+' ' for c in ds[:sz*n]).strip()
original = np.fromstring(original, dtype=int, sep=' ')
original = original.reshape((original.shape[0]//n, n)).transpose()
for i in range(original.shape[1]):
res = ''.join([str(original[j,i]) for j in range(original.shape[0])])
#assert flag
dataset = (np.ones((n+2, original.shape[1]))).astype(int)
dataset[1:-1] = original
dataset[0] = dataset[0]*3
dataset[-1] = dataset[-1]*2
print(dataset.shape, batch_size)
assert dataset.shape[1] >= sz
ds = dataset[:, :batch_size*int(1.0*dataset.shape[1]/batch_size)]
return torch.from_numpy(ds).cuda()
# ------------------------------------------------------------------------
# ------------ classes: RNN, GAMs, WhiteNoise with filter ----------------
def repackage_hidden(h):
"""detach vars from their history."""
return tuple(Variable(h[i].data) for i in range(len(h)))
def init(module, weight_init, bias_init, gain=1):
weight_init(module.weight.data, gain=gain)
bias_init(module.bias.data)
return module
# some part of the language model architecture from https://github.com/NVIDIA/DeepLearningExamples/blob/master/PyTorch/LanguageModel/
class RNNModel(nn.Module):
def __init__(self, ntoken, ninp, nhid, nlayers, dropout=0.5, policy=False, policy_log=False):
super(RNNModel, self).__init__()
self.drop = nn.Dropout(dropout)
self.encoder = nn.Embedding(ntoken, ninp)
# 0 1 <EOS> <BOS> PAD
one_hot_vecs = np.array([[1,0,0], [0,1,0], [0,0,1], [0,0,0], [0,0,0]])
self.encoder.weight.data.copy_(torch.from_numpy(one_hot_vecs))
self.freeze_layer(self.encoder)
self.rnn = nn.LSTM(ninp, nhid, nlayers, dropout=dropout)
# <bos> is not in the output vocabulary
self.decoder = nn.Linear(nhid, ninp)
self.policy = policy
if policy and ('crit' in args.train2 or 'ac_dpg' in args.train2):
init_ = lambda m: init(m, nn.init.orthogonal_, lambda x: nn.init.
constant_(x, 0))
# spit out values of Z(s) leaves
if 'ac_dpg_a' in args.train2:
zn_out = ninp
else:
zn_out = 1
if policy_log:
# log_Z(s)
self.critic = nn.Sequential(init_(nn.Linear(nhid, nhid)), nn.Tanh(), init_(nn.Linear(nhid, zn_out)))
else:
# Z(s)
self.critic = nn.Sequential(init_(nn.Linear(nhid, nhid)), nn.Tanh(), init_(nn.Linear(nhid, zn_out)), nn.ReLU())
self.init_weights()
self.nhid = nhid
self.nlayers = nlayers
def freeze_layer(self, layer):
for param in layer.parameters():
param.requires_grad = False
def init_weights(self):
initrange = 0.1
self.decoder.bias.data.fill_(0)
self.decoder.weight.data.uniform_(-initrange, initrange)
def forward(self, input, hidden, len_inp, mask, critic=False):
emb = self.drop(self.encoder(input))
output, hidden = self.rnn(emb, hidden)
output = self.drop(output) # [seq_len ,batch, nhid]
# [seq_len*batch, ntok]
decoded = self.decoder(output.view(output.size(0)*output.size(1), output.size(2)))
decoded = torch.mul(decoded.view(output.size(0), output.size(1), decoded.size(1)), mask)
if self.policy and ('crit' in args.train2 or 'ac_dpg' in args.train2) and critic:
