Genomics, Machine Learning, and Data for Bioinformatics
gmdbioinformaticsGMD Bioinformatics - from dalloliogm
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gmdbioinformatics.substack.comLatest Issues
The CAFA6 Challenge: predicting protein function from sequence
Now that the Arc Virtual Cell Challenge has finished, my attention has shifted to a different type of computational biology-related competition: the CAFA6 challenge, hosted on Kaggle.
The task in the CAFA6 challenge is to predict the funct...
Arc Virtual Cell Challenge - part 4: Winners announced!
The Winners of the first Arc Virtual Cell Challenge have been announced! Congratulations to all the teams.
This wrap-up blog post on the Challenge’s website gives plenty of details about the winners and their strategies, along with some co...
New preprint: Multi-agent AI enables evidence-based cell annotation in single-cell transcriptomics
I’m pleased to announce that the CyteType pre-print is out on bioArXiv!
Main figure of the paper, showing the architecture of the agentic system and its results.
CyteType is an agentic framework for annotation of cell types in single-cell...
Arc Virtual Cell Challenge part 3: how to train your own Virtual Cell Model
Here is my third article covering the Arc Virtual Cell Challenge (see first and second).
Right at the beginning of the challenge, the organizers released a Colab Notebook to help participants get started. This notebook shows how to train S...
Arc Virtual Cell Challenge part 2: What the Leaderboard Collapse Reveals About Model Evaluation
The Arc Virtual Challenge is coming to an end, with the deadline in a mid November 2025.
However, the challenge’s Discord forums are in turmoil. Some participants have discovered a trick to get to the top of the leaderboard: by simply appl...
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The writers behind this newsletter.
GMD Bioinformatics provides consulting on Genomics, Machine Learning, and Data for Bioinformatics.
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