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Patrick Aloy

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Open access Jul 2026

Task-adapted biological foundation models uncover perturbation-centric representations

Fine-tuned scGPT, a transformer pre-trained on over 30 million single-cell transcriptomes, was fine-tuned on more than three million LINCS L1000 perturbation profiles using a supervised objective that predicts perturbation identity and spontaneously captured orthogonal biological relationships never provided during tra...

Elena Pareja-Lorente, Patrick Aloy · 0 citations

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