Edge-Labeling Graph Neural Network (EGNN)
In this paper, we propose a novel edge-labeling graph neural network (EGNN), which adapts a deep neural network on the edge-labeling graph, for few-shot learning. The previous graph neural network (GNN) approaches in few-shot learning have been based on the node-labeling framework, which implicitly models the intra-cluster similarity and the inter-cluster dissimilarity. In contrast, the proposed EGNN learns to predict the edge-labels rather than the node-labels on the graph that enables the evolution of an explicit clustering by iteratively updating the edge-labels with direct exploitation of both intra-cluster similarity and the inter-cluster dissimilarity. It is also well suited for performing on various numbers of classes without retraining, and can be easily extended to perform a transductive inference. The parameters of the EGNN are learned by episodic training with an edge-labeling loss to obtain a well-generalizable model for unseen low-data problem. On both of the supervised and semi-supervised few-shot image classification tasks with two benchmark datasets, the proposed EGNN significantly improves the performances over the existing GNNs. …

Predictive Clustering
We show how to convert any clustering into a prediction set. This has the effect of converting the clustering into a (possibly overlapping) union of spheres or ellipsoids. The tuning parameters can be chosen to minimize the size of the prediction set. When applied to k-means clustering, this method solves several problems: the method tells us how to choose k, how to merge clusters and how to replace the Voronoi partition with more natural shapes. We show that the same reasoning can be applied to other clustering methods. …

Meta-Analysis for Pathway Enrichment (MAPE)
Motivation: Many pathway analysis (or gene set enrichment analysis) methods have been developed to identify enriched pathways under different biological states within a genomic study. As more and more microarray datasets accumulate, meta-analysis methods have also been developed to integrate information among multiple studies. Currently, most meta-analysis methods for combining genomic studies focus on biomarker detection and meta-analysis for pathway analysis has not been systematically pursued.
Results: We investigated two approaches of meta-analysis for pathway enrichment (MAPE) by combining statistical significance across studies at the gene level (MAPE_G) or at the pathway level (MAPE_P). Simulation results showed increased statistical power of meta-analysis approaches compared to a single study analysis and showed complementary advantages of MAPE_G and MAPE_P under different scenarios. We also developed an integrated method (MAPE_I) that incorporates advantages of both approaches. Comprehensive simulations and applications to real data on drug response of breast cancer cell lines and lung cancer tissues were evaluated to compare the performance of three MAPE variations. MAPE_P has the advantage of not requiring gene matching across studies. When MAPE_G and MAPE_P show complementary advantages, the hybrid version of MAPE_I is generally recommended. …

Recurrent Transformer Network (RTN)
We present recurrent transformer networks (RTNs) for obtaining dense correspondences between semantically similar images. Our networks accomplish this through an iterative process of estimating spatial transformations between the input images and using these transformations to generate aligned convolutional activations. By directly estimating the transformations between an image pair, rather than employing spatial transformer networks to independently normalize each individual image, we show that greater accuracy can be achieved. This process is conducted in a recursive manner to refine both the transformation estimates and the feature representations. In addition, a technique is presented for weakly-supervised training of RTNs that is based on a proposed classification loss. With RTNs, state-of-the-art performance is attained on several benchmarks for semantic correspondence. …