Gradient Descent
Gradient descent is an iterative algorithm that aims to find values for the parameters of a function of interest which minimizes the output of a cost function with respect to a given dataset. Gradient...
View ArticleBig data, big challenge – part 2
This post follows my previous post on big data. Even though the latter did not result in a big virtual discussion, I was pleased to read some comments regarding the situation in other areas of...
View ArticleA Week of Deep Learning
From August 21 to 25, IVADO and the MILA held their first edition of the École d'été francophone en apprentissage profond. The aim of this summer school was to "give [the participants] the theoretical...
View ArticleLet it roam free ! Releasing your code into the wild…
Today, I thought I'd do something a little different and talk about what one might expect from publicly releasing some code. I figured it might be nice to interview someone from our group which has...
View ArticleOverfitting and Regularization
This series of articles on machine learning wouldn't be complete without dipping our toes in overfitting and regularization. Overfitting The Achille's heel of machine learning is overfitting. As...
View ArticleA multiprocessing example and more
Recently, I had to search a given chemical structure into a list of structures. Using the python chemoinformatics packages pybel and rdkit, I was easily able to do so but the operation took a little...
View ArticleThink like a computer
Let's say all your results for a given project are stored in Excel files named exp1.xlsx, exp2_20170708.xlsx, exp_prolif_072017.xlsx... Inside file exp1.xlsx, you have this : This might be a...
View ArticleUnderstanding how kallisto works
In 2016, Bray et al. introduced a new k-mer based method to estimate isoform abundance from RNA-Seq data. Their method, called kallisto, provided a significant improvement in speed and memory usage...
View ArticleA word about unwanted variability
Experiments are influenced by various variables: the one we are interested in, and many others. Variability in the data can be related to differences in technical or biological variables, such as the...
View ArticleDocument your work by adding parameters to your shell scripts
At some point during your bioinformatics career, you're going to start writing shell scripts, it's kind of inevitable ! So let us discuss a strategy to add parameters to your scripts in order make them...
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