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Creating large imbalanced data benchmarks
Tutorial with OpenML
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Load-balanced parallel machine learning benchmarks
A new approach using filelock and batchtools
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Debrief May 2025
Zurich, Munich, Mons
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Parallel machine learning benchmarks
A new approach using targets and crew.cluster
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New parallel computing frameworks
batchtools, clustermq, rush, mirai, crew, targets
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Centralized vs de-centralized parallelization
Exploring rush
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mlr3 tutorials
Links to other blogs
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Comparing change-point pruning methods using square loss
Pruned Exact Linear Time (PELT) and Functional Pruning Optimal Partitioning (FPOP)
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Organizing computational research projects
Guide for research students
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Volcano plots
Redesign of SOAK paper results
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Torch learning with binary classification
Implementing AUM loss in mlr3torch
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Creating imbalanced data benchmarks
Tutorial with MNIST
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Comparing neural network architectures using mlr3torch
Convolutional network versus linear model
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Comparing pruning methods for optimal partitioning
Pruned Exact Linear Time (PELT) and Functional Pruning Optimal Partitioning (FPOP)
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Are pipe operations linear or quadratic?
A demonstration of atime on mlr3torch
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Bike ride map and time series data viz
A demonstration of animint2 and sf
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Configuring eduroam
On cell phones and linux
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Benchmarking data.table with polars, duckdb, and pandas
Demonstrating advantages of data.table
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Implementing optimal partitioning in R
Comparison with Pruned Exact Linear Time (PELT)
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Cross-validation experiments with torch learners
Demonstration of mlr3torch + mlr3resampling
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Overhead of auto-grad in torch
Comparison with explicit gradients
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AUC and AUM in torch
Demonstration of auto-grad
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Ordinary least squares algorithms
Comparing computation time in R
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Collaborations not allowed
Parsing a web page with regex
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Code of conduct / conduite
Lecture obligatoire pour participants du labo LASSO / Required reading for LASSO lab participants
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Visualizing prediction error
And clearly showing differences between algorithms
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History of supervised change-point detection
Using git bisect to find a survival bug
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Generate publications page
Parsing bibtex and generating markdown
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Writing comprehensible tests
Documenting key code magic numbers in animint2 tests
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Rust versus Go
Similarities and Differences
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How reproducible are benchmarks?
Comparing atime results on different computers
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Collapse reshape benchmark
Comparison with data.table
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Porting base R regex code to nc
Case study with a complex regex
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Benchmarking a change in data.table
Progress reporting for group by operations
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Mammouth tutorial
Cluster computing for students at UdeS
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Research student application
Please read if you want to do research under my supervision
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HTML to Markdown
Regex for porting my lab web site
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Short bio
Some text to use for talk introductions
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Directions to my office in Sherbrooke
With a map in English!
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New code for various kinds of cross-validation
Cross-validation in R with mlr3
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Capturing regular expressions
Extracting data from loosely structured text
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The importance of hyper-parameter tuning
And parallellizing machine learning experiments in R
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When is it useful to train with combined subsets?
An exploration using cross-validation
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Parsing check logs using regular expressions
A demonstration of nc R package
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Unable to load shared object, Undefined symbol
Creating and explaining a linker error
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Reshape performance comparison
Demonstration of asymptotic timing comparisons
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Cross-validation with variable size train sets
Determining how many samples are necessary for optimal prediction
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Upgrading R arrow
More build debugging
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Partial matching on data frame row names
Comparing efficiency using atime
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Interpretable learning algorithms with built-in feature selection
Regularized linear model and decision tree
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Generalization to new subsets in R
Coding non-standard cross-validation
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Comparing machine learning frameworks in R
for loop, mlr3, tidymodels
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data.table CRAN diffs
Verifying consistency between CRAN and github
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data.table asymptotic timings
Motivational figures
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Debugging python code in emacs
Fixing a bug and building old emacs
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Count unique students
Regex and data table summarization
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Essential emacs key commands
Cheat sheet for my students
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Splitting an R package
Recommendations from experience with spatstat
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Installing Rmpi on the cluster
This package needs special treatment on compute nodes
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Segfault using R arrow
Reproducing and fixing an error
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Re-building vignettes on windows
Fixing mysterious error
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Modifying default gcc compilation flags
When compiling R packages
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Installing Ubuntu on an old Mac
Step by step instructions
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spack package manager
contrast with conda
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Checking R package on M1 Mac
Web services for R package developers
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Comparing asymptotic timings of CSV read/write functions
Some surprising differences
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Debugging C code
valgrind and gdb are essential tools
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CRAN Meta-data
Backing up MRAN
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Cross-validation experiments on the cluster
NAU monsoon tutorial
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Generalization to new subsets
Cross-validation in python
