I have a CNN model that I need to train for a large scale genomics application. It is working well with a subset of my training data. I have scaled up to a subset of about 130 million examples and training time is very long, about 3 hours per epoch. I plan to scale up to the hundreds of billions of training examples and I anticipate training time to be not be feasible with my current design. I would appreciate feedback on how I can streamline the training or improve some aspect of my design that I may not be considering. Currently, I am training from a MongoDB. The training examples are not very large. Here is an example.

    'added': datetime.datetime(2019, 11, 1, 6, 13, 13, 340000),
    '_id': ObjectId('5dbbccf92464af872756022e'),
    'label': 0,
    'accession': 'GM_0001',
    'data': '34363,30450,9019,19152,8726,22128,59881,17670,15803,64454,64579,28103,52442,64951,29783,64574,652,19243,33498,14775,18803,4700,55446,53912,47645,41465,48257,16305,62071,12334,44698,24371,46515,8445,3000,61849,43228,18120,23587,11105,5453,42707,42739,46122,31285,40773,48162,16653,58783,2928,2836,21330,46947,6719,26992,8852,14520,46212,47362,43554,2147,39372,33885,59716,37384,14825,53387,58763,18065,34070,23278,15641,40237,47950,58811,40015,36880,29841,45351,14904,49660,48224,54638,50358,17202,10701,3564,4829,62655,5684,37207,49724,16369,6769,37827,38144,63885,5070,42882,48960,16178,35758,50554,54253,34556,2383,39431,30176,11482,24459,4472,53825,7764,44500,4869,50875,33037,56353,46848,30769,18729,46026,41409,2826,12092,17086',
    'name': 'Example_1'

The relevant data is the 'data' field which is a string of 126 integers where each integer is a value between 0 and about 65,000. The other fields are convenient, but not necessary except for the 'label' field. But even this I could insert into the front of the data field. I mention this because I don't think I necessarily need to train from a MongoDB database.

I am using Keras 2.3.0 with TensorFlow 2.0.0. Below is an example of my code. The workflow is 1) Load a text file containing the document ids of all training examples in the MongoDB collection. I do this so I can shuffle the examples before sending them to the model for training. 2) I load the examples in batches of 50,000 using my Custom_Generator class. This class pulls the documents from the MongoDB using the list of document ids. 3) The model is trained. I use 5 epochs. I currently have 5-fold cross-validation but I know this is not feasible on the full training set. For that I will do a single train-test split. I am currently performing this on a Google Cloud instance with 2 Tesla T4 GPUs. The database is on a bucket. With the cloud I have flexibility of hardware architectures. I would appreciate any insight. This is a rather large engineering challenge for me.

Additional background to the problem: The objective is to classify organisms into broad classes quickly for downstream analysis. The pool of organisms I want to classify is very large (10s of thousands) and very diverse. I'm essentially reading the genomes of the organisms like a book. The genome (a series of "A", "T", "C", or "G") is processed in chunks through a hash function producing integer strings as shown above. Depending on the size of the organism genome, thousands to millions of these integer strings may be produced. So I have many thousands of organisms producing many thousands to millions of examples. To be successful, I feel like I need to capture the diversity of the genomes in the organism pool. To give an example, even though Ecoli and Salmonella are both bacteria, their genomes are quite distinct. I feel like I need to have them both represented in the training set to distinguish them from other organisms I would label as a different class. As far as reducing the dataset, I think I can get by with only training on a representative organism for a give species (since there are many unique genomes available for Ecoli, for example). This will help considerably, but I think the training data set will likely still be in the billions of examples.

import sys
import time
from keras.utils import Sequence, to_categorical, multi_gpu_model
from keras.models import Sequential
from keras.layers import Dense
from keras.layers import Flatten
from keras.layers import Embedding
from keras.layers.convolutional import Conv1D
from keras.layers.convolutional import MaxPooling1D
from sklearn.model_selection import KFold
from keras.preprocessing.sequence import pad_sequences
import numpy as np
import random
from pymongo import MongoClient
from bson import ObjectId
from sklearn.metrics import classification_report, confusion_matrix

class Custom_Generator(Sequence) :

    def __init__(self, document_ids, batch_size) :
        self.document_ids = document_ids
        self.batch_size = batch_size

    def __len__(self) :
        return (np.ceil(len(self.document_ids) / float(self.batch_size))).astype(np.int)

    def __getitem__(self, idx) :
        client = MongoClient(port=27017)
        db = client[database]
        document_ids = self.document_ids[idx * self.batch_size : (idx+1) * self.batch_size]
        query_results = db[collection].find({'_id': {'$in': document_ids}})
        batch_x, batch_y = [], []
        for result in query_results:
            kmer_list = result['kmers'].split(',')
            label = result['label']
            x = [x for x in kmer_list if len(x) > 0]
            if len(x) < 1:
            one_hot_y = to_categorical(label, 5)
        batch_x = pad_sequences(batch_x, maxlen=126, padding='post')
        return np.array(batch_x), np.array(batch_y)

