Index Query Research Articles

Disproportionality analysis of flutamide- or bicalutamide-induced liver injury with and without steroids by using the Japanese Adverse Drug Event Report database.

Although the mechanism underlying flutamide- or bicalutamide-induced liver injury may be immune related, the details remain unclear. If this mechanism is immune related, steroid use may be considered as a treatment option. Disproportionality analysis was conducted to evaluate the effect of concomitant steroid use on flutamide- and bicalutamide-induced liver injury. Male patients aged 20years or older who were receiving nonsteroidal anti-androgens from April 2004 to October 2023 were screened from the Japanese Adverse Drug Event Report database. Data on liver injury, age, weight, height, steroid use, obesity, hepatic stenosis, alcohol-related hepatic disorders, hepatitis B and C, and common drugs known to cause drug-induced liver injury were analyzed. Liver injury was defined by the Standardized Medical Dictionary for Regulatory Activities query index (code 20000006, version 27.0). Among 142,430 patients, 2,316 were administered nonsteroidal anti-androgens. Reports of liver injury were disproportionate depending on the agents used (reporting odds ratio [ROR], 1.29; 95% confidence intervals [CI], 1.13-1.46), especially among flutamide or bicalutamide users (flutamide: ROR, 6.09; 95% CI, 4.51-8.23; bicalutamide: ROR, 1.24; 95% CI, 1.05-1.48). Multivariable logistic regression analysis correlated steroid use with a lower risk of flutamide- or bicalutamide-induced liver injury (flutamide: odds ratio, 0.07; 95% CI, 0.01-0.52; bicalutamide: odds ratio, 0.45; 95% CI, 0.21-0.96). Our findings suggest that flutamide and bicalutamide may increase the risk of liver injury compared to enzalutamide, apalutamide, and darolutamide. Furthermore, our study indicated that steroid use could aid in the management of liver injury.

Learned index for non-key queries

Learned index for non-key queries

On Querying Historical Connectivity in Temporal Graphs

We study the historical connectivity query in temporal graphs where edges continuously arrive. Given an arbitrary time window, and two query vertices, the problem aims to identify if two vertices are connected by a path in the snapshot of the window. The state-of-the-art method designs an index based on the two-hop cover, and updating the index is costly when new edges arrive. In this paper, we propose a new framework and design a novel forest-based index for historical connectivity queries. The index enables us to answer queries by searching if two vertices are connected in the forest. We update the index by modifying a forest structure. Our techniques also work for connectivity query processing in a sliding window of temporal graphs. Extensive experiments have been conducted to show the considerable advantages of our approach compared with the state-of-the-art methods in both historical connectivity queries and sliding-window connectivity queries.

Readon: a novel algorithm to identify read-through transcripts with long-read sequencing data.

There are many clustered transcriptionally active regions in the human genome, in which the transcription complex cannot immediately terminate transcription at the upstream gene termination site, but instead continues to transcribe intergenic regions and downstream genes, resulting in read-through transcripts. Several studies have demonstrated the regulatory roles of read-through transcripts in tumorigenesis and development. However, limited by the read length of next-generation sequencing, discovery of read-through transcripts has been slow. For long but also erroneous third-generation sequencing data, this study developed a novel minimizer sketch algorithm to accurately and quickly identify read-through transcripts. Readon initially splits the reference sequence into distinct active regions. It employs a sliding window approach within each region, calculates minimizers, and constructs the specialized structured arrays for query indexing. Following initial alignment anchor screening of candidate read-through transcripts, further confirmation steps are executed. Comparative assessments against existing software reveal Readon's superior performance on both simulated and validated real data. Additionally, two downstream tools are provided: one for predicting whether a read-through transcript is likely to undergo nonsense-mediated decay or encodes a protein, and another for visualizing splicing patterns. Readon is freely available on GitHub (https://github.com/Bulabula45/Readon).

MEM-based pangenome indexing for k-mer queries.

Pangenomes are growing in number and size, thanks to the prevalence of high-quality long-read assemblies. However, current methods for studying sequence composition and conservation within pangenomes have limitations. Methods based on graph pangenomes require a computationally expensive multiple-alignment step, which can leave out some variation. Indexes based on k-mers and de Bruijn graphs are limited to answering questions at a specific substring length k. We present Maximal Exact Match Ordered (MEMO), a pangenome indexing method based on maximal exact matches (MEMs) between sequences. A single MEMO index can handle arbitrary-length queries over pangenomic windows. MEMO enables both queries that test k-mer presence/absence (membership queries) and that count the number of genomes containing k-mers in a window (conservation queries). MEMO's index for a pangenome of 89 human autosomal haplotypes fits in 2.04 GB, 8.8× smaller than a comparable KMC3 index and 11.4× smaller than a PanKmer index. MEMO indexes can be made smaller by sacrificing some counting resolution, with our decile-resolution HPRC index reaching 0.67 GB. MEMO can conduct a conservation query for 31-mers over the human leukocyte antigen locus in 13.89 seconds, 2.5x faster than other approaches. MEMO's small index size, lack of k-mer length dependence, and efficient queries make it a flexible tool for studying and visualizing substring conservation in pangenomes.

