Application of kernel functions for accurate similarity search in large chemical databases

Background Similaritysearch in chemical structure databases is an important problem with many applications in chemical genomics, drug design, and efficient chemical probe screening among others. It is widely believed that structure based methods provide an efficient way to do the query. Recently various graph kernel functions have been designed to capture the intrinsic similarity of graphs. Though successful in constructing accurate predictive and classification models, graph kernel functions can not be applied to large chemical compound database due to the high computational complexity and the difficulties in indexing similarity search for large databases. Results To bridge graph kernel function and similarity search in chemical databases, we applied a novel kernel-based similarity measurement, developed in our team, to measure similarity of graph represented chemicals. In our method, we utilize a hash table to support new graph kernel function definition, efficient storage and fast search. We have applied our method, named G-hash, to large chemical databases. Our results show that the G-hash method achieves state-of-the-art performance for k-nearest neighbor (k-NN) classification. Moreover, the similarity measurement and the index structure is scalable to large chemical databases with smaller indexing size, and faster query processing time as compared to state-of-the-art indexing methods such as Daylight fingerprints, C-tree and GraphGrep. Conclusions Efficient similarity query processing method for large chemical databases is challenging since we need to balance running time efficiency and similarity search accuracy. Our previous similarity search method, G-hash, provides a new way to perform similarity search in chemical databases. Experimental study validates the utility of G-hash in chemical databases

The Metric Nearness Problem

Metric nearness refers to the problem of optimally restoring metric properties to distance measurements that happen to be nonmetric due to measurement errors or otherwise. Metric data can be important in various settings, for example, in clustering, classification, metric-based indexing, query processing, and graph theoretic approximation algorithms. This paper formulates and solves the metric nearness problem: Given a set of pairwise dissimilarities, find a “nearest” set of distances that satisfy the properties of a metric—principally the triangle inequality. For solving this problem, the paper develops efficient triangle fixing algorithms that are based on an iterative projection method. An intriguing aspect of the metric nearness problem is that a special case turns out to be equivalent to the all pairs shortest paths problem. The paper exploits this equivalence and develops a new algorithm for the latter problem using a primal-dual method. Applications to graph clustering are provided as an illustration. We include experiments that demonstrate the computational superiority of triangle fixing over general purpose convex programming software. Finally, we conclude by suggesting various useful extensions and generalizations to metric nearness

Incremental dimension reduction of tensors with random index

We present an incremental, scalable and efficient dimension reduction technique for tensors that is based on sparse random linear coding. Data is stored in a compactified representation with fixed size, which makes memory requirements low and predictable. Component encoding and decoding are performed on-line without computationally expensive re-analysis of the data set. The range of tensor indices can be extended dynamically without modifying the component representation. This idea originates from a mathematical model of semantic memory and a method known as random indexing in natural language processing. We generalize the random-indexing algorithm to tensors and present signal-to-noise-ratio simulations for representations of vectors and matrices. We present also a mathematical analysis of the approximate orthogonality of high-dimensional ternary vectors, which is a property that underpins this and other similar random-coding approaches to dimension reduction. To further demonstrate the properties of random indexing we present results of a synonym identification task. The method presented here has some similarities with random projection and Tucker decomposition, but it performs well at high dimensionality only (n>10^3). Random indexing is useful for a range of complex practical problems, e.g., in natural language processing, data mining, pattern recognition, event detection, graph searching and search engines. Prototype software is provided. It supports encoding and decoding of tensors of order >= 1 in a unified framework, i.e., vectors, matrices and higher order tensors.Comment: 36 pages, 9 figure

TopCom: Index for Shortest Distance Query in Directed Graph

Finding shortest distance between two vertices in a graph is an important problem due to its numerous applications in diverse domains, including geo-spatial databases, social network analysis, and information retrieval. Classical algorithms (such as, Dijkstra) solve this problem in polynomial time, but these algorithms cannot provide real-time response for a large number of bursty queries on a large graph. So, indexing based solutions that pre-process the graph for efficiently answering (exactly or approximately) a large number of distance queries in real-time is becoming increasingly popular. Existing solutions have varying performance in terms of index size, index building time, query time, and accuracy. In this work, we propose T OP C OM , a novel indexing-based solution for exactly answering distance queries. Our experiments with two of the existing state-of-the-art methods (IS-Label and TreeMap) show the superiority of T OP C OM over these two methods considering scalability and query time. Besides, indexing of T OP C OM exploits the DAG (directed acyclic graph) structure in the graph, which makes it significantly faster than the existing methods if the SCCs (strongly connected component) of the input graph are relatively small

Investigation into Indexing XML Data Techniques

The rapid development of XML technology improves the WWW, since the XML data has many advantages and has become a common technology for transferring data cross the internet. Therefore, the objective of this research is to investigate and study the XML indexing techniques in terms of their structures. The main goal of this investigation is to identify the main limitations of these techniques and any other open issues. Furthermore, this research considers most common XML indexing techniques and performs a comparison between them. Subsequently, this work makes an argument to find out these limitations. To conclude, the main problem of all the XML indexing techniques is the trade-off between the size and the efficiency of the indexes. So, all the indexes become large in order to perform well, and none of them is suitable for all users’ requirements. However, each one of these techniques has some advantages in somehow

Non-hierarchical Structures: How to Model and Index Overlaps?

Overlap is a common phenomenon seen when structural components of a digital object are neither disjoint nor nested inside each other. Overlapping components resist reduction to a structural hierarchy, and tree-based indexing and query processing techniques cannot be used for them. Our solution to this data modeling problem is TGSA (Tree-like Graph for Structural Annotations), a novel extension of the XML data model for non-hierarchical structures. We introduce an algorithm for constructing TGSA from annotated documents; the algorithm can efficiently process non-hierarchical structures and is associated with formal proofs, ensuring that transformation of the document to the data model is valid. To enable high performance query analysis in large data repositories, we further introduce an extension of XML pre-post indexing for non-hierarchical structures, which can process both reachability and overlapping relationships.Comment: The paper has been accepted at the Balisage 2014 conferenc