Kaggle competition: OSIC Pulmonary Fibrosis Progression
<SOS> metric: LaplaceLogLikelihood Kaggle data source: osic-pulmonary-fibrosis-progression<feature_engineering>
!pip install.. /input/kerasapplications/keras-team-keras-applications-3b180cb -f./ --no-index
!pip install.. /input/efficientnet/efficientnet-1.1.0/ -f./ --no-index
def build_vocab(texts):
sentences = texts.apply(lambda x: x.split() ).values
vocab = {}
for sentence in sentences:
for word in sentence:
try:
vocab[word] += 1
except KeyError:
vocab[word] = 1
return vocab
vocab = build_vocab(df['question_text'] )<define_variables>
import os
import cv2
import pydicom
import pandas as pd
import numpy as np
import tensorflow as tf
import matplotlib.pyplot as plt
import random
from tqdm.notebook import tqdm
from sklearn.model_selection import train_test_split, KFold
from sklearn.metrics import mean_absolute_error
from tensorflow_addons.optimizers import RectifiedAdam
from tensorflow.keras import Model
import tensorflow.keras.backend as K
import tensorflow.keras.layers as L
import tensorflow.keras.models as M
from tensorflow.keras.optimizers import Nadam
import seaborn as sns
import plotly.express as px
import plotly.graph_objects as go
from PIL import Image
sin = len(df_train[df_train["target"]==0])
 insin = len(df_train[df_train["target"]==1])
 persin =(sin/(sin+insin)) *100
perinsin =(insin/(sin+insin)) *100
print("
print("<feature_engineering>
def seed_everything(seed=2020):
random.seed(seed)
 os.environ['PYTHONHASHSEED'] = str(seed)
 np.random.seed(seed)
 tf.random.set_seed(seed )
def build_vocab(texts):
sentences = texts.apply(lambda x: x.split() ).values
vocab = {}
for sentence in sentences:
for word in sentence:
try:
vocab[word] += 1
except KeyError:
vocab[word] = 1
return vocab
def known_contractions(embed):
known = []
for contract in contraction_mapping:
if contract in embed:
known.append(contract)
 return known
def clean_contractions(text, mapping):
specials = ["’", "‘", "´", "`"]
for s in specials:
text = text.replace(s, "'")
 text = ' '.join([mapping[t] if t in mapping else t for t in text.split(" ")])
 return text
def correct_spelling(x, dic):
for word in dic.keys() :
x = x.replace(word, dic[word])
 return x
def unknown_punct(embed, punct):
unknown = ''
for p in punct:
if p not in embed:
unknown += p
unknown += ' '
return unknown
def clean_numbers(x):
x = re.sub('[0-9]{5,}', '
x = re.sub('[0-9]{4}', '
x = re.sub('[0-9]{3}', '
x = re.sub('[0-9]{2}', '
return x
def clean_special_chars(text, punct, mapping):
for p in mapping:
text = text.replace(p, mapping[p])
 for p in punct:
text = text.replace(p, f' {p} ')
 specials = {'\u200b': ' ', '…': '...', '\ufeff': '', 'करना': '', 'है': ''}
for s in specials:
text = text.replace(s, specials[s])
 return text
def add_lower(embedding, vocab):
count = 0
for word in vocab:
if word in embedding and word.lower() not in embedding:
embedding[word.lower() ] = embedding[word]
count += 1
print(f"Added {count} words to embedding" )<define_variables>
seed_everything(42 )
puncts = [',', '.', '"', ':', ')', '(', '-', '!', '?', '|', ';', "'", '$', '&', '/', '[', ']', '>', '%', '=', '
'·', '_', '{', '}', '©', '^', '®', '`', '<', '→', '°', '€', '™', '›', '♥', '←', '×', '§', '″', '′', 'Â', '█', '½', 'à', '…',
'“', '★', '”', '–', '●', 'â', '►', '−', '¢', '²', '¬', '░', '¶', '↑', '±', '¿', '▾', '═', '¦', '║', '―', '¥', '▓', '—', '‹', '─',
'▒', '：', '¼', '⊕', '▼', '▪', '†', '■', '’', '▀', '¨', '▄', '♫', '☆', 'é', '¯', '♦', '¤', '▲', 'è', '¸', '¾', 'Ã', '⋅', '‘', '∞',
'∙', '）', '↓', '、', '│', '（', '»', '，', '♪', '╩', '╚', '³', '・', '╦', '╣', '╔', '╗', '▬', '❤', 'ï', 'Ø', '¹', '≤', '‡', '√', ]
def clean_text(x):
x = str(x)
 for punct in puncts:
x = x.replace(punct, f' {punct} ')
 return x
def clean_numbers(x):
x = re.sub('[0-9]{5,}', '
x = re.sub('[0-9]{4}', '
x = re.sub('[0-9]{3}', '
x = re.sub('[0-9]{2}', '
return x
mispell_dict = {"ain't": "is not", "aren't": "are not","can't": "cannot", "'cause": "because", "could've": "could have", "couldn't": "could not", "didn't": "did not", "doesn't": "does not", "don't": "do not", "hadn't": "had not", "hasn't": "has not", "haven't": "have not", "he'd": "he would","he'll": "he will", "he's": "he is", "how'd": "how did", "how'd'y": "how do you", "how'll": "how will", "how's": "how is", "I'd": "I would", "I'd've": "I would have", "I'll": "I will", "I'll've": "I will have","I'm": "I am", "I've": "I have", "i'd": "i would", "i'd've": "i would have", "i'll": "i will", "i'll've": "i will have","i'm": "i am", "i've": "i have", "isn't": "is not", "it'd": "it would", "it'd've": "it would have", "it'll": "it will", "it'll've": "it will have","it's": "it is", "let's": "let us", "ma'am": "madam", "mayn't": "may not", "might've": "might have","mightn't": "might not","mightn't've": "might not have", "must've": "must have", "mustn't": "must not", "mustn't've": "must not have", "needn't": "need not", "needn't've": "need not have","o'clock": "of the clock", "oughtn't": "ought not", "oughtn't've": "ought not have", "shan't": "shall not", "sha'n't": "shall not", "shan't've": "shall not have", "she'd": "she would", "she'd've": "she would have", "she'll": "she will", "she'll've": "she will have", "she's": "she is", "should've": "should have", "shouldn't": "should not", "shouldn't've": "should not have", "so've": "so have","so's": "so as", "this's": "this is","that'd": "that would", "that'd've": "that would have", "that's": "that is", "there'd": "there would", "there'd've": "there would have", "there's": "there is", "here's": "here is","they'd": "they would", "they'd've": "they would have", "they'll": "they will", "they'll've": "they will have", "they're": "they are", "they've": "they have", "to've": "to have", "wasn't": "was not", "we'd": "we would", "we'd've": "we would have", "we'll": "we will", "we'll've": "we will have", "we're": "we are", "we've": "we have", "weren't": "were not", "what'll": "what will", "what'll've": "what will have", "what're": "what are", "what's": "what is", "what've": "what have", "when's": "when is", "when've": "when have", "where'd": "where did", "where's": "where is", "where've": "where have", "who'll": "who will", "who'll've": "who will have", "who's": "who is", "who've": "who have", "why's": "why is", "why've": "why have", "will've": "will have", "won't": "will not", "won't've": "will not have", "would've": "would have", "wouldn't": "would not", "wouldn't've": "would not have", "y'all": "you all", "y'all'd": "you all would","y'all'd've": "you all would have","y'all're": "you all are","y'all've": "you all have","you'd": "you would", "you'd've": "you would have", "you'll": "you will", "you'll've": "you will have", "you're": "you are", "you've": "you have", 'colour': 'color', 'centre': 'center', 'favourite': 'favorite', 'travelling': 'traveling', 'counselling': 'counseling', 'theatre': 'theater', 'cancelled': 'canceled', 'labour': 'labor', 'organisation': 'organization', 'wwii': 'world war 2', 'citicise': 'criticize', 'youtu ': 'youtube ', 'Qoura': 'Quora', 'sallary': 'salary', 'Whta': 'What', 'narcisist': 'narcissist', 'howdo': 'how do', 'whatare': 'what are', 'howcan': 'how can', 'howmuch': 'how much', 'howmany': 'how many', 'whydo': 'why do', 'doI': 'do I', 'theBest': 'the best', 'howdoes': 'how does', 'mastrubation': 'masturbation', 'mastrubate': 'masturbate', "mastrubating": 'masturbating', 'pennis': 'penis', 'Etherium': 'Ethereum', 'narcissit': 'narcissist', 'bigdata': 'big data', '2k17': '2017', '2k18': '2018', 'qouta': 'quota', 'exboyfriend': 'ex boyfriend', 'airhostess': 'air hostess', "whst": 'what', 'watsapp': 'whatsapp', 'demonitisation': 'demonetization', 'demonitization': 'demonetization', 'demonetisation': 'demonetization'}
def _get_mispell(mispell_dict):
mispell_re = re.compile('(%s)' % '|'.join(mispell_dict.keys()))
return mispell_dict, mispell_re
mispellings, mispellings_re = _get_mispell(mispell_dict)
 def replace_typical_misspell(text):
def replace(match):
return mispellings[match.group(0)]
return mispellings_re.sub(replace, text )<feature_engineering>
config = tf.compat.v1.ConfigProto()
config.gpu_options.allow_growth = True
session = tf.compat.v1.Session(config=config )
def add_features(df):
df['question_text'] = df['question_text'].progress_apply(lambda x:str(x))
df['total_length'] = df['question_text'].progress_apply(len)
 df['capitals'] = df['question_text'].progress_apply(lambda comment: sum(1 for c in comment if c.isupper()))