est_z = self.critic(output.view(output.size(0)*output.size(1), output.size(2)))
est_z = torch.mul(est_z.view(output.size(0), output.size(1), est_z.size(1)), mask)
return decoded, hidden, est_z
else:
return decoded, hidden
def init_hidden(self, bsz):
weight = next(self.parameters()).data
return (Variable(weight.new(self.nlayers, bsz, self.nhid).zero_()),
Variable(weight.new(self.nlayers, bsz, self.nhid).zero_()))
class White_noise_filter(nn.Module):
# biased white noise with filter for strings
# of length!=n and not containing the motif
def __init__(self, probs, feat, motifs):
super(White_noise_filter, self).__init__()
self.drop = nn.Dropout(dropout)
self.feat = feat
self.motifs = motifs
self.encoder = nn.Embedding(ntoken, 1)
one_hot_vecs = np.array([[pi] for pi in probs+[1, 1]])
self.encoder.weight.data.copy_(torch.from_numpy(one_hot_vecs))
# probs for: 0 1 <EOS> <BOS> PAD
self.probs = torch.tensor(probs).cuda()
self.freeze_layer(self.encoder)
def freeze_layer(self, layer):
for param in layer.parameters():
param.requires_grad = False
def init_hidden(self, bsz):
return (None, None)
def forward(self, input, hidden, len_tar, mask):
# [seq x batch x 1]
probs = self.encoder(input)
# 1 = no motif
x_feat = get_features(input, self.motifs, self.feat)[:,0]
if 'no_motif' in args.debug_opt:
x_feat = x_feat*0
log_lin = 0
#len_tar, _,_,_ = get_length_mask(input)
# 1 = length different from n
if 'i' in args.feat:
len_feat = (torch.abs(len_tar-(args.n+1))>=10).float()
else:
x_feat += (len_tar!=(args.n+1)).float()
infs = -torch.ones(probs.size(1)).cuda()*float('Inf')
if 'rew1' in args.debug_opt:
logits = torch.zeros(probs.size(1)).cuda()
else:
logits = torch.log(probs).sum(0).squeeze()
if 'i' in args.feat:
log_05 = np.log(0.5)
logits = torch.where(((x_feat==0) | (x_feat==0.5)) & (len_feat==0), logits, infs)
logits = torch.where(((x_feat==0.5) & (len_feat==0))|((x_feat==0) & (len_tar!=(args.n+1))), logits+log_05, logits)
if np.random.rand()<0.001:
print('X', input[:,:5], 'feat', x_feat[:5], logits[:5])
else:
x_feat = torch.clamp(x_feat, min=0, max=1)
# if all features are on - use logits, else prob is 0
logits = torch.where(x_feat==0, logits, infs)
#print(logits[:10].data.cpu().numpy(), len_tar[:10], (len_tar!=(args.n+1))[:10], args.n+1)
# [batch]
return logits.unsqueeze(1), None, log_lin
class GAMModel(nn.Module):
def __init__(self, ntoken, ninp, nhid, nlayers, feat, motifs, dropout=0.5):
super(GAMModel, self).__init__()
self.drop = nn.Dropout(dropout)
self.feat = feat
self.motifs = motifs
self.encoder = nn.Embedding(ntoken, ninp)
# 0 1 <eos> <bos> PAD
one_hot_vecs = np.array([[1,0,0], [0,1,0], [0,0,1], [0,0,0], [0,0,0]])
self.encoder.weight.data.copy_(torch.from_numpy(one_hot_vecs))
self.freeze_layer(self.encoder)
self.rnn = nn.LSTM(ninp, nhid, nlayers, dropout=dropout)
# <bos> is not in the output vocabulary
self.decoder = nn.Linear(nhid, ninp)
