FORest Graph-Embedded deep feedforward NETwork (forgeNet) google
A unique challenge in predictive model building for omics data has been the small number of samples $(n)$ versus the large amount of features $(p)$. This ‘$n\ll p$’ property brings difficulties for disease outcome classification using deep learning techniques. Sparse learning by incorporating external gene network information such as the graph-embedded deep feedforward network (GEDFN) model has been a solution to this issue. However, such methods require an existing feature graph, and potential mis-specification of the feature graph can be harmful on classification and feature selection. To address this limitation and develop a robust classification model without relying on external knowledge, we propose a \underline{for}est \underline{g}raph-\underline{e}mbedded deep feedforward \underline{net}work (forgeNet) model, to integrate the GEDFN architecture with a forest feature graph extractor, so that the feature graph can be learned in a supervised manner and specifically constructed for a given prediction task. To validate the method’s capability, we experimented the forgeNet model with both synthetic and real datasets. The resulting high classification accuracy suggests that the method is a valuable addition to sparse deep learning models for omics data. …

Evolutionary Subspace Clustering google
The problem of organizing data that evolves over time into clusters is encountered in a number of practical settings. We introduce evolutionary subspace clustering, a method whose objective is to cluster a collection of evolving data points that lie on a union of low-dimensional evolving subspaces. To learn the parsimonious representation of the data points at each time step, we propose a non-convex optimization framework that exploits the self-expressiveness property of the evolving data while taking into account representation from the preceding time step. To find an approximate solution to the aforementioned non-convex optimization problem, we develop a scheme based on alternating minimization that both learns the parsimonious representation as well as adaptively tunes and infers a smoothing parameter reflective of the rate of data evolution. The latter addresses a fundamental challenge in evolutionary clustering — determining if and to what extent one should consider previous clustering solutions when analyzing an evolving data collection. Our experiments on both synthetic and real-world datasets demonstrate that the proposed framework outperforms state-of-the-art static subspace clustering algorithms and existing evolutionary clustering schemes in terms of both accuracy and running time, in a range of scenarios. …

Variational Time Series Feature Extractor (VTSFE) google
We propose a Variational Time Series Feature Extractor (VTSFE), inspired by the VAE-DMP model of Chen et al., to be used for action recognition and prediction. Our method is based on variational autoencoders. It improves VAE-DMP in that it has a better noise inference model, a simpler transition model constraining the acceleration in the trajectories of the latent space, and a tighter lower bound for the variational inference. We apply the method for classification and prediction of whole-body movements on a dataset with 7 tasks and 10 demonstrations per task, recorded with a wearable motion capture suit. The comparison with VAE and VAE-DMP suggests the better performance of our method for feature extraction. An open-source software implementation of each method with TensorFlow is also provided. In addition, a more detailed version of this work can be found in the indicated code repository. Although it was meant to, the VTSFE hasn’t been tested for action prediction, due to a lack of time in the context of Maxime Chaveroche’s Master thesis at INRIA. …

Joint Association and Classification Analysis (JACA) google
Multi-view data, that is matched sets of measurements on the same subjects, have become increasingly common with technological advances in genomics and other fields. Often, the subjects are separated into known classes, and it is of interest to find associations between the views that are related to the class membership. Existing classification methods can either be applied to each view separately, or to the concatenated matrix of all views without taking into account between-views associations. On the other hand, existing association methods can not directly incorporate class information. In this work we propose a framework for Joint Association and Classification Analysis of multi-view data (JACA). We support the methodology with theoretical guarantees for estimation consistency in high-dimensional settings, and numerical comparisons with existing methods. In addition to joint learning framework, a distinct advantage of our approach is its ability to use partial information: it can be applied both in the settings with missing class labels, and in the settings with missing subsets of views. We apply JACA to colorectal cancer data from The Cancer Genome Atlas project, and quantify the association between RNAseq and miRNA views with respect to consensus molecular subtypes of colorectal cancer. …

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