The number of web APIs is growing rapidly. API adoption is increasing across all industries with executives prioritizing investments in the API economy. Each API provider offers API documentation which includes complex descriptions. In order to collect and understand the applications and operations of diverse APIs, software engineers read lengthy and complicated API documentations. Understanding the variety of API documentations is a labor intensive and error-prone process. In this paper, we introduce a data-centric web crawler service to collect, analyze, and construct a large corpus of API documentations. The generated API Corpus can be used in machine programming (i.e., code generation, code search). The proposed API web-crawler intelligently harvests more than 2.8M API documentation pages where it uses a machine-learning-based approach with an accuracy of 91.32% to select only web API pages (REST). We also conducted an extensive and end-to-end real-world evaluation, where the proposed API web-crawler not only collects a sheer number of API pages, but also successfully validates 1,222 APIs out of 1,521 target APIs with a success rate of 80.34%.

The number and variety of Web APIs is growing exponentially. Software engineers need to expend a significant amount of time and effort reading and understanding the accompanying documentation. In addition, system automation may use API to interact with each other. However, this is not always a simple task since the API documentation of a provider can be anything from a single HTML page description through to a complex structure with information spanning several pages. Understanding this wide variety of API documentation structures and styles is therefore a labor intensive and error-prone task for engineers. By providing a machine-learning platform that can extract and standardize API usage information, however, we believe we can accelerate the creation of API-enabled systems by using automation to simplify the task of understanding. In this paper we introduce a novel approach to automating and standardizing usage information about APIs, combining several machine-learning algorithms in order to extract key attributes from API documentation and generate a machine readable Open API Specification (OAS). We develop i) a content-based learning model that identifies the context of a block of extracted API features; ii) a signature-based machine learning model that recognizes a sequence of successful/unsuccessful extracted API endpoints; and iii) a deep mapping model that pinpoints fine-grained mapping of extracted API attributes to OAS objects. Results of our experiments show that the proposed approach successfully works with an accuracy of 99%, 94% and 97% for content-based learning, signature-based learning, and Deep Mapping of API attributes respectively. We then use the models to produce OAS compliant API Specifications for more than 2,585 public APIs, validate them via API calls and finally deploy the validated APIs to the RunMyProcess software automation platform.

This is an editorial report of the supplements to BMC Bioinformatics that includes 6 papers selected from the BIOCOMP'19-The 2019 International Conference on Bioinformatics and Computational Biology. These articles reflect current trend and development in bioinformatics research.

With the advent of the Internet, the amount of Semantic Web documents that describe real-world entities and their inter-links as a set of statements have grown considerably. These descriptions are usually lengthy, which makes the utilization of the underlying entities a difficult task. Entity summarization, which aims to create summaries for real-world entities, has gained increasing attention in recent years. In this paper, we propose a probabilistic topic model, ES-LDA, that combines prior knowledge with statistical learning techniques within a single framework to create more reliable and representative summaries for entities. We demonstrate the effectiveness of our approach by conducting extensive experiments and show that our model outperforms the state-of-the-art techniques and enhances the quality of the entity summaries.

This paper aims to investigate and compare the accuracy of different data mining classification schemes, employing Ensemble Machine Learning Techniques, for the prediction of heart disease. The Cleveland data set for heart diseases, containing 303 instances, has been used as the main database for the training and testing of the developed system. 10-Fold Cross-Validation has been applied in order to increase the amount of data, which would otherwise have been limited. Different classifiers, namely Decision Tree (DT), Naïve Bayes (NB), Multilayer Perceptron (MLP), K-Nearest Neighbor (K-NN), Single Conjunctive Rule Learner (SCRL), Radial Basis Function (RBF) and Support Vector Machine (SVM), have been employed. Moreover, the ensemble prediction of classifiers, bagging, boosting and stacking, has been applied to the dataset. The results of the experiments indicate that the SVM method using the boosting technique outperforms the other aforementioned methods.

Advances of high-throughput technologies have rapidly produced more and more data from DNAs and RNAs to proteins, especially large volumes of genome-scale data. However, connection of the genomic information to cellular functions and biological behaviours relies on the development of effective approaches at higher systems level. In particular, advances in RNA-Seq technology has helped the studies of transcriptome, RNA expressed from the genome, while systems biology on the other hand provides more comprehensive pictures, from which genes and proteins actively interact to lead to cellular behaviours and physiological phenotypes. As biological interactions mediate many biological processes that are essential for cellular function or disease development, it is important to systematically identify genomic information including genetic mutations from GWAS (genome-wide association study), differentially expressed genes, bidirectional promoters, intrinsic disordered proteins (IDP) and protein interactions to gain deep insights into the underlying mechanisms of gene regulations and networks. Furthermore, bidirectional promoters can co-regulate many biological pathways, where the roles of bidirectional promoters can be studied systematically for identifying co-regulating genes at interactive network level. Combining information from different but related studies can ultimately help revealing the landscape of molecular mechanisms underlying complex diseases such as cancer.

