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

GraphMatch: Efficient Large-Scale Graph Construction for Structure from Motion

We present GraphMatch, an approximate yet efficient method for building the matching graph for large-scale structure-from-motion (SfM) pipelines. Unlike modern SfM pipelines that use vocabulary (Voc.) trees to quickly build the matching graph and avoid a costly brute-force search of matching image pairs, GraphMatch does not require an expensive offline pre-processing phase to construct a Voc. tree. Instead, GraphMatch leverages two priors that can predict which image pairs are likely to match, thereby making the matching process for SfM much more efficient. The first is a score computed from the distance between the Fisher vectors of any two images. The second prior is based on the graph distance between vertices in the underlying matching graph. GraphMatch combines these two priors into an iterative "sample-and-propagate" scheme similar to the PatchMatch algorithm. Its sampling stage uses Fisher similarity priors to guide the search for matching image pairs, while its propagation stage explores neighbors of matched pairs to find new ones with a high image similarity score. Our experiments show that GraphMatch finds the most image pairs as compared to competing, approximate methods while at the same time being the most efficient.Comment: Published at IEEE 3DV 201

Effective and Efficient Similarity Search in Scientific Workflow Repositories

International audienceScientific workflows have become a valuable tool for large-scale data processing and analysis. This has led to the creation of specialized online repositories to facilitate worflkow sharing and reuse. Over time, these repositories have grown to sizes that call for advanced methods to support workflow discovery, in particular for similarity search. Effective similarity search requires both high quality algorithms for the comparison of scientific workflows and efficient strategies for indexing, searching, and ranking of search results. Yet, the graph structure of scientific workflows poses severe challenges to each of these steps. Here, we present a complete system for effective and efficient similarity search in scientific workflow repositories, based on the Layer Decompositon approach to scientific workflow comparison. Layer Decompositon specifically accounts for the directed dataflow underlying scientific workflows and, compared to other state-of-the-art methods, delivers best results for similarity search at comparably low runtimes. Stacking Layer Decomposition with even faster, structure-agnostic approaches allows us to use proven, off-the-shelf tools for workflow indexing to further reduce runtimes and scale similarity search to sizes of current repositories

On Ranked Approximate Matching Of Large Attributed Graphs

Many emerging database applications entail sophisticated graph based query manipulation, predominantly evident in large-scale scientific applications. To access the information embedded in graphs, efficient graph matching tools and algorithms have become of prime importance. Although the prohibitively expensive time complexity associated with exact sub-graph isomorphism techniques has limited its efficacy in the application domain, approximate yet efficient graph matching techniques have received much attention due to their pragmatic applicability. Since public domain databases are noisy and incomplete in nature, inexact graph matching techniques have proven to be more promising in terms of inferring knowledge from numerous structural data repositories. Contemporary algorithms for approximate graph matching incur substantial cost to generate candidates, and then test and rank them for possible match. Leading algorithms balance processing time and overall resource consumption cost by leveraging sophisticated data structures and graph properties to improve overall performance. In this dissertation, we propose novel techniques for approximate graph matching based on two different techniques called TraM or Top-k Graph Matching and Approximate Network Matching or AtoM respectively. While TraM off-loads a significant amount of its processing on to the database making the approach viable for large graphs, AtoM provides improved turn around time by means of graph summarization prior to matching. The summarization process is aided by domain sensitive similarity matrices, which in turn helps improve the matching performance. The vector space embedding of the graphs and efficient filtration of the search space enables computation of approximate graph similarity at a throw-away cost. We combine domain similarity and topological similarity to obtain overall graph similarity and compare them with neighborhood biased segments of the data-graph for proper matches. We show that our approach can naturally support the emerging trend in graph pattern queries and discuss its suitability for large networks as it can be seamlessly transformed to adhere to map-reduce framework. We have conducted thorough experiments on several synthetic and real data sets, and have demonstrated the effectiveness and efficiency of the proposed method

Image Stream Similarity Search in GPU Clusters

Images are an important part of today’s society. They are everywhere on the internet and computing, from news articles to diverse areas such as medicine, autonomous vehicles and social media. This enormous amount of images requires massive amounts of processing power to process, upload, download and search for images. The ability to search an image, and find similar images in a library of millions of others empowers users with great advantages. Different fields have different constraints, but all benefit from the quick processing that can be achieved. Problems arise when creating a solution for this. The similarity calculation between several images, performing thousands of comparisons every second, is a challenge. The results of such computations are very large, and pose a challenge when attempting to process. Solutions for these problems often take advantage of graphs in order to index images and their similarity. The graph can then be used for the querying process. Creating and processing such a graph in an acceptable time frame poses yet another challenge. In order to tackle these challenges, we take advantage of a cluster of machines equipped with Graphics Processing Units (GPUs), enabling us to parallelize the process of describing an image visually and finding other images similar to it in an acceptable time frame. GPUs are incredibly efficient at processing data such as images and graphs, through algorithms that are heavily parallelizable. We propose a scalable and modular system that takes advantage of GPUs, distributed computing and fine-grained parallellism to detect image features, index images in a graph and allow users to search for similar images. The solution we propose is able to compare up to 5000 images every second. It is also able to query a graph with thousands of nodes and millions of edges in a matter of milliseconds, achieving a very efficient query speed. The modularity of our solution allows the interchangeability of algorithms and different steps in the solution, which provides great adaptability to any needs

Off the Beaten Path: Let's Replace Term-Based Retrieval with k-NN Search

Retrieval pipelines commonly rely on a term-based search to obtain candidate records, which are subsequently re-ranked. Some candidates are missed by this approach, e.g., due to a vocabulary mismatch. We address this issue by replacing the term-based search with a generic k-NN retrieval algorithm, where a similarity function can take into account subtle term associations. While an exact brute-force k-NN search using this similarity function is slow, we demonstrate that an approximate algorithm can be nearly two orders of magnitude faster at the expense of only a small loss in accuracy. A retrieval pipeline using an approximate k-NN search can be more effective and efficient than the term-based pipeline. This opens up new possibilities for designing effective retrieval pipelines. Our software (including data-generating code) and derivative data based on the Stack Overflow collection is available online

FLASH: Randomized Algorithms Accelerated over CPU-GPU for Ultra-High Dimensional Similarity Search

We present FLASH (\textbf{F}ast \textbf{L}SH \textbf{A}lgorithm for \textbf{S}imilarity search accelerated with \textbf{H}PC), a similarity search system for ultra-high dimensional datasets on a single machine, that does not require similarity computations and is tailored for high-performance computing platforms. By leveraging a LSH style randomized indexing procedure and combining it with several principled techniques, such as reservoir sampling, recent advances in one-pass minwise hashing, and count based estimations, we reduce the computational and parallelization costs of similarity search, while retaining sound theoretical guarantees. We evaluate FLASH on several real, high-dimensional datasets from different domains, including text, malicious URL, click-through prediction, social networks, etc. Our experiments shed new light on the difficulties associated with datasets having several million dimensions. Current state-of-the-art implementations either fail on the presented scale or are orders of magnitude slower than FLASH. FLASH is capable of computing an approximate k-NN graph, from scratch, over the full webspam dataset (1.3 billion nonzeros) in less than 10 seconds. Computing a full k-NN graph in less than 10 seconds on the webspam dataset, using brute-force ($n^2D$), will require at least 20 teraflops. We provide CPU and GPU implementations of FLASH for replicability of our results