How to Solve Classification and Regression Problems on High-Dimensional Data with a Supervised Extension of Slow Feature Analysis

Supervised learning from high-dimensional data, e.g., multimedia data, is a challenging task. We propose an extension of slow feature analysis (SFA) for supervised dimensionality reduction called graph-based SFA (GSFA). The algorithm extracts a label-predictive low-dimensional set of features that can be post-processed by typical supervised algorithms to generate the final label or class estimation. GSFA is trained with a so-called training graph, in which the vertices are the samples and the edges represent similarities of the corresponding labels. A new weighted SFA optimization problem is introduced, generalizing the notion of slowness from sequences of samples to such training graphs. We show that GSFA computes an optimal solution to this problem in the considered function space, and propose several types of training graphs. For classification, the most straightforward graph yields features equivalent to those of (nonlinear) Fisher discriminant analysis. Emphasis is on regression, where four different graphs were evaluated experimentally with a subproblem of face detection on photographs. The method proposed is promising particularly when linear models are insufficient, as well as when feature selection is difficult

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

Spectral Graph Convolutions for Population-based Disease Prediction

Exploiting the wealth of imaging and non-imaging information for disease prediction tasks requires models capable of representing, at the same time, individual features as well as data associations between subjects from potentially large populations. Graphs provide a natural framework for such tasks, yet previous graph-based approaches focus on pairwise similarities without modelling the subjects' individual characteristics and features. On the other hand, relying solely on subject-specific imaging feature vectors fails to model the interaction and similarity between subjects, which can reduce performance. In this paper, we introduce the novel concept of Graph Convolutional Networks (GCN) for brain analysis in populations, combining imaging and non-imaging data. We represent populations as a sparse graph where its vertices are associated with image-based feature vectors and the edges encode phenotypic information. This structure was used to train a GCN model on partially labelled graphs, aiming to infer the classes of unlabelled nodes from the node features and pairwise associations between subjects. We demonstrate the potential of the method on the challenging ADNI and ABIDE databases, as a proof of concept of the benefit from integrating contextual information in classification tasks. This has a clear impact on the quality of the predictions, leading to 69.5% accuracy for ABIDE (outperforming the current state of the art of 66.8%) and 77% for ADNI for prediction of MCI conversion, significantly outperforming standard linear classifiers where only individual features are considered.Comment: International Conference on Medical Image Computing and Computer-Assisted Interventions (MICCAI) 201

Mining the Demographics of Political Sentiment from Twitter Using Learning from Label Proportions

Opinion mining and demographic attribute inference have many applications in social science. In this paper, we propose models to infer daily joint probabilities of multiple latent attributes from Twitter data, such as political sentiment and demographic attributes. Since it is costly and time-consuming to annotate data for traditional supervised classification, we instead propose scalable Learning from Label Proportions (LLP) models for demographic and opinion inference using U.S. Census, national and state political polls, and Cook partisan voting index as population level data. In LLP classification settings, the training data is divided into a set of unlabeled bags, where only the label distribution in of each bag is known, removing the requirement of instance-level annotations. Our proposed LLP model, Weighted Label Regularization (WLR), provides a scalable generalization of prior work on label regularization to support weights for samples inside bags, which is applicable in this setting where bags are arranged hierarchically (e.g., county-level bags are nested inside of state-level bags). We apply our model to Twitter data collected in the year leading up to the 2016 U.S. presidential election, producing estimates of the relationships among political sentiment and demographics over time and place. We find that our approach closely tracks traditional polling data stratified by demographic category, resulting in error reductions of 28-44% over baseline approaches. We also provide descriptive evaluations showing how the model may be used to estimate interactions among many variables and to identify linguistic temporal variation, capabilities which are typically not feasible using traditional polling methods

Manifold Elastic Net: A Unified Framework for Sparse Dimension Reduction

It is difficult to find the optimal sparse solution of a manifold learning based dimensionality reduction algorithm. The lasso or the elastic net penalized manifold learning based dimensionality reduction is not directly a lasso penalized least square problem and thus the least angle regression (LARS) (Efron et al. \cite{LARS}), one of the most popular algorithms in sparse learning, cannot be applied. Therefore, most current approaches take indirect ways or have strict settings, which can be inconvenient for applications. In this paper, we proposed the manifold elastic net or MEN for short. MEN incorporates the merits of both the manifold learning based dimensionality reduction and the sparse learning based dimensionality reduction. By using a series of equivalent transformations, we show MEN is equivalent to the lasso penalized least square problem and thus LARS is adopted to obtain the optimal sparse solution of MEN. In particular, MEN has the following advantages for subsequent classification: 1) the local geometry of samples is well preserved for low dimensional data representation, 2) both the margin maximization and the classification error minimization are considered for sparse projection calculation, 3) the projection matrix of MEN improves the parsimony in computation, 4) the elastic net penalty reduces the over-fitting problem, and 5) the projection matrix of MEN can be interpreted psychologically and physiologically. Experimental evidence on face recognition over various popular datasets suggests that MEN is superior to top level dimensionality reduction algorithms.Comment: 33 pages, 12 figure

Collaborative Deep Learning for Speech Enhancement: A Run-Time Model Selection Method Using Autoencoders

We show that a Modular Neural Network (MNN) can combine various speech enhancement modules, each of which is a Deep Neural Network (DNN) specialized on a particular enhancement job. Differently from an ordinary ensemble technique that averages variations in models, the propose MNN selects the best module for the unseen test signal to produce a greedy ensemble. We see this as Collaborative Deep Learning (CDL), because it can reuse various already-trained DNN models without any further refining. In the proposed MNN selecting the best module during run time is challenging. To this end, we employ a speech AutoEncoder (AE) as an arbitrator, whose input and output are trained to be as similar as possible if its input is clean speech. Therefore, the AE can gauge the quality of the module-specific denoised result by seeing its AE reconstruction error, e.g. low error means that the module output is similar to clean speech. We propose an MNN structure with various modules that are specialized on dealing with a specific noise type, gender, and input Signal-to-Noise Ratio (SNR) value, and empirically prove that it almost always works better than an arbitrarily chosen DNN module and sometimes as good as an oracle result

Scientific Information Extraction with Semi-supervised Neural Tagging

This paper addresses the problem of extracting keyphrases from scientific articles and categorizing them as corresponding to a task, process, or material. We cast the problem as sequence tagging and introduce semi-supervised methods to a neural tagging model, which builds on recent advances in named entity recognition. Since annotated training data is scarce in this domain, we introduce a graph-based semi-supervised algorithm together with a data selection scheme to leverage unannotated articles. Both inductive and transductive semi-supervised learning strategies outperform state-of-the-art information extraction performance on the 2017 SemEval Task 10 ScienceIE task.Comment: accepted by EMNLP 201