BL: An Efficient Index for Reachability Queries on Large Graphs

BL: An Efficient Index for Reachability Queries on Large Graphs

A bitemporal RDF index based on skip list

The Resource Description Framework (RDF) is a framework for expressing information about resources in the form of triples (subject, predicate, object). The information represented by the standard RDF is static, i.e., that does not change over time. To better deal with a large amount of time-related information, temporal RDF is proposed. Consequently, how to explore index technology to efficiently query temporal information has become an important research issue, but the research on the index of temporal RDF is still short, especially the index of bitemporal RDF. BitemporalRDF can represent more complicated situations (e.g., RDF triples with both validtime and transactiontime). Indexes for bitemporal RDF can further expand the application scenarios and functions of temporal RDF. In this paper, we propose an efficient index for bitemporal RDF queries. The index innovatively introduces and re-designs skip list structure into the bitemporal RDF query. We also investigate how to cover almost all query patterns with as few indexes as possible. In addition, although the proposed index is conceived for temporal RDF, it also takes into account the performance of standard RDF queries when the time element is unknown. Finally, we run experiments with synthetic data sets of different sizes using the Lehigh University Benchmark (LUBM), and results prove that the proposed index is scalable and effective.

Fulgor: a fast and compact k-mer index for large-scale matching and color queries.

The problem of sequence identification or matching-determining the subset of reference sequences from a given collection that are likely to contain a short, queried nucleotide sequence-is relevant for many important tasks in Computational Biology, such as metagenomics and pangenome analysis. Due to the complex nature of such analyses and the large scale of the reference collections a resource-efficient solution to this problem is of utmost importance. This poses the threefold challenge of representing the reference collection with a data structure that is efficient to query, has light memory usage, and scales well to large collections. To solve this problem, we describe an efficient colored de Bruijn graph index, arising as the combination of a k-mer dictionary with a compressed inverted index. The proposed index takes full advantage of the fact that unitigs in the colored compacted de Bruijn graph are monochromatic (i.e., all k-mers in a unitig have the same set of references of origin, or color). Specifically, the unitigs are kept in the dictionary in color order, thereby allowing for the encoding of the map from k-mers to their colors in as little as 1 + o(1) bits per unitig. Hence, one color per unitig is stored in the index with almost no space/time overhead. By combining this property with simple but effective compression methods for integer lists, the index achieves very small space. We implement these methods in a tool called Fulgor, and conduct an extensive experimental analysis to demonstrate the improvement of our tool over previous solutions. For example, compared to Themisto-the strongest competitor in terms of index space vs. query time trade-off-Fulgor requires significantly less space (up to 43% less space for a collection of 150,000 Salmonella enterica genomes), is at least twice as fast for color queries, and is 2-6[Formula: see text] faster to construct.

LK-Index: A Learned Index for KNN Queries

LK-Index: A Learned Index for KNN Queries

Searchable encryption algorithm based on key aggregation of multiple data owners in data sharing

Searchable encryption allows data owners to outsource their encrypted data to cloud servers and provide a searchable encryption service without exposing their sensitive information. Existing searchable encryption schemes provide the service for users to query the encrypted data of a single data owner. However, these schemes ignore the problem of query matching efficiency when users query the encrypted data of multiple data owners simultaneously. Specifically, for the same content encrypted by different data owners, users need to generate different query trapdoors in the query phase and match the different query trapdoors and indexes in the matching phase. In this paper, we propose a searchable encryption algorithm based on the key aggregation of multiple data owners. The algorithm first generates keys for multiple data owners using the mutual inversion of elements in a finite field to ensure the consistency of ciphertext processing. Then, it generates index keys to build encrypted indexes and ensure the searchability of the ciphertext. Finally, it generates query trapdoors based on multi-key aggregation to match the encrypted indexes of multiple data owners. The theoretical analysis and simulation results show that the proposed algorithm improves the query efficiency and protects the query indexes and trapdoors.

