GitHub Repository Research Articles

Interpreting protein abundance in Saccharomyces cerevisiae through relational learning.

Proteomic profiles reflect the functional readout of the physiological state of an organism. An increased understanding of what controls and defines protein abundances is of high scientific interest. Saccharomyces cerevisiae is a well-studied model organism, and there is a large amount of structured knowledge on yeast systems biology in databases such as the Saccharomyces Genome Database, and highly curated genome-scale metabolic models like Yeast8. These datasets, the result of decades of experiments, are abundant in information, and adhere to semantically meaningful ontologies. By representing this knowledge in an expressive Datalog database we generated data descriptors using relational learning that, when combined with supervised machine learning, enables us to predict protein abundances in an explainable manner. We learnt predictive relationships between protein abundances, function and phenotype; such as α-amino acid accumulations and deviations in chronological lifespan. We further demonstrate the power of this methodology on the proteins His4 and Ilv2, connecting qualitative biological concepts to quantified abundances. All data and processing scripts are available at the following Github repository: https://github.com/DanielBrunnsaker/ProtPredict.

Ds-Seq: An Integrated Pipeline for In Silico Small RNA Se-quence Analysis for Host-pathogen Interaction Studies

Plant-pathogen interactions activate molecular activities wherein the host defends the pathogen while the pathogen tries to suppress the plant response. Small RNAs (sRNAs) mediate major mechanisms, including post-transcriptional gene silencing, histone modification and DNA methylation by which plants respond to the presence of pathogens. Genome-wide profiling of host and pathogen sRNAs is therefore pivotal to uncovering the mechanisms underlying the host-pathogen interaction and mechanisms for host resistance. sRNA high throughput sequencing (HTS) data analysis often involves multiple stages/tools. Most necessary tools are accessible only through the command line, making it challenging for those without a high level of Unix/Linux skills. Furthermore, installation of some of these tools may become difficult due to dependencies and software version compatibility. We have developed an integrated open-source pipeline, Ds-Seq, for end-to-end in silico analysis of sRNA HTS data with improved reproducibility. The pipeline combines in-house scripts and public tools in a shell script, which can be invoked with a single command. The pipeline's usefulness has been demonstrated with testing on publicly available and published data from independent sRNA-seq datasets of host-pathogen interaction studies. Ds-Seq is available on GitHub, while a Docker image can be obtained from the Docker hub.Availability: Ds-Seq is freely available from the GitHub repository at https://github.com/CEPHAS-01/small-RNASeq.ngs and Docker hub with ID cephas/ds-seq (https://hub.docker.com/r/cephas/ds-seq).

RI−Calc: A user friendly software and web server for refractive index calculation

The refractive index of an optical medium is essential for studying a variety of physical phenomena. One useful method for determining the refractive index of scalar materials (i.e., materials which are characterized by a scalar dielectric function) is to employ the Kramers−Kronig (K−K) relations. The K−K method is particularly useful in cases where ellipsometric measurements are unavailable, a situation that frequently occurs in many laboratories. Although some packages can perform this calculation, they usually lack a graphical interface and are complex to implement and use. Those deficiencies inhibit their utilization by a plethora of researchers unfamiliar with programming languages. To address the aforementioned gap, we have developed the Refractive Index Calculator (RI−Calc) program that provides an intuitive and user−friendly interface. The RI−Calc program allows users to input the absorption coefficient spectrum and then easily calculate the complex refractive index and the complex relative permittivity of a broad range of thin films, including of molecules, polymers, blends, and perovskites. The program has been thoroughly tested, taking into account the Lorentz oscillator model and experimental data from a materials' refractive index database, demonstrating consistent outcomes. It is compatible with Windows, Unix, and macOS operating systems. You can download the RI−Calc binaries from our GitHub repository or conveniently access the program through our dedicated web server at nanocalc.org.

Dynamic Associations Between Centers for Disease Control and Prevention Social Media Contents and Epidemic Measures During COVID-19: Infoveillance Study.

