The paper investigates adapting the HiFiC generative image compression model, originally designed for natural photographs, to compress Hi‑C chromatin contact maps while preserving biologically relevant features. By replacing HiFiC’s distortion term with a spatially‑weighted MSE that emphasizes loops, TAD boundaries, stripes, and compartments, and adding an insulation‑score loss, the authors fine‑tune a pretrained HiFiC checkpoint in a three‑phase strategy to create HiFiC‑G. Evaluation on two cell lines shows HiFiC‑G better retains local structures such as stripes and TAD boundaries, though long‑range A/B compartment preservation remains limited due to architectural constraints.
arXiv:2607. 14163v1 Announce Type: cross Abstract: Most single-cell foundation models are adapted from language models, representing each cell as a sequence of gene tokens.
arXiv:2609.31204v1 Announce Type: cross Abstract: Recent fMRI foundation models differ substantially in the spatial scale at which they represent brain activity. ROI- and connectivity-based models ar...
arXiv:2608. 06240v1 Announce Type: cross Abstract: Unpaired image-to-image translation must decide, per image, what to change and what to preserve without paired supervision.
arXiv:2603. 13432v4 Announce Type: replace-cross Abstract: Spatial Transcriptomics (ST) profiles thousands of gene expression values at discrete spots with precise coordinates on tissue sections, preserving spatial context essential for clinical and pathological studies.
arXiv:2607. 27712v1 Announce Type: new Abstract: Standard masked-language-model fine-tuning applies a uniform masking probability across every token position, assuming reconstruction difficulty is position-agnostic.
arXiv:2608. 14710v1 Announce Type: cross Abstract: Predicting spatial gene expression from hematoxylin and eosin (H\&E)-stained images offers a cost-effective alternative to spatial transcriptomics (ST).
The paper introduces GenDA, a bidirectional discrete diffusion model designed for genomic sequence reconstruction, hypothesizing that entropy-guided span placement would improve variant-effect prediction and functional sequence generation. While the 202‑million‑parameter GenDA model achieves a higher ClinVar SNV AUROC (0.774) than a comparable autoregressive model, the improvement is not attributable to entropy guidance, and the model fails to outperform a shuffled‑gap baseline in zero‑shot functional inpainting across various genomic regions. The authors identify limitations such as tokenization granularity, span length caps, and the mismatch between local sequence complexity and functional importance, concluding that variant prediction, corruption priors, and functional generation are distinct tasks requiring separate validation.
arXiv:2609.36429v1 Announce Type: new Abstract: Predicting gene expression from H&E-stained histology images offers a scalable alternative to costly spatial transcriptomics, yet most existing methods...
arXiv:2608.07632v2 Announce Type: replace-cross Abstract: Image-based profiling captures rich phenotypic signatures for drug discovery and functional genomics. Large public datasets like JUMP Cell Pa...
arXiv:2603. 01568v2 Announce Type: replace Abstract: Efficient coding theory predicts that biological perceptual systems compress sensory input optimally under resource constraints, with the systematic structure of errors reflecting the geometry of that compression.
The paper introduces CP‑BG‑Bench, a paired‑view evaluation framework for Cell Painting vision encoders that fixes a central cell across four matched views (raw crop, segmented, and density‑augmented variants). Using this framework on three datasets and three encoders, the authors show that standard single‑metric rankings (e.g., replicate mAP) vary systematically across protocols, revealing disagreements along axes of cell versus background, morphology versus context, and within‑study versus across‑batch performance. The study demonstrates that segmented views can outperform crops in certain tasks and that background‑driven gains are largely determined by experimental design rather than encoder choice.
arXiv:2610.00860v1 Announce Type: cross Abstract: Background and Objectives: Fluorescence-labeled cellular arbors provide readouts of neuronal and microglial morphology, but fine and weakly labeled p...