Learning to propagate labels on graphs: An iterative multitask regression framework for semi-supervised hyperspectral dimensionality reduction.

Hyperspectral dimensionality reduction (HDR), an important preprocessing step prior to high-level data analysis, has been garnering growing attention in the remote sensing community. Although a variety of methods, both unsupervised and supervised models, have been proposed for this task, yet the discriminative ability in feature representation still remains limited due to the lack of a powerful tool that effectively exploits the labeled and unlabeled data in the HDR process. A semi-supervised HDR approach, called iterative multitask regression (IMR), is proposed in this paper to address this need. IMR aims at learning a low-dimensional subspace by jointly considering the labeled and unlabeled data, and also bridging the learned subspace with two regression tasks: labels and pseudo-labels initialized by a given classifier. More significantly, IMR dynamically propagates the labels on a learnable graph and progressively refines pseudo-labels, yielding a well-conditioned feedback system. Experiments conducted on three widely-used hyperspectral image datasets demonstrate that the dimension-reduced features learned by the proposed IMR framework with respect to classification or recognition accuracy are superior to those of related state-of-the-art HDR approaches.

Bayesian learning of feature spaces for multitask regression.

This paper introduces a novel approach to learn multi-task regression models with constrained architecture complexity. The proposed model, named RFF-BLR, consists of a randomised feedforward neural network with two fundamental characteristics: a single hidden layer whose units implement the random Fourier features that approximate an RBF kernel, and a Bayesian formulation that optimises the weights connecting the hidden and output layers. The RFF-based hidden layer inherits the robustness of kernel methods. The Bayesian formulation enables promoting multioutput sparsity: all tasks interplay during the optimisation to select a compact subset of the hidden layer units that serve as common non-linear mapping for every tasks. The experimental results show that the RFF-BLR framework can lead to significant performance improvements compared to the state-of-the-art methods in multitask nonlinear regression, especially in small-sized training dataset scenarios.

Multitask Learning Radiomics on Longitudinal Imaging to Predict Survival Outcomes following Risk-Adaptive Chemoradiation for Non-Small Cell Lung Cancer.

Medical imaging provides quantitative and spatial information to evaluate treatment response in the management of patients with non-small cell lung cancer (NSCLC). High throughput extraction of radiomic features on these images can potentially phenotype tumors non-invasively and support risk stratification based on survival outcome prediction. The prognostic value of radiomics from different imaging modalities and time points prior to and during chemoradiation therapy of NSCLC, relative to conventional imaging biomarker or delta radiomics models, remains uncharacterized. We investigated the utility of multitask learning of multi-time point radiomic features, as opposed to single-task learning, for improving survival outcome prediction relative to conventional clinical imaging feature model benchmarks. Survival outcomes were prospectively collected for 45 patients with unresectable NSCLC enrolled on the FLARE-RT phase II trial of risk-adaptive chemoradiation and optional consolidation PD-L1 checkpoint blockade (NCT02773238). FDG-PET, CT, and perfusion SPECT imaging pretreatment and week 3 mid-treatment was performed and 110 IBSI-compliant pyradiomics shape-/intensity-/texture-based features from the metabolic tumor volume were extracted. Outcome modeling consisted of a fused Laplacian sparse group LASSO with component-wise gradient boosting survival regression in a multitask learning framework. Testing performance under stratified 10-fold cross-validation was evaluated for multitask learning radiomics of different imaging modalities and time points. Multitask learning models were benchmarked against conventional clinical imaging and delta radiomics models and evaluated with the concordance index (c-index) and index of prediction accuracy (IPA). FDG-PET radiomics had higher prognostic value for overall survival in test folds (c-index 0.71 [0.67, 0.75]) than CT radiomics (c-index 0.64 [0.60, 0.71]) or perfusion SPECT radiomics (c-index 0.60 [0.57, 0.63]). Multitask learning of pre-/mid-treatment FDG-PET radiomics (c-index 0.71 [0.67, 0.75]) outperformed benchmark clinical imaging (c-index 0.65 [0.59, 0.71]) and FDG-PET delta radiomics (c-index 0.52 [0.48, 0.58]) models. Similarly, the IPA for multitask learning FDG-PET radiomics (30%) was higher than clinical imaging (26%) and delta radiomics (15%) models. Radiomics models performed consistently under different voxel resampling conditions. Multitask learning radiomics for outcome modeling provides a clinical decision support platform that leverages longitudinal imaging information. This framework can reveal the relative importance of different imaging modalities and time points when designing risk-adaptive cancer treatment strategies.

Kernel Multitask Regression for Toxicogenetics.

The development of high-throughput in vitro assays to study quantitatively the toxicity of chemical compounds on genetically characterized human-derived cell lines paves the way to predictive toxicogenetics, where one would be able to predict the toxicity of any particular compound on any particular individual. In this paper we present a machine learning-based approach for that purpose, kernel multitask regression (KMR), which combines chemical characterizations of molecular compounds with genetic and transcriptomic characterizations of cell lines to predict the toxicity of a given compound on a given cell line. We demonstrate the relevance of the method on the recent DREAM8 Toxicogenetics challenge, where it ranked among the best state-of-the-art models, and discuss the importance of choosing good descriptors for cell lines and chemicals.