Health agencies have been widely adopting social media to disseminate important information, educate the public on emerging health issues, and understand public opinions. The Centers for Disease Control and Prevention (CDC) widely used social media platforms during the COVID-19 pandemic to communicate with the public and mitigate the disease in the United States. It is crucial to understand the relationships between the CDC's social media communications and the actual epidemic metrics to improve public health agencies' communication strategies during health emergencies. This study aimed to identify key topics in tweets posted by the CDC during the pandemic, investigate the temporal dynamics between these key topics and the actual COVID-19 epidemic measures, and make recommendations for the CDC's digital health communication strategies for future health emergencies. Two types of data were collected: (1) a total of 17,524 COVID-19-related English tweets posted by the CDC between December 7, 2019, and January 15, 2022, and (2) COVID-19 epidemic measures in the United States from the public GitHub repository of Johns Hopkins University from January 2020 to July 2022. Latent Dirichlet allocation topic modeling was applied to identify key topics from all COVID-19-related tweets posted by the CDC, and the final topics were determined by domain experts. Various multivariate time series analysis techniques were applied between each of the identified key topics and actual COVID-19 epidemic measures to quantify the dynamic associations between these 2 types of time series data. Four major topics from the CDC's COVID-19 tweets were identified: (1) information on the prevention of health outcomes of COVID-19; (2) pediatric intervention and family safety; (3) updates of the epidemic situation of COVID-19; and (4) research and community engagement to curb COVID-19. Multivariate analyses showed that there were significant variabilities of progression between the CDC's topics and the actual COVID-19 epidemic measures. Some CDC topics showed substantial associations with the COVID-19 measures over different time spans throughout the pandemic, expressing similar temporal dynamics between these 2 types of time series data. Our study is the first to comprehensively investigate the dynamic associations between topics discussed by the CDC on Twitter and the COVID-19 epidemic measures in the United States. We identified 4 major topic themes via topic modeling and explored how each of these topics was associated with each major epidemic measure by performing various multivariate time series analyses. We recommend that it is critical for public health agencies, such as the CDC, to update and disseminate timely and accurate information to the public and align major topics with key epidemic measures over time. We suggest that social media can help public health agencies to inform the public on health emergencies and to mitigate them effectively.

A hyperspectral unmixing approach for ink mismatch detection in unbalanced clusters

Detecting ink mismatch is a significant challenge in verifying the authenticity of documents, especially when dealing with uneven ink distribution. Conventional imaging methods frequently fail to distinguish visually similar inks. Our study presents a novel hyperspectral unmixing approach to detect ink mismatches in unbalanced clusters. The proposed method identifies unique spectral characteristics of different inks employing k-means clustering and Gaussian mixture models (GMMs) to perform color segmentation on different ink types and utilizes elbow estimation and silhouette coefficient to evaluate the number of inks estimation precisely. For a more accurate estimation of quantity, which is generally not an attribute of clustering methods, we employed entropy calculations in the red, green, and blue depth channels for precise abundance estimation of ink. This unique combination of basic techniques in conjunction exhibits better efficacy in performing ink unmixing and provides a real-world document forensic solution compared to current methods that rely on assumptions like prior knowledge of the inks used in a document and deep learning-based methods that rely heavily on abundant training datasets. We evaluate our approach on the iVision handwritten hyperspectral images dataset (iVision HHID), which is a comprehensive and rich dataset that surpasses the commonly-used UWA writing inks hyperspectral images (WIHSI) database in size and diversity. This study has accomplished the unmixing task with three main challenges: unmixing of diverse ink spectral signatures (149 spectral bands instead of 33 bands in the previous dataset), without using prior knowledge and assumptions about the number of inks used in the questioned document, and not requiring large training data for performing unmixing. Furthermore, the security of the proposed document authentication methodology to address the likelihood of forgeries or manipulations in questioned documents is enhanced as compared to previous works relying on known inks and known spectrum. Randomization techniques and anomaly detection mechanisms are used in our methodology which increases the difficulty for adversaries to predict and manipulate specific aspects of the input data in questioned documents, thereby enhancing the robustness of our method. The code for conducting this research can be accessed at GitHub repository.

