In this paper, we aim to eliminate the inductive bias imposed by the embedding space geometry.

Learning useful representations is a key ingredient to the success of modern machine learning. Currently, representation learning mostly relies on embedding data into Euclidean space. However, recent work has shown that data in some domains is better modeled by non-euclidean metric spaces, and inappropriate geometry can result in inferior performance. In this paper, we aim to eliminate the inductive bias imposed by the embedding space geometry. Namely, we propose to map data into more general non-vector metric spaces: a weighted graph with a shortest path distance. By design, such graphs can model arbitrary geometry with a proper configuration of edges and weights. Our main contribution is PRODIGE: a method that learns a weighted graph representation of data end-to-end by gradient descent. Greater generality and fewer model assumptions make PRODIGE more powerful than existing embedding-based approaches. We confirm the superiority of our method via extensive experiments on a wide range of tasks, including classification, compression, and collaborative filtering.

Neural Information Processing Systems http://nips.cc/

We thank the reviewers for their constructive feedback and address their comments below. In this paper, we focus on the models with low memory budgets. Empirically, we also observe that edge probabilities converge to 0 or 1. Y es, in our model edge indicators are independent random variables. Furthermore, PRODIGE is a general method that works for a variety of tasks (e.g. If accepted, we will include a more detailed comparison of the two methods with explanation.

Learning useful representations is a key ingredient to the success of modern machine learning. Currently, representation learning mostly relies on embedding data into Euclidean space. However, recent work has shown that data in some domains is better modeled by non-euclidean metric spaces, and inappropriate geometry can result in inferior performance. In this paper, we aim to eliminate the inductive bias imposed by the embedding space geometry. Namely, we propose to map data into more general non-vector metric spaces: a weighted graph with a shortest path distance.

Learning useful representations is a key ingredient to the success of modern machine learning. Currently, representation learning mostly relies on embedding data into Euclidean space. However, recent work has shown that data in some domains is better modeled by non-euclidean metric spaces, and inappropriate geometry can result in inferior performance. In this paper, we aim to eliminate the inductive bias imposed by the embedding space geometry. Namely, we propose to map data into more general non-vector metric spaces: a weighted graph with a shortest path distance.

Learning useful representations is a key ingredient to the success of modern machine learning. Currently, representation learning mostly relies on embedding data into Euclidean space. However, recent work has shown that data in some domains is better modeled by non-euclidean metric spaces, and inappropriate geometry can result in inferior performance. In this paper, we aim to eliminate the inductive bias imposed by the embedding space geometry. Namely, we propose to map data into more general non-vector metric spaces: a weighted graph with a shortest path distance. By design, such graphs can model arbitrary geometry with a proper configuration of edges and weights. Our main contribution is PRODIGE: a method that learns a weighted graph representation of data end-to-end by gradient descent. Greater generality and fewer model assumptions make PRODIGE more powerful than existing embedding-based approaches. We confirm the superiority of our method via extensive experiments on a wide range of tasks, including classification, compression, and collaborative filtering.

Elucidating the genetic basis of human diseases is a central goal of genetics and molecular biology. While traditional linkage analysis and modern high-throughput techniques often provide long lists of tens or hundreds of disease gene candidates, the identification of disease genes among the candidates remains time-consuming and expensive. Efficient computational methods are therefore needed to prioritize genes within the list of candidates, by exploiting the wealth of information available about the genes in various databases. Here we propose ProDiGe, a novel algorithm for Prioritization of Disease Genes. ProDiGe implements a novel machine learning strategy based on learning from positive and unlabeled examples, which allows to integrate various sources of information about the genes, to share information about known disease genes across diseases, and to perform genome-wide searches for new disease genes. Experiments on real data show that ProDiGe outperforms state-of-the-art methods for the prioritization of genes in human diseases.