Laurent Jacob

Antoine Villié, Philippe Veber, Yohann de Castro et al.

Over the past decade, neural networks have been successful at making predictions from biological sequences, especially in the context of regulatory genomics. As in other fields of deep learning, tools have been devised to extract features such as sequence motifs that can explain the predictions made by a trained network. Here we intend to go beyond explainable machine learning and introduce SEISM, a selective inference procedure to test the association between these extracted features and the predicted phenotype. In particular, we discuss how training a one-layer convolutional network is formally equivalent to selecting motifs maximizing some association score. We adapt existing sampling-based selective inference procedures by quantizing this selection over an infinite set to a large but finite grid. Finally, we show that sampling under a specific choice of parameters is sufficient to characterize the composite null hypothesis typically used for selective inference-a result that goes well beyond our particular framework. We illustrate the behavior of our method in terms of calibration, power and speed and discuss its power/speed trade-off with a simpler data-split strategy. SEISM paves the way to an easier analysis of neural networks used in regulatory genomics, and to more powerful methods for genome wide association studies (GWAS).

Dexiong Chen, Laurent Jacob, Julien Mairal

We introduce a family of multilayer graph kernels and establish new links between graph convolutional neural networks and kernel methods. Our approach generalizes convolutional kernel networks to graph-structured data, by representing graphs as a sequence of kernel feature maps, where each node carries information about local graph substructures. On the one hand, the kernel point of view offers an unsupervised, expressive, and easy-to-regularize data representation, which is useful when limited samples are available. On the other hand, our model can also be trained end-to-end on large-scale data, leading to new types of graph convolutional neural networks. We show that our method achieves competitive performance on several graph classification benchmarks, while offering simple model interpretation. Our code is freely available at https://github.com/claying/GCKN.

Dexiong Chen, Laurent Jacob, Julien Mairal

Substring kernels are classical tools for representing biological sequences or text. However, when large amounts of annotated data are available, models that allow end-to-end training such as neural networks are often preferred. Links between recurrent neural networks (RNNs) and substring kernels have recently been drawn, by formally showing that RNNs with specific activation functions were points in a reproducing kernel Hilbert space (RKHS). In this paper, we revisit this link by generalizing convolutional kernel networks---originally related to a relaxation of the mismatch kernel---to model gaps in sequences. It results in a new type of recurrent neural network which can be trained end-to-end with backpropagation, or without supervision by using kernel approximation techniques. We experimentally show that our approach is well suited to biological sequences, where it outperforms existing methods for protein classification tasks.