# MongoDB database, collection, and document ids of collection
database = 'db'
collection = 'collection_subset2'
docids_file = 'docids_collection_subset2.txt'
id_ls = []
# Convert docids strings to MongoDB ObjectID
with open(docids_file) as f:
    for line in f:

# Model
model = Sequential()
model.add(Embedding(65521, 100, input_length=126))
model.add(Conv1D(filters=25, kernel_size=5, activation='relu'))
model.add(Conv1D(filters=30, kernel_size=3, activation='relu'))
model.add(Dense(1000, activation='relu'))
model.add(Dense(5, kernel_initializer="normal", activation="softmax"))
parallel_model = multi_gpu_model(model, gpus=2)
parallel_model.compile(loss='categorical_crossentropy', optimizer='adam', metrics=['accuracy'])

seed = 7
batch_size = 50000

# Currently training with 5-fold CV. Will only use single test train split 
# on the full-scale dataset.
kfold = KFold(n_splits=5, shuffle=True, random_state=seed)
kfold_stats = {}
accuracy_ls = []
val_accuracy_ls = []
confusion_ls = []
for fold_idx, (train_idx, test_idx) in enumerate(kfold.split(id_ls)):
    ids_train = np.array(id_ls)[train_idx].tolist()
    ids_test = np.array(id_ls)[test_idx].tolist()
    training_batch_generator = Custom_Generator(ids_train, batch_size)
    validation_batch_generator = Custom_Generator(ids_test, batch_size)
    print('Number of train files: %d' % len(ids_train))
    print('Number of test files: %d' % len(ids_test))
    start = time.time()
    history = parallel_model.fit_generator(
        steps_per_epoch = int(len(ids_train) // batch_size),
        epochs = 5,
        verbose = 2,
        validation_data = validation_batch_generator,
        validation_steps = int(len(ids_test) // batch_size),
    sys.stderr.write("time to train model (seconds): %d\n"%(time.time() - start))
    fold_name = 'kfold_%s' % str(fold_idx)
    kfold_stats.update({fold_name: history.history})
    parallel_model.save('model_output_kfold_%s.h5' % str(fold_idx))
    print("Kfold %s finished" % str(fold_idx))
    Y_pred = parallel_model.predict_generator(validation_batch_generator)
    y_pred = np.argmax(Y_pred, axis=1)
    y_true = np.concatenate([np.argmax(batch[1], axis=1) for batch in validation_batch_generator])  
    print('Confusion Matrix')
    conf = confusion_matrix(y_true, y_pred)
    print('Classification Report')
    target_names = ['Class_name_1', 'Class_name_2', 'Class_name_3', 'Class_name_4', 'Class_name_5']
    report = classification_report(y_true, y_pred, target_names=target_names)

  • $\begingroup$ I would suggest using as little data as possible to help speed up the process. You are right you don't need the database. Although it does help with the problem of organizing the data it may create some latency. $\endgroup$ Nov 15, 2019 at 0:42
  • $\begingroup$ Thanks @MichaelHearn. It's true, I should do some learning curves to see how much I need. $\endgroup$ Nov 15, 2019 at 3:01

1 Answer 1


First of all, you should add the argument workers = n in the fit generator call. n should be bigger than 1 to prefetch data. As your data processing requires the data be taken from a server or port, you should do pre fetching data as that would fetch the next data while GPU is processing.

If you call fit_generator with workers > 1 , use_multiprocessing=True , we will prefetch queue_size batches.

Source: https://github.com/keras-team/keras/issues/12847

Secondly, as @MichaelHearn mentioned, you should plot a graph to see how many data is needed. You task should not require several billion data samples. A couple hundred thousand data should be enough. If the model is not getting a good accuracy from a couple hundred thousand data samples, perhaps you can try changing up the model architecture instead of adding more data. Maybe you can add drop out layers.

Hope I can help you.

  • $\begingroup$ Thanks for the advice for prefetching @ClementHui. I thought creating a parallel model and including multiprocessing arguments were redundant, but now I see how they work. Concerning dropout layers, I thought those were just to prevent overfitting. So far I have not seen that problem as my train and test performance is closely matched. Also, I edited my question with some background to hopefully make it more clear why I think my training set needs to be so large. However, I could be wrong and each class may be distinct enough that I can get by with less. I will do some learning curves. Thanks! $\endgroup$ Nov 15, 2019 at 18:43
  • $\begingroup$ If the genomes are so different, you may try choosing the most important part of the genome to input to the network, instead of using all of it. Maybe you can do some kind of input selection. $\endgroup$
    – Clement
    Nov 16, 2019 at 3:22

You must log in to answer this question.

Not the answer you're looking for? Browse other questions tagged .