Kaggle competition: APTOS 2019 Blindness Detection
<SOS> metric: QuadraticWeightedKappa Kaggle data source: aptos-2019-blindness-detection<train_model>
%matplotlib inline
m2.fit(0,600000,3,2000,loss='binary_crossentropy', metrics=['accuracy', f1],
optimizer=Adam(lr=1e-3))
m2.fit(0,1250000,5,2000,loss='binary_crossentropy', metrics=['accuracy', f1],
optimizer=Adam(lr=3e-4))
m2.unfreeze()
m2.fit(0,1250000,14,2000,loss='binary_crossentropy', metrics=['accuracy', f1],
optimizer=Adam(lr=3e-5))<prepare_x_and_y>
np.random.seed(2019)
 tf.set_random_seed(2019 )
lval=1250000
y_v=y_train.tolist() [lval:]
x_v=x_train[lval:] 
<prepare_output>
train_df = pd.read_csv('.. /input/aptos2019-blindness-detection/train.csv')
 test_df = pd.read_csv('.. /input/aptos2019-blindness-detection/test.csv')
 print(train_df.shape)
 print(test_df.shape)
 train_df.head()
u1=m1.predvec(x_v)
 u2=m2.predvec(x_v )<compute_test_metric>
def get_pad_width(im, new_shape, is_rgb=True):
pad_diff = new_shape - im.shape[0], new_shape - im.shape[1]
t, b = math.floor(pad_diff[0]/2), math.ceil(pad_diff[0]/2)
 l, r = math.floor(pad_diff[1]/2), math.ceil(pad_diff[1]/2)
 if is_rgb:
pad_width =(( t,b),(l,r),(0, 0))
else:
pad_width =(( t,b),(l,r))
return pad_width
def preprocess_image(image_path, desired_size=224):
im = Image.open(image_path)
 im = im.resize(( desired_size,)*2, resample=Image.LANCZOS)
 return im
def qf1(t,vv):
tp=0
fp=0
fn=0
yt=y_train.tolist()
for i in range(len(vv)) :
if vv[-i]>t:
if yt[-i]==1:
tp+=1
else:
fp+=1
else:
if yt[-i]==1:
fn+=1
return(2*tp/(2*tp+fn+fp))
def best(vv):
cc=0.35
a=0
for i in range(10):
r= qf1(cc+0.01*i,vv)
 if(r>a):
ii=i
a=r
a=0
for i in range(10):
r= qf1(cc+0.01*(ii-1)+0.002*i,vv)
 if(r>a):
iii=i
a=r
print(a)
 return(cc+0.01*(ii-1)+0.002*iii)
<find_best_params>
N = train_df.shape[0]
x_train = np.empty(( N, 224, 224, 3), dtype=np.uint8)
 for i, image_id in enumerate(tqdm(train_df['id_code'])) :
x_train[i, :, :, :] = preprocess_image(
 f'.. /input/aptos2019-blindness-detection/train_images/{image_id}.png'
)
bt=best(( u1+u2)/2)
 print(bt )<categorify>
N = test_df.shape[0]
x_test = np.empty(( N, 224, 224, 3), dtype=np.uint8)
 for i, image_id in enumerate(tqdm(test_df['id_code'])) :
x_test[i, :, :, :] = preprocess_image(
 f'.. /input/aptos2019-blindness-detection/test_images/{image_id}.png'
)
def ans(v,tr):
res=np.zeros(len(v))
for i in range(len(v)) :
if v[i]>tr:
res[i]=1
return res<compute_test_metric>
y_train = pd.get_dummies(train_df['diagnosis'] ).values
print(x_train.shape)
 print(y_train.shape)
 print(x_test.shape )
v1=m1.predvec(x_test)
 v2=m2.predvec(x_test)
 vv=ans(( v1+v2)/2,bt )<save_to_csv>
y_train_multi = np.empty(y_train.shape, dtype=y_train.dtype)
 y_train_multi[:, 4] = y_train[:, 4]
for i in range(3, -1, -1):
y_train_multi[:, i] = np.logical_or(y_train[:, i], y_train_multi[:, i+1])
 print("Original y_train:", y_train.sum(axis=0))
print("Multilabel version:", y_train_multi.sum(axis=0))
out = np.column_stack(( test['qid'].values,vv))
np.savetxt('submission.csv', out, header="qid,prediction",
comments="", fmt="%s,%d" )<import_modules>
x_train, x_val, y_train, y_val = train_test_split(
 x_train, y_train_multi,
test_size=0.15,
random_state=2019
)
tqdm.pandas(desc='Progress')
<define_variables>
class MixupGenerator() :
def __init__(self, X_train, y_train, batch_size=32, alpha=0.2, shuffle=True, datagen=None):
self.X_train = X_train
self.y_train = y_train
self.batch_size = batch_size
self.alpha = alpha
self.shuffle = shuffle
self.sample_num = len(X_train)
 self.datagen = datagen
def __call__(self):
while True:
indexes = self.__get_exploration_order()
itr_num = int(len(indexes)//(self.batch_size * 2))
for i in range(itr_num):
batch_ids = indexes[i * self.batch_size * 2:(i + 1)* self.batch_size * 2]
X, y = self.__data_generation(batch_ids)
 yield X, y
def __get_exploration_order(self):
indexes = np.arange(self.sample_num)
 if self.shuffle:
np.random.shuffle(indexes)
 return indexes
def __data_generation(self, batch_ids):
_, h, w, c = self.X_train.shape
l = np.random.beta(self.alpha, self.alpha, self.batch_size)
 X_l = l.reshape(self.batch_size, 1, 1, 1)
 y_l = l.reshape(self.batch_size, 1)
 X1 = self.X_train[batch_ids[:self.batch_size]]
