JUMP-lite: Compact, reproducible benchmarking of cell representations
Read the original on arXiv Computer Vision →The Flow has not summarised this story yet — read it at arXiv Computer Vision.
The Flow has not summarised this story yet — read it at arXiv Computer Vision.
arXiv:2603. 13377v2 Announce Type: replace-cross Abstract: Representation learning has driven major advances in natural image analysis by enabling models to acquire high-level semantic features.
arXiv:2606. 05139v1 Announce Type: new Abstract: The rapid advancement of high-throughput sequencing has led to large, high-dimensional omics datasets.
The paper presents MoCoP v2, an enhanced contrastive pretraining method that aligns small molecule embeddings with deep‑learning‑derived cell morphology profiles. By replacing CellProfiler fingerprints with richer image‑encoded features, the new embeddings better capture how molecules alter cell morphology, leading to improved QSAR, toxicity, ADME, and activity predictions. Performance scales log‑linearly with training data size, indicating further gains with larger datasets.
The study evaluates self‑supervised learning (SSL) models pretrained on ImageNet‑1k and the Human Protein Atlas (HPA) Field‑of‑View (FOV) for protein localization in microscopy images. DINO‑based Vision Transformer backbones pretrained on either dataset transfer well to the OpenCell dataset, achieving strong performance even without fine‑tuning and improving further when fine‑tuned (0.704 ± 0.027 macro F1 on 17 classes). At the single‑cell level, the HPA‑pretrained model outperforms others in k‑nearest‑neighbor classification across all neighborhood sizes (macro F1 ≥ 0.515).
The paper presents a 3D foundation model for light sheet fluorescence microscopy (LSM) that is pretrained on a large curated set of 3D images from various organisms, stains, and imaging protocols. By jointly optimizing for masked reconstruction and image‑text alignment, the model learns transferable volumetric representations that dramatically reduce the need for annotated data. The pretrained backbone enables efficient few‑shot adaptation to downstream tasks such as segmentation, classification, and deblurring, consistently outperforming baselines according to standard metrics and expert evaluation.
arXiv:2608. 14293v1 Announce Type: cross Abstract: High-content microscopy enables systematic profiling of cellular responses to chemical perturbations, but the scale of the chemical space makes exhaustive phenotypic characterization experimentally infeasible.