df['caps_vs_length'] = df.progress_apply(lambda row: float(row['capitals'])/float(row['total_length']),
axis=1)
 df['num_words'] = df.question_text.str.count('\S+')
 df['num_unique_words'] = df['question_text'].progress_apply(lambda comment: len(set(w for w in comment.split())))
 df['words_vs_unique'] = df['num_unique_words'] / df['num_words']
return df
def load_and_prec() :
train_df = pd.read_csv(".. /input/train.csv")
 test_df = pd.read_csv(".. /input/test.csv")
 print("Train shape : ",train_df.shape)
 print("Test shape : ",test_df.shape)
 train_df["question_text"] = train_df["question_text"].progress_apply(lambda x: clean_text(x))
test_df["question_text"] = test_df["question_text"].apply(lambda x: clean_text(x))
train_df["question_text"] = train_df["question_text"].progress_apply(lambda x: clean_numbers(x))
test_df["question_text"] = test_df["question_text"].apply(lambda x: clean_numbers(x))
train_df["question_text"] = train_df["question_text"].progress_apply(lambda x: replace_typical_misspell(x))
test_df["question_text"] = test_df["question_text"].apply(lambda x: replace_typical_misspell(x))
train = add_features(train_df)
 test = add_features(test_df)
 train_df["question_text"] = train_df["question_text"].apply(lambda x: x.lower())
 test_df["question_text"] = test_df["question_text"].apply(lambda x: x.lower())
 train_X = train_df["question_text"].fillna("_
test_X = test_df["question_text"].fillna("_
features = train[['caps_vs_length', 'words_vs_unique']].fillna(0)
 test_features = test[['caps_vs_length', 'words_vs_unique']].fillna(0)
 ss = StandardScaler()
ss.fit(np.vstack(( features, test_features)))
 features = ss.transform(features)
 test_features = ss.transform(test_features)
 tokenizer = Tokenizer(num_words=max_features)
 tokenizer.fit_on_texts(list(train_X))
train_X = tokenizer.texts_to_sequences(train_X)
 test_X = tokenizer.texts_to_sequences(test_X)
 train_X = pad_sequences(train_X, maxlen=maxlen)
 test_X = pad_sequences(test_X, maxlen=maxlen)
 train_y = train_df['target'].values
np.random.seed(SEED)
 trn_idx = np.random.permutation(len(train_X))
train_X = train_X[trn_idx]
train_y = train_y[trn_idx]
features = features[trn_idx]
return train_X, test_X, train_y, features, test_features, tokenizer.word_index 
<train_model>
Dropout_model = 0.3855
FVC_weight = 0.2
Confidence_weight = 0.2
x_train, x_test, y_train, features, test_features, word_index = load_and_prec() 
<save_model>
train = pd.read_csv('.. /input/osic-pulmonary-fibrosis-progression/train.csv' )
np.save("x_train",x_train)
 np.save("x_test",x_test)
 np.save("y_train",y_train)
 np.save("features",features)
 np.save("test_features",test_features)
 np.save("word_index.npy",word_index )<load_pretrained>
def get_tab(df):
vector = [(df.Age.values[0] - 30)/ 30]
if df.Sex.values[0] == 'male':
vector.append(0)
 else:
vector.append(1)
 if df.SmokingStatus.values[0] == 'Never smoked':
vector.extend([0,0])
 elif df.SmokingStatus.values[0] == 'Ex-smoker':
vector.extend([1,1])
 elif df.SmokingStatus.values[0] == 'Currently smokes':
vector.extend([0,1])
 else:
vector.extend([1,0])
 return np.array(vector )
x_train = np.load("x_train.npy")
 x_test = np.load("x_test.npy")
 y_train = np.load("y_train.npy")
 features = np.load("features.npy")
 test_features = np.load("test_features.npy")
 word_index = np.load("word_index.npy" ).item()<normalization>
A = {}
TAB = {}
P = []
for i, p in tqdm(enumerate(train.Patient.unique())) :
sub = train.loc[train.Patient == p, :]
fvc = sub.FVC.values
weeks = sub.Weeks.values
c = np.vstack([weeks, np.ones(len(weeks)) ] ).T
a, b = np.linalg.lstsq(c, fvc)[0]
A[p] = a
TAB[p] = get_tab(sub)
 P.append(p )
seed_everything()
glove_embeddings = load_glove(word_index)
 paragram_embeddings = load_para(word_index)
 fasttext_embeddings = load_fasttext(word_index)
 embedding_matrix = np.mean([glove_embeddings, paragram_embeddings, fasttext_embeddings], axis=0)
 del glove_embeddings, paragram_embeddings, fasttext_embeddings
gc.collect()
np.shape(embedding_matrix )<split>
class IGenerator(Sequence):
BAD_ID = ['ID00011637202177653955184', 'ID00052637202186188008618']
def __init__(self, keys, a, tab, batch_size=32):
self.keys = [k for k in keys if k not in self.BAD_ID]
self.a = a
self.tab = tab
self.batch_size = batch_size
self.train_data = {}
for p in train.Patient.values:
self.train_data[p] = os.listdir(f'.. /input/osic-pulmonary-fibrosis-progression/train/{p}/')
 def __len__(self):
return 1000
def __getitem__(self, idx):
x = []
a, tab = [], []
keys = np.random.choice(self.keys, size = self.batch_size)
 for k in keys:
try:
i = np.random.choice(self.train_data[k], size=1)[0]
img = get_img(f'.. /input/osic-pulmonary-fibrosis-progression/train/{k}/{i}')
 x.append(img)
 a.append(self.a[k])
 tab.append(self.tab[k])
 except:
print(k, i)
 x,a,tab = np.array(x), np.array(a), np.array(tab)
 x = np.expand_dims(x, axis=-1)
 return [x, tab] , a
splits = list(StratifiedKFold(n_splits=n_splits, shuffle=True, random_state=SEED ).split(x_train, y_train))
splits[:3]<choose_model_class>
Dense, Dropout, Activation, Flatten, Input, BatchNormalization, GlobalAveragePooling2D, Add, Conv2D, AveragePooling2D,
LeakyReLU, Concatenate 
)
 def get_efficientnet(model, shape):
models_dict = {
'b0': efn.EfficientNetB0(input_shape=shape,weights=None,include_top=False),
'b1': efn.EfficientNetB1(input_shape=shape,weights=None,include_top=False),
'b2': efn.EfficientNetB2(input_shape=shape,weights=None,include_top=False),
'b3': efn.EfficientNetB3(input_shape=shape,weights=None,include_top=False),
'b4': efn.EfficientNetB4(input_shape=shape,weights=None,include_top=False),
'b5': efn.EfficientNetB5(input_shape=shape,weights=None,include_top=False),
'b6': efn.EfficientNetB6(input_shape=shape,weights=None,include_top=False),
'b7': efn.EfficientNetB7(input_shape=shape,weights=None,include_top=False)
 }
return models_dict[model]
def build_model(shape=(512, 512, 1), model_class=None):
inp = Input(shape=shape)
 base = get_efficientnet(model_class, shape)
 x = base(inp)
 x = GlobalAveragePooling2D()(x)
 inp2 = Input(shape=(4,))
x2 = tf.keras.layers.GaussianNoise(0.2 )(inp2)
 x = Concatenate()([x, x2])
 x = Dropout(Dropout_model )(x)
 x = Dense(1 )(x)
 model = Model([inp, inp2] , x)
 weights = [w for w in os.listdir('.. /input/osic-model-weights')if model_class in w][0]
model.load_weights('.. /input/osic-model-weights/' + weights)
 return model
model_classes = ['b5']
models = [build_model(shape=(512, 512, 1), model_class=m)for m in model_classes]
print('Number of models: ' + str(len(models)) )
class CyclicLR(object):
def __init__(self, optimizer, base_lr=1e-3, max_lr=6e-3,
step_size=2000, mode='triangular', gamma=1.,
scale_fn=None, scale_mode='cycle', last_batch_iteration=-1):
if not isinstance(optimizer, Optimizer):
raise TypeError('{} is not an Optimizer'.format(
 type(optimizer ).__name__))
self.optimizer = optimizer
if isinstance(base_lr, list)or isinstance(base_lr, tuple):
if len(base_lr)!= len(optimizer.param_groups):
raise ValueError("expected {} base_lr, got {}".format(
 len(optimizer.param_groups), len(base_lr)))
 self.base_lrs = list(base_lr)
 else:
self.base_lrs = [base_lr] * len(optimizer.param_groups)
 if isinstance(max_lr, list)or isinstance(max_lr, tuple):
if len(max_lr)!= len(optimizer.param_groups):
raise ValueError("expected {} max_lr, got {}".format(
 len(optimizer.param_groups), len(max_lr)))
 self.max_lrs = list(max_lr)
 else:
self.max_lrs = [max_lr] * len(optimizer.param_groups)
 self.step_size = step_size
if mode not in ['triangular', 'triangular2', 'exp_range'] \
and scale_fn is None:
raise ValueError('mode is invalid and scale_fn is None')
 self.mode = mode
self.gamma = gamma
if scale_fn is None:
if self.mode == 'triangular':
self.scale_fn = self._triangular_scale_fn
self.scale_mode = 'cycle'
elif self.mode == 'triangular2':
self.scale_fn = self._triangular2_scale_fn
self.scale_mode = 'cycle'
elif self.mode == 'exp_range':
self.scale_fn = self._exp_range_scale_fn
self.scale_mode = 'iterations'
else:
self.scale_fn = scale_fn
self.scale_mode = scale_mode
self.batch_step(last_batch_iteration + 1)
 self.last_batch_iteration = last_batch_iteration
def batch_step(self, batch_iteration=None):
if batch_iteration is None:
batch_iteration = self.last_batch_iteration + 1
self.last_batch_iteration = batch_iteration
for param_group, lr in zip(self.optimizer.param_groups, self.get_lr()):
param_group['lr'] = lr
def _triangular_scale_fn(self, x):
return 1.