X2 = self.X_train[batch_ids[self.batch_size:]]
X = X1 * X_l + X2 *(1 - X_l)
 if self.datagen:
for i in range(self.batch_size):
X[i] = self.datagen.random_transform(X[i])
 X[i] = self.datagen.standardize(X[i])
 if isinstance(self.y_train, list):
y = []
for y_train_ in self.y_train:
y1 = y_train_[batch_ids[:self.batch_size]]
y2 = y_train_[batch_ids[self.batch_size:]]
y.append(y1 * y_l + y2 *(1 - y_l))
else:
y1 = self.y_train[batch_ids[:self.batch_size]]
y2 = self.y_train[batch_ids[self.batch_size:]]
y = y1 * y_l + y2 *(1 - y_l)
 return X, y
embed_size = 300
max_features = 120000
maxlen = 70
batch_size = 512
n_epochs = 5
n_splits = 5
SEED = 1029<set_options>
BATCH_SIZE = 32
def create_datagen() :
return ImageDataGenerator(
 zoom_range=0.15,
fill_mode='constant',
cval=0.,
horizontal_flip=True,
vertical_flip=True, 
)
 data_generator = create_datagen().flow(x_train, y_train, batch_size=BATCH_SIZE, seed=2019)
 mixup_generator = MixupGenerator(x_train, y_train, batch_size=BATCH_SIZE, alpha=0.2, datagen=create_datagen() )()
def seed_everything(seed=1029):
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()<features_selection>
true_labels = np.array([1, 0, 1, 1, 0, 1])
 pred_labels = np.array([1, 0, 0, 0, 0, 1] )
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')[:300]
embeddings_index = dict(get_coefs(*o.split(" ")) for o in open(EMBEDDING_FILE))
all_embs = np.stack(embeddings_index.values())
 emb_mean,emb_std = -0.005838499,0.48782197
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 = -0.0053247833,0.49346462
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<load_from_csv>
accuracy_score(true_labels, pred_labels )
df_train = pd.read_csv(".. /input/train.csv")
 df_test = pd.read_csv(".. /input/test.csv")
 df = pd.concat([df_train ,df_test],sort=True )<feature_engineering>
cohen_kappa_score(true_labels, pred_labels )
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>
class Metrics(Callback):
def on_train_begin(self, logs={}):
self.val_kappas = []
def on_epoch_end(self, epoch, logs={}):
X_val, y_val = self.validation_data[:2]
y_val = y_val.sum(axis=1)- 1
y_pred = self.model.predict(X_val)> 0.5
y_pred = y_pred.astype(int ).sum(axis=1)- 1
_val_kappa = cohen_kappa_score(
 y_val,
y_pred,
weights='quadratic' 
)
 self.val_kappas.append(_val_kappa)
 print(f"val_kappa: {_val_kappa:.4f}")
 if _val_kappa == max(self.val_kappas):
print("Validation Kappa has improved.Saving model.")
 self.model.save('model.h5')
 return
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>
densenet = DenseNet121(
 weights='.. /input/densenet-keras/DenseNet-BC-121-32-no-top.h5',
include_top=False,
input_shape=(224,224,3)
 )
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>
def build_model() :
model = Sequential()
model.add(densenet)
 model.add(layers.GlobalAveragePooling2D())
 model.add(layers.Dropout(0.5))
model.add(layers.Dense(5, activation='sigmoid'))
model.compile(
 loss='binary_crossentropy',
optimizer=Adam(lr=0.00005),
metrics=['accuracy'] 
)
 return model
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>
kappa_metrics = Metrics()
history = model.fit_generator(
 data_generator,
steps_per_epoch=x_train.shape[0] / BATCH_SIZE,
epochs=15,
validation_data=(x_val, y_val),
callbacks=[kappa_metrics]
)
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"].apply(lambda x: x.lower())
 test_df["question_text"] = test_df["question_text"].apply(lambda x: x.lower())
 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_X = train_df["question_text"].fillna("_
test_X = test_df["question_text"].fillna("_
train = add_features(train_df)
 test = add_features(test_df)
 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>
model.load_weights('model.h5')
 y_val_pred = model.predict(x_val)
 def compute_score_inv(threshold):
y1 = y_val_pred > threshold
y1 = y1.astype(int ).sum(axis=1)- 1
y2 = y_val.sum(axis=1)- 1
score = cohen_kappa_score(y1, y2, weights='quadratic')
 return 1 - score
simplex = scipy.optimize.minimize(
 compute_score_inv, 0.5, method='nelder-mead' 
)
 best_threshold = simplex['x'][0]
<save_model><EOS> 
y_test = model.predict(x_test)> 0.5
y_test = y_test.astype(int ).sum(axis=1)- 1
test_df['diagnosis'] = y_test
test_df.to_csv('submission.csv',index=False )