BACKGROUND: Kidney Renal Clear Cell Carcinoma (KIRC) is one of fatal genitourinary diseases and accounts for most malignant kidney tumours. KIRC has been shown resistance to radiotherapy and chemotherapy. Like many types of cancers, there is no curative treatment for metastatic KIRC. Using advanced sequencing technologies, The Cancer Genome Atlas (TCGA) project of NIH/NCI-NHGRI has produced large-scale sequencing data, which provide unprecedented opportunities to reveal new molecular mechanisms of cancer. We combined differentially expressed genes, pathways and network analyses to gain new insights into the underlying molecular mechanisms of the disease development. RESULTS: Followed by the experimental design for obtaining significant genes and pathways, comprehensive analysis of 537 KIRC patients' sequencing data provided by TCGA was performed. Differentially expressed genes were obtained from the RNA-Seq data. Pathway and network analyses were performed. We identified 186 differentially expressed genes with significant p-value and large fold changes (P < 0.01, |log(FC)| > 5). The study not only confirmed a number of identified differentially expressed genes in literature reports, but also provided new findings. We performed hierarchical clustering analysis utilizing the whole genome-wide gene expressions and differentially expressed genes that were identified in this study. We revealed distinct groups of differentially expressed genes that can aid to the identification of subtypes of the cancer. The hierarchical clustering analysis based on gene expression profile and differentially expressed genes suggested four subtypes of the cancer. We found enriched distinct Gene Ontology (GO) terms associated with these groups of genes. Based on these findings, we built a support vector machine based supervised-learning classifier to predict unknown samples, and the classifier achieved high accuracy and robust classification results. In addition, we identified a number of pathways (P < 0.04) that were significantly influenced by the disease. We found that some of the identified pathways have been implicated in cancers from literatures, while others have not been reported in the cancer before. The network analysis leads to the identification of significantly disrupted pathways and associated genes involved in the disease development. Furthermore, this study can provide a viable alternative in identifying effective drug targets. CONCLUSIONS: Our study identified a set of differentially expressed genes and pathways in kidney renal clear cell carcinoma, and represents a comprehensive computational approach to analysis large-scale next-generation sequencing data. The pathway and network analyses suggested that information from distinctly expressed genes can be utilized in the identification of aberrant upstream regulators. Identification of distinctly expressed genes and altered pathways are important in effective biomarker identification for early cancer diagnosis and treatment planning. Combining differentially expressed genes with pathway and network analyses using intelligent computational approaches provide an unprecedented opportunity to identify upstream disease causal genes and effective drug targets.

The five papers in this special issue cover a broad range of topics, from analytic methods for DNA/RNA sequences, gene expression analysis, to protein function predictions.

Summary form only given. Inherent limitations on the computational power of sequential uniprocessor systems have led to the development of parallel multiprocessor systems. The two major issues in the formulation and design of parallel multiprocessor systems are algorithm design and architecture design. The parallel multiprocessor systems should be so designed so as to facilitate the design and implementation of the efficient parallel algorithms that exploit optimally the capabilities of the system. From an architectural point of view, the system should have low hardware complexity, be capable of being built of components that can be easily replicated, should exhibit desirable cost-performance characteristics, be cost effective and exhibit good scalability in terms of hardware complexity and cost with increasing problem size. In distributed memory multiprocessor systems, the processing elements can be considered to be nodes that are connected together via an interconnection network. In order to facilitate algorithm and architecture design, we require that the interconnection network have a low diameter, the system be symmetric and each node in the system have low degree of connectivity. Further, it is also desirable that the system configuration and behavior be amenable to a suitable and tractable mathematical description. The requirement of network symmetry ensures that each node in the network is identical to any other, thereby greatly reducing the architecture and algorithm design effort. For most symmetric network topologies, however, the requirements of low degree of connectivity for each node and low network diameter are often conflicting. Low network diameter often entails that each node in the network have a high degree of connectivity resulting in a drastic increase in the number of inter-processor connection links. A low degree of connectivity on the other hand, results in a high network diameter which in turn results in high inter-processor communication overhead and reduced efficiency of parallelism. Reconfigurable networks attempt to address this tradeoff. In a reconfigurable network each node has a fixed degree of connectivity irrespective of the network size. The network diameter is restricted by allowing the network to reconfigure itself into different configurations. Broadly speaking, a reconfigurable system needs to satisfy the following criteria in order to be considered practically viable: (a) In each configuration the nodes in the network should have a fixed degree of connectivity irrespective of network size, (b) The network diameter should be kept low via the reconfiguration mechanism and (c) The hardware for the reconfiguration mechanism (i.e., switch) should be of reasonable complexity. In this presentation, we discuss our design of a reconfigurable network topology that is targeted at medical applications. We present some results and discuss the future roadmap of this project.