 def _triangular2_scale_fn(self, x):
return 1 /(2.**(x - 1))
def _exp_range_scale_fn(self, x):
return self.gamma**(x)
 def get_lr(self):
step_size = float(self.step_size)
 cycle = np.floor(1 + self.last_batch_iteration /(2 * step_size))
x = np.abs(self.last_batch_iteration / step_size - 2 * cycle + 1)
 lrs = []
param_lrs = zip(self.optimizer.param_groups, self.base_lrs, self.max_lrs)
 for param_group, base_lr, max_lr in param_lrs:
base_height =(max_lr - base_lr)* np.maximum(0,(1 - x))
if self.scale_mode == 'cycle':
lr = base_lr + base_height * self.scale_fn(cycle)
 else:
lr = base_lr + base_height * self.scale_fn(self.last_batch_iteration)
 lrs.append(lr)
 return lrs 
<choose_model_class>
tr_p, vl_p = train_test_split(P, shuffle=True, train_size = 0.8 )
embedding_dim = 300
embedding_path = '.. /save/embedding_matrix.npy'
use_pretrained_embedding = True
hidden_size = 60
gru_len = hidden_size
Routings = 4
Num_capsule = 5
Dim_capsule = 5
dropout_p = 0.25
rate_drop_dense = 0.28
LR = 0.001
T_epsilon = 1e-7
num_classes = 30
class Embed_Layer(nn.Module):
def __init__(self, embedding_matrix=None, vocab_size=None, embedding_dim=300):
super(Embed_Layer, self ).__init__()
self.encoder = nn.Embedding(vocab_size + 1, embedding_dim)
 if use_pretrained_embedding:
self.encoder.weight.data.copy_(t.from_numpy(embedding_matrix))
def forward(self, x, dropout_p=0.25):
return nn.Dropout(p=dropout_p )(self.encoder(x))
class GRU_Layer(nn.Module):
def __init__(self):
super(GRU_Layer, self ).__init__()
self.gru = nn.GRU(input_size=300,
hidden_size=gru_len,
bidirectional=True)

def init_weights(self):
ih =(param.data for name, param in self.named_parameters() if 'weight_ih' in name)
 hh =(param.data for name, param in self.named_parameters() if 'weight_hh' in name)
 b =(param.data for name, param in self.named_parameters() if 'bias' in name)
 for k in ih:
nn.init.xavier_uniform_(k)
 for k in hh:
nn.init.orthogonal_(k)
 for k in b:
nn.init.constant_(k, 0)
 def forward(self, x):
return self.gru(x)
 class Caps_Layer(nn.Module):
def __init__(self, input_dim_capsule=gru_len * 2, num_capsule=Num_capsule, dim_capsule=Dim_capsule, \
routings=Routings, kernel_size=(9, 1), share_weights=True,
activation='default', **kwargs):
super(Caps_Layer, self ).__init__(**kwargs)
 self.num_capsule = num_capsule
self.dim_capsule = dim_capsule
self.routings = routings
self.kernel_size = kernel_size
self.share_weights = share_weights
if activation == 'default':
self.activation = self.squash
else:
self.activation = nn.ReLU(inplace=True)
 if self.share_weights:
self.W = nn.Parameter(
 nn.init.xavier_normal_(t.empty(1, input_dim_capsule, self.num_capsule * self.dim_capsule)))
 else:
self.W = nn.Parameter(
 t.randn(BATCH_SIZE, input_dim_capsule, self.num_capsule * self.dim_capsule))
def forward(self, x):
if self.share_weights:
u_hat_vecs = t.matmul(x, self.W)
 else:
print('add later')
 batch_size = x.size(0)
 input_num_capsule = x.size(1)
 u_hat_vecs = u_hat_vecs.view(( batch_size, input_num_capsule,
self.num_capsule, self.dim_capsule))
u_hat_vecs = u_hat_vecs.permute(0, 2, 1, 3)
 b = t.zeros_like(u_hat_vecs[:, :, :, 0])
 for i in range(self.routings):
b = b.permute(0, 2, 1)
 c = F.softmax(b, dim=2)
 c = c.permute(0, 2, 1)
 b = b.permute(0, 2, 1)
 outputs = self.activation(t.einsum('bij,bijk->bik',(c, u_hat_vecs)))
 if i < self.routings - 1:
b = t.einsum('bik,bijk->bij',(outputs, u_hat_vecs))
return outputs
def squash(self, x, axis=-1):
s_squared_norm =(x ** 2 ).sum(axis, keepdim=True)
 scale = t.sqrt(s_squared_norm + T_epsilon)
 return x / scale
class Capsule_Main(nn.Module):
def __init__(self, embedding_matrix=None, vocab_size=None):
super(Capsule_Main, self ).__init__()
self.embed_layer = Embed_Layer(embedding_matrix, vocab_size)
 self.gru_layer = GRU_Layer()
self.gru_layer.init_weights()
self.caps_layer = Caps_Layer()
self.dense_layer = Dense_Layer()
def forward(self, content):
content1 = self.embed_layer(content)
 content2, _ = self.gru_layer(
 content1)
 content3 = self.caps_layer(content2)
 output = self.dense_layer(content3)
 return output 
<normalization>
def score(fvc_true, fvc_pred, sigma):
sigma_clip = np.maximum(sigma, 70)
 delta = np.abs(fvc_true - fvc_pred)
 delta = np.minimum(delta, 1000)
 sq2 = np.sqrt(2)
 metric =(delta / sigma_clip)*sq2 + np.log(sigma_clip* sq2)
 return np.mean(metric )
class Attention(nn.Module):
def __init__(self, feature_dim, step_dim, bias=True, **kwargs):
super(Attention, self ).__init__(**kwargs)
 self.supports_masking = True
self.bias = bias
self.feature_dim = feature_dim
self.step_dim = step_dim
self.features_dim = 0
weight = torch.zeros(feature_dim, 1)
 nn.init.xavier_uniform_(weight)
 self.weight = nn.Parameter(weight)
 if bias:
self.b = nn.Parameter(torch.zeros(step_dim))
def forward(self, x, mask=None):
feature_dim = self.feature_dim
step_dim = self.step_dim
eij = torch.mm(
 x.contiguous().view(-1, feature_dim),
self.weight
).view(-1, step_dim)
 if self.bias:
eij = eij + self.b
eij = torch.tanh(eij)
 a = torch.exp(eij)
 if mask is not None:
a = a * mask
a = a / torch.sum(a, 1, keepdim=True)+ 1e-10
weighted_input = x * torch.unsqueeze(a, -1)
 return torch.sum(weighted_input, 1)
 class NeuralNet(nn.Module):
def __init__(self):
super(NeuralNet, self ).__init__()
fc_layer = 16
fc_layer1 = 16
self.embedding = nn.Embedding(max_features, embed_size)
 self.embedding.weight = nn.Parameter(torch.tensor(embedding_matrix, dtype=torch.float32))
self.embedding.weight.requires_grad = False
self.embedding_dropout = nn.Dropout2d(0.1)
 self.lstm = nn.LSTM(embed_size, hidden_size, bidirectional=True, batch_first=True)
 self.gru = nn.GRU(hidden_size * 2, hidden_size, bidirectional=True, batch_first=True)
 self.lstm2 = nn.LSTM(hidden_size * 2, hidden_size, bidirectional=True, batch_first=True)
 self.lstm_attention = Attention(hidden_size * 2, maxlen)
 self.gru_attention = Attention(hidden_size * 2, maxlen)
 self.bn = nn.BatchNorm1d(16, momentum=0.5)
 self.linear = nn.Linear(hidden_size*8+3, fc_layer1)
 self.relu = nn.ReLU()
self.dropout = nn.Dropout(0.1)
 self.fc = nn.Linear(fc_layer**2,fc_layer)
 self.out = nn.Linear(fc_layer, 1)
 self.lincaps = nn.Linear(Num_capsule * Dim_capsule, 1)
 self.caps_layer = Caps_Layer()
def forward(self, x):
h_embedding = self.embedding(x[0])
 h_embedding = torch.squeeze(
 self.embedding_dropout(torch.unsqueeze(h_embedding, 0)))
 h_lstm, _ = self.lstm(h_embedding)
 h_gru, _ = self.gru(h_lstm)
 content3 = self.caps_layer(h_gru)
 content3 = self.dropout(content3)
 batch_size = content3.size(0)
 content3 = content3.view(batch_size, -1)
 content3 = self.relu(self.lincaps(content3))
h_lstm_atten = self.lstm_attention(h_lstm)
 h_gru_atten = self.gru_attention(h_gru)
 avg_pool = torch.mean(h_gru, 1)
 max_pool, _ = torch.max(h_gru, 1)
 f = torch.tensor(x[1], dtype=torch.float ).cuda()
conc = torch.cat(( h_lstm_atten, h_gru_atten,content3, avg_pool, max_pool,f), 1)
 conc = self.relu(self.linear(conc))
conc = self.bn(conc)
 conc = self.dropout(conc)
 out = self.out(conc)
 return out<categorify>
subs = []
for model in models:
metric = []
for q in tqdm(range(1, 10)) :
m = []
for p in vl_p:
x = []
tab = []
if p in ['ID00011637202177653955184', 'ID00052637202186188008618']:
continue
ldir = os.listdir(f'.. /input/osic-pulmonary-fibrosis-progression/train/{p}/')
 for i in ldir:
if int(i[:-4])/ len(ldir)< 0.8 and int(i[:-4])/ len(ldir)> 0.15:
x.append(get_img(f'.. /input/osic-pulmonary-fibrosis-progression/train/{p}/{i}'))
tab.append(get_tab(train.loc[train.Patient == p, :]))
if len(x)< 1:
continue
tab = np.array(tab)
 x = np.expand_dims(x, axis=-1)
 _a = model.predict([x, tab])
 a = np.quantile(_a, q / 10)
 percent_true = train.Percent.values[train.Patient == p]
fvc_true = train.FVC.values[train.Patient == p]
weeks_true = train.Weeks.values[train.Patient == p]
fvc = a *(weeks_true - weeks_true[0])+ fvc_true[0]
percent = percent_true[0] - a * abs(weeks_true - weeks_true[0])
 m.append(score(fvc_true, fvc, percent))
print(np.mean(m))
metric.append(np.mean(m))
q =(np.argmin(metric)+ 1)/ 10
sub = pd.read_csv('.. /input/osic-pulmonary-fibrosis-progression/sample_submission.csv')
 test = pd.read_csv('.. /input/osic-pulmonary-fibrosis-progression/test.csv')
 A_test, B_test, P_test,W, FVC= {}, {}, {},{},{}
STD, WEEK = {}, {}
for p in test.Patient.unique() :
x = []
tab = []
ldir = os.listdir(f'.. /input/osic-pulmonary-fibrosis-progression/test/{p}/')
 for i in ldir:
if int(i[:-4])/ len(ldir)< 0.8 and int(i[:-4])/ len(ldir)> 0.15:
x.append(get_img(f'.. /input/osic-pulmonary-fibrosis-progression/test/{p}/{i}'))
tab.append(get_tab(test.loc[test.Patient == p, :]))
if len(x)<= 1:
continue
tab = np.array(tab)
 x = np.expand_dims(x, axis=-1)
 _a = model.predict([x, tab])
 a = np.quantile(_a, q)
 A_test[p] = a
B_test[p] = test.FVC.values[test.Patient == p] - a*test.Weeks.values[test.Patient == p]
P_test[p] = test.Percent.values[test.Patient == p]
WEEK[p] = test.Weeks.values[test.Patient == p]
for k in sub.Patient_Week.values:
p, w = k.split('_')
 w = int(w)
 fvc = A_test[p] * w + B_test[p]
sub.loc[sub.Patient_Week == k, 'FVC'] = fvc
sub.loc[sub.Patient_Week == k, 'Confidence'] =(
 P_test[p] - A_test[p] * abs(WEEK[p] - w)
)
 _sub = sub[["Patient_Week","FVC","Confidence"]].copy()
subs.append(_sub )
class MyDataset(Dataset):
def __init__(self,dataset):
self.dataset = dataset
def __getitem__(self, index):
data, target = self.dataset[index]
return data, target, index
def __len__(self):
return len(self.dataset )<compute_train_metric>
N = len(subs)
 sub = subs[0].copy()
sub["FVC"] = 0
sub["Confidence"] = 0
for i in range(N):
sub["FVC"] += subs[0]["FVC"] *(1/N)
 sub["Confidence"] += subs[0]["Confidence"] *(1/N )
class FocalLoss(nn.Module):
def __init__(self, alpha=1, gamma=2, logits=True, reduction='elementwise_mean'):
super(FocalLoss, self ).__init__()
self.alpha = alpha
self.gamma = gamma
self.logits = logits
self.reduction = reduction
def forward(self, inputs, targets):
if self.logits:
BCE_loss = F.binary_cross_entropy_with_logits(inputs, targets, reduction='none')
 else:
BCE_loss = F.binary_cross_entropy(inputs, targets, reduction='none')
 pt = torch.exp(-BCE_loss)
 F_loss = self.alpha *(1-pt)**self.gamma * BCE_loss
if self.reduction is None:
return F_loss
else:
return torch.mean(F_loss )<define_variables>
sub[["Patient_Week","FVC","Confidence"]].to_csv("submission_img.csv", index=False )
def sigmoid(x):
return 1 /(1 + np.exp(-x))
train_preds = np.zeros(( len(x_train)))
 test_preds = np.zeros(( len(df_test)))
 seed_everything()
x_test_cuda = torch.tensor(x_test, dtype=torch.long ).cuda()
test = torch.utils.data.TensorDataset(x_test_cuda)
 test_loader = torch.utils.data.DataLoader(test, batch_size=batch_size, shuffle=False)
 avg_losses_f = []
avg_val_losses_f = []<data_type_conversions>
img_sub = sub[["Patient_Week","FVC","Confidence"]].copy()
for i,(train_idx, valid_idx)in enumerate(splits):
x_train = np.array(x_train)
 y_train = np.array(y_train)
 features = np.array(features)
 x_train_fold = torch.tensor(x_train[train_idx.astype(int)], dtype=torch.long ).cuda()
y_train_fold = torch.tensor(y_train[train_idx.astype(int), np.newaxis], dtype=torch.float32 ).cuda()
kfold_X_features = features[train_idx.astype(int)]
kfold_X_valid_features = features[valid_idx.astype(int)]
x_val_fold = torch.tensor(x_train[valid_idx.astype(int)], dtype=torch.long ).cuda()
y_val_fold = torch.tensor(y_train[valid_idx.astype(int), np.newaxis], dtype=torch.float32 ).cuda()
model = NeuralNet()
model.cuda()
gamma = 1.1 + i/16
loss_fn = FocalLoss(gamma=gamma)
 step_size = 300
base_lr, max_lr = 0.001, 0.003
optimizer = torch.optim.Adam(filter(lambda p: p.requires_grad, model.parameters()),
lr=max_lr)
 scheduler = CyclicLR(optimizer, base_lr=base_lr, max_lr=max_lr,
step_size=step_size, mode='exp_range',
gamma=0.99994)
 train = torch.utils.data.TensorDataset(x_train_fold, y_train_fold)
 valid = torch.utils.data.TensorDataset(x_val_fold, y_val_fold)
 train = MyDataset(train)
 valid = MyDataset(valid)
 train_loader = torch.utils.data.DataLoader(train, batch_size=batch_size, shuffle=True)
 valid_loader = torch.utils.data.DataLoader(valid, batch_size=batch_size, shuffle=False)
 print(f'Fold {i + 1}')
 for epoch in range(n_epochs):
start_time = time.time()
model.train()
avg_loss = 0.
