The CausalBench challenge: A machine learning contest for gene network inference from single-cell perturbation data
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| Main Authors: | , , , , , , , , , , , , , , , , , |
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| Format: | Preprint |
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2023
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| _version_ | 1866910952109113344 |
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| author | Chevalley, Mathieu Sackett-Sanders, Jacob Roohani, Yusuf Notin, Pascal Bakulin, Artemy Brzezinski, Dariusz Deng, Kaiwen Guan, Yuanfang Hong, Justin Ibrahim, Michael Kotlowski, Wojciech Kowiel, Marcin Misiakos, Panagiotis Nazaret, Achille Püschel, Markus Wendler, Chris Mehrjou, Arash Schwab, Patrick |
| author_facet | Chevalley, Mathieu Sackett-Sanders, Jacob Roohani, Yusuf Notin, Pascal Bakulin, Artemy Brzezinski, Dariusz Deng, Kaiwen Guan, Yuanfang Hong, Justin Ibrahim, Michael Kotlowski, Wojciech Kowiel, Marcin Misiakos, Panagiotis Nazaret, Achille Püschel, Markus Wendler, Chris Mehrjou, Arash Schwab, Patrick |
| contents | In drug discovery, mapping interactions between genes within cellular systems is a crucial early step. Such maps are not only foundational for understanding the molecular mechanisms underlying disease biology but also pivotal for formulating hypotheses about potential targets for new medicines. Recognizing the need to elevate the construction of these gene-gene interaction networks, especially from large-scale, real-world datasets of perturbed single cells, the CausalBench Challenge was initiated. This challenge aimed to inspire the machine learning community to enhance state-of-the-art methods, emphasizing better utilization of expansive genetic perturbation data. Using the framework provided by the CausalBench benchmark, participants were tasked with refining the current methodologies or proposing new ones. This report provides an analysis and summary of the methods submitted during the challenge to give a partial image of the state of the art at the time of the challenge. Notably, the winning solutions significantly improved performance compared to previous baselines, establishing a new state of the art for this critical task in biology and medicine. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2308_15395 |
| institution | arXiv |
| publishDate | 2023 |
| record_format | arxiv |
| spellingShingle | The CausalBench challenge: A machine learning contest for gene network inference from single-cell perturbation data Chevalley, Mathieu Sackett-Sanders, Jacob Roohani, Yusuf Notin, Pascal Bakulin, Artemy Brzezinski, Dariusz Deng, Kaiwen Guan, Yuanfang Hong, Justin Ibrahim, Michael Kotlowski, Wojciech Kowiel, Marcin Misiakos, Panagiotis Nazaret, Achille Püschel, Markus Wendler, Chris Mehrjou, Arash Schwab, Patrick Machine Learning Molecular Networks Quantitative Methods In drug discovery, mapping interactions between genes within cellular systems is a crucial early step. Such maps are not only foundational for understanding the molecular mechanisms underlying disease biology but also pivotal for formulating hypotheses about potential targets for new medicines. Recognizing the need to elevate the construction of these gene-gene interaction networks, especially from large-scale, real-world datasets of perturbed single cells, the CausalBench Challenge was initiated. This challenge aimed to inspire the machine learning community to enhance state-of-the-art methods, emphasizing better utilization of expansive genetic perturbation data. Using the framework provided by the CausalBench benchmark, participants were tasked with refining the current methodologies or proposing new ones. This report provides an analysis and summary of the methods submitted during the challenge to give a partial image of the state of the art at the time of the challenge. Notably, the winning solutions significantly improved performance compared to previous baselines, establishing a new state of the art for this critical task in biology and medicine. |
| title | The CausalBench challenge: A machine learning contest for gene network inference from single-cell perturbation data |
| topic | Machine Learning Molecular Networks Quantitative Methods |
| url | https://arxiv.org/abs/2308.15395 |