Storage and Query Indexing Methods on Big Data

Storage and Query Indexing Methods on Big Data

WISK: A Workload-aware Learned Index for Spatial Keyword Queries

Spatial objects often come with textual information, such as Points of Interest (POIs) with their descriptions, which are referred to as geo-textual data. To retrieve such data, spatial keyword queries that take into account both spatial proximity and textual relevance have been extensively studied. Existing indexes designed for spatial keyword queries are mostly built based on the geo-textual data without considering the distribution of queries already received. However, previous studies have shown that utilizing the known query distribution can improve the index structure for future query processing. In this paper, we propose WISK, a learned index for spatial keyword queries, which self-adapts for optimizing querying costs given a query workload. One key challenge is how to utilize both structured spatial attributes and unstructured textual information during learning the index. We first divide the data objects into partitions, aiming to minimize the processing costs of the given query workload. We prove the NP-hardness of the partitioning problem and propose a machine learning model to find the optimal partitions. Then, to achieve more pruning power, we build a hierarchical structure based on the generated partitions in a bottom-up manner with a reinforcement learning-based approach. We conduct extensive experiments on real-world datasets and query workloads with various distributions, and the results show that WISK outperforms all competitors, achieving up to 8× speedup in querying time with comparable storage overhead.

Dual-Layer Index for Efficient Traceability Query of Food Supply Chain Based on Blockchain.

Blockchain techniques have been introduced to achieve decentralized and transparent traceability systems, which are critical components of food supply chains. Academia and industry have tried to enhance the efficiency of blockchain-based food supply chain traceability queries. However, the cost of traceability queries remains high. In this paper, we propose a dual-layer index structure for optimizing traceability queries in blockchain, which consists of an external and an internal index. The dual-layer index structure accelerates the external block jump and internal transaction search while preserving the original characteristics of the blockchain. We establish an experimental environment by modeling the blockchain storage module for extensive simulation experiments. The results show that although the dual-layer index structure introduces a little extra storage and construction time, it significantly improves the efficiency of traceability queries. Specifically, the dual-layer index improves the traceability query rate by seven to eight times compared with that of the original blockchain.

HINT: a hierarchical interval index for Allen relationships

Indexing intervals is a fundamental problem, finding a wide range of applications, most notably in temporal and uncertain databases. We propose HINT, a novel and efficient in-memory index for range selection queries over interval collections. HINT applies a hierarchical partitioning approach, which assigns each interval to at most two partitions per level and has controlled space requirements. We reduce the information stored at each partition to the absolutely necessary by dividing the intervals in it, based on whether they begin inside or before the partition boundaries. In addition, our index includes storage optimization techniques for the effective handling of data sparsity and skewness. We show how HINT can be used to efficiently process queries based on Allen’s relationships. Experiments on real and synthetic interval sets of different characteristics show that HINT is typically one order of magnitude faster than existing interval indexing methods.

Personalized PageRank on Evolving Graphs with an Incremental Index-Update Scheme

\em Personalized PageRank (PPR) stands as a fundamental proximity measure in graph mining. Given an input graph G with the probability of decay α, a source node s and a target node t, the PPR score π(s,t) of target t with respect to source s is the probability that an α-decay random walk starting from s stops at t. A \em single-source PPR (SSPPR) query takes an input graph G with decay probability α and a source s, and then returns the PPR π(s,v) for each node v ∈ V. Since computing an exact SSPPR query answer is prohibitive, most existing solutions turn to approximate queries with guarantees. The state-of-the-art solutions for approximate SSPPR queries are index-based and mainly focus on static graphs, while real-world graphs are usually dynamically changing. However, existing index-update schemes can not achieve a sub-linear update time. Motivated by this, we present an efficient indexing scheme for single-source PPR queries on evolving graphs. Our proposed solution is based on a classic framework that combines the forward-push technique with a random walk index for approximate PPR queries. Thus, our indexing scheme is similar to existing solutions in the sense that we store pre-sampled random walks for efficient query processing. One of our main contributions is an incremental updating scheme to maintain indexed random walks in expected O(1) time after each graph update. To achieve O(1) update cost, we need to maintain auxiliary data structures for both vertices and edges. To reduce the space consumption, we further revisit the sampling methods and propose a new sampling scheme to remove the auxiliary data structure for vertices while still supporting O(1) index update cost on evolving graphs. Extensive experiments show that our update scheme achieves orders of magnitude speed-up on update performance over existing index-based dynamic schemes without sacrificing the query efficiency.