if args.theta_fixed:
self.freeze_layer(self.decoder)
self.freeze_layer(self.rnn)
self.motifs = motifs
nfeat = sum([sum([int(e!='0') for e in el]) for el in feat])
self.lin_lambda = nn.Linear(nfeat, 1)
self.lin_lambda.bias.data = self.lin_lambda.bias.data * 0
self.lin_lambda.bias.requires_grad = False
self.lin_lambda.weight.data = self.lin_lambda.weight.data * 0
self.init_weights()
self.nhid = nhid
self.nlayers = nlayers
def freeze_layer(self, layer):
for param in layer.parameters():
param.requires_grad = False
def init_weights(self):
initrange = 0.1
self.decoder.bias.data.fill_(0)
self.decoder.weight.data.uniform_(-initrange, initrange)
def forward(self, input, hidden, len_inp, mask):
emb = self.encoder(input)
emb_pack = torch.nn.utils.rnn.pack_padded_sequence(emb, len_inp, batch_first=False)
out_pack, hidden = self.rnn(emb_pack, hidden)
output, _ = torch.nn.utils.rnn.pad_packed_sequence(out_pack, batch_first=False)
output = torch.mul(output, mask)
# [seq_len x batch x nhid]
output = self.drop(output)
# [ seq_len*batch x ntok]
decoded = self.decoder(output.view(output.size(0)*output.size(1), output.size(2)))
x_feat = get_features(input, self.motifs, self.feat)
log_lin = self.lin_lambda(x_feat)
decoded = torch.mul(decoded.view(output.size(0), output.size(1), decoded.size(1)), mask)
return decoded, hidden, log_lin
def init_hidden(self, bsz):
weight = next(self.parameters()).data
return (Variable(weight.new(self.nlayers, bsz, self.nhid).zero_()),
Variable(weight.new(self.nlayers, bsz, self.nhid).zero_()))
def oracle_features(s, motifs, feat):
# s: seq_len x 1
# output: [ nfeat ]
# (motif, supermotif, submotif__2, 1st bit==0, 10101_len_m, 1001001_le_m_2, 00110011_len_m__2)
out = []
idx = min(1, len(s)-1)
nfeat = sum([sum([int(e!='0') for e in el]) for el in feat])
i = 0
for j in range(len(feat[i])):
if feat[i][j] == '1':
# correlated features
if j < len(args.feat)-4:
if args.nmotifs == 1:
if j == len(args.feat)-7:
# motif
if args.mtype == 'm':
out += [1 - int(motifs[i] in s)]
elif args.mtype == 'mult':
if s[0] == '3':
digits = s[1:]
else:
digits = s
end_idx = digits.find('2')
if end_idx != -1:
digits = digits[:end_idx]
if digits:
out += [1-int(int('0b'+digits,2)%args.motif == 0 and int('0b'+digits,2)!=0)]
else:
out += [1]
elif j == len(args.feat)-6:
# supermotif
motif_j = motifs[i] + '0'*1
out += [1 - int(motif_j in s)]
elif j == len(args.feat)-5:
# submotif
motif_j = motifs[i][:len(motifs[i])//2]
out += [1 - int(motif_j in s)]
elif args.nmotifs == 2:
if j in [j == len(args.feat)-8, j == len(args.feat)-6]:
# motif
out += [1 - int(motifs[max(0, j-1)] in s)]
elif j in [j == len(args.feat)-7, j == len(args.feat)-5]:
# submotif
motif_j = motifs[max(0, j-2)][:len(motifs[max(0, j-2)])//2]
out += [1 - int(motif_j in s)]
else:
# distractive features
if j == len(args.feat)-4:
# first bit
out += [1 - int(s[idx]=='1')]
# distractor
elif j == len(args.feat)-3:
pref = '10101'
