Biomarker Prioritisation and Power Estimation Using Ensemble Gene Regulatory Network Inference

Inferring the topology of a gene regulatory network (GRN) from gene expression data is a challenging but important undertaking for gaining a better understanding of gene regulation. Key challenges include working with noisy data and dealing with a higher number of genes than samples. Although a number of different methods have been proposed to infer the structure of a GRN, there are large discrepancies among the different inference algorithms they adopt, rendering their meaningful comparison challenging. In this study, we used two methods, namely the MIDER (Mutual Information Distance and Entropy Reduction) and the PLSNET (Partial least square based feature selection) methods, to infer the structure of a GRN directly from data and computationally validated our results. Both methods were applied to different gene expression datasets resulting from inflammatory bowel disease (IBD), pancreatic ductal adenocarcinoma (PDAC), and acute myeloid leukaemia (AML) studies. For each case, gene regulators were successfully identified. For example, for the case of the IBD dataset, the UGT1A family genes were identified as key regulators while upon analysing the PDAC dataset, the SULF1 and THBS2 genes were depicted. We further demonstrate that an ensemble-based approach, that combines the output of the MIDER and PLSNET algorithms, can infer the structure of a GRN from data with higher accuracy. We have also estimated the number of the samples required for potential future validation studies. Here, we presented our proposed analysis framework that caters not only to candidate regulator genes prediction for potential validation experiments but also an estimation of the number of samples required for these experiments

Modeling User-Affected Software Properties for Open Source Software Supply Chains

Background: Open Source Software development community relies heavily on users of the software and contributors outside of the core developers to produce top-quality software and provide long-term support. However, the relationship between a software and its contributors in terms of exactly how they are related through dependencies and how the users of a software affect many of its properties are not very well understood. Aim: My research covers a number of aspects related to answering the overarching question of modeling the software properties affected by users and the supply chain structure of software ecosystems, viz. 1) Understanding how software usage affect its perceived quality; 2) Estimating the effects of indirect usage (e.g. dependent packages) on software popularity; 3) Investigating the patch submission and issue creation patterns of external contributors; 4) Examining how the patch acceptance probability is related to the contributors\u27 characteristics. 5) A related topic, the identification of bots that commit code, aimed at improving the accuracy of these and other similar studies was also investigated. Methodology: Most of the Research Questions are addressed by studying the NPM ecosystem, with data from various sources like the World of Code, GHTorrent, and the GiHub API. Different supervised and unsupervised machine learning models, including Regression, Random Forest, Bayesian Networks, and clustering, were used to answer appropriate questions. Results: 1) Software usage affects its perceived quality even after accounting for code complexity measures. 2) The number of dependents and dependencies of a software were observed to be able to predict the change in its popularity with good accuracy. 3) Users interact (contribute issues or patches) primarily with their direct dependencies, and rarely with transitive dependencies. 4) A user\u27s earlier interaction with the repository to which they are contributing a patch, and their familiarity with related topics were important predictors impacting the chance of a pull request getting accepted. 5) Developed BIMAN, a systematic methodology for identifying bots. Conclusion: Different aspects of how users and their characteristics affect different software properties were analyzed, which should lead to a better understanding of the complex interaction between software developers and users/ contributors

On Finding Optimal Discretizations for Two Attributes

We show that finding optimal discretization of instances of decision tables with two attributes with real values and binary decisions is computationally hard. This is done by abstracting the problem in such a way that it regards partitioning points in the plane into regions, subject to certain minimality restrictions, and proving them to be NP-hard. We also propose a new method to find optimal discretizations