Scalable Similarity Search for Molecular Descriptors

Similarity search over chemical compound databases is a fundamental task in the discovery and design of novel drug-like molecules. Such databases often encode molecules as non-negative integer vectors, called molecular descriptors, which represent rich information on various molecular properties. While there exist efficient indexing structures for searching databases of binary vectors, solutions for more general integer vectors are in their infancy. In this paper we present a time- and space- efficient index for the problem that we call the succinct intervals-splitting tree algorithm for molecular descriptors (SITAd). Our approach extends efficient methods for binary-vector databases, and uses ideas from succinct data structures. Our experiments, on a large database of over 40 million compounds, show SITAd significantly outperforms alternative approaches in practice.Comment: To be appeared in the Proceedings of SISAP'1

Search Efficient Binary Network Embedding

Traditional network embedding primarily focuses on learning a dense vector representation for each node, which encodes network structure and/or node content information, such that off-the-shelf machine learning algorithms can be easily applied to the vector-format node representations for network analysis. However, the learned dense vector representations are inefficient for large-scale similarity search, which requires to find the nearest neighbor measured by Euclidean distance in a continuous vector space. In this paper, we propose a search efficient binary network embedding algorithm called BinaryNE to learn a sparse binary code for each node, by simultaneously modeling node context relations and node attribute relations through a three-layer neural network. BinaryNE learns binary node representations efficiently through a stochastic gradient descent based online learning algorithm. The learned binary encoding not only reduces memory usage to represent each node, but also allows fast bit-wise comparisons to support much quicker network node search compared to Euclidean distance or other distance measures. Our experiments and comparisons show that BinaryNE not only delivers more than 23 times faster search speed, but also provides comparable or better search quality than traditional continuous vector based network embedding methods

Topic Similarity Networks: Visual Analytics for Large Document Sets

We investigate ways in which to improve the interpretability of LDA topic models by better analyzing and visualizing their outputs. We focus on examining what we refer to as topic similarity networks: graphs in which nodes represent latent topics in text collections and links represent similarity among topics. We describe efficient and effective approaches to both building and labeling such networks. Visualizations of topic models based on these networks are shown to be a powerful means of exploring, characterizing, and summarizing large collections of unstructured text documents. They help to "tease out" non-obvious connections among different sets of documents and provide insights into how topics form larger themes. We demonstrate the efficacy and practicality of these approaches through two case studies: 1) NSF grants for basic research spanning a 14 year period and 2) the entire English portion of Wikipedia.Comment: 9 pages; 2014 IEEE International Conference on Big Data (IEEE BigData 2014

Chemical structure matching using correlation matrix memories

This paper describes the application of the Relaxation By Elimination (RBE) method to matching the 3D structure of molecules in chemical databases within the frame work of binary correlation matrix memories. The paper illustrates that, when combined with distributed representations, the method maps well onto these networks, allowing high performance implementation in parallel systems. It outlines the motivation, the neural architecture, the RBE method and presents some results of matching small molecules against a database of 100,000 models

The Parallelism Motifs of Genomic Data Analysis

Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these genomic data analysis problems require large scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high end parallel systems today and place different requirements on programming support, software libraries, and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high performance genomics analysis, including alignment, profiling, clustering, and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or motifs that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing