# FACET: Factorized Asymmetric Conditioning for Efficient Transport in High-Fidelity Fluorescence Microscopy Synthesis

arXiv: https://arxiv.org/abs/2610.05353 · HTML: https://mlsanity.com/paper/2610.05353/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 23 of its 49 references that are in the map.
- First posted on arXiv 4 Oct 2026.

## Builds on (most cited first, 23 of 23)

- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [High-Resolution Image Synthesis with Latent Diffusion Models](https://mlsanity.com/paper/2112.10752/) (2021)
- [Denoising Diffusion Implicit Models](https://mlsanity.com/paper/2010.02502/) (2020)
- [Score-Based Generative Modeling through Stochastic Differential Equations](https://mlsanity.com/paper/2011.13456/) (2020)
- [Flow Matching for Generative Modeling](https://mlsanity.com/paper/2210.02747/) (2022)
- [Adding Conditional Control to Text-to-Image Diffusion Models](https://mlsanity.com/paper/2302.05543/) (2023)
- [On Calibration of Modern Neural Networks](https://mlsanity.com/paper/1706.04599/) (2017)
- [Flow Straight and Fast: Learning to Generate and Transfer Data with Rectified Flow](https://mlsanity.com/paper/2209.03003/) (2022)
- [Elucidating the Design Space of Diffusion-Based Generative Models](https://mlsanity.com/paper/2206.00364/) (2022)
- [Domain-Adversarial Training of Neural Networks](https://mlsanity.com/paper/1505.07818/) (2015)
- [FiLM: Visual Reasoning with a General Conditioning Layer](https://mlsanity.com/paper/1709.07871/) (2017)
- [Shortcut Learning in Deep Neural Networks](https://mlsanity.com/paper/2004.07780/) (2020)
- [Stochastic Interpolants: A Unifying Framework for Flows and Diffusions](https://mlsanity.com/paper/2303.08797/) (2023)
- [Improving and generalizing flow-based generative models with minibatch optimal transport](https://mlsanity.com/paper/2302.00482/) (2023)
- [What Makes Training Multi-Modal Classification Networks Hard?](https://mlsanity.com/paper/1905.12681/) (2019)
- [Ladder Variational Autoencoders](https://mlsanity.com/paper/1602.02282/) (2016)
- [Balanced Multimodal Learning via On-the-fly Gradient Modulation](https://mlsanity.com/paper/2203.15332/) (2022)
- [Modality Competition: What Makes Joint Training of Multi-modal Network Fail in Deep Learning? (Provably)](https://mlsanity.com/paper/2203.12221/) (2022)
- [PMR: Prototypical Modal Rebalance for Multimodal Learning](https://mlsanity.com/paper/2211.07089/) (2022)
- [Diff2Flow: Training Flow Matching Models via Diffusion Model Alignment](https://mlsanity.com/paper/2506.02221/) (2025)
- [B'ezierFlow: Learning B'ezier Stochastic Interpolant Schedulers for Few-Step Generation](https://mlsanity.com/paper/2512.13255/) (2025)
- [PRISM: Enhancing Protein Inverse Folding through Fine-Grained Retrieval on Structure-Sequence Multimodal Representations](https://mlsanity.com/paper/2510.11750/) (2025)
- [Retrieval-Augmented Interpretable Learning: Towards Task-Specific Zero-Shot Models in Healthcare](https://mlsanity.com/paper/2607.17508/) (2026)

## Abstract (arXiv)

Fluorescence microscopy reveals where proteins localize, but only a limited number of proteins can be imaged in the same cell; generating these images from amino-acid sequence and the cell's morphological context enables in silico localization of unimaged proteins. The two conditions, however, play asymmetric roles: morphological context is spatially aligned with the target, whereas sequence is non-spatial and must specify protein-dependent localization within it, with recurring coarse patterns shared across proteins and finer protein-specific variation. Existing generators condition on both jointly, without separating what each explains. We introduce FACET (Factorized Asymmetric Conditioning for Efficient Transport), a probabilistic generative framework that encodes this structure as an explicit inductive bias: sequence semantics are learned from what context leaves unexplained, coarse localization regularities are shared across proteins through a semantic memory, and protein-specific variation is a bounded residual around them. A variance-preserving state projection further lets FACET perform continuous stochastic transport through a pretrained diffusion predictor with minimal parameter overhead. On held-out proteins, FACET improves spatial overlap by 34.3% on the Human Protein Atlas and 14.0% on OpenCell over a backbone-matched baseline, and reduces FID by 27.2% and 46.5%, respectively, with 75% fewer network evaluations. It also substantially improves protein-association structure recovery and yields better-calibrated predictions, while detailed ablations show complementary contributions from its design choices. These results identify factorized asymmetric conditioning, rather than generator capacity alone, as a key lever for high-fidelity, efficient, and biologically meaningful cellular image synthesis.