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Open-source Tools for CryoET Particle Picking Machine Learning Competitions

Harrington, K. I.; Zhao, Z.; Schwartz, J.; Kandel, S.; Ermel, U.; Paraan, M.; Potter, C.; Carragher, B.

2024-11-05 bioinformatics
10.1101/2024.11.04.621608 bioRxiv
Show abstract

We are launching a machine learning (ML) competition focused on particle picking in cryo-electron tomography (cryoET) data, a crucial task in structural biology. To support this, we have created a comprehensive suite of open-source tools to develop resources for our competition, including copick for dataset management, napari plugins for interactive visualization, utilities for converting particle picks to segmentation masks, and PyTorch tools for custom dataset sampling. These resources streamline the processes of data handling, labeling, and visualization, allowing participants to focus on model development. By leveraging these tools, competitors will be better equipped to tackle the unique challenges of cryoET data and push forward advancements in particle picking techniques.

Matching journals

The top 4 journals account for 50% of the predicted probability mass.

1
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Top 0.8%
23.0%
2
Journal of Structural Biology
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13.3%
3
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12.2%
4
Acta Crystallographica Section D Structural Biology
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Top 0.1%
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50% of probability mass above
5
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Top 0.1%
3.3%
6
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Top 3%
3.3%
7
PLOS Computational Biology
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Top 10%
3.3%
8
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Top 0.1%
2.7%
9
BMC Bioinformatics
○ 457 papers in training set
Top 3%
2.5%
10
Nature Methods
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Top 3%
2.5%
11
GigaScience
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Top 2%
1.8%
12
Computational and Structural Biotechnology Journal
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Top 5%
1.2%
13
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Top 0.7%
1.2%
14
Nature Communications
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Top 52%
1.1%
15
Bioinformatics Advances
◐ 203 papers in training set
Top 4%
1.1%
16
Journal of Open Source Software
● 25 papers in training set
Top 0.3%
1.1%
17
Journal of Molecular Biology
○ 232 papers in training set
Top 3%
1.0%
18
Nucleic Acids Research
◐ 1281 papers in training set
Top 13%
0.9%
19
PLOS ONE
● 5266 papers in training set
Top 60%
0.9%
20
Cell Reports Methods
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Top 4%
0.9%
21
Protein Science
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Top 4%
0.6%
22
Frontiers in Bioinformatics
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0.6%
23
eLife
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Top 67%
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24
Genome Biology
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Top 9%
0.6%