EAR-Oracle: On Efficient Indexing for Distance Queries between Arbitrary Points on Terrain Surface

Due to the advancement of geo-positioning technology, the terrain data has become increasingly popular and has drawn a lot of research effort from both academia and industry. The distance computation on the terrain surface is a fundamental and important problem that is widely applied in geographical information systems and 3D modeling. As could be observed from the existing studies, online computation of the distance on the terrain surface is very expensive. All existing index-based methods are only efficient under the case where the distance query must be performed among a small set of predefined points-of-interest known apriori. But, in general cases, they could not scale up to sizable datasets due to their intolerable oracle building time and space consumption. In this paper, we studied the arbitrary point-to-arbitrary point distance query on the terrain surface in which no assumption is imposed on the query points, and the distance query could be performed between any two arbitrary points. We propose an indexing structure, namely Efficient Arbitrary Point-to-Arbitrary Point Distance Oracle (EAR-Oracle), with theoretical guarantee on the accuracy, oracle building time, oracle size and query time. Our experiments demonstrate that our oracle enjoys excellent scalability and it scales up to enormous terrain surfaces but none of the existing index-based methods could be able to. Besides, it significantly outperforms all existing online computation methods by orders of magnitude in terms of the query time.

A hash-based index for processing frequent updates and continuous location-based range queries

A hash-based index for processing frequent updates and continuous location-based range queries

A Dynamic Grid Index for CkNN Queries on Large-Scale Road Networks with Moving Objects

As the Internet of Things devices are deployed on a large scale, location-based services are being increasingly utilized. Among these services, kNN (k-nearest neighbor) queries based on road network constraints have gained importance. This study focuses on the CkNN (continuous k-nearest neighbor) queries for non-uniformly distributed moving objects with large-scale dynamic road network constraints, where CkNN objects are continuously and periodically queried based on their motion evolution. The present CkNN high-concurrency query under the constraints of a super-large road network faces problems, such as high computational cost and low query efficiency. The aim of this study is to ensure high concurrency nearest neighbor query requests while shortening the query response time and reducing global computation costs. To address this issue, we propose the DVTG-Index (Dynamic V-Tree Double-Layer Grid Index), which intelligently adjusts the index granularity by continuously merging and splitting subgraphs as the objects move, thereby filtering unnecessary vertices. Based on DVTG-Index, we further propose the DVTG-CkNN algorithm to calculate the initial kNN query and utilize the existing results to speed up the CkNN query. Finally, extensive experiments on real road networks confirm the superior performance of our proposed method, which has significant practical applications in large-scale dynamic road network constraints with non-uniformly distributed moving objects.

A Trie Based Set Similarity Query Algorithm

Set similarity query is a primitive for many applications, such as data integration, data cleaning, and gene sequence alignment. Most of the existing algorithms are inverted index based, they usually filter unqualified sets one by one and do not have sufficient support for duplicated sets, thus leading to low efficiency. To solve this problem, this paper designs T-starTrie, an efficient trie based index for set similarity query, which can naturally group sets with the same prefix into one node, and can filter all sets corresponding to the node at a time, thereby significantly improving the candidates generation efficiency. In this paper, we find that the set similarity query problem can be transformed into matching nodes of the first-layer (FMNodes) detecting problem on T-starTrie. Therefore, an efficient FLMNode detection algorithm is designed. Based on this, an efficient set similarity query algorithm, TT-SSQ, is implemented by developing a variety of filtering techniques. Experimental results show that TT-SSQ can be up to 3.10x faster than existing algorithms.

Ontology-based semantic retrieval of documents using Word2vec model

Semantic retrieval of engineering knowledge is crucial in various engineering activities, such as process development and product model planning. To make a solution for this issue, previously, a few word-based semantic enabling existing approaches such as Lexical Retrieval Model with Semantic Residual Embedding’s (LR-SRE), Document Retrieval Model through Semantic Linking (DR-MTS), Semantic Term Matching in Axiomatic Approaches to Information Retrieval (STM-IR) and Hybrid Ontology for Semantic Information Retrieval Model using Keyword Matching Indexing System (HOS-IR) were utilized. But, they all have shown less query-based accuracy results than the required value. In our proposed Information Retrieval (IR) design, the semantic knowledge-based retrieval scheme has been implemented. For query, entered by a user and processed for finding the dominated word. Word is then compared for its similarity equations, and similarity values are then computed to give output. Highly similar values are obtained as the class value. From class, the respective clusters are selected. Then, documents in that cluster are retrieved and ranked according to the relevance of the user. To support the accuracy level performance of this IR system, a word2vec model has been employed with the benefits of Horse Herd Optimization (HHO), which helps to extract vectors as features for classification. These results are stored as a .csv file for further retrieval. By implementing the proposed IR-word2vec model, the results showed that it outperforms other existing techniques by improved similarity index and accuracy for query results in an execution time of 1.7 s.