 for i,(x_batch, y_batch, index)in enumerate(train_loader):
f = kfold_X_features[index]
y_pred = model([x_batch,f])
 if scheduler:
scheduler.batch_step()
loss = loss_fn(y_pred, y_batch)
 optimizer.zero_grad()
loss.backward()
optimizer.step()
avg_loss += loss.item() / len(train_loader)
 model.eval()
valid_preds_fold = np.zeros(( x_val_fold.size(0)))
 test_preds_fold = np.zeros(( len(df_test)))
 avg_val_loss = 0.
 for i,(x_batch, y_batch, index)in enumerate(valid_loader):
f = kfold_X_valid_features[index]
y_pred = model([x_batch,f] ).detach()
avg_val_loss += loss_fn(y_pred, y_batch ).item() / len(valid_loader)
 valid_preds_fold[i * batch_size:(i+1)* batch_size] = sigmoid(y_pred.cpu().numpy())[:, 0]
elapsed_time = time.time() - start_time
print('Epoch {}/{} \t loss={:.4f} \t val_loss={:.4f} \t time={:.2f}s'.format(
 epoch + 1, n_epochs, avg_loss, avg_val_loss, elapsed_time))
avg_losses_f.append(avg_loss)
 avg_val_losses_f.append(avg_val_loss)
 for i,(x_batch,)in enumerate(test_loader):
f = test_features[i * batch_size:(i+1)* batch_size]
y_pred = model([x_batch,f] ).detach()
test_preds_fold[i * batch_size:(i+1)* batch_size] = sigmoid(y_pred.cpu().numpy())[:, 0]
train_preds[valid_idx] = valid_preds_fold
test_preds += test_preds_fold / len(splits)
 print('All \t loss={:.4f} \t val_loss={:.4f} \t '.format(np.average(avg_losses_f),np.average(avg_val_losses_f)))
<compute_test_metric>
ROOT = ".. /input/osic-pulmonary-fibrosis-progression"
BATCH_SIZE=128
tr = pd.read_csv(f"{ROOT}/train.csv")
 tr.drop_duplicates(keep=False, inplace=True, subset=['Patient','Weeks'])
 chunk = pd.read_csv(f"{ROOT}/test.csv")
 print("add infos")
 sub = pd.read_csv(f"{ROOT}/sample_submission.csv")
 sub['Patient'] = sub['Patient_Week'].apply(lambda x:x.split('_')[0])
 sub['Weeks'] = sub['Patient_Week'].apply(lambda x: int(x.split('_')[-1]))
sub = sub[['Patient','Weeks','Confidence','Patient_Week']]
sub = sub.merge(chunk.drop('Weeks', axis=1), on="Patient" )
def bestThresshold(y_train,train_preds):
tmp = [0,0,0]
delta = 0
for tmp[0] in tqdm(np.arange(0.3, 0.601, 0.001)) :
tmp[1] = f1_score(y_train, np.array(train_preds)>tmp[0])
 if tmp[1] > tmp[2]:
delta = tmp[0]
tmp[2] = tmp[1]
print('best threshold is {:.4f} with F1 score: {:.4f}'.format(delta, tmp[2]))
return delta
delta = bestThresshold(y_train,train_preds )<save_to_csv>
tr['WHERE'] = 'train'
chunk['WHERE'] = 'val'
sub['WHERE'] = 'test'
data = tr.append([chunk, sub] )
submission = df_test[['qid']].copy()
submission['prediction'] =(test_preds > delta ).astype(int)
 submission.to_csv('submission.csv', index=False )<define_variables>
print(tr.shape, chunk.shape, sub.shape, data.shape)
 print(tr.Patient.nunique() , chunk.Patient.nunique() , sub.Patient.nunique() ,
data.Patient.nunique() )
embed_size = 300
max_features = 95000
maxlen = 70<import_modules>
data['min_week'] = data['Weeks']
data.loc[data.WHERE=='test','min_week'] = np.nan
data['min_week'] = data.groupby('Patient')['min_week'].transform('min' )
import os
import time
import numpy as np
import pandas as pd
from tqdm import tqdm
import math
from sklearn.model_selection import train_test_split
from sklearn import metrics
from sklearn.model_selection import GridSearchCV, StratifiedKFold
from sklearn.metrics import f1_score, roc_auc_score
from sklearn.decomposition import PCA
from keras.preprocessing.text import Tokenizer
from keras.preprocessing.sequence import pad_sequences
from keras.layers import Dense, Input, CuDNNLSTM, Embedding, Dropout, Activation, CuDNNGRU, Conv1D
from keras.layers import Bidirectional, GlobalMaxPool1D, GlobalMaxPooling1D, GlobalAveragePooling1D
from keras.layers import Input, Embedding, Dense, Conv2D, MaxPool2D, concatenate
from keras.layers import Reshape, Flatten, Concatenate, Dropout, SpatialDropout1D
from keras.optimizers import Adam
from keras.models import Model
from keras import backend as K
from keras.engine.topology import Layer
from keras import initializers, regularizers, constraints, optimizers, layers
from keras.layers import concatenate
from keras.callbacks import *<load_from_csv>
base = data.loc[data.Weeks == data.min_week]
base = base[['Patient','FVC']].copy()
base.columns = ['Patient','min_FVC']
base['nb'] = 1
base['nb'] = base.groupby('Patient')['nb'].transform('cumsum')
 base = base[base.nb==1]
base.drop('nb', axis=1, inplace=True )
def load_and_prec() :
train_df = pd.read_csv(".. /input/train.csv")
 test_df = pd.read_csv(".. /input/test.csv")
 print("Train shape : ",train_df.shape)
 print("Test shape : ",test_df.shape)
 train_X = train_df["question_text"].fillna("_
test_X = test_df["question_text"].fillna("_
tokenizer = Tokenizer(num_words=max_features)
 tokenizer.fit_on_texts(list(train_X))
train_X = tokenizer.texts_to_sequences(train_X)
 test_X = tokenizer.texts_to_sequences(test_X)
 train_X = pad_sequences(train_X, maxlen=maxlen)
 test_X = pad_sequences(test_X, maxlen=maxlen)
 train_y = train_df['target'].values
np.random.seed(2018)
 trn_idx = np.random.permutation(len(train_X))
train_X = train_X[trn_idx]
train_y = train_y[trn_idx]
return train_X, test_X, train_y, tokenizer.word_index<statistical_test>
data = data.merge(base, on='Patient', how='left')
 data['base_week'] = data['Weeks'] - data['min_week']
del base
def load_glove(word_index):
EMBEDDING_FILE = '.. /input/embeddings/glove.840B.300d/glove.840B.300d.txt'
def get_coefs(word,*arr): return word, np.asarray(arr, dtype='float32')
 embeddings_index = dict(get_coefs(*o.split(" ")) for o in open(EMBEDDING_FILE))
all_embs = np.stack(embeddings_index.values())
 emb_mean,emb_std = all_embs.mean() , all_embs.std()
embed_size = all_embs.shape[1]
nb_words = min(max_features, len(word_index))
embedding_matrix = np.random.normal(emb_mean, emb_std,(nb_words, embed_size))
for word, i in word_index.items() :
if i >= max_features: continue
embedding_vector = embeddings_index.get(word)
 if embedding_vector is not None: embedding_matrix[i] = embedding_vector
return embedding_matrix
def load_fasttext(word_index):
EMBEDDING_FILE = '.. /input/embeddings/wiki-news-300d-1M/wiki-news-300d-1M.vec'
def get_coefs(word,*arr): return word, np.asarray(arr, dtype='float32')
 embeddings_index = dict(get_coefs(*o.split(" ")) for o in open(EMBEDDING_FILE)if len(o)>100)
 all_embs = np.stack(embeddings_index.values())
 emb_mean,emb_std = all_embs.mean() , all_embs.std()
embed_size = all_embs.shape[1]
nb_words = min(max_features, len(word_index))
embedding_matrix = np.random.normal(emb_mean, emb_std,(nb_words, embed_size))
for word, i in word_index.items() :
if i >= max_features: continue
embedding_vector = embeddings_index.get(word)
 if embedding_vector is not None: embedding_matrix[i] = embedding_vector
return embedding_matrix
def load_para(word_index):
EMBEDDING_FILE = '.. /input/embeddings/paragram_300_sl999/paragram_300_sl999.txt'
def get_coefs(word,*arr): return word, np.asarray(arr, dtype='float32')
 embeddings_index = dict(get_coefs(*o.split(" ")) for o in open(EMBEDDING_FILE, encoding="utf8", errors='ignore')if len(o)>100)
 all_embs = np.stack(embeddings_index.values())
 emb_mean,emb_std = all_embs.mean() , all_embs.std()
embed_size = all_embs.shape[1]
nb_words = min(max_features, len(word_index))
embedding_matrix = np.random.normal(emb_mean, emb_std,(nb_words, embed_size))
for word, i in word_index.items() :
if i >= max_features: continue
embedding_vector = embeddings_index.get(word)
 if embedding_vector is not None: embedding_matrix[i] = embedding_vector
return embedding_matrix<choose_model_class>
COLS = ['Sex','SmokingStatus']
FE = []
for col in COLS:
for mod in data[col].unique() :
FE.append(mod)
 data[mod] =(data[col] == mod ).astype(int )
class Attention(Layer):
def __init__(self, step_dim,
W_regularizer=None, b_regularizer=None,
W_constraint=None, b_constraint=None,
bias=True, **kwargs):
self.supports_masking = True
self.init = initializers.get('glorot_uniform')
 self.W_regularizer = regularizers.get(W_regularizer)
 self.b_regularizer = regularizers.get(b_regularizer)
 self.W_constraint = constraints.get(W_constraint)
 self.b_constraint = constraints.get(b_constraint)
 self.bias = bias
self.step_dim = step_dim
self.features_dim = 0
super(Attention, self ).__init__(**kwargs)
 def build(self, input_shape):
assert len(input_shape)== 3
self.W = self.add_weight(( input_shape[-1],),
initializer=self.init,
name='{}_W'.format(self.name),
regularizer=self.W_regularizer,
constraint=self.W_constraint)
 self.features_dim = input_shape[-1]
if self.bias:
self.b = self.add_weight(( input_shape[1],),
initializer='zero',
name='{}_b'.format(self.name),
regularizer=self.b_regularizer,
constraint=self.b_constraint)
 else:
self.b = None
self.built = True
def compute_mask(self, input, input_mask=None):
return None
def call(self, x, mask=None):
features_dim = self.features_dim
step_dim = self.step_dim
eij = K.reshape(K.dot(K.reshape(x,(-1, features_dim)) ,
K.reshape(self.W,(features_dim, 1))),(-1, step_dim))
if self.bias:
eij += self.b
eij = K.tanh(eij)
 a = K.exp(eij)
 if mask is not None:
a *= K.cast(mask, K.floatx())
 a /= K.cast(K.sum(a, axis=1, keepdims=True)+ K.epsilon() , K.floatx())
 a = K.expand_dims(a)
 weighted_input = x * a
return K.sum(weighted_input, axis=1)
 def compute_output_shape(self, input_shape):
return input_shape[0], self.features_dim<train_model>
data['age'] =(data['Age'] - data['Age'].min())/(data['Age'].max() - data['Age'].min())
 data['BASE'] =(data['min_FVC'] - data['min_FVC'].min())/(data['min_FVC'].max() - data['min_FVC'].min())
 data['week'] =(data['base_week'] - data['base_week'].min())/(data['base_week'].max() - data['base_week'].min())
 data['percent'] =(data['Percent'] - data['Percent'].min())/(data['Percent'].max() - data['Percent'].min())
 FE += ['age','percent','week','BASE']
class CyclicLR(Callback):

 def __init__(self, base_lr=0.001, max_lr=0.006, step_size=2000., mode='triangular',
gamma=1., scale_fn=None, scale_mode='cycle'):
super(CyclicLR, self ).__init__()
self.base_lr = base_lr
self.max_lr = max_lr
self.step_size = step_size
self.mode = mode
self.gamma = gamma
if scale_fn == None:
if self.mode == 'triangular':
self.scale_fn = lambda x: 1.
