MetaAnalyst: a user-friendly tool for metagenomic biomarker detection and phenotype classification.

BACKGROUND: Many metagenomic studies have linked the imbalance in microbial abundance profiles to a wide range of diseases. These studies suggest utilizing the microbial abundance profiles as potential markers for metagenomic-associated conditions. Due to the inevitable importance of biomarkers in understanding the disease progression and the development of possible therapies, various computational tools have been proposed for metagenomic biomarker detection. However, most existing tools require prior scripting knowledge and lack user friendly interfaces, causing considerable time and effort to install, configure, and run these tools. Besides, there is no available all-in-one solution for running and comparing various metagenomic biomarker detection simultaneously. In addition, most of these tools just present the suggested biomarkers without any statistical evaluation for their quality. RESULTS: To overcome these limitations, this work presents MetaAnalyst, a software package with a simple graphical user interface (GUI) that (i) automates the installation and configuration of 28 state-of-the-art tools, (ii) supports flexible study design to enable studying the dataset under different scenarios smoothly, iii) runs and evaluates several algorithms simultaneously iv) supports different input formats and provides the user with several preprocessing capabilities, v) provides a variety of metrics to evaluate the quality of the suggested markers, and vi) presents the outcomes in the form of publication quality plots with various formatting capabilities as well as Excel sheets. CONCLUSIONS: The utility of this tool has been verified through studying a metagenomic dataset under four scenarios. The executable file for MetaAnalyst along with its user manual are made available at https://github.com/mshawaqfeh/MetaAnalyst .

Unsupervised anomaly appraisal of cleft faces using a StyleGAN2-based model adaptation technique.

A novel machine learning framework that is able to consistently detect, localize, and measure the severity of human congenital cleft lip anomalies is introduced. The ultimate goal is to fill an important clinical void: to provide an objective and clinically feasible method of gauging baseline facial deformity and the change obtained through reconstructive surgical intervention. The proposed method first employs the StyleGAN2 generative adversarial network with model adaptation to produce a normalized transformation of 125 faces, and then uses a pixel-wise subtraction approach to assess the difference between all baseline images and their normalized counterparts (a proxy for severity of deformity). The pipeline of the proposed framework consists of the following steps: image preprocessing, face normalization, color transformation, heat-map generation, morphological erosion, and abnormality scoring. Heatmaps that finely discern anatomic anomalies visually corroborate the generated scores. The proposed framework is validated through computer simulations as well as by comparison of machine-generated versus human ratings of facial images. The anomaly scores yielded by the proposed computer model correlate closely with human ratings, with a calculated Pearson's r score of 0.89. The proposed pixel-wise measurement technique is shown to more closely mirror human ratings of cleft faces than two other existing, state-of-the-art image quality metrics (Learned Perceptual Image Patch Similarity and Structural Similarity Index). The proposed model may represent a new standard for objective, automated, and real-time clinical measurement of faces affected by congenital cleft deformity.