motif_j = (pref*args.n)[:len(motifs[i])]
out += [1 - int(motif_j in s)]
elif j == len(args.feat)-2:
pref = '1001001'
motif_j = (pref*args.n)[:len(motifs[i])+2]
out += [1 - int(motif_j in s)]
elif j == len(args.feat)-1:
pref = '00110011'
motif_j = (pref*args.n)[:len(motifs[i])//2]
out += [1 - int(motif_j in s)]
elif feat[i][j] == 'e':
# edit distance
out += [get_edit_frc(s, motifs[i])]
elif feat[i][j] == 's':
out += [get_longestsubstr_frc(s, motifs[i])]
elif feat[i][j] == 'l':
out += [int(np.abs(len(s)-args.n-1)>=3)]
elif feat[i][j] == 'M':
out += [(len(s)*1.0)/args.max_len]
elif feat[i][j] == 'v':
out += [(1.0*len(s)**2)/(args.max_len**2)]
elif feat[i][j] == 'm':
out += [get_longestsubstr_frc(s, motifs[i]) + get_edit_frc(s, motifs[i])]
elif feat[i][j] == 'i':
val = get_longestsubstr(s, motifs[i])
if np.abs(val-len(motifs[i]))==0:
out += [0]
elif np.abs(val-len(motifs[i]))<=3:
out += [0.5]
else:
out += [1]
if np.random.rand()<0.00001:
print('X', s, 'val', val, np.abs(val-len(motifs[i])), out)
return out
def get_longestsubstr(s, motif):
n, m = len(s)+1, len(motif)+1
#assert m<=n
e = np.zeros((m,n))
max_lss = 0
for j in range(1,m):
for i in range(1,n):
e_ij = []
if s[i-1]!=motif[j-1]:
e[j,i]=0
else:
e[j,i] = 1 + e[j-1,i-1]
max_lss = max(max_lss, e[j,i])
return max_lss
def get_longestsubstr_frc(s, motif):
max_lss = get_longestsubstr(s, motif)
return 1-(1.*max_lss)/len(motif)
def get_edit_frc(s, motif):
def edit_distance(subs, motif):
n, m = len(subs)+1, len(motif)+1
#assert m<=n
e = np.zeros((m,n))
e[0,0] = 0
for j in range(1,m):
e[j,0]= j
for j in range(1,m):
for i in range(1,n):
e_ij = []
if j>0:
e_ij += [e[j-1,i]+1]
if i>0:
e_ij += [e[j,i-1]+1]
if j>0 and i>0:
e_ij += [e[j-1, i-1]+ int(subs[i-1]!=motif[j-1])]
if e_ij:
e[j,i] = min(e_ij)
return 1.0*min(e[-1,:])
ed_dist = edit_distance(s, motif)
edit_frac = ed_dist/len(motif)
assert edit_frac<=1
return edit_frac
def get_edit_frc1(s, motif):
def edit_distance(subs, motif):
n, m = len(subs)+1, len(motif)+1
#assert m<=n
e = np.ones((m,n))*m
e[0,0] = 0
for j in range(1,m):
e[j,0]=j
for i in range(1,n):
e[0,i]=i
for j in range(1,m):
for i in range(1,n):
e_ij = []
if j>0:
e_ij += [e[j-1,i]+1]
if i>0:
e_ij += [e[j,i-1]+1]
if j>0 and i>0:
e_ij += [e[j-1, i-1]+ int(subs[i-1]!=motif[j-1])]
if e_ij:
e[j,i] = min(e_ij)
return 1.0*min(e[-1,:])
ed_dist = len(motif)
for i in range(len(s)):
for j in range(i, len(s)):
ed_dist = min(ed_dist, edit_distance(s[i:i+j], motif))#
edit_frac = ed_dist/len(motif)
assert edit_frac<=1
return edit_frac
def get_features(var, motifs, feat):
# returns the results of identifying oracle features in the input binary sequence
# 0 = feature exists
# var: [ seq_len x batch ]
# output: [batch x nfeat]
def var_to_str(a):
a = a.data.cpu().numpy()
b = []
for i in range(a.shape[1]):
b += [''.join([str(el) for el in a[:,i]])]
return b
x = var_to_str(var)
out = []
for b in x:
out += [oracle_features(b, motifs, feat)]