 self.scale_mode = 'cycle'
elif self.mode == 'triangular2':
self.scale_fn = lambda x: 1/(2.**(x-1))
self.scale_mode = 'cycle'
elif self.mode == 'exp_range':
self.scale_fn = lambda x: gamma**(x)
 self.scale_mode = 'iterations'
else:
self.scale_fn = scale_fn
self.scale_mode = scale_mode
self.clr_iterations = 0.
 self.trn_iterations = 0.
 self.history = {}
self._reset()
def _reset(self, new_base_lr=None, new_max_lr=None,
new_step_size=None):

 if new_base_lr != None:
self.base_lr = new_base_lr
if new_max_lr != None:
self.max_lr = new_max_lr
if new_step_size != None:
self.step_size = new_step_size
self.clr_iterations = 0.
 def clr(self):
cycle = np.floor(1+self.clr_iterations/(2*self.step_size))
x = np.abs(self.clr_iterations/self.step_size - 2*cycle + 1)
 if self.scale_mode == 'cycle':
return self.base_lr +(self.max_lr-self.base_lr)*np.maximum(0,(1-x)) *self.scale_fn(cycle)
 else:
return self.base_lr +(self.max_lr-self.base_lr)*np.maximum(0,(1-x)) *self.scale_fn(self.clr_iterations)
 def on_train_begin(self, logs={}):
logs = logs or {}
if self.clr_iterations == 0:
K.set_value(self.model.optimizer.lr, self.base_lr)
 else:
K.set_value(self.model.optimizer.lr, self.clr())
 def on_batch_end(self, epoch, logs=None):
logs = logs or {}
self.trn_iterations += 1
self.clr_iterations += 1
self.history.setdefault('lr', [] ).append(K.get_value(self.model.optimizer.lr))
self.history.setdefault('iterations', [] ).append(self.trn_iterations)
 for k, v in logs.items() :
self.history.setdefault(k, [] ).append(v)
 K.set_value(self.model.optimizer.lr, self.clr())
 def f1(y_true, y_pred):

 def recall(y_true, y_pred):

 true_positives = K.sum(K.round(K.clip(y_true * y_pred, 0, 1)))
 possible_positives = K.sum(K.round(K.clip(y_true, 0, 1)))
 recall = true_positives /(possible_positives + K.epsilon())
 return recall
def precision(y_true, y_pred):

 true_positives = K.sum(K.round(K.clip(y_true * y_pred, 0, 1)))
 predicted_positives = K.sum(K.round(K.clip(y_pred, 0, 1)))
 precision = true_positives /(predicted_positives + K.epsilon())
 return precision
precision = precision(y_true, y_pred)
 recall = recall(y_true, y_pred)
 return 2*(( precision*recall)/(precision+recall+K.epsilon())) 
<define_search_model>
tr = data.loc[data.WHERE=='train']
chunk = data.loc[data.WHERE=='val']
sub = data.loc[data.WHERE=='test']
del data
def model_lstm_atten(embedding_matrix):
inp = Input(shape=(maxlen,))
x = Embedding(max_features, embed_size, weights=[embedding_matrix], trainable=False )(inp)
 x = SpatialDropout1D(0.1 )(x)
 x = Bidirectional(CuDNNLSTM(40, return_sequences=True))(x)
 y = Bidirectional(CuDNNGRU(40, return_sequences=True))(x)
 atten_1 = Attention(maxlen )(x)
 atten_2 = Attention(maxlen )(y)
 avg_pool = GlobalAveragePooling1D()(y)
 max_pool = GlobalMaxPooling1D()(y)
 conc = concatenate([atten_1, atten_2, avg_pool, max_pool])
 conc = Dense(16, activation="relu" )(conc)
 conc = Dropout(0.1 )(conc)
 outp = Dense(1, activation="sigmoid" )(conc)
 model = Model(inputs=inp, outputs=outp)
 model.compile(loss='binary_crossentropy', optimizer='adam', metrics=[f1])
 return model<predict_on_test>
C1, C2 = tf.constant(70, dtype='float32'), tf.constant(1000, dtype="float32")
 def score(y_true, y_pred):
tf.dtypes.cast(y_true, tf.float32)
 tf.dtypes.cast(y_pred, tf.float32)
 sigma = y_pred[:, 2] - y_pred[:, 0]
fvc_pred = y_pred[:, 1]
sigma_clip = tf.maximum(sigma, C1)
 delta = tf.abs(y_true[:, 0] - fvc_pred)
 delta = tf.minimum(delta, C2)
 sq2 = tf.sqrt(tf.dtypes.cast(2, dtype=tf.float32))
metric =(delta / sigma_clip)*sq2 + tf.math.log(sigma_clip* sq2)
 return K.mean(metric)
 def qloss(y_true, y_pred):
qs = [0.2, 0.50, 0.8]
q = tf.constant(np.array([qs]), dtype=tf.float32)
 e = y_true - y_pred
v = tf.maximum(q*e,(q-1)*e)
 return K.mean(v)
 def mloss(_lambda):
def loss(y_true, y_pred):
return _lambda * qloss(y_true, y_pred)+(1 - _lambda)*score(y_true, y_pred)
 return loss
def make_model(nh):
z = L.Input(( nh,), name="Patient")
 x = L.Dense(100, activation="relu", name="d1" )(z)
 x = L.Dense(100, activation="relu", name="d2" )(x)
 p1 = L.Dense(3, activation="linear", name="p1" )(x)
 p2 = L.Dense(3, activation="relu", name="p2" )(x)
 preds = L.Lambda(lambda x: x[0] + tf.cumsum(x[1], axis=1),
name="preds" )([p1, p2])
 model = M.Model(z, preds, name="CNN")
 model.compile(loss=mloss(0.65), optimizer=tf.keras.optimizers.Adam(lr=0.1, beta_1=0.9, beta_2=0.999, epsilon=None, decay=0.01, amsgrad=False), metrics=[score])
 return model
def train_pred(model, train_X, train_y, val_X, val_y, epochs=2, callback=None):
for e in range(epochs):
model.fit(train_X, train_y, batch_size=512, epochs=1, validation_data=(val_X, val_y), callbacks = callback, verbose=0)
 pred_val_y = model.predict([val_X], batch_size=1024, verbose=0)
 best_score = metrics.f1_score(val_y,(pred_val_y > 0.33 ).astype(int))
print("Epoch: ", e, "- Val F1 Score: {:.4f}".format(best_score))
pred_test_y = model.predict([test_X], batch_size=1024, verbose=0)
 print('=' * 60)
 return pred_val_y, pred_test_y, best_score<split>
y = tr['FVC'].values
z = tr[FE].values
ze = sub[FE].values
nh = z.shape[1]
pe = np.zeros(( ze.shape[0], 3))
pred = np.zeros(( z.shape[0], 3))
train_X, test_X, train_y, word_index = load_and_prec()
embedding_matrix_1 = load_glove(word_index)
 embedding_matrix_3 = load_para(word_index )<normalization>
NFOLD = 5
kf = KFold(n_splits=NFOLD )
embedding_matrix = np.mean([embedding_matrix_1, embedding_matrix_3], axis = 0)
 np.shape(embedding_matrix )<normalization>
%%time
cnt = 0
EPOCHS = 855
for tr_idx, val_idx in kf.split(z):
cnt += 1
print(f"FOLD {cnt}")
 net = make_model(nh)
 net.fit(z[tr_idx], y[tr_idx], batch_size=BATCH_SIZE, epochs=EPOCHS,
validation_data=(z[val_idx], y[val_idx]), verbose=0)
 print("train", net.evaluate(z[tr_idx], y[tr_idx], verbose=0, batch_size=BATCH_SIZE))
print("val", net.evaluate(z[val_idx], y[val_idx], verbose=0, batch_size=BATCH_SIZE))
print("predict val...")
 pred[val_idx] = net.predict(z[val_idx], batch_size=BATCH_SIZE, verbose=0)
 print("predict test...")
 pe += net.predict(ze, batch_size=BATCH_SIZE, verbose=0)/ NFOLD
pca_dims = PCA()
pca_dims.fit(embedding_matrix)
 cumsum = np.cumsum(pca_dims.explained_variance_ratio_)
 embed_size = np.argmax(cumsum >= 0.95)+ 1
print("new embed_size", embed_size)
 pca = PCA(n_components=embed_size)
 embedding_matrix = pca.fit_transform(embedding_matrix )<compute_train_metric>
sigma_opt = mean_absolute_error(y, pred[:, 1])
 unc = pred[:,2] - pred[:, 0]
sigma_mean = np.mean(unc)
 print(sigma_opt, sigma_mean )
def threshold_search(y_true, y_proba):
best_threshold = 0
best_score = 0
for threshold in [i * 0.01 for i in range(100)]:
score = f1_score(y_true=y_true, y_pred=y_proba > threshold)
 if score > best_score:
best_threshold = threshold
best_score = score
search_result = {'threshold': best_threshold, 'f1': best_score}
return search_result<split>
sub['FVC1'] = 1.*pe[:, 1]
sub['Confidence1'] = pe[:, 2] - pe[:, 0]
subm = sub[['Patient_Week','FVC','Confidence','FVC1','Confidence1']].copy()
subm.loc[~subm.FVC1.isnull() ].head(10 )
DATA_SPLIT_SEED = 2018
clr = CyclicLR(base_lr=0.001, max_lr=0.002,
step_size=300., mode='exp_range',
gamma=0.99994)
 train_meta = np.zeros(train_y.shape)
 test_meta = np.zeros(test_X.shape[0])
 splits = list(StratifiedKFold(n_splits=4, shuffle=True, random_state=DATA_SPLIT_SEED ).split(train_X, train_y))
for idx,(train_idx, valid_idx)in enumerate(splits):
X_train = train_X[train_idx]
y_train = train_y[train_idx]
X_val = train_X[valid_idx]
y_val = train_y[valid_idx]
model = model_lstm_atten(embedding_matrix)
 pred_val_y, pred_test_y, best_score = train_pred(model, X_train, y_train, X_val, y_val, epochs = 8, callback = [clr,])
 train_meta[valid_idx] = pred_val_y.reshape(-1)
 test_meta += pred_test_y.reshape(-1)/ len(splits )<save_to_csv>
subm.loc[~subm.FVC1.isnull() ,'FVC'] = subm.loc[~subm.FVC1.isnull() ,'FVC1']
if sigma_mean<70:
subm['Confidence'] = sigma_opt
else:
subm.loc[~subm.FVC1.isnull() ,'Confidence'] = subm.loc[~subm.FVC1.isnull() ,'Confidence1']
sub = pd.read_csv('.. /input/sample_submission.csv')
 sub.prediction = test_meta > 0.33
sub.to_csv("submission.csv", index=False )<compute_test_metric>
otest = pd.read_csv('.. /input/osic-pulmonary-fibrosis-progression/test.csv')
 for i in range(len(otest)) :
subm.loc[subm['Patient_Week']==otest.Patient[i]+'_'+str(otest.Weeks[i]), 'FVC'] = otest.FVC[i]
subm.loc[subm['Patient_Week']==otest.Patient[i]+'_'+str(otest.Weeks[i]), 'Confidence'] = 0.1
f1_score(y_true=train_y, y_pred=train_meta > 0.33 )<set_options>
subm[["Patient_Week","FVC","Confidence"]].to_csv("submission_regression.csv", index=False )
%matplotlib inline
pd.set_option('max_colwidth',400)
 warnings.filterwarnings("ignore", message="F-score is ill-defined and being set to 0.0 due to no predicted samples.")