IDSL_MINT: a deep learning framework to predict molecular fingerprints from mass spectra

The majority of tandem mass spectrometry (MS/MS) spectra in untargeted metabolomics and exposomics studies lack any annotation. Our deep learning framework, Integrated Data Science Laboratory for Metabolomics and Exposomics—Mass INTerpreter (IDSL_MINT) can translate MS/MS spectra into molecular fingerprint descriptors. IDSL_MINT allows users to leverage the power of the transformer model for mass spectrometry data, similar to the large language models. Models are trained on user-provided reference MS/MS libraries via any customizable molecular fingerprint descriptors. IDSL_MINT was benchmarked using the LipidMaps database and improved the annotation rate of a test study for MS/MS spectra that were not originally annotated using existing mass spectral libraries. IDSL_MINT may improve the overall annotation rates in untargeted metabolomics and exposomics studies. The IDSL_MINT framework and tutorials are available in the GitHub repository at https://github.com/idslme/IDSL_MINT.Scientific contributionStructural annotation of MS/MS spectra from untargeted metabolomics and exposomics datasets is a major bottleneck in gaining new biological insights. Machine learning models to convert spectra into molecular fingerprints can help in the annotation process. Here, we present IDSL_MINT, a new, easy-to-use and customizable deep-learning framework to train and utilize new models to predict molecular fingerprints from spectra for the compound annotation workflows.

A gentle introduction to computer vision-based specimen classification in ecological datasets.

Classifying specimens is a critical component of ecological research, biodiversity monitoring and conservation. However, manual classification can be prohibitively time-consuming and expensive, limiting how much data a project can afford to process. Computer vision, a form of machine learning, can help overcome these problems by rapidly, automatically and accurately classifying images of specimens. Given the diversity of animal species and contexts in which images are captured, there is no universal classifier for all species and use cases. As such, ecologists often need to train their own models. While numerous software programs exist to support this process, ecologists need a fundamental understanding of how computer vision works to select appropriate model workflows based on their specific use case, data types, computing resources and desired performance capabilities. Ecologists may also face characteristic quirks of ecological datasets, such as long-tail distributions, 'unknown' species, similarity between species and polymorphism within species, which impact the efficacy of computer vision. Despite growing interest in computer vision for ecology, there are few resources available to help ecologists face the challenges they are likely to encounter. Here, we present a gentle introduction for species classification using computer vision. In this manuscript and associated GitHub repository, we demonstrate how to prepare training data, basic model training procedures, and methods for model evaluation and selection. Throughout, we explore specific considerations ecologists should make when training classification models, such as data domains, feature extractors and class imbalances. With these basics, ecologists can adjust their workflows to achieve research goals and/or account for uncertainty in downstream analysis. Our goal is to provide guidance for ecologists for getting started in or improving their use of machine learning for visual classification tasks.

CAPTVRED: an automated pipeline for viral tracking and discovery from capture-based metagenomics samples

Abstract Summary Target Enrichment Sequencing or Capture-based metagenomics has emerged as an approach of interest for viral metagenomics in complex samples. However, these datasets are usually analyzed with standard downstream Bioinformatics analyses. CAPTVRED (Capture-based metagenomics Analysis Pipeline for tracking ViRal species from Environmental Datasets), has been designed to assess the virome present in complex samples, specially focused on those obtained by Target Enrichment Sequencing approach. This work aims to provide a user-friendly tool that complements this sequencing approach for the total or partial virome description, especially from environmental matrices. It includes a setup module which allows preparation and adjustment of the pipeline to any capture panel directed to a set of species of interest. The tool also aims to reduce time and computational cost, as well as to provide comprehensive, reproducible, and accessible results while being easy to costume, set up, and install. Availability and implementation Source code and test datasets are freely available at github repository: https://github.com/CompGenLabUB/CAPTVRED.git

MvlearnR and Shiny App for multiview learning.

The package mvlearnR and accompanying Shiny App is intended for integrating data from multiple sources or views or modalities (e.g. genomics, proteomics, clinical, and demographic data). Most existing software packages for multiview learning are decentralized and offer limited capabilities, making it difficult for users to perform comprehensive integrative analysis. The new package wraps statistical and machine learning methods and graphical tools, providing a convenient and easy data integration workflow. For users with limited programming language, we provide a Shiny Application to facilitate data integration anywhere and on any device. The methods have potential to offer deeper insights into complex disease mechanisms. mvlearnR is available from the following GitHub repository: https://github.com/lasandrall/mvlearnR. The web application is hosted on shinyapps.io and available at: https://multi-viewlearn.shinyapps.io/MultiView_Modeling/.

