Predicting the sequence specificities of DNA-and RNA-binding proteins by deep learning, Nature biotechnology, vol.33, issue.8, pp.831-838, 2015. ,
Deep learning for computational biology, Molecular Systems Biology, vol.12, issue.7, p.878, 2016. ,
A global reference for human genetic variation, Nature, vol.526, pp.68-74, 2015. ,
Biological sequence modeling with convolutional kernel networks, Bioinformatics, vol.35, issue.18, p.2019 ,
URL : https://hal.archives-ouvertes.fr/hal-01632912
Learning phrase representations using rnn encoder-decoder for statistical machine translation, Conference on Empirical Methods in Natural Language Processing (EMNLP), 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01433235
Kernel methods for deep learning, Advances in Neural Information Processing Systems (NIPS), 2009. ,
Computational pan-genomics: status, promises and challenges, Briefings in Bioinformatics, vol.19, issue.1, p.2016 ,
The Unreasonable Effectiveness of Convolutional Neural Networks in Population Genetic Inference, Molecular Biology and Evolution, vol.36, issue.2, pp.220-238, 2018. ,
Collected matrix derivative results for forward and reverse mode algorithmic differentiation, Advances in Automatic Differentiation, pp.35-44, 2008. ,
Motif kernel generated by genetic programming improves remote homology and fold detection, BMC bioinformatics, vol.8, issue.1, p.23, 2007. ,
Convolution kernels on discrete structures, 1999. ,
Amino acid substitution matrices from protein blocks, Proceedings of the National Academy of Sciences, vol.89, pp.10915-10919, 1992. ,
Fast model-based protein homology detection without alignment, Bioinformatics, vol.23, issue.14, pp.1728-1736, 2007. ,
Long short-term memory, Neural computation, vol.9, issue.8, pp.1735-1780, 1997. ,
DeepSF: deep convolutional neural network for mapping protein sequences to folds, Bioinformatics, vol.34, issue.8, p.2017 ,
High-performance medicine: the convergence of human and artificial intelligence, Nature Medicine, p.25, 2019. ,
Using the fisher kernel method to detect remote protein homologies, Conference on Intelligent Systems for Molecular Biology (ISMB), 1999. ,
A convolutional neural network for modelling sentences, Association for Computational Linguistics (ACL), 2014. ,
Backpropagation applied to handwritten zip code recognition, Neural computation, vol.1, issue.4, pp.541-551, 1989. ,
Deriving neural architectures from sequence and graph kernels, International Conference on Machine Learning (ICML), 2017. ,
The spectrum kernel: A string kernel for svm protein classification, Biocomputing, pp.564-575, 2001. ,
Mismatch string kernels for discriminative protein classification, Bioinformatics, vol.20, issue.4, pp.467-476, 2004. ,
Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships, Journal of computational biology, vol.10, issue.6, pp.857-868, 2003. ,
Text classification using string kernels, Journal of Machine Learning Research, vol.2, pp.419-444, 2002. ,
End-to-End Kernel Learning with Supervised Convolutional Kernel Networks, Advances in Neural Information Processing Systems (NIPS), 2016. ,
Regularizing and optimizing lstm language models, International Conference on Learning Representations (ICLR), 2018. ,
Convolutional kitchen sinks for transcription factor binding site prediction, 2017. ,
Generalized max pooling, Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 2014. ,
Scop: a structural classification of proteins database for the investigation of sequences and structures, Journal of molecular biology, vol.247, issue.4, pp.536-540, 1995. ,
Random features for large-scale kernel machines, Adv. in Neural Information Processing Systems (NIPS), 2008. ,
Profile-based direct kernels for remote homology detection and fold recognition, Bioinformatics, vol.21, issue.23, pp.4239-4247, 2005. ,
Protein homology detection using string alignment kernels, Bioinformatics, vol.20, issue.11, pp.1682-1689, 2004. ,
URL : https://hal.archives-ouvertes.fr/hal-00433587
Learning with kernels: support vector machines, regularization, optimization, and beyond, 2002. ,
Kernel methods in computational biology, 2004. ,
Marginalized kernels for biological sequences, Bioinformatics, vol.18, issue.suppl_1, pp.268-275, 2002. ,
Convolution and local alignment kernels. Kernel methods in computational biology, pp.131-154, 2004. ,
Dynamic alignment kernels, Advances in Neural Information Processing Systems (NIPS), 1999. ,
Using the Nyström method to speed up kernel machines, Advances in Neural Information Processing Systems (NIPS), 2001. ,
Improved nyström low-rank approximation and error analysis, International Conference on Machine Learning (ICML), 2008. ,
Convexified convolutional neural networks, International Conference on Machine Learning (ICML), 2017. ,
Predicting effects of noncoding variants with deep learning-based sequence model, Nature Methods, vol.12, issue.10, pp.931-934, 2015. ,