 np.seterr(divide='ignore')
<load_from_csv>
reg_sub = subm[["Patient_Week","FVC","Confidence"]].copy()
path = '.. /input/'
train = pd.read_csv(os.path.join(path,"train.csv"))
test = pd.read_csv(os.path.join(path,"test.csv"))
sub = pd.read_csv(os.path.join(path,'sample_submission.csv'))<count_values>
df1 = img_sub.sort_values(by=['Patient_Week'], ascending=True ).reset_index(drop=True)
 df2 = reg_sub.sort_values(by=['Patient_Week'], ascending=True ).reset_index(drop=True )
train["target"].value_counts()<split>
df = df1[['Patient_Week']].copy()
df['FVC'] = FVC_weight*df1['FVC'] +(1-FVC_weight)*df2['FVC']
df['Confidence'] = Confidence_weight*df1['Confidence'] +(1-Confidence_weight)*df2['Confidence']
df.head()
print('Average word length of questions in train is {0:.0f}.'.format(np.mean(train['question_text'].apply(lambda x: len(x.split())))))
 print('Average word length of questions in test is {0:.0f}.'.format(np.mean(test['question_text'].apply(lambda x: len(x.split())))) )<string_transform>
df.to_csv('submission.csv', index=False )
print('Max word length of questions in train is {0:.0f}.'.format(np.max(train['question_text'].apply(lambda x: len(x.split())))))
 print('Max word length of questions in test is {0:.0f}.'.format(np.max(test['question_text'].apply(lambda x: len(x.split())))) )<compute_test_metric>
df_issa1 = df.copy()
print('Average character length of questions in train is {0:.0f}.'.format(np.mean(train['question_text'].apply(lambda x: len(x)))))
 print('Average character length of questions in test is {0:.0f}.'.format(np.mean(test['question_text'].apply(lambda x: len(x)))) )<define_variables>
Dropout_model = 0.385
FVC_weight = 0.2
Confidence_weight = 0
!pip install.. /input/kerasapplications/keras-team-keras-applications-3b180cb -f./ --no-index
!pip install.. /input/efficientnet/efficientnet-1.1.0/ -f./ --no-index
puncts = [',', '.', '"', ':', ')', '(', '-', '!', '?', '|', ';', "'", '$', '&', '/', '[', ']', '>', '%', '=', '
'·', '_', '{', '}', '©', '^', '®', '`', '<', '→', '°', '€', '™', '›', '♥', '←', '×', '§', '″', '′', 'Â', '█', '½', 'à', '…',
'“', '★', '”', '–', '●', 'â', '►', '−', '¢', '²', '¬', '░', '¶', '↑', '±', '¿', '▾', '═', '¦', '║', '―', '¥', '▓', '—', '‹', '─',
'▒', '：', '¼', '⊕', '▼', '▪', '†', '■', '’', '▀', '¨', '▄', '♫', '☆', 'é', '¯', '♦', '¤', '▲', 'è', '¸', '¾', 'Ã', '⋅', '‘', '∞',
'∙', '）', '↓', '、', '│', '（', '»', '，', '♪', '╩', '╚', '³', '・', '╦', '╣', '╔', '╗', '▬', '❤', 'ï', 'Ø', '¹', '≤', '‡', '√', ]
def clean_text(x):
x = str(x)
 for punct in puncts:
x = x.replace(punct, f' {punct} ')
 return x
def clean_numbers(x):
if bool(re.search(r'\d', x)) :
x = re.sub('[0-9]{5,}', '
x = re.sub('[0-9]{4}', '
x = re.sub('[0-9]{3}', '
x = re.sub('[0-9]{2}', '
return x
mispell_dict = {"aren't" : "are not",
"can't" : "cannot",
"couldn't" : "could not",
"didn't" : "did not",
"doesn't" : "does not",
"don't" : "do not",
"hadn't" : "had not",
"hasn't" : "has not",
"haven't" : "have not",
"he'd" : "he would",
"he'll" : "he will",
"he's" : "he is",
"i'd" : "I would",
"i'd" : "I had",
"i'll" : "I will",
"i'm" : "I am",
"isn't" : "is not",
"it's" : "it is",
"it'll":"it will",
"i've" : "I have",
"let's" : "let us",
"mightn't" : "might not",
"mustn't" : "must not",
"shan't" : "shall not",
"she'd" : "she would",
"she'll" : "she will",
"she's" : "she is",
"shouldn't" : "should not",
"that's" : "that is",
"there's" : "there is",
"they'd" : "they would",
"they'll" : "they will",
"they're" : "they are",
"they've" : "they have",
"we'd" : "we would",
"we're" : "we are",
"weren't" : "were not",
"we've" : "we have",
"what'll" : "what will",
"what're" : "what are",
"what's" : "what is",
"what've" : "what have",
"where's" : "where is",
"who'd" : "who would",
"who'll" : "who will",
"who're" : "who are",
"who's" : "who is",
"who've" : "who have",
"won't" : "will not",
"wouldn't" : "would not",
"you'd" : "you would",
"you'll" : "you will",
"you're" : "you are",
"you've" : "you have",
"'re": " are",
"wasn't": "was not",
"we'll":" will",
"didn't": "did not",
"tryin'":"trying",
'\u200b': '',
'…': '',
'\ufeff': '',
'करना': '',
'है': ''}
for coin in ['Litecoin', 'altcoin', 'altcoins', 'coinbase', 'litecoin', 'Unocoin', 'Dogecoin', 'cryptocoin', 'Altcoins', 'filecoin', 'Altcoin', 'cryptocoins',
'Altacoin', 'Dentacoin', 'Bytecoin', 'Siacoin', 'Onecoin', 'dogecoin', 'unocoin', 'siacoin', 'litecoins', 'Filecoin', 'Buyucoin', 'Litecoins',
'Laxmicoin', 'shtcoins', 'Sweatcoin', 'Skycoin', 'vitrocoin', 'Monacoin', 'Litcoin', 'reddcoin', 'freebitcoin', 'Namecoin', 'plexcoin', 'Onecoins',
'daikicoin', 'Gainbitcoin', 'Gatecoin', 'Plexcoin', 'peercoin', 'coinsecure', 'dogecoins', 'cointries', 'Zcoin', 'genxcoin', 'Frazcoin', 'frazcoin',
'coinify', 'Nagricoin', 'OKcoin', 'Presscoins', 'Dagcoin', 'batcoin', 'Spectrocoin', 'Travelflexcoin', 'ecoin', 'Minexcoin', 'Kashhcoin', 'coinone',
'octacoin', 'coinsides', 'zabercoin', 'ADZcoin', 'cyptocoin', 'bitecoin', 'Bitecoin', 'Emercoin', 'tegcoin', 'flipcoin', 'Gridcoin', 'Facecoin',
'Ravencoins', 'digicoin', 'bitcoincash', 'Vitrocoin', 'Livecoin', 'dashcoin', 'Fedcoin', 'litcoins', 'Webcoin', 'coinspot', 'bitoxycoin', 'peercoins',
'Ucoin', 'ALTcoins', 'coincidece', 'dagcoin', 'Giracoin', 'coincheck', 'Swisscoin', 'butcoin', 'neocoin', 'mintcoin', 'Myriadcoin', 'Viacoin', 'jiocoin',
'Potcoin', 'bibitcoin', 'gainbitcoin', 'altercoins', 'coinburn', 'Kodakcoin', 'Bcoin', 'Kucoin', 'Operacoin', 'Lomocoin', 'dentacoin', 'Nyancoin',
'Jiocoin', 'Indicoin', 'coinsidered', 'Vertcoin', 'Maidsafecoin', 'coindelta', 'coinfirm', 'coinvest', 'bixcoin', 'litcoin', 'Dogecoins', 'Unicoin',
'Rothscoin', 'localbitcoins', 'groestlcoin', 'sibcoin', 'Travelercoin', 'Vericoin', 'bytecoin', 'Bananacoin', 'PACcoin']:
mispell_dict[coin] = 'bitcoin'
def _get_mispell(mispell_dict):
mispell_re = re.compile('(%s)' % '|'.join(mispell_dict.keys()))
return mispell_dict, mispell_re
mispellings, mispellings_re = _get_mispell(mispell_dict)
 def replace_typical_misspell(text):
def replace(match):
return mispellings[match.group(0)]
return mispellings_re.sub(replace, text)
 train["question_text"] = train["question_text"].apply(lambda x: clean_text(x.lower()))
test["question_text"] = test["question_text"].apply(lambda x: clean_text(x.lower()))
train["question_text"] = train["question_text"].apply(lambda x: clean_numbers(x))
test["question_text"] = test["question_text"].apply(lambda x: clean_numbers(x))
train["question_text"] = train["question_text"].apply(lambda x: replace_typical_misspell(x))
test["question_text"] = test["question_text"].apply(lambda x: replace_typical_misspell(x))<train_model>
def seed_everything(seed=2020):
random.seed(seed)
 os.environ['PYTHONHASHSEED'] = str(seed)
 np.random.seed(seed)
 tf.random.set_seed(seed)
 seed_everything(42)
 config = tf.compat.v1.ConfigProto()
config.gpu_options.allow_growth = True
session = tf.compat.v1.Session(config=config)
 train = pd.read_csv('.. /input/osic-pulmonary-fibrosis-progression/train.csv' )
max_features = 120000
tk = Tokenizer(lower = True, filters='', num_words=max_features)
 full_text = list(train['question_text'].values)+ list(test['question_text'].values)
 tk.fit_on_texts(full_text )<string_transform>
def expandFVC_Percent(DS):
DS['FVC_Percent'] = DS['FVC'] / DS['Percent']
return DS
train_tokenized = tk.texts_to_sequences(train['question_text'].fillna('missing'))
test_tokenized = tk.texts_to_sequences(test['question_text'].fillna('missing'))<string_transform>
def expandFE(data_set):
data_set['MinWeeks'] = data_set.groupby('Patient')['Weeks'].transform('min')
 sub_tr = data_set.loc[data_set['Weeks']==data_set['MinWeeks']]
sub_tr['MinFVC'] = sub_tr['FVC']
sub_tr = sub_tr[['Patient', 'MinFVC']]
merged = data_set.merge(sub_tr, on='Patient', how='outer')
 data_set=merged
data_set['MinFVC'] =(data_set['MinFVC'] - data_set['MinFVC'].min())/(data_set['MinFVC'].max() -data_set['MinFVC'].min())
 print(data_set.sample(5))
return data_set
max_len = 72
X_train = pad_sequences(train_tokenized, maxlen=max_len)
 X_test = pad_sequences(test_tokenized, maxlen=max_len )<prepare_x_and_y>
train = expandFE(train)
y_train = train['target'].values<compute_test_metric>
class IGenerator(Sequence):
BAD_ID = ['ID00011637202177653955184', 'ID00052637202186188008618']
def __init__(self, keys, a, tab, batch_size=8):
self.keys = [k for k in keys if k not in self.BAD_ID]
self.a = a
self.tab = tab
self.batch_size = batch_size
self.train_data = {}
