Efficient entry point encoding and decoding algorithms on 2D Hilbert space filling curve.

The Hilbert curve is an important method for mapping high-dimensional spatial information into one-dimensional spatial information while preserving the locality in the high-dimensional space. Entry points of a Hilbert curve can be used for image compression, dimensionality reduction, corrupted image detection and many other applications. As far as we know, there is no specific algorithms developed for entry points. To address this issue, in this paper we present an efficient entry point encoding algorithm (EP-HE) and a corresponding decoding algorithm (EP-HD). These two algorithms are efficient by exploiting the m consecutive 0s in the rear part of an entry point. We further found that the outputs of these two algorithms are a certain multiple of a certain bit of s, where s is the starting state of these m levels. Therefore, the results of these m levels can be directly calculated without iteratively encoding and decoding. The experimental results show that these two algorithms outperform their counterparts in terms of processing entry points.

Nomogram models for the prognosis of cervical cancer: A SEER-based study.

Background: Cervical cancer (CC) is one of the most common cancers in women. This study aimed to investigate the clinical and non-clinical features that may affect the prognosis of patients with CC and to develop accurate prognostic models with respect to overall survival (OS) and cancer-specific survival (CSS). Methods: We identified 11,148 patients with CC from the SEER (Surveillance, Epidemiology, and End Results) database from 2010 to 2016. Univariate and multivariate Cox regression models were used to identify potential predictors of patients' survival outcomes (OS and CSS). We selected meaningful independent parameters and developed nomogram models for 1-, 3-, and 5-year OS and CSS via R tools. Model performance was evaluated by C-index and receiver operating characteristic curve. Furthermore, calibration curves were plotted to compare the predictions of nomograms with observed outcomes, and decision curve analysis (DCA) and clinical impact curves (CICs) were used to evaluate the clinical effectiveness of the nomograms. Results: All eligible patients (n=11148) were randomized at a 7:3 ratio into training (n=7803) and validation (n=3345) groups. Ten variables were identified as common independent predictors of OS and CSS: insurance status, grade, histology, chemotherapy, metastasis number, tumor size, regional nodes examined, International Federation of Obstetrics and Gynecology stage, lymph vascular space invasion (LVSI), and radiation. The C-index values for OS (0.831 and 0.824) and CSS (0.844 and 0.841) in the training cohorts and validation cohorts, respectively, indicated excellent discrimination performance of the nomograms. The internal and external calibration plots indicated excellent agreement between nomogram prediction and actual survival, and the DCA and CICs reflected favorable potential clinical effects. Conclusions: We constructed nomograms that could predict 1-, 3-, and 5-year OS and CSS in patients with CC. These tools showed near-perfect accuracy and clinical utility; thus, they could lead to better patient counseling and personalized and tailored treatment to improve clinical prognosis.

Drug repositioning based on individual bi-random walks on a heterogeneous network.

BACKGROUND: Traditional drug research and development is high cost, time-consuming and risky. Computationally identifying new indications for existing drugs, referred as drug repositioning, greatly reduces the cost and attracts ever-increasing research interests. Many network-based methods have been proposed for drug repositioning and most of them apply random walk on a heterogeneous network consisted with disease and drug nodes. However, these methods generally adopt the same walk-length for all nodes, and ignore the different contributions of different nodes. RESULTS: In this study, we propose a drug repositioning approach based on individual bi-random walks (DR-IBRW) on the heterogeneous network. DR-IBRW firstly quantifies the individual work-length of random walks for each node based on the network topology and knowledge that similar drugs tend to be associated with similar diseases. To account for the inner structural difference of the heterogeneous network, it performs bi-random walks with the quantified walk-lengths, and thus to identify new indications for approved drugs. Empirical study on public datasets shows that DR-IBRW achieves a much better drug repositioning performance than other related competitive methods. CONCLUSIONS: Using individual random walk-lengths for different nodes of heterogeneous network indeed boosts the repositioning performance. DR-IBRW can be easily generalized to prioritize links between nodes of a network.

ClusterMI: Detecting High-Order SNP Interactions Based on Clustering and Mutual Information.

Identifying single nucleotide polymorphism (SNP) interactions is considered as a popular and crucial way for explaining the missing heritability of complex diseases in genome-wide association studies (GWAS). Many approaches have been proposed to detect SNP interactions. However, existing approaches generally suffer from the high computational complexity resulting from the explosion of candidate high-order interactions. In this paper, we propose a two-stage approach (called ClusterMI) to detect high-order genome-wide SNP interactions based on significant pairwise SNP combinations. In the screening stage, to alleviate the huge computational burden, ClusterMI firstly applies a clustering algorithm combined with mutual information to divide SNPs into different clusters. Then, ClusterMI utilizes conditional mutual information to screen significant pairwise SNP combinations in each cluster. In this way, there is a higher probability of identifying significant two-locus combinations in each group, and the computational load for the follow-up search can be greatly reduced. In the search stage, two different search strategies (exhaustive search and improved ant colony optimization search) are provided to detect high-order SNP interactions based on the cardinality of significant two-locus combinations. Extensive simulation experiments show that ClusterMI has better performance than other related and competitive approaches. Experiments on two real case-control datasets from Wellcome Trust Case Control Consortium (WTCCC) also demonstrate that ClusterMI is more capable of identifying high-order SNP interactions from genome-wide data.

Protein-Protein Interactions Prediction Using a Novel Local Conjoint Triad Descriptor of Amino Acid Sequences.

Protein-protein interactions (PPIs) play crucial roles in almost all cellular processes. Although a large amount of PPIs have been verified by high-throughput techniques in the past decades, currently known PPIs pairs are still far from complete. Furthermore, the wet-lab experiments based techniques for detecting PPIs are time-consuming and expensive. Hence, it is urgent and essential to develop automatic computational methods to efficiently and accurately predict PPIs. In this paper, a sequence-based approach called DNN-LCTD is developed by combining deep neural networks (DNNs) and a novel local conjoint triad description (LCTD) feature representation. LCTD incorporates the advantage of local description and conjoint triad, thus, it is capable to account for the interactions between residues in both continuous and discontinuous regions of amino acid sequences. DNNs can not only learn suitable features from the data by themselves, but also learn and discover hierarchical representations of data. When performing on the PPIs data of Saccharomyces cerevisiae, DNN-LCTD achieves superior performance with accuracy as 93.12%, precision as 93.75%, sensitivity as 93.83%, area under the receiver operating characteristic curve (AUC) as 97.92%, and it only needs 718 s. These results indicate DNN-LCTD is very promising for predicting PPIs. DNN-LCTD can be a useful supplementary tool for future proteomics study.

[Service Middleware of Medical Information Integration and Exchange Based on HL7 and DICOM].

Medical information exchange and integration is the effective method to solve the interoperability and medical information island, and is the basis of medical information sharing. In this paper, we take medical texts and medical images as the basic integrated objects, DICOM, HL7 messages and datasets as the integrated units, efficient DI-COM, HL7 message construction and parsing methods as basis, design and realize a universal medical information integration and exchange service middleware. Experimental results show that the prototype system could perform medical information integration and exchange among relational database, HL7 and DICOM message, provide a feasible scheme to solve the medical information island and lay a good foundation for establishing the unified medical information integration and sharing platform. The middleware has been applied in the project named "development and demonstration of opened medical information integration system".