Gene-Level Representation Learning via Interventional Style Transfer in Optical Pooled Screening

Optical pooled screening (OPS) combines automated microscopy and genetic perturbations to systematically study gene function in a scalable and cost-effective way. Leveraging the resulting data requires extracting biologically informative representations of cellular perturbation phenotypes from images. We employ a style-transfer approach to learn gene-level feature representations from images of genetically perturbed cells obtained via OPS. Our method outperforms widely used engineered features in clustering gene representations according to gene function, demonstrating its utility for uncovering latent biological relationships. This approach offers a promising alternative to investigate the role of genes in health and disease.

Data Alignment for Zero-Shot Concept Generation in Dermatology AI

AI in dermatology is evolving at a rapid pace but the major limitation to training trustworthy classifiers is the scarcity of data with ground-truth concept level labels, which are meta-labels semantically meaningful to humans. Foundation models like CLIP providing zero-shot capabilities can help alleviate this challenge by leveraging vast amounts of image-caption pairs available on the internet. CLIP can be fine-tuned using domain specific image-caption pairs to improve classification performance. However, CLIP's pre-training data is not well-aligned with the medical jargon that clinicians use to perform diagnoses. The development of large language models (LLMs) in recent years has led to the possibility of leveraging the expressive nature of these models to generate rich text. Our goal is to use these models to generate caption text that aligns well with both the clinical lexicon and with the natural human language used in CLIP's pre-training data. Starting with captions used for images in PubMed articles, we extend them by passing the raw captions through an LLM fine-tuned on the field's several textbooks. We find that using captions generated by an expressive fine-tuned LLM like GPT-3.5 improves downstream zero-shot concept classification performance.

MIMIC: Masked Image Modeling with Image Correspondences

Many pixelwise dense prediction tasks-depth estimation and semantic segmentation in computer vision today rely on pretrained image representations. Therefore, curating effective pretraining datasets is vital. Unfortunately, the effective pretraining datasets are those with multi-view scenes and have only been curated using annotated 3D meshes, point clouds, and camera parameters from simulated environments. We propose a dataset-curation mechanism that does not require any annotations. We mine two datasets: MIMIC-1M with 1.3M and MIMIC-3M with 3.1M multi-view image pairs from open-sourced video datasets and from synthetic 3D environments. We train multiple self-supervised models with different masked image modeling objectives to showcase the following findings: Representations trained on MIMIC-3M outperform those mined using annotations on multiple downstream tasks, including depth estimation, semantic segmentation, surface normals, and pose estimation. They also outperform representations that are frozen and when downstream training data is limited to few-shot. Larger dataset (MIMIC-3M) significantly improves performance, which is promising since our curation method can arbitrarily scale to produce even larger datasets. MIMIC code, dataset, and pretrained models are open-sourced at https://github.com/RAIVNLab/MIMIC.