Optimal linear ensemble of binary classifiers.

The integration of vast, complex biological data with computational models offers profound insights and predictive accuracy. Yet, such models face challenges: poor generalization and limited labeled data. To overcome these difficulties in binary classification tasks, we developed the Method for Optimal Classification by Aggregation (MOCA) algorithm, which addresses the problem of generalization by virtue of being an ensemble learning method and can be used in problems with limited or no labeled data. We developed both an unsupervised (uMOCA) and a supervised (sMOCA) variant of MOCA. For uMOCA, we show how to infer the MOCA weights in an unsupervised way, which are optimal under the assumption of class-conditioned independent classifier predictions. When it is possible to use labels, sMOCA uses empirically computed MOCA weights. We demonstrate the performance of uMOCA and sMOCA using simulated data as well as actual data previously used in Dialogue on Reverse Engineering and Methods (DREAM) challenges. We also propose an application of sMOCA for transfer learning where we use pre-trained computational models from a domain where labeled data are abundant and apply them to a different domain with less abundant labeled data. GitHub repository, https://github.com/robert-vogel/moca.

Synphage: a pipeline for phage genome synteny graphics focused on gene conservation.

Visualization and comparison of genome maps of bacteriophages can be very effective, but none of the tools available on the market allow visualization of gene conservation between multiple sequences at a glance. In addition, most bioinformatic tools running locally are command line only, making them hard to setup, debug, and monitor. To address these motivations, we developed synphage, an easy-to-use and intuitive tool to generate synteny diagrams from GenBank files. This software has a user-friendly interface and uses metadata to monitor the progress and success of the data transformation process. The output plot features colour-coded genes according to their degree of conservation among the group of displayed sequences. The strength of synphage lies also in its modularity and the ability to generate multiple plots with different configurations without having to re-process all the data. In conclusion, synphage reduces the bioinformatic workload of users and allows them to focus on analysis, the most impactful area of their work. The synphage tool is implemented in the Python language and is available from the GitHub repository at https://github.com/vestalisvirginis/synphage. This software is released under an Apache-2.0 licence. A PyPI synphage package is available at https://pypi.org/project/synphage/ and a containerized version is available at https://hub.docker.com/r/vestalisvirginis/synphage. Contributions to the software are welcome whether it is reporting a bug or proposing new features and the contribution guidelines are available at https://github.com/vestalisvirginis/synphage/blob/main/CONTRIBUTING.md.

JobEdKG: An uncertain knowledge graph-based approach for recommending online courses and predicting in-demand skills based on career choices

Modern job markets often require an intricate combination of multi-disciplinary skills or specialist and technical knowledge, even for entry-level positions. Such requirements pose increased pressure on students, new graduates, and job seekers to find suitable sources of information to enhance their employability. Unlike standard competence management systems, this paper presents JobEdKG, which helps job seekers from various backgrounds choose online courses based on their prospective careers in addition to predicting different skills that may be required in their chosen career path. While existing solutions focus on internal institutional data, such as previous student experiences and a fixed set of skills provided by curated datasets, JobEdKG considers external data, recommending online courses that best cover the knowledge and skills required by selected job roles, in addition to extracting and predicting skills of that particular job roles. To achieve this, we first extract skills from job postings and online courses. These skills are linked to job titles, online courses, and other concepts in order to create a knowledge graph (KG). We assign an uncertainty score to each fact in the KG based on the prevalence of the fact in the source data (i.e. job listings and online courses), which results in an uncertain KG (UKG). Finally, we model the constructed UKG in order to infer different relations between the different concepts. The code and the data are available on our GitHub repository (https://github.com/team611/JobEd) and a user interface to browse the KG is available at (http://jobed.datanets.org/).

M-Ionic: prediction of metal-ion-binding sites from sequence using residue embeddings.