Over the last two decades, the Delaunay triangulation has been the only choice for most geographical information system (GIS) users and researchers to build triangulated irregular networks (TINs). The classical Delaunay triangulation for creating TINs only considers the 2D distribution of data points. Recent research efforts have been devoted to generating data-dependent triangulation which incorporate information on both distribution and values of input data in the triangulation process. This paper compares the traditional Delaunay triangulations with several variant data-dependent triangulations based on Lawson's local optimization procedure (LOP). Two USGS digital elevation models (DEMs) are used in the comparison. It is clear from the experiments that the quality of TINs not only depends on the vertex placement but also on the vertex connection. Traditonal two step processes for TIN construction, which separate point selection from the triangulation, generate far worse results than the methods which iteratively select points during the triangulation process. A pure data-dependent triangulation contains a large amount of slivers and steep triangles, which greatly affect the quality of TINs constructed. Among the triangulation methods tested, the classical Delaunay triangulation is still the most successful technique for constructing TINs for approximating natural terrain surfaces.

A novel reconfigurable architecture based on a multiring multiprocessor network is described. The reconfigurability of the architecture is shown to result in a low network diameter and also a low degree of connectivity for each node in the network. The mathematical properties of the network topology and the hardware for the reconfiguration switch are described. Primitive parallel operations on the network topology are described and analyzed. The architecture is shown to contain 2D mesh topologies of varying sizes and also a single one factor of the Boolean hypercube in any given configuration. A large class of algorithms for the 2D mesh and the Boolean n-cube are shown to map efficiently on the proposed architecture without loss of performance. The architecture is shown to be well suited for a number of problems in low and intermediate level computer vision such as the FFT, edge detection, template matching, and the Hough transform. Timing results for typical low and intermediate level vision algorithms on a transputer based prototype are presented.

This paper addresses the problem of parallelizing one of the most computationally intensive imaging tasks, namely, the stereocorrelation operation. Stereocorrelation is a statistical procedure utilized to automatically derive the depth information from a pair of digitized pictures taken from the same scene but at different positions. Thus, the operation automatically generates the third dimension (z-coordinate) of each pixel of the image of the scene. The paper presents a simple but novel distributed stereocorrelation algorithm which uses a data farming approach to balance the work load.

In this paper we describe a reconfigurable architecture for image processing and computer vision based on a multi-ring network which we call a Reconfigurable Multi-Ring System (RMRS). We describe the reconfiguration switch for the RMRS and also describe its VLSI implementation. The RMRS topology is shown to be regular and scalable and hence well-suited for VLSI implementation. We prove some important properties of the RMRS topology and show that a broad class of algorithms for the n-cube can be mapped to the RMRS in a simple and elegant manner. We design and analyze a class of procedural primitives for the SIMD RMRS and show how these primitives can be used as building blocks for more complex parallel operations. We demonstrate the usefulness of the RMRS for problems in image processing and computer vision by considering two important operations—the Fast Fourier Transform (FFT) and the Hough transform for detection of linear features in an image. Parallel algorithms for the FFT and the Hough transform on the SIMD RMRS are designed using the aforementioned procedural primitives. The analysis of the complexity of these algorithms shows that the SIMD RMRS is a viable architecture for problems in computer vision and image processing.

A novel reconfigurable architecture based on a multi-ring multiprocessor network is described. The reconfigurable architecture is shown to combine low network diameter with a low degree of connectivity for each node in the network. The mathematical properties of the network topology and the hardware for the reconfiguration switch are described. Primitive parallel operations on the network topology are described and analyzed. A large class of algorithms for the Boolean n-cube and the 2-D mesh is shown to map efficiently on the proposed architecture without loss of performance. The architecture is shown to be well suited for a number of problems in computer vision.

A novel reconfigurable architecture based on a multi-ring multiprocessor network is described. The reconfigurability of the architecture is shown to result in a low network diameter and also a low degree of connectivity for each node in the network. The mathematical properties of the network topology and the hardware for the reconfiguration switch are described. Primitive parallel operations on the network topology are described and analyzed. The architecture is shown to contain a single 1-factor of the Boolean hypercube in any given configuration. A large class of algorithms for the Boolean n-cube and the 2-D mesh is shown to map efficiently on the proposed architecture without loss of performance. The architecture is shown to be well suited for a number of problems in robot vision.>

Abstract Algorithms for the translation and scaling of a digitised image are described. The algorithms have been designed to work on a transputer network which has a simple topology. This transputer network was originally proposed for the arbitrary rotation operation on digitised images1. The data structure used to represent the image is closely related to mnlength encoding. Both operations can be performed in real time on non trivial images.

Abstract An algorithm for the rotation of a raster image by an arbitrary angle is described. The image data structure is closely related to runlength code. The algorithm has been designed to exploit SIMD parallel architectures. It has been implemented on an ICL DAP on which non trivial images can be rotated in times very close to real time.

An algorithm for the rotation of a digitised image is presented. This algorithm has been designed to work on a transputer network which has a simple topology. The data structure used to represent the image is closely related to run-length encodement. Tests have been made on a simulation of the network.

Abstract Algorithms for fast operations on a raster image data structure are described. The data structure and algorithms have been designed to exploit SIMD parallel architectures. Images of lines, discs and circles can be created efficiently. Images can be translated, scaled, and combined. The data structure is closely related to runlength encodement. The algorithms have been implemented on an ICL DAP on which the operations can be done in real time (on non‐trivial images).