return torch.tensor(out).cuda().float()
def argmax_quadratic(left,right,a,b):
'''
Find the argmax of $ax^2 + bx$ on the interval [left,right]
'''
if a < 0:
global_argmax = -b/(2*a)
if left < global_argmax and global_argmax < right:
return global_argmax
else:
return np.argmax([a*left**2 + b*left, a*right**2 + b*right])
else:
return np.argmax([a*left**2 + b*left, a*right**2 + b*right])
# -----------------------------------------------
# -------------------- utils --------------------
def to_one_hot(y, n_dims=None):
""" Take an integer vector (tensor of variable) and convert it to 1-hot matrix. """
y_tensor = y.data if isinstance(y, Variable) else y
y_tensor = y_tensor.type(torch.LongTensor).view(-1, 1)
n_dims = n_dims if n_dims is not None else ninp
y_one_hot = torch.zeros(y_tensor.size(0), n_dims).scatter_(1, y_tensor, 1).cuda()
return Variable(y_one_hot) if isinstance(y, Variable) else y_one_hot
def get_log_r(r_output, ce_target, mask_tar, ce_criterion):
# get logits from the AMs output layer for a specific target sequence
# r_output: [seq_len x batch x ninp] -> log_r_seq: [seq_len x batch x 1]
# ce_target: [seq_len x batch]; indices
# mask PAD symbol to keep short output vocabulary
ce_target = torch.mul(ce_target.float(), mask_tar[:,:,0]).long()
# [(n+1) x batch x 1]
r_output = torch.nn.functional.log_softmax(r_output, dim=2)
log_r_seq = torch.sum(r_output.view(-1, ninp) * to_one_hot(ce_target.view(-1)), dim = 1)
log_r_seq = torch.mul(log_r_seq.view(mask_tar.size()), mask_tar)
# [seq_len x batch x 1]
return log_r_seq
def get_lr(optimizer):
for param_group in optimizer.param_groups:
return param_group['lr']
def init_rnn_from_proposal(model_r, policy_log, policy):
# copy model_r to model_q
model_q = RNNModel(ntoken, ninp, nhid, nlayers, dropout, policy=policy, policy_log=policy_log)
model_q.cuda()
pretrained_dict = model_r.state_dict()
model_dict = model_q.state_dict()
pretrained_dict = {k: v for k, v in pretrained_dict.items() if k in model_dict}
# 2. overwrite entries in the existing state dict
model_dict.update(pretrained_dict)
# 3. load the new state dict
model_q.load_state_dict(model_dict)
return model_q
def cat_variable_length(a, b):
seq_len = max(a.size()[0], b.size()[0])
if a.size()[0] < seq_len:
padding = torch.ones((seq_len-a.size()[0], a.size(1))).long()*PAD
if a.is_cuda:
padding = padding.cuda()
a = torch.cat((a, padding), dim=0)
if b.size()[0] < seq_len:
padding = torch.ones((seq_len-b.size()[0], b.size(1))).long()*PAD
if a.is_cuda:
padding = padding.cuda()
b = torch.cat((b, padding), dim=0)
return torch.cat((a,b), dim=1)
def isfinite(x):
"""
Quick pytorch test that there are no nan's or infs.
note: torch now has torch.isnan
url: https://gist.github.com/wassname/df8bc03e60f81ff081e1895aabe1f519
"""
not_inf = ((x + 1) != x)
not_nan = (x == x)
return not_inf & not_nan
def sample_from_rnn(model):
n = args.n
motifs = all_motifs[args.n].split('.')
