Inferring gene ontologies from pairwise similarity data.

MotivationWhile the manually curated Gene Ontology (GO) is widely used, inferring a GO directly from -omics data is a compelling new problem. Recognizing that ontologies are a directed acyclic graph (DAG) of terms and hierarchical relations, algorithms are needed that: analyze a full matrix of gene-gene pairwise similarities from -omics data; infer true hierarchical structure in these data rather than enforcing hierarchy as a computational artifact; and respect biological pleiotropy, by which a term in the hierarchy can relate to multiple higher level terms. Methods addressing these requirements are just beginning to emerge-none has been evaluated for GO inference.MethodsWe consider two algorithms [Clique Extracted Ontology (CliXO), LocalFitness] that uniquely satisfy these requirements, compared with methods including standard clustering. CliXO is a new approach that finds maximal cliques in a network induced by progressive thresholding of a similarity matrix. We evaluate each method's ability to reconstruct the GO biological process ontology from a similarity matrix based on (a) semantic similarities for GO itself or (b) three -omics datasets for yeast.ResultsFor task (a) using semantic similarity, CliXO accurately reconstructs GO (>99% precision, recall) and outperforms other approaches (<20% precision, <20% recall). For task (b) using -omics data, CliXO outperforms other methods using two -omics datasets and achieves ∼30% precision and recall using YeastNet v3, similar to an earlier approach (Network Extracted Ontology) and better than LocalFitness or standard clustering (20-25% precision, recall).ConclusionThis study provides algorithmic foundation for building gene ontologies by capturing hierarchical and pleiotropic structure embedded in biomolecular data

Physics Inspired Optimization on Semantic Transfer Features: An Alternative Method for Room Layout Estimation

In this paper, we propose an alternative method to estimate room layouts of cluttered indoor scenes. This method enjoys the benefits of two novel techniques. The first one is semantic transfer (ST), which is: (1) a formulation to integrate the relationship between scene clutter and room layout into convolutional neural networks; (2) an architecture that can be end-to-end trained; (3) a practical strategy to initialize weights for very deep networks under unbalanced training data distribution. ST allows us to extract highly robust features under various circumstances, and in order to address the computation redundance hidden in these features we develop a principled and efficient inference scheme named physics inspired optimization (PIO). PIO's basic idea is to formulate some phenomena observed in ST features into mechanics concepts. Evaluations on public datasets LSUN and Hedau show that the proposed method is more accurate than state-of-the-art methods.Comment: To appear in CVPR 2017. Project Page: https://sites.google.com/view/st-pio

Breaking Sticks and Ambiguities with Adaptive Skip-gram

Recently proposed Skip-gram model is a powerful method for learning high-dimensional word representations that capture rich semantic relationships between words. However, Skip-gram as well as most prior work on learning word representations does not take into account word ambiguity and maintain only single representation per word. Although a number of Skip-gram modifications were proposed to overcome this limitation and learn multi-prototype word representations, they either require a known number of word meanings or learn them using greedy heuristic approaches. In this paper we propose the Adaptive Skip-gram model which is a nonparametric Bayesian extension of Skip-gram capable to automatically learn the required number of representations for all words at desired semantic resolution. We derive efficient online variational learning algorithm for the model and empirically demonstrate its efficiency on word-sense induction task