Distributional Inclusion Vector Embedding for Unsupervised Hypernymy Detection

Modeling hypernymy, such as poodle is-a dog, is an important generalization aid to many NLP tasks, such as entailment, coreference, relation extraction, and question answering. Supervised learning from labeled hypernym sources, such as WordNet, limits the coverage of these models, which can be addressed by learning hypernyms from unlabeled text. Existing unsupervised methods either do not scale to large vocabularies or yield unacceptably poor accuracy. This paper introduces distributional inclusion vector embedding (DIVE), a simple-to-implement unsupervised method of hypernym discovery via per-word non-negative vector embeddings which preserve the inclusion property of word contexts in a low-dimensional and interpretable space. In experimental evaluations more comprehensive than any previous literature of which we are aware-evaluating on 11 datasets using multiple existing as well as newly proposed scoring functions-we find that our method provides up to double the precision of previous unsupervised embeddings, and the highest average performance, using a much more compact word representation, and yielding many new state-of-the-art results.Comment: NAACL 201

Laplacian Mixture Modeling for Network Analysis and Unsupervised Learning on Graphs

Laplacian mixture models identify overlapping regions of influence in unlabeled graph and network data in a scalable and computationally efficient way, yielding useful low-dimensional representations. By combining Laplacian eigenspace and finite mixture modeling methods, they provide probabilistic or fuzzy dimensionality reductions or domain decompositions for a variety of input data types, including mixture distributions, feature vectors, and graphs or networks. Provable optimal recovery using the algorithm is analytically shown for a nontrivial class of cluster graphs. Heuristic approximations for scalable high-performance implementations are described and empirically tested. Connections to PageRank and community detection in network analysis demonstrate the wide applicability of this approach. The origins of fuzzy spectral methods, beginning with generalized heat or diffusion equations in physics, are reviewed and summarized. Comparisons to other dimensionality reduction and clustering methods for challenging unsupervised machine learning problems are also discussed.Comment: 13 figures, 35 reference

ProtNN: Fast and Accurate Nearest Neighbor Protein Function Prediction based on Graph Embedding in Structural and Topological Space

Studying the function of proteins is important for understanding the molecular mechanisms of life. The number of publicly available protein structures has increasingly become extremely large. Still, the determination of the function of a protein structure remains a difficult, costly, and time consuming task. The difficulties are often due to the essential role of spatial and topological structures in the determination of protein functions in living cells. In this paper, we propose ProtNN, a novel approach for protein function prediction. Given an unannotated protein structure and a set of annotated proteins, ProtNN finds the nearest neighbor annotated structures based on protein-graph pairwise similarities. Given a query protein, ProtNN finds the nearest neighbor reference proteins based on a graph representation model and a pairwise similarity between vector embedding of both query and reference protein-graphs in structural and topological spaces. ProtNN assigns to the query protein the function with the highest number of votes across the set of k nearest neighbor reference proteins, where k is a user-defined parameter. Experimental evaluation demonstrates that ProtNN is able to accurately classify several datasets in an extremely fast runtime compared to state-of-the-art approaches. We further show that ProtNN is able to scale up to a whole PDB dataset in a single-process mode with no parallelization, with a gain of thousands order of magnitude of runtime compared to state-of-the-art approaches