Systematic adaptation of dynamically generated source code via domain-specific examples

In modern web-based applications, an increasing amount of source code is generated dynamically at runtime. Web applications commonly execute dynamically generated code (DGC) emitted by third-party, black-box generators, run at remote sites. Web developers often need to adapt DGC before it can be executed: embedded HTML can be vulnerable to cross-site scripting attacks; an API may be incompatible with some browsers; and the program\u27s state created by DGC may not be persisting. Lacking any systematic approaches for adapting DGC, web developers resort to ad-hoc techniques that are unsafe and error-prone. This study presents an approach for adapting DGC systematically that follows the program-transformation-byexample paradigm. The proposed approach provides predefined, domain-specific before/after examples that capture the variability of commonly used adaptations. By approving or rejecting these examples, web developers determine the required adaptation transformations, which are encoded in an adaptation script operating on the generated code\u27s abstract syntax tree. The proposed approach is a suite of practical JavaScript program adaptations and their corresponding before/after examples. The authors have successfully applied the approach to real web applications to adapt third-party generated JavaScript code for security, browser compatibility, and persistence

Reusable Enterprise Metadata with Pattern-Based Structural Expressions

An essential part of modern enterprise software development is metadata. Mainstream metadata formats, including XML deployment descriptors and Java 5 annotations, suffer from a number of limitations that complicate the development and maintenance of enterprise applications. Their key problem is that they make it impossible to reuse metadata specifications not only across different applications but even across smaller program constructs such as classes or methods. To provide better enterprise metadata, we present patternbased structural expressions (PBSE), a novel metadata representation that offers conciseness and maintainability advantages and is reusable. To apply PBSE to enterprise applications, we translate PBSE specifications to Java annotations, with annotating classes automatically as an intermediate build step. We demonstrate the advantages of the new metadata format by assessing its conciseness and reusability, as compared to XML and annotations, in the task of expressing metadata of J2EE reference applications and a mid-size, commercial, enterprise application

MegaD: Deep Learning for Rapid and Accurate Disease Status Prediction of Metagenomic Samples

The diversity within different microbiome communities that drive biogeochemical processes influences many different phenotypes. Analyses of these communities and their diversity by countless microbiome projects have revealed an important role of metagenomics in understanding the complex relation between microbes and their environments. This relationship can be understood in the context of microbiome composition of specific known environments. These compositions can then be used as a template for predicting the status of similar environments. Machine learning has been applied as a key component to this predictive task. Several analysis tools have already been published utilizing machine learning methods for metagenomic analysis. Despite the previously proposed machine learning models, the performance of deep neural networks is still under-researched. Given the nature of metagenomic data, deep neural networks could provide a strong boost to growth in the prediction accuracy in metagenomic analysis applications. To meet this urgent demand, we present a deep learning based tool that utilizes a deep neural network implementation for phenotypic prediction of unknown metagenomic samples. (1) First, our tool takes as input taxonomic profiles from 16S or WGS sequencing data. (2) Second, given the samples, our tool builds a model based on a deep neural network by computing multi-level classification. (3) Lastly, given the model, our tool classifies an unknown sample with its unlabeled taxonomic profile. In the benchmark experiments, we deduced that an analysis method facilitating a deep neural network such as our tool can show promising results in increasing the prediction accuracy on several samples compared to other machine learning models

Tool Support for Improving Software Quality in Machine Learning Programs

Machine learning (ML) techniques discover knowledge from large amounts of data. Modeling in ML is becoming essential to software systems in practice. The accuracy and efficiency of ML models have been focused on ML research communities, while there is less attention on validating the qualities of ML models. Validating ML applications is a challenging and time-consuming process for developers since prediction accuracy heavily relies on generated models. ML applications are written by relatively more data-driven programming based on the black box of ML frameworks. All of the datasets and the ML application need to be individually investigated. Thus, the ML validation tasks take a lot of time and effort. To address this limitation, we present a novel quality validation technique that increases the reliability for ML models and applications, called MLVal. Our approach helps developers inspect the training data and the generated features for the ML model. A data validation technique is important and beneficial to software quality since the quality of the input data affects speed and accuracy for training and inference. Inspired by software debugging/validation for reproducing the potential reported bugs, MLVal takes as input an ML application and its training datasets to build the ML models, helping ML application developers easily reproduce and understand anomalies in the ML application. We have implemented an Eclipse plugin for MLVal that allows developers to validate the prediction behavior of their ML applications, the ML model, and the training data on the Eclipse IDE. In our evaluation, we used 23,500 documents in the bioengineering research domain. We assessed the ability of the MLVal validation technique to effectively help ML application developers: (1) investigate the connection between the produced features and the labels in the training model, and (2) detect errors early to secure the quality of models from better data. Our approach reduces the cost of engineering efforts to validate problems, improving data-centric workflows of the ML application development