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R Package Release History
Extracting and plotting data from CRAN web site
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Submitting python jobs on monsoon
And anaconda setup
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Cloud Storage
Different options for internal and external sharing
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Indirect reverse dependencies
Computing the entire graph, and histogram tutorial
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GUI for WSL on Windows 10
use cygwin instead of vcxsrv
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Reformatting NEWS files
Regular expression example
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R packages on github
How to query CRAN meta-data
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Positive and negative log transform
Non-linear transformations for heat maps and signed p-values
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Research Mentorship Plan
Required reading for potential students
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Historical reverse imports
Analysis of R package usage over time
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Learning with Area Under the Min
How to use torch with a non-standard loss
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Torch randomness
Reproducible neural network learning
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No argument unpacking in C
But there is in R and Python
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AUM in Torch
Auto-grad of a non-differentiable loss function
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Erdos number
A distance calculator
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Plotting the probability simplex
An application of matrix inversion
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Link-time optimization
Fixing warnings from CRAN checks
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Finding symbols in object files
Using objdump to find cerr
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Ten years of R project in Google Summer of Code
Some success stories from my participation
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Simple methods for defining small data by row
Comparison with base R and tribble
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The C book
Documentation of stringize macros
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Evidential machine learning
An alternative to probability
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Stress testing reshape operations on list columns
Advantages of updated data.table::melt
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Defining data by row and regex by sub-pattern
Avoiding separation of related concepts in code
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Update about data reshaping and visualization in R and python
data.table, tidyr, nc, pandas, datatable, plotnine, altair, bokeh
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Convex clustering theory
Recent results on trees and cluster shapes
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R packages that depend on system libraries
How to pass CRAN checks
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The UCR Time Series Archive
A benchmark for classification algorithms
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Multi-threaded sorting
Thread safety of qsort variants
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Faster AUM computation?
Log-linear C++ STL containers vs linear time radix sort
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New ideas for classification
Weston-Watkins multiclass SVM and AUC optimization
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Emulating the python interactive console
My hack using the code module
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New packages for data storage and reshaping
tidyfast, tidyfst, fst, arrow, feather, parquet
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Computing K-means train/validation error
Alternatives to for loops in R
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Parsing CRAN maintainers
Regular expressions using nc R package
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emacspeak
Teaching my son to type in emacs
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Random train/validation/test assignment
Different methods tried by my students
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C/C++ completion in emacs
Configuration details
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Data manipulation libraries
Translating between data.table, pandas, dplyr
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Custom evaluation metrics in TensorFlow
Implementing the exact area under the ROC curve
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Fast parameter exploration
Caching and parallel execution
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binsegRcpp inside a C++ program
Embedding Rcpp code into a main function
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Embedding R
Compiling a program that links to R
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R batchtools on Monsoon
Cluster computing tutorial for NAU students
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Arizona time
Why does internet tell people the wrong time?
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Emacs local variables
Custom configurations for R
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Ubuntu setup and LaTeX debugging
Installing and configuring a 10 year old Mac
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X forwarding on windows
Installing and configuring cygwin
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Scientific poster suggestions
A helpful video
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Tinyverse
Complex software dependencies considered harmful
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useR 2019 debrief
Interesting talks I saw in Toulouse
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R in Docker on Mac
Reproducing valgrind messages using an R-hub image
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R package installation on windows considered harmful
Warning for unsuccessful DLL copy should be an error
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tikzDevice on windows
Fixing missing packages
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future.batchtools
Simple parallel R code on a computer cluster
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OpenMP
Simple parallel for loops in C++
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gdb with R
how to find line numbers of assertion errors
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Eigen and UNDEBUG
Turning on runtime assertion errors for compiled code in R packages
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survivalsvm
Support vector machine for survival analysis
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Testing PeakSegPipeline on Travis with SLURM
Also batchtools and texinfo
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Tweet when donation received
My first google script
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Setting default web browser in LXDE
Need to create a .desktop file
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Keyboard remapping on windows
Changing caps lock to control on windows
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Training Benchmark for Deep neural networks
A new benchmark data set for neural network training
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The biglasso package
An on-disk implementation for huge data
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True reproducibility in R
The switchr package and manifests
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Seasonal temperature variations where I have lived
Using R to download and plot temperature data from wikipedia
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Loon
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What Science Is
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Compiling R
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R-GSOC-2017
R project in Google Summer of Code 2017
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useR! 2017 debrief
summary of interesting work I saw in Brussels
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Combining data tables in R
rbind inside the for loop is much slower than outside
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new web site
now more complete and informative
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