Towards scientific discovery with dictionary learning: Extracting biological concepts from microscopy foundation models

• URL: http://arxiv.org/abs/2412.16247v2
• Date: Tue, 11 Feb 2025 16:54:45 GMT
• Title: Towards scientific discovery with dictionary learning: Extracting biological concepts from microscopy foundation models
• Authors: Konstantin Donhauser, Kristina Ulicna, Gemma Elyse Moran, Aditya Ravuri, Kian Kenyon-Dean, Cian Eastwood, Jason Hartford,
• Abstract summary: We propose Iterative Codebook Feature Learning(ICFL) and combine it with a pre-processing step which uses PCA whitening from a control dataset. We show that both ICFL and PCA improve the selectivity of extracted features compared to TopK sparse autoencoders.
• Score: 6.136186137141521
• License:
• Abstract: Dictionary learning (DL) has emerged as a powerful interpretability tool for large language models. By extracting known concepts (e.g., Golden-Gate Bridge) from human-interpretable data (e.g., text), sparse DL can elucidate a model's inner workings. In this work, we ask if DL can also be used to discover unknown concepts from less human-interpretable scientific data (e.g., cell images), ultimately enabling modern approaches to scientific discovery. As a first step, we use DL algorithms to study microscopy foundation models trained on multi-cell image data, where little prior knowledge exists regarding which high-level concepts should arise. We show that sparse dictionaries indeed extract biologically-meaningful concepts such as cell type and genetic perturbation type. We also propose Iterative Codebook Feature Learning~(ICFL) and combine it with a pre-processing step which uses PCA whitening from a control dataset. In our experiments, we demonstrate that both ICFL and PCA improve the selectivity of extracted features compared to TopK sparse autoencoders.

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