ReSeg: A Recurrent Neural Network-based Model for Semantic Segmentation

We propose a structured prediction architecture, which exploits the local generic features extracted by Convolutional Neural Networks and the capacity of Recurrent Neural Networks (RNN) to retrieve distant dependencies. The proposed architecture, called ReSeg, is based on the recently introduced ReNet model for image classification. We modify and extend it to perform the more challenging task of semantic segmentation. Each ReNet layer is composed of four RNN that sweep the image horizontally and vertically in both directions, encoding patches or activations, and providing relevant global information. Moreover, ReNet layers are stacked on top of pre-trained convolutional layers, benefiting from generic local features. Upsampling layers follow ReNet layers to recover the original image resolution in the final predictions. The proposed ReSeg architecture is efficient, flexible and suitable for a variety of semantic segmentation tasks. We evaluate ReSeg on several widely-used semantic segmentation datasets: Weizmann Horse, Oxford Flower, and CamVid; achieving state-of-the-art performance. Results show that ReSeg can act as a suitable architecture for semantic segmentation tasks, and may have further applications in other structured prediction problems. The source code and model hyperparameters are available on https://github.com/fvisin/reseg.Comment: In CVPR Deep Vision Workshop, 201

A non-homogeneous dynamic Bayesian network with sequentially coupled interaction parameters for applications in systems and synthetic biology

An important and challenging problem in systems biology is the inference of gene regulatory networks from short non-stationary time series of transcriptional profiles. A popular approach that has been widely applied to this end is based on dynamic Bayesian networks (DBNs), although traditional homogeneous DBNs fail to model the non-stationarity and time-varying nature of the gene regulatory processes. Various authors have therefore recently proposed combining DBNs with multiple changepoint processes to obtain time varying dynamic Bayesian networks (TV-DBNs). However, TV-DBNs are not without problems. Gene expression time series are typically short, which leaves the model over-flexible, leading to over-fitting or inflated inference uncertainty. In the present paper, we introduce a Bayesian regularization scheme that addresses this difficulty. Our approach is based on the rationale that changes in gene regulatory processes appear gradually during an organism's life cycle or in response to a changing environment, and we have integrated this notion in the prior distribution of the TV-DBN parameters. We have extensively tested our regularized TV-DBN model on synthetic data, in which we have simulated short non-homogeneous time series produced from a system subject to gradual change. We have then applied our method to real-world gene expression time series, measured during the life cycle of Drosophila melanogaster, under artificially generated constant light condition in Arabidopsis thaliana, and from a synthetically designed strain of Saccharomyces cerevisiae exposed to a changing environment