for p in train.Patient.values:
self.train_data[p] = os.listdir(f'.. /input/osic-pulmonary-fibrosis-progression/train/{p}/')
 def __len__(self):
return math.ceil(len(self.keys)/ float(self.batch_size))
def __getitem__(self, idx):
x = []
a, tab = [], []
keys = np.random.choice(self.keys, size = self.batch_size)
 for k in keys:
try:
self.train_data[k].sort()
mx_len = len(self.train_data[k])
 i = np.random.choice(self.train_data[k][mx_len//3:mx_len//3*2], size=1)[0]
img = get_img(f'.. /input/osic-pulmonary-fibrosis-progression/train/{k}/{i}')
 x.append(img)
 a.append(self.a[k])
 tab.append(self.tab[k])
 except:
print(k, i)
 x, a, tab = np.array(x), np.array(a), np.array(tab)
 x = np.expand_dims(x, axis=-1)
 return [x, tab] , a
def sigmoid(x):
return 1 /(1 + np.exp(-x))<split>
Dense, Dropout, Activation, Flatten, Input, BatchNormalization, GlobalAveragePooling2D, Add, Conv2D, AveragePooling2D,
LeakyReLU, Concatenate 
)
 def get_efficientnet(model, shape):
models_dict = {
'b0': efn.EfficientNetB0(input_shape=shape,weights=None,include_top=False),
'b1': efn.EfficientNetB1(input_shape=shape,weights=None,include_top=False),
'b2': efn.EfficientNetB2(input_shape=shape,weights=None,include_top=False),
'b3': efn.EfficientNetB3(input_shape=shape,weights=None,include_top=False),
'b4': efn.EfficientNetB4(input_shape=shape,weights=None,include_top=False),
'b5': efn.EfficientNetB5(input_shape=shape,weights=None,include_top=False),
'b6': efn.EfficientNetB6(input_shape=shape,weights=None,include_top=False),
'b7': efn.EfficientNetB7(input_shape=shape,weights=None,include_top=False)
 }
return models_dict[model]
def build_model(shape=(512, 512, 1), model_class=None):
inp = Input(shape=shape)
 base = get_efficientnet(model_class, shape)
 x = base(inp)
 x = GlobalAveragePooling2D()(x)
 inp2 = Input(shape=(5,))
x2 = tf.keras.layers.GaussianNoise(0.2 )(inp2)
 x = Concatenate()([x, x2])
 x = Dropout(Dropout_model )(x)
 x = Dense(1 )(x)
 model = Model([inp, inp2] , x)
 return model
splits = list(StratifiedKFold(n_splits=5, shuffle=True, random_state=10 ).split(X_train, y_train))<statistical_test>
efn_path = ".. /input/trainefn/efn.ckpt"
model.load_weights(efn_path )
embed_size = 300
embedding_path = ".. /input/embeddings/glove.840B.300d/glove.840B.300d.txt"
def get_coefs(word,*arr): return word, np.asarray(arr, dtype='float32')
 embedding_index = dict(get_coefs(*o.split(" ")) for o in open(embedding_path, encoding='utf-8', errors='ignore'))
emb_mean,emb_std = -0.005838499, 0.48782197
word_index = tk.word_index
nb_words = min(max_features, len(word_index))
embedding_matrix = np.random.normal(emb_mean, emb_std,(nb_words + 1, embed_size))
for word, i in word_index.items() :
if i >= max_features: continue
embedding_vector = embedding_index.get(word)
 if embedding_vector is not None: embedding_matrix[i] = embedding_vector<compute_train_metric>
def score(fvc_true, fvc_pred, sigma):
sigma_clip = np.maximum(sigma, 70)
 delta = np.abs(fvc_true - fvc_pred)
 delta = np.minimum(delta, 1000)
 sq2 = np.sqrt(2)
 metric =(delta / sigma_clip)*sq2 + np.log(sigma_clip* sq2)
 return np.mean(metric)
 subs = []
q = -1
embedding_path = ".. /input/embeddings/paragram_300_sl999/paragram_300_sl999.txt"
def get_coefs(word,*arr): return word, np.asarray(arr, dtype='float32')
 embedding_index = dict(get_coefs(*o.split(" ")) for o in open(embedding_path, encoding='utf-8', errors='ignore')if len(o)>100)
 emb_mean,emb_std = -0.0053247833, 0.49346462
embedding_matrix1 = np.random.normal(emb_mean, emb_std,(nb_words + 1, embed_size))
for word, i in word_index.items() :
if i >= max_features: continue
embedding_vector = embedding_index.get(word)
 if embedding_vector is not None: embedding_matrix1[i] = embedding_vector<statistical_test>
q = -1
with open('.. /input/trainefn/q.txt', 'r')as f:
q=float(f.readlines() [0].strip())
 print(q )
embedding_path = ".. /input/embeddings/wiki-news-300d-1M/wiki-news-300d-1M.vec"
def get_coefs(word,*arr): return word, np.asarray(arr, dtype='float32')
 embedding_index = dict(get_coefs(*o.split(" ")) for o in open(embedding_path, encoding='utf-8', errors='ignore')if len(o)>100)
 emb_mean,emb_std = -0.0033469985, 0.109855495
embedding_matrix2 = np.random.normal(emb_mean, emb_std,(nb_words + 1, embed_size))
for word, i in word_index.items() :
if i >= max_features: continue
embedding_vector = embedding_index.get(word)
 if embedding_vector is not None: embedding_matrix2[i] = embedding_vector<compute_test_metric>
sub = pd.read_csv('.. /input/osic-pulmonary-fibrosis-progression/sample_submission.csv')
 test = pd.read_csv('.. /input/osic-pulmonary-fibrosis-progression/test.csv')
 A_test, B_test, P_test,W, FVC= {}, {}, {},{},{}
STD, WEEK = {}, {}
embedding_matrix = np.mean([embedding_matrix, embedding_matrix1, embedding_matrix2], axis=0)
 print(embedding_matrix.shape)
 del embedding_matrix1, embedding_matrix2<normalization>
N = len(subs)
 print(N)
 sub = subs[0].copy()
sub["FVC"] = 0
sub["Confidence"] = 0
for i in range(N):
sub["FVC"] += subs[0]["FVC"] *(1/N)
 sub["Confidence"] += subs[0]["Confidence"] *(1/N)
 sub[["Patient_Week","FVC","Confidence"]].to_csv("submission_img.csv", index=False)
 img_sub = sub[["Patient_Week","FVC","Confidence"]].copy()
print(img_sub.sample(5))
class Attention(nn.Module):
def __init__(self, feature_dim, step_dim, bias=True, **kwargs):
super(Attention, self ).__init__(**kwargs)
 self.supports_masking = True
self.bias = bias
self.feature_dim = feature_dim
self.step_dim = step_dim
self.features_dim = 0
weight = torch.zeros(feature_dim, 1)
 nn.init.xavier_uniform_(weight)
 self.weight = nn.Parameter(weight)
 if bias:
self.b = nn.Parameter(torch.zeros(step_dim))
def forward(self, x, mask=None):
feature_dim = self.feature_dim
step_dim = self.step_dim
eij = torch.mm(
 x.contiguous().view(-1, feature_dim),
self.weight
).view(-1, step_dim)
 if self.bias:
eij = eij + self.b
eij = torch.tanh(eij)
 a = torch.exp(eij)
 if mask is not None:
a = a * mask
a = a / torch.sum(a, 1, keepdim=True)+ 1e-10
weighted_input = x * torch.unsqueeze(a, -1)
 return torch.sum(weighted_input, 1)
 class NeuralNet(nn.Module):
def __init__(self):
super(NeuralNet, self ).__init__()
hidden_size = 128
self.embedding = nn.Embedding(max_features, embed_size)
 self.embedding.weight = nn.Parameter(torch.tensor(embedding_matrix, dtype=torch.float32))
self.embedding.weight.requires_grad = False
self.embedding_dropout = nn.Dropout2d(0.1)
 self.lstm = nn.LSTM(embed_size, hidden_size, bidirectional=True, batch_first=True)
 self.gru = nn.GRU(hidden_size*2, hidden_size, bidirectional=True, batch_first=True)
 self.lstm_attention = Attention(hidden_size*2, max_len)
 self.gru_attention = Attention(hidden_size*2, max_len)
 self.linear = nn.Linear(1536, 256)
 self.linear1 = nn.Linear(256, 32)
 self.relu = nn.ReLU()
self.dropout = nn.Dropout(0.1)
 self.out = nn.Linear(32, 1)
 def forward(self, x):
h_embedding = self.embedding(x)
 h_embedding = torch.squeeze(self.embedding_dropout(torch.unsqueeze(h_embedding, 0)))
 h_lstm, _ = self.lstm(h_embedding)
 h_gru, _ = self.gru(h_lstm)
 h_lstm_atten = self.lstm_attention(h_lstm)
 h_gru_atten = self.gru_attention(h_gru)
 avg_pool_g = torch.mean(h_gru, 1)
 max_pool_g, _ = torch.max(h_gru, 1)
 avg_pool_l = torch.mean(h_lstm, 1)
 max_pool_l, _ = torch.max(h_lstm, 1)
 conc = torch.cat(( h_lstm_atten, h_gru_atten, avg_pool_g, max_pool_g, avg_pool_l, max_pool_l), 1)
 conc = self.relu(self.linear(conc))
conc = self.dropout(conc)
 conc = self.relu(self.linear1(conc))
out = self.out(conc)
 return out<feature_engineering>
ROOT = ".. /input/osic-pulmonary-fibrosis-progression"
BATCH_SIZE=128
tr = pd.read_csv(f"{ROOT}/train.csv")
 tr.drop_duplicates(keep=False, inplace=True, subset=['Patient','Weeks'])
 chunk = pd.read_csv(f"{ROOT}/test.csv")
 print("add infos")
 sub = pd.read_csv(f"{ROOT}/sample_submission.csv")
 sub['Patient'] = sub['Patient_Week'].apply(lambda x:x.split('_')[0])
 sub['Weeks'] = sub['Patient_Week'].apply(lambda x: int(x.split('_')[-1]))
sub = sub[['Patient','Weeks','Confidence','Patient_Week']]
sub = sub.merge(chunk.drop('Weeks', axis=1), on="Patient")
 tr['WHERE'] = 'train'
chunk['WHERE'] = 'val'
sub['WHERE'] = 'test'
data = tr.append([chunk, sub])
 print(tr.shape, chunk.shape, sub.shape, data.shape)
 print(tr.Patient.nunique() , chunk.Patient.nunique() , sub.Patient.nunique() ,
data.Patient.nunique() )
m = NeuralNet()
x_test_cuda = torch.tensor(X_test, dtype=torch.long ).cuda()
