Spatially Aware Dictionary Learning and Coding for Fossil Pollen Identification

We propose a robust approach for performing automatic species-level recognition of fossil pollen grains in microscopy images that exploits both global shape and local texture characteristics in a patch-based matching methodology. We introduce a novel criteria for selecting meaningful and discriminative exemplar patches. We optimize this function during training using a greedy submodular function optimization framework that gives a near-optimal solution with bounded approximation error. We use these selected exemplars as a dictionary basis and propose a spatially-aware sparse coding method to match testing images for identification while maintaining global shape correspondence. To accelerate the coding process for fast matching, we introduce a relaxed form that uses spatially-aware soft-thresholding during coding. Finally, we carry out an experimental study that demonstrates the effectiveness and efficiency of our exemplar selection and classification mechanisms, achieving $86.13\%$ accuracy on a difficult fine-grained species classification task distinguishing three types of fossil spruce pollen.Comment: CVMI 201

Weighted Heuristic Ensemble of Filters

Feature selection has become increasingly important in data mining in recent years due to the rapid increase in the dimensionality of big data. However, the reliability and consistency of feature selection methods (filters) vary considerably on different data and no single filter performs consistently well under various conditions. Therefore, feature selection ensemble has been investigated recently to provide more reliable and effective results than any individual one but all the existing feature selection ensemble treat the feature selection methods equally regardless of their performance. In this paper, we present a novel framework which applies weighted feature selection ensemble through proposing a systemic way of adding different weights to the feature selection methods-filters. Also, we investigate how to determine the appropriate weight for each filter in an ensemble. Experiments based on ten benchmark datasets show that theoretically and intuitively adding more weight to ‘good filters’ should lead to better results but in reality it is very uncertain. This assumption was found to be correct for some examples in our experiment. However, for other situations, filters which had been assumed to perform well showed bad performance leading to even worse results. Therefore adding weight to filters might not achieve much in accuracy terms, in addition to increasing complexity, time consumption and clearly decreasing the stability

Modified Frank-Wolfe Algorithm for Enhanced Sparsity in Support Vector Machine Classifiers

This work proposes a new algorithm for training a re-weighted L2 Support Vector Machine (SVM), inspired on the re-weighted Lasso algorithm of Cand\`es et al. and on the equivalence between Lasso and SVM shown recently by Jaggi. In particular, the margin required for each training vector is set independently, defining a new weighted SVM model. These weights are selected to be binary, and they are automatically adapted during the training of the model, resulting in a variation of the Frank-Wolfe optimization algorithm with essentially the same computational complexity as the original algorithm. As shown experimentally, this algorithm is computationally cheaper to apply since it requires less iterations to converge, and it produces models with a sparser representation in terms of support vectors and which are more stable with respect to the selection of the regularization hyper-parameter

Deep Learning versus Classical Regression for Brain Tumor Patient Survival Prediction

Deep learning for regression tasks on medical imaging data has shown promising results. However, compared to other approaches, their power is strongly linked to the dataset size. In this study, we evaluate 3D-convolutional neural networks (CNNs) and classical regression methods with hand-crafted features for survival time regression of patients with high grade brain tumors. The tested CNNs for regression showed promising but unstable results. The best performing deep learning approach reached an accuracy of 51.5% on held-out samples of the training set. All tested deep learning experiments were outperformed by a Support Vector Classifier (SVC) using 30 radiomic features. The investigated features included intensity, shape, location and deep features. The submitted method to the BraTS 2018 survival prediction challenge is an ensemble of SVCs, which reached a cross-validated accuracy of 72.2% on the BraTS 2018 training set, 57.1% on the validation set, and 42.9% on the testing set. The results suggest that more training data is necessary for a stable performance of a CNN model for direct regression from magnetic resonance images, and that non-imaging clinical patient information is crucial along with imaging information.Comment: Contribution to The International Multimodal Brain Tumor Segmentation (BraTS) Challenge 2018, survival prediction tas