AffinityNet: semi-supervised few-shot learning for disease type prediction

While deep learning has achieved great success in computer vision and many other fields, currently it does not work very well on patient genomic data with the "big p, small N" problem (i.e., a relatively small number of samples with high-dimensional features). In order to make deep learning work with a small amount of training data, we have to design new models that facilitate few-shot learning. Here we present the Affinity Network Model (AffinityNet), a data efficient deep learning model that can learn from a limited number of training examples and generalize well. The backbone of the AffinityNet model consists of stacked k-Nearest-Neighbor (kNN) attention pooling layers. The kNN attention pooling layer is a generalization of the Graph Attention Model (GAM), and can be applied to not only graphs but also any set of objects regardless of whether a graph is given or not. As a new deep learning module, kNN attention pooling layers can be plugged into any neural network model just like convolutional layers. As a simple special case of kNN attention pooling layer, feature attention layer can directly select important features that are useful for classification tasks. Experiments on both synthetic data and cancer genomic data from TCGA projects show that our AffinityNet model has better generalization power than conventional neural network models with little training data. The code is freely available at https://github.com/BeautyOfWeb/AffinityNet .Comment: 14 pages, 6 figure

Discriminatively Trained Latent Ordinal Model for Video Classification

We study the problem of video classification for facial analysis and human action recognition. We propose a novel weakly supervised learning method that models the video as a sequence of automatically mined, discriminative sub-events (eg. onset and offset phase for "smile", running and jumping for "highjump"). The proposed model is inspired by the recent works on Multiple Instance Learning and latent SVM/HCRF -- it extends such frameworks to model the ordinal aspect in the videos, approximately. We obtain consistent improvements over relevant competitive baselines on four challenging and publicly available video based facial analysis datasets for prediction of expression, clinical pain and intent in dyadic conversations and on three challenging human action datasets. We also validate the method with qualitative results and show that they largely support the intuitions behind the method.Comment: Paper accepted in IEEE TPAMI. arXiv admin note: substantial text overlap with arXiv:1604.0150