test = torch.utils.data.TensorDataset(x_test_cuda)
 batch_size = 512
test_loader = torch.utils.data.DataLoader(test, batch_size=batch_size, shuffle=False)
 seed=1029
def seed_everything(seed=1234):
random.seed(seed)
 os.environ['PYTHONHASHSEED'] = str(seed)
 np.random.seed(seed)
 torch.manual_seed(seed)
 torch.cuda.manual_seed(seed)
 torch.backends.cudnn.deterministic = True
seed_everything(seed )<train_model>
data['min_week'] = data['Weeks']
data.loc[data.WHERE=='test','min_week'] = np.nan
data['min_week'] = data.groupby('Patient')['min_week'].transform('min')
 base = data.loc[data.Weeks == data.min_week]
base = base[['Patient','FVC']].copy()
base.columns = ['Patient','min_FVC']
base['nb'] = 1
base['nb'] = base.groupby('Patient')['nb'].transform('cumsum')
 base = base[base.nb==1]
base.drop('nb', axis=1, inplace=True)
 data = data.merge(base, on='Patient', how='left')
 data['base_week'] = data['Weeks'] - data['min_week']
del base
COLS = ['Sex','SmokingStatus']
FE = []
for col in COLS:
for mod in data[col].unique() :
FE.append(mod)
 data[mod] =(data[col] == mod ).astype(int)
 data['age'] =(data['Age'] - data['Age'].min())/(data['Age'].max() - data['Age'].min())
 data['BASE'] =(data['min_FVC'] - data['min_FVC'].min())/(data['min_FVC'].max() - data['min_FVC'].min())
 data['week'] =(data['base_week'] - data['base_week'].min())/(data['base_week'].max() - data['base_week'].min())
 data['percent'] =(data['Percent'] - data['Percent'].min())/(data['Percent'].max() - data['Percent'].min())
 data['FVC_Percent'] = data['FVC'] / data['Percent']
FE += ['age','percent','week','BASE']
tr = data.loc[data.WHERE=='train']
chunk = data.loc[data.WHERE=='val']
sub = data.loc[data.WHERE=='test']
del data
C1, C2 = tf.constant(70, dtype='float32'), tf.constant(1000, dtype="float32")
 def score(y_true, y_pred):
tf.dtypes.cast(y_true, tf.float32)
 tf.dtypes.cast(y_pred, tf.float32)
 sigma = y_pred[:, 2] - y_pred[:, 0]
fvc_pred = y_pred[:, 1]
sigma_clip = tf.maximum(sigma, C1)
 delta = tf.abs(y_true[:, 0] - fvc_pred)
 delta = tf.minimum(delta, C2)
 sq2 = tf.sqrt(tf.dtypes.cast(2, dtype=tf.float32))
metric =(delta / sigma_clip)*sq2 + tf.math.log(sigma_clip* sq2)
 return K.mean(metric)
 def qloss(y_true, y_pred):
qs = [0.2, 0.50, 0.8]
q = tf.constant(np.array([qs]), dtype=tf.float32)
 e = y_true - y_pred
v = tf.maximum(q*e,(q-1)*e)
 return K.mean(v)
 def mloss(_lambda):
def loss(y_true, y_pred):
return _lambda * qloss(y_true, y_pred)+(1 - _lambda)*score(y_true, y_pred)
 return loss
def make_model(nh):
z = L.Input(( nh,), name="Patient")
 x = L.Dense(100, activation="relu", name="d1" )(z)
 x = L.Dense(100, activation="relu", name="d2" )(x)
 p1 = L.Dense(3, activation="linear", name="p1" )(x)
 p2 = L.Dense(3, activation="relu", name="p2" )(x)
 preds = L.Lambda(lambda x: x[0] + tf.cumsum(x[1], axis=1),
name="preds" )([p1, p2])
 model = M.Model(z, preds, name="CNN")
 model.compile(loss=mloss(0.65), optimizer=tf.keras.optimizers.Adam(lr=0.1, beta_1=0.9, beta_2=0.999, epsilon=None, decay=0.01, amsgrad=False), metrics=[score])
 return model
print(FE )
def train_model_full(X_train=X_train, y_train=y_train, splits=splits, n_epochs=5, batch_size=batch_size, validate=False):
train_preds = np.zeros(len(X_train))
test_preds = np.zeros(( len(test), len(splits)))
 scores = []
for i,(train_idx, valid_idx)in enumerate(splits):
print(f'Fold {i + 1}.{time.ctime() }')
 x_train_fold = torch.tensor(X_train[train_idx], dtype=torch.long ).cuda()
y_train_fold = torch.tensor(y_train[train_idx, np.newaxis], dtype=torch.float32 ).cuda()
x_val_fold = torch.tensor(X_train[valid_idx], dtype=torch.long ).cuda()
y_val_fold = torch.tensor(y_train[valid_idx, np.newaxis], dtype=torch.float32 ).cuda()
seed_everything(seed + i)
 model = NeuralNet()
model.cuda()
optimizer = torch.optim.Adam(model.parameters())
 loss_fn = torch.nn.BCEWithLogitsLoss(reduction='mean' ).cuda()
train_dataset = torch.utils.data.TensorDataset(x_train_fold, y_train_fold)
 valid_dataset = torch.utils.data.TensorDataset(x_val_fold, y_val_fold)
 train_loader = torch.utils.data.DataLoader(train_dataset, batch_size=batch_size, shuffle=True)
 valid_loader = torch.utils.data.DataLoader(valid_dataset, batch_size=batch_size, shuffle=False)
 best_f1 = 0
best_model_name = ''
for epoch in range(n_epochs):
print()
print(f'Epoch {epoch}.{time.ctime() }')
 model.train()
avg_loss = 0.
 for x_batch, y_batch in train_loader:
y_pred = model(x_batch)
 loss = loss_fn(y_pred, y_batch)
 optimizer.zero_grad()
loss.backward()
optimizer.step()
avg_loss += loss.item() / len(train_loader)
 model.eval()
valid_preds = np.zeros(( x_val_fold.size(0)))
 if validate:
avg_val_loss = 0.
 for j,(x_batch, y_batch)in enumerate(valid_loader):
y_pred = model(x_batch ).detach()
avg_val_loss += loss_fn(y_pred, y_batch ).item() / len(valid_loader)
 valid_preds[j * batch_size:(j+1)* batch_size] = sigmoid(y_pred.cpu().numpy())[:, 0]
best_th, score = scoring(y_val_fold.cpu().numpy() , valid_preds, verbose=True)
 valid_preds = np.zeros(( x_val_fold.size(0)))
 avg_val_loss = 0.
 for j,(x_batch, y_batch)in enumerate(valid_loader):
y_pred = model(x_batch ).detach()
avg_val_loss += loss_fn(y_pred, y_batch ).item() / len(valid_loader)
 valid_preds[j * batch_size:(j+1)* batch_size] = sigmoid(y_pred.cpu().numpy())[:, 0]
best_th, score = scoring(y_val_fold.cpu().numpy() , valid_preds, verbose=True)
 scores.append(score)
 test_preds_fold = np.zeros(( len(test_loader.dataset)))
 for j,(x_batch,)in enumerate(test_loader):
y_pred = model(x_batch ).detach()
test_preds_fold[j * batch_size:(j+1)* batch_size] = sigmoid(y_pred.cpu().numpy())[:, 0]
train_preds[valid_idx] = valid_preds
test_preds[:, i] = test_preds_fold
print(f'Finished training at {time.ctime() }')
 print(f'Mean validation f1-score: {np.mean(scores)}.Std: {np.std(scores)}')
 return train_preds, test_preds<compute_train_metric>
y = tr['FVC'].values
z = tr[FE].values
print(z.shape)
 ze = sub[FE].values
print(ze.shape)
 nh = z.shape[1]
print(nh)
 pe = np.zeros(( ze.shape[0], 3))
pred = np.zeros(( z.shape[0], 3))
net = make_model(nh)
 print(net.summary())
 print(net.count_params())
 NFOLD = 5
kf = KFold(n_splits=NFOLD )
def scoring(y_true, y_proba, verbose=True):
def threshold_search1(y_true, y_proba):
precision , recall, thresholds = precision_recall_curve(y_true, y_proba)
 thresholds = np.append(thresholds, 1.001)
 F = 2 /(1/precision + 1/recall)
 best_score = np.max(F)
 best_th = thresholds[np.argmax(F)]
return best_th
rkf = RepeatedStratifiedKFold(n_splits=5, n_repeats=10)
 scores = []
ths = []
for train_index, test_index in rkf.split(y_true, y_true):
y_prob_train, y_prob_test = y_proba[train_index], y_proba[test_index]
y_true_train, y_true_test = y_true[train_index], y_true[test_index]
best_threshold = threshold_search1(y_true_train, y_prob_train)
 sc = f1_score(y_true_test,(y_prob_test >= best_threshold ).astype(int))
scores.append(sc)
 ths.append(best_threshold)
 best_th = np.mean(ths)
 score = np.mean(scores)
 if verbose: print(f'Best threshold: {np.round(best_th, 4)}, Score: {np.round(score,5)}')
 return best_th, score<train_model>
cnt = 0
EPOCHS = 800
y = y.astype(np.float32)
 for tr_idx, val_idx in kf.split(z):
cnt += 1
print(f"FOLD {cnt}")
 net = make_model(nh)
 net.fit(z[tr_idx], y[tr_idx], batch_size=BATCH_SIZE, epochs=EPOCHS,
validation_data=(z[val_idx], y[val_idx]), verbose=0)
 print("train", net.evaluate(z[tr_idx], y[tr_idx], verbose=0, batch_size=BATCH_SIZE))
print("val", net.evaluate(z[val_idx], y[val_idx], verbose=0, batch_size=BATCH_SIZE))
print("predict val...")
 pred[val_idx] = net.predict(z[val_idx], batch_size=BATCH_SIZE, verbose=0)
 print("predict test...")
 pe += net.predict(ze, batch_size=BATCH_SIZE, verbose=0)/ NFOLD
train_preds, test_preds = train_model_full(X_train=X_train, y_train=y_train, splits=splits, n_epochs=5, batch_size=batch_size, validate=True )<save_to_csv>
df_issa2 = df.copy()
best_th, score = scoring(y_train, train_preds)
 sub['prediction'] = test_preds.mean(1)> best_th
sub.to_csv("submission.csv", index=False )<set_options>
df_issa1.to_csv('df_issa1.csv', index=False)
 df_issa2.to_csv('df_issa2.csv', index=False )
tqdm.pandas(desc='Progress')
<define_variables>
x = 0.8
df = df_issa1.copy()
df['FVC'] = x*df_issa1['FVC'] +(1-x)*df_issa2['FVC']
df['Confidence'] = x*df_issa1['Confidence'] +(1-x)*df_issa2['Confidence']
df.head()
<define_variables><EOS> 
df.to_csv('submission.csv', index=False )