Peter DeWeirdt
@pdeweirdt.bsky.social
PhD student @mit studying anti-phage defense systems using machine learning
Also congrats to @audeber.bsky.social and co. on their work using ML to predict anti-phage defense systems: www.biorxiv.org/content/10.1...
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Protein and genomic language models chart a vast landscape of antiphage defenses
The bacterial pangenome encodes an immense array of antiphage systems, yet much of their diversity remains uncharted. In this study, we developed language models to predict novel antiphage proteins in...
www.biorxiv.org
January 9, 2025 at 7:32 PM
Also congrats to @audeber.bsky.social and co. on their work using ML to predict anti-phage defense systems: www.biorxiv.org/content/10.1...
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Congrats Mike Laub and Emily Mahoney!
Lots more in the manuscript: www.biorxiv.org/content/10.1...
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Lots more in the manuscript: www.biorxiv.org/content/10.1...
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DefensePredictor: A Machine Learning Model to Discover Novel Prokaryotic Immune Systems
Anti-phage defense systems protect bacteria from viruses. Studying defense systems has begun to reveal the evolutionary roots of eukaryotic innate immunity and produced important biotechnologies such ...
www.biorxiv.org
January 9, 2025 at 7:32 PM
Congrats Mike Laub and Emily Mahoney!
Lots more in the manuscript: www.biorxiv.org/content/10.1...
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Lots more in the manuscript: www.biorxiv.org/content/10.1...
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When applied to 500 diverse bacterial assemblies, DefensePredictor revealed thousands of additional candidate systems awaiting validation.
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January 9, 2025 at 7:32 PM
When applied to 500 diverse bacterial assemblies, DefensePredictor revealed thousands of additional candidate systems awaiting validation.
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Among the systems were 7 protein domains that we newly validated in defense, including in DS-8 and DS-9, which have homology to the human innate immune protein SMPDL3A.
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January 9, 2025 at 7:32 PM
Among the systems were 7 protein domains that we newly validated in defense, including in DS-8 and DS-9, which have homology to the human innate immune protein SMPDL3A.
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We tested the model’s predictions in lab and identified 45 novel defense systems, observing a strong correlation between the validation rate and defense probability.
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January 9, 2025 at 7:32 PM
We tested the model’s predictions in lab and identified 45 novel defense systems, observing a strong correlation between the validation rate and defense probability.
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DefensePredictor demonstrates strong performance on a held-out set of defense genes and leverages biological patterns like low GC content to make its predictions.
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January 9, 2025 at 7:32 PM
DefensePredictor demonstrates strong performance on a held-out set of defense genes and leverages biological patterns like low GC content to make its predictions.
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We compiled a dataset of known defense systems and trained a gradient boosting model to distinguish defense from non-defense genes, using ESM2 embeddings and genomic features of each gene and its neighbors.
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January 9, 2025 at 7:32 PM
We compiled a dataset of known defense systems and trained a gradient boosting model to distinguish defense from non-defense genes, using ESM2 embeddings and genomic features of each gene and its neighbors.
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