Recent Releases of topolow
topolow - v2.0.0
Topolow v2.0.0 is a major update introducing the wizard function Euclidify, which gets the dissimilarity matrix, carries out the entire optimization pipeline, and produces coordinates in a space with optimal dimensionality.
Stability improvements, fewer dependencies, examples from various fields, and a vignette are some of the improvements in this version.
- R
Published by omid-arhami 7 months ago
topolow - v1.0.0
This is the version submitted to CRAN.
- Examples: Examples for most functions have been updated.
- File Writing: Functions no longer write to user directories by default. Functions where writing a file is the main purpose now require the user to specify an output directory.
- Functionality: The complex distributed processing functionality (SLURM) has been removed, as it was not essential for typical use cases.
- Citation: The link to our paper published in Bioinformatics and citation information have been updated.
- R
Published by omid-arhami 8 months ago
topolow - v0.2.2
Previously, Topolow would report the mean NLL over folds for each set of parameters and dataset, basically, NLL of the total data points divided by the number of folds. It was just a division by a constant and NLL values have no meaning individually, so, the results remain unchanged. However, to make it more mathematically accurate and allow for true comparison between different datasets, now Topolow reports NLL for all data.
- R
Published by omid-arhami 11 months ago
topolow - v0.2.1
In this release interfaces of some functions were simplified. Please refer to the documentation for the updated syntax. https://github.com/omid-arhami/topolow/blob/main/build/topolow-manual.pdf
The improvements include: - Simpler function arguments for parallelization - shorter run times.
- R
Published by omid-arhami 11 months ago
topolow - v0.1.3
The third revision in the first minor version of Topolow. 15X speed increase and improved parallel processing robustness across platforms. topolow-manual.pdf
- R
Published by omid-arhami 11 months ago
topolow - v0.1.2
TopoLow v0.1.2
This version introduces a major speed increase (about 6X) by employing vectorization feature in R.
Documentations and usage are the same as previous version. You just need to update the package if you have installed previous versions.
The public release of the TopoLow algorithm for antigenic cartography mapping and analysis. This version implements a physics-inspired approach combining spring forces and repulsive interactions to optimize point configurations in high-dimensional spaces.
Key Features
- Core optimization algorithm with configurable parameters
- Support for both SLURM clusters and local machines (Windows/Unix)
- Handling of missing and thresholded measurements
- Interactive visualization tools
- Cross-validation and error analysis capabilities
- Network structure analysis
- Comprehensive test coverage and validation
Installation
Windows users should use the .zip binary, while Unix/Mac users can install from the .tar.gz source package. For direct installation from GitHub:
r
devtools::install_github("omid-arhami/topolow")
Documentation
Full documentation is available for each function. Examples of using various functionalities of Topolow on different data sets are provided in the directory "reproduction_examples".
Validation
All functions and methodologies have been extensively tested and validated as described in the paper. If you use Topolow, please cite: TOPOLOW: A MAPPING ALGORITHM FOR ANTIGENIC CROSS-REACTIVITY AND BINDING AFFINITY ASSAY RESULTS Omid Arhami, Pejman Rohani bioRxiv 2025.02.09.637307; doi: https://doi.org/10.1101/2025.02.09.637307 (under peer review)
Notes
- This is the version referenced in the manuscript submitted for peer review
- Requires R ≥ 4.1.0
- SLURM functionality is available and needed for cluster computing for large-scale problems
Bug Reports
Please report any issues at: https://github.com/omid-arhami/topolow/issues
- R
Published by omid-arhami 12 months ago
topolow - v0.1.1
TopoLow v0.1.1
First public release of the TopoLow algorithm for antigenic cartography mapping and analysis. This version implements a physics-inspired approach combining spring forces and repulsive interactions to optimize point configurations in high-dimensional spaces.
Key Features
- Core optimization algorithm with configurable parameters
- Support for both SLURM clusters and local machines (Windows/Unix)
- Handling of missing and thresholded measurements
- Interactive visualization tools
- Cross-validation and error analysis capabilities
- Network structure analysis
- Comprehensive test coverage and validation
Installation
Windows users should use the .zip binary, while Unix/Mac users can install from the .tar.gz source package. For direct installation from GitHub:
r
devtools::install_github("omid-arhami/topolow")
Documentation
Full documentation is available for each function. Examples of using various functionalities of Topolow on different data sets are provided in the directory "reproduction_examples".
Validation
All functions and methodologies have been extensively tested and validated as described in the paper. If you use Topolow, please cite: TOPOLOW: A MAPPING ALGORITHM FOR ANTIGENIC CROSS-REACTIVITY AND BINDING AFFINITY ASSAY RESULTS Omid Arhami, Pejman Rohani bioRxiv 2025.02.09.637307; doi: https://doi.org/10.1101/2025.02.09.637307 (under peer review)
Notes
- This is the version referenced in the manuscript submitted for peer review
- Requires R ≥ 4.1.0
- SLURM functionality is available and needed for cluster computing for large-scale problems
Bug Reports
Please report any issues at: https://github.com/omid-arhami/topolow/issues
- R
Published by omid-arhami about 1 year ago
topolow - topolow v0.1.0
TopoLow v0.1.0
First public release of the TopoLow algorithm for antigenic cartography mapping and analysis. This version implements a physics-inspired approach combining spring forces and repulsive interactions to optimize point configurations in high-dimensional spaces.
Key Features
- Core optimization algorithm with configurable parameters
- Support for both SLURM clusters and local machines (Windows/Unix)
- Handling of missing and thresholded measurements
- Interactive visualization tools
- Cross-validation and error analysis capabilities
- Network structure analysis
- Comprehensive test coverage and validation
Installation
Windows users should use the .zip binary, while Unix/Mac users can install from the .tar.gz source package. For direct installation from GitHub:
r
devtools::install_github("omid-arhami/topolow")
Documentation
Full documentation is available within the package:
r
library(topolow)
?topolow
Validation
All functions and methodologies have been extensively tested and validated as described in: Arhami and Rohani (2025) [Topolow: Topological optimization for continuous phenotype mapping], Journal
Notes
- This is the version referenced in the manuscript submitted for peer review
- Requires R ≥ 4.1.0
- SLURM functionality is available and only needed for cluster computing for large-scale problems
Bug Reports
Please report any issues at: https://github.com/omid-arhami/topolow/issues
- R
Published by omid-arhami about 1 year ago