Computational Biology with Deep Learning
Keywords:
Cellular imaging, Computational biology, Deep learning, Machine learning, Regulatory genomicsAbstract
Technological advances in genomics and imaging have resulted in an explosion of molecular and cellular profiling data from large numbers of samples. Conventional analytic methodologies are being tested by the increasing expansion of biological data dimension and acquisition rate. Modern machine learning technologies, such as deep learning, promise to make accurate predictions and identify underlying structure in very huge data sets. In this study, we look at how regulatory genomics and cellular imaging can benefit from this new breed of analysis tools. We give an overview of what deep learning is and how it may be used to obtain biological insights in different situations. We emphasise probable hazards and restrictions to guide you, in addition to presenting real applications and providing recommendations for practical use. We point out potential problems and limitations to help computational biologists decide when and how to use this new technique. We emphasise potential dangers and limitations to assist computational biologists when and how to make the most of this new tool, in addition to showing specific applications and providing practical recommendations.
References
Angermueller, Christof, et al. "Deep learning for computational biology." Molecular systems biology 12.7 (2016): 878.
Yu, Dong, and Li Deng. "Deep learning and its applications to signal and information processing [exploratory dsp]." IEEE Signal Processing Magazine 28.1 (2010): 145–154.
Fukushima, Kunihiko. "A self-organizing neural network model for a mechanism of pattern recognition unaffected by shift in position." Biol. Cybern. 36 (1980): 193–202.
Hinton, G.E., S. Osindero, and Y.W. Teh. "A quick learning calculation for profound conviction nets." Neural Computation 18.7 (2006): 1527–1554.
Hinton, Geoffrey E., and Ruslan R. Salakhutdinov. "Reducing the dimensionality of data with neural networks." science 313.5786 (2006): 504–507.
Cios, Krzysztof J., et al. "Computational intelligence in solving bioinformatics problems." (2005).
Längkvist, Martin, Lars Karlsson, and Amy Loutfi. "A review of unsupervised feature learning and deep learning for time-series modeling." Pattern Recognition Letters 42 (2014): 11–24.
Krizhevsky, Alex, Ilya Sutskever, and Geoffrey E. Hinton. "Imagenet classification with deep convolutional neural networks." Advances in neural information processing systems 25 (2012).
Asgari, Ehsaneddin, and Mohammad RK Mofrad. "Protvec: A continuous distributed representation of biological sequences." Computer Science 10.11 (2010): e0141287.
Cao, Chensi, et al. "Deep learning and its applications in biomedicine." Genomics, proteomics & bioinformatics 16.1 (2018): 17–32.
Graves, Alex. "Practical variational inference for neural networks." Advances in neural information processing systems 24 (2011).
Bengio, Yoshua, Patrice Simard, and Paolo Frasconi. "Learning long-term dependencies with gradient descent is difficult." IEEE transactions on neural networks 5.2 (1994): 157–166.
LeCun, Yann, Yoshua Bengio, and Geoffrey Hinton. "Deep learning." nature 521.7553 (2015): 436–444.
Cires, D.C., et al. "High Performance Convolutional Neural Networks for Image Classification." Proceedings of 22nd International Joint Conference on Artificial Intelligence.
Hinton, Geoffrey, et al. "Deep neural networks for acoustic modeling in speech recognition: The shared views of four research groups." IEEE Signal processing magazine 29.6 (2012): 82–97.
Cireşan, Dan Claudiu, et al. "Deep, big, simple neural nets for handwritten digit recognition." Neural computation 22.12 (2010): 3207–3220.
Raina, Rajat, Anand Madhavan, and Andrew Y. Ng. "Large-scale deep unsupervised learning using graphics processors." Proceedings of the 26th annual international conference on machine learning. 2009.
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