Understanding metal-protein interaction can provide structural and functional insights into cellular processes. As the number of protein sequences increases, developing fast yet precise computational approaches to predict and annotate metal-binding sites becomes imperative. Quick and resource-efficient pre-trained protein language model (pLM) embeddings have successfully predicted binding sites from protein sequences despite not using structural or evolutionary features (multiple sequence alignments). Using residue-level embeddings from the pLMs, we have developed a sequence-based method (M-Ionic) to identify metal-binding proteins and predict residues involved in metal binding. On independent validation of recent proteins, M-Ionic reports an area under the curve (AUROC) of 0.83 (recall = 84.6%) in distinguishing metal binding from non-binding proteins compared to AUROC of 0.74 (recall = 61.8%) of the next best method. In addition to comparable performance to the state-of-the-art method for identifying metal-binding residues (Ca2+, Mg2+, Mn2+, Zn2+), M-Ionic provides binding probabilities for six additional ions (i.e. Cu2+, Po43-, So42-, Fe2+, Fe3+, Co2+). We show that the pLM embedding of a single residue contains sufficient information about its neighbours to predict its binding properties. M-Ionic can be used on your protein of interest using a Google Colab Notebook (https://bit.ly/40FrRbK). The GitHub repository (https://github.com/TeamSundar/m-ionic) contains all code and data.

Open source and reproducible and inexpensive infrastructure for data challenges and education

Data sharing is necessary to maximize the actionable knowledge generated from research data. Data challenges can encourage secondary analyses of datasets. Data challenges in biomedicine often rely on advanced cloud-based computing infrastructure and expensive industry partnerships. Examples include challenges that use Google Cloud virtual machines and the Sage Bionetworks Dream Challenges platform. Such robust infrastructures can be financially prohibitive for investigators without substantial resources. Given the potential to develop scientific and clinical knowledge and the NIH emphasis on data sharing and reuse, there is a need for inexpensive and computationally lightweight methods for data sharing and hosting data challenges. To fill that gap, we developed a workflow that allows for reproducible model training, testing, and evaluation. We leveraged public GitHub repositories, open-source computational languages, and Docker technology. In addition, we conducted a data challenge using the infrastructure we developed. In this manuscript, we report on the infrastructure, workflow, and data challenge results. The infrastructure and workflow are likely to be useful for data challenges and education.

Computational reproducibility of Jupyter notebooks from biomedical publications.

Jupyter notebooks facilitate the bundling of executable code with its documentation and output in one interactive environment, and they represent a popular mechanism to document and share computational workflows, including for research publications. The reproducibility of computational aspects of research is a key component of scientific reproducibility but has not yet been assessed at scale for Jupyter notebooks associated with biomedical publications. We address computational reproducibility at 2 levels: (i) using fully automated workflows, we analyzed the computational reproducibility of Jupyter notebooks associated with publications indexed in the biomedical literature repository PubMed Central. We identified such notebooks by mining the article's full text, trying to locate them on GitHub, and attempting to rerun them in an environment as close to the original as possible. We documented reproduction success and exceptions and explored relationships between notebook reproducibility and variables related to the notebooks or publications. (ii) This study represents a reproducibility attempt in and of itself, using essentially the same methodology twice on PubMed Central over the course of 2 years, during which the corpus of Jupyter notebooks from articles indexed in PubMed Central has grown in a highly dynamic fashion. Out of 27,271 Jupyter notebooks from 2,660 GitHub repositories associated with 3,467 publications, 22,578 notebooks were written in Python, including 15,817 that had their dependencies declared in standard requirement files and that we attempted to rerun automatically. For 10,388 of these, all declared dependencies could be installed successfully, and we reran them to assess reproducibility. Of these, 1,203 notebooks ran through without any errors, including 879 that produced results identical to those reported in the original notebook and 324 for which our results differed from the originally reported ones. Running the other notebooks resulted in exceptions. We zoom in on common problems and practices, highlight trends, and discuss potential improvements to Jupyter-related workflows associated with biomedical publications.