batch_size = 5000
x, log_pi, inp, len_inp, action, mask_tar = sample_data_inp_targ_vary(model,
batch_size, max_len=500)
avg_len = np.round(len_inp.float().mean().data.cpu().numpy(),decimals=1)
print('avg len ', avg_len)
x = x.data.cpu().numpy()
count = 0
for i in range(x.shape[1]):
res = ''.join([str(x[j,i]) for j in range(x.shape[0])])
curr_count = 0
if args.mtype == 'mult':
if res[0] == '3':
digits=res[1:]
else:
digits=res
end_idx = digits.find('2')
if end_idx != -1:
digits = digits[:end_idx]
if digits:
curr_count += int(int('0b'+digits,2)%args.motif == 0 and int('0b'+digits,2)!=0)
else:
for motif in motifs:
if motif in res:
curr_count += 1
count += min(1, curr_count)
print('%d motifs in total %d' % (count, x.shape[1]))
motif_freq = (1.0*count)/x.shape[1]
return motif_freq, avg_len
def logsumexp(x, dim=None):
if dim is None:
xmax = x.max()
xmax_ = x.max()
return xmax_ + numpy.log(torch.exp(x - xmax).sum())
else:
xmax, _ = x.max(dim, keepdim=True)
xmax_, _ = x.max(dim)
return xmax_ + torch.log(torch.exp(x - xmax).sum(dim))
# -----------------------------------------------
# -------------- sampling from LM ---------------
def sample_lm_vary(model, batch_size_i, max_len=None, critic=False):
# sample strings of varying length
# output: [ seq_len x batch ]
model.eval()
# [ 1 x batch ]
# <pad> idx = 4
if not max_len:
max_len=args.n*2+1
EOS = 2; BOS = 3
out = [(torch.ones(1)*BOS).cuda().long()]*batch_size_i # contains sequences of variable lenght
symb = start_symbol[:,:batch_size_i]
hidden = model.init_hidden(batch_size_i)
len_inp = torch.ones((batch_size_i), dtype=torch.int64).cuda()
mask = torch.ones((1, batch_size_i, 1)).cuda()
all_logits = torch.ones((0, batch_size_i, ninp)).cuda()
if critic:
all_z = torch.zeros((0, batch_size_i, 1)).cuda()
for i in range(max_len):
# [1 x batch x ntok]
if critic:
logits, hidden, est_z = model(symb, hidden, len_inp, mask, critic=critic)
else:
logits, hidden = model(symb, hidden, len_inp, mask)[:2]
probs = softm(logits)
cat_dist = torch.distributions.Categorical(probs=probs)
# [ 1 x batch ]
symb = cat_dist.sample()
flag = False
for b in range(batch_size_i):
# if the sequence has not terminated yet
if i==0 or (i>0 and out[b][-1] != EOS):
out[b] = torch.cat((out[b], symb[:1,b]), dim=0)
flag = True
if not flag:
break
# TODO: instead of cat write into predefined array
all_logits = torch.cat((all_logits, logits), dim=0)
if critic:
all_z = torch.cat((all_z, est_z), dim=0)
out = torch.nn.utils.rnn.pad_sequence(out, batch_first=False, padding_value=PAD)
model.train()
# <bos> 010010101 <eos>
if critic:
return out, all_logits, all_z
else:
return out, all_logits
def sample_lm_vary_new(model, batch_size_i, max_len=None, critic=False):
# sample strings of varying length
# out: [ seq_len+1 x batch ]
# all_logits: [ seq_len x batch x ninp ]
# all_z: [ seq_len x batch x 1]
model.eval()
if not max_len:
max_len=args.n*2+1
EOS = 2; BOS = 3
symb = start_symbol[:,:batch_size_i]
hidden = model.init_hidden(batch_size_i)
len_inp = torch.ones((batch_size_i), dtype=torch.int64).cuda()
mask = torch.ones((1, batch_size_i, 1)).cuda()
all_logits = torch.ones((max_len, batch_size_i, ninp)).cuda()