Rworkflows: automating reproducible practices for the R community

Despite calls to improve reproducibility in research, achieving this goal remains elusive even within computational fields. Currently, >50% of R packages are distributed exclusively through GitHub. While the trend towards sharing open-source software has been revolutionary, GitHub does not have any default built-in checks for minimal coding standards or software usability. This makes it difficult to assess the current quality R packages, or to consistently use them over time and across platforms. While GitHub-native solutions are technically possible, they require considerable time and expertise for each developer to write, implement, and maintain. To address this, we develop rworkflows; a suite of tools to make robust continuous integration and deployment (https://github.com/neurogenomics/rworkflows). rworkflows can be implemented by developers of all skill levels using a one-time R function call which has both sensible defaults and extensive options for customisation. Once implemented, any updates to the GitHub repository automatically trigger parallel workflows that install all software dependencies, run code checks, generate a dedicated documentation website, and deploy a publicly accessible containerised environment. By making the rworkflows suite free, automated, and simple to use, we aim to promote widespread adoption of reproducible practices across a continually growing R community.

Meta-Scaler: A Meta-Learning Framework for the Selection of Scaling Techniques.

Dataset scaling, a.k.a. normalization, is an essential preprocessing step in a machine learning (ML) pipeline. It aims to adjust the scale of attributes in a way that they all vary within the same range. This transformation is known to improve the performance of classification models. Still, there are several scaling techniques (STs) to choose from, and no ST is guaranteed to be the best for a dataset regardless of the classifier chosen. It is thus a problem-and classifier-dependent decision. Furthermore, there can be a huge difference in performance when selecting the wrong technique; hence, it should not be neglected. That said, the trial-and-error process of finding the most suitable technique for a particular dataset can be unfeasible. As an alternative, we propose the Meta-scaler, which uses meta-learning (MtL) to build meta-models to automatically select the best ST for a given dataset and classification algorithm. The meta-models learn to represent the relationship between meta-features extracted from the datasets and the performance of specific classification algorithms on these datasets when scaled with different techniques. Our experiments using 12 base classifiers, 300 datasets, and five STs demonstrate the feasibility and effectiveness of the approach. When using the ST selected by the Meta-scaler for each dataset, 10 of 12 base models tested achieved statistically significantly better classification performance than any fixed choice of a single ST. The Meta-scaler also outperforms state-of-the-art MtL approaches for ST selection. The source code, data, and results from the experiments in this article are available at a GitHub repository (http://github.com/amorimlb/meta_scaler).

Augmenting a training dataset of the generative diffusion model for molecular docking with artificial binding pockets.

This study introduces the PocketCFDM generative diffusion model, aimed at improving the prediction of small molecule poses in the protein binding pockets. The model utilizes a novel data augmentation technique, involving the creation of numerous artificial binding pockets that mimic the statistical patterns of non-bond interactions found in actual protein-ligand complexes. An algorithmic method was developed to assess and replicate these interaction patterns in the artificial binding pockets built around small molecule conformers. It is shown that the integration of artificial binding pockets into the training process significantly enhanced the model's performance. Notably, PocketCFDM surpassed DiffDock in terms of non-bond interaction and steric clash numbers, and the inference speed. Future developments and optimizations of the model are discussed. The inference code and final model weights of PocketCFDM are accessible publicly via the GitHub repository: https://github.com/vtarasv/pocket-cfdm.git.

A MACHINE LEARNING BASED CLASSIFICATION AND PREDICTION TECHNIQUE FOR DDOS ATTACKS

Distributed network attacks are referred to, usually, as Distributed Denial of Service (DDoS) attacks. These attacks take advantage of specific limitations that apply to any arrangement asset, such as the framework of the authorized organization's site. In the existing research study, the author worked on an old KDD dataset. It is necessary to work with the latest dataset to identify the current state of DDoS attacks. This paper, used a machine learning approach for DDoS attack types classification and prediction. For this purpose, used Random Forest and XGBoost classication algorithms. To access the research proposed a complete framework for DDoS attacks prediction. For the proposed work, the UNWS-np-15 dataset was extracted from the GitHub repository and Python was used as a simulator. After applying the machine learning models, we generated a confusion matrix for identification of the model performance. In the first classification, the results showed that both Precision (PR) and Recall (RE) are 89% for the Random Forest algorithm. The average Accuracy (AC) of our proposed model is 89% which is superb and enough good. In the second classification, the results showed that both Precision (PR) and Recall (RE) are approximately 90% for the XGBoost algorithm. The average Accuracy (AC) of our suggested model is 90%. By comparing our work to the existing research works, the accuracy of the defect determination was significantly improved which is approximately 85% and 79%, respectively.

DUNE Computing Tutorials

DUNE Computing Tutorials