out = torch.ones((max_len+1, batch_size_i)).cuda().long()
out[0,:] = out[0,:]*BOS
if critic:
all_z = torch.zeros((max_len, batch_size_i, 1)).cuda()
for i in range(max_len):
# [1 x batch x ntok]
if critic:
logits, hidden, est_z = model(symb, hidden, len_inp, mask, critic=critic)
else:
logits, hidden = model(symb, hidden, len_inp, mask)[:2]
probs = softm(logits)
cat_dist = torch.distributions.Categorical(probs=probs)
# [ 1 x batch ]
symb = cat_dist.sample()
out[i+1:i+2] = symb[:1]
all_logits[i:i+1] = logits
if critic:
all_z[i:i+1] = est_z
max_seq_len = 0
for b in range(batch_size_i):
ends = (out[:,b] == EOS).nonzero()
if ends.size(0) == 0:
continue # string does not contain EOS
idx = ends[0,0]
if idx == max_len:
max_seq_len = max_len
out[idx+1:,b] = out[idx+1:,b]*0 + PAD
all_logits[idx:,b] = all_logits[idx:,b]*0
if critic:
all_z[idx:,b] = all_z[idx:,b]*0
max_seq_len = max(max_seq_len, idx)
out = out[:max_seq_len+1]
all_logits = all_logits[:max_seq_len]
if critic:
all_z = all_z[:max_seq_len]
model.train()
# <bos> 010010101 <eos>
if critic:
return out, all_logits, all_z
else:
return out, all_logits
def sample_lm_vary_hid(model, batch_size_i, max_len=None, critic=False):
# output: [ seq_len x batch ]
model.eval()
# [ 1 x batch ]
# <pad> idx = 4
if not max_len:
max_len=args.n*2+1
out = [(torch.ones(1)*3).cuda().long()]*batch_size_i # contains sequences of variable lenght
symb = start_symbol[:,:batch_size_i]
hidden = model.init_hidden(batch_size_i)
len_inp = torch.ones((batch_size_i), dtype=torch.int64)
mask = torch.ones((1, batch_size_i, 1)).cuda()
all_logits = torch.ones((0, batch_size_i, ninp)).cuda()
hids = torch.zeros(model.nlayers, 0, model.nhid)
c_hids = torch.zeros(model.nlayers, 0, model.nhid)
if critic:
all_z = torch.zeros((0, batch_size_i, 1)).cuda()
for i in range(max_len):
# [1 x batch x ntok]
if critic:
logits, hidden, est_z = model(symb, hidden, len_inp, mask, critic=critic)
else:
logits, hidden = model(symb, hidden, len_inp, mask)[:2]
probs = softm(logits)
cat_dist = torch.distributions.Categorical(probs=probs)
# [ 1 x batch ]
symb = cat_dist.sample()
flag = False
for b in range(batch_size_i):
if i==0 or (i>0 and out[b][-1] != 2):
out[b] = torch.cat((out[b], symb[:1,b]), dim=0)
flag = True
if not flag:
break
hids = torch.cat((hids, hidden[0].cpu()), dim=1).detach()
c_hids = torch.cat((c_hids, hidden[1].cpu()), dim=1).detach()
all_logits = torch.cat((all_logits, logits), dim=0)
if critic:
all_z = torch.cat((all_z, est_z), dim=0)
out = torch.nn.utils.rnn.pad_sequence(out, batch_first=False, padding_value=PAD)
# <bos> 010010101 <eos>
model.train()
if critic:
return out, all_logits, hids, c_hids, all_z
else:
return out, all_logits, hids, c_hids
def sample_wn(model, batch_size_i, max_len=None):
# sample strings of varying length from white noise model
# output: [ seq_len x batch ]
# [ 1 x batch ]
# <pad> idx = 4
if not max_len:
max_len=args.n*2+1
out = [(torch.ones(1)*3).cuda().long()]*batch_size_i # contains sequences of variable lenght
all_logits = torch.ones((0, batch_size_i, ninp)).cuda()
# [1 x batch x ntok]
probs = model.probs.repeat(1, batch_size_i).view(1, -1, ninp)
logits = torch.log(probs)