# Joint Flow Matching Enables Continuous Dose-Conditioned Cell Morphing

arXiv: https://arxiv.org/abs/2608.16424 · HTML: https://mlsanity.com/paper/2608.16424/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Flow matching, time series and science, one of 14 directions in Diffusion models.
- Builds on 25 of its 44 references that are in the map.
- First posted on arXiv 17 Aug 2026.

## Placed in

- Diffusion models / [Flow matching, time series and science](https://mlsanity.com/diffusion/flow-matching-time-series-and-science/)

## Builds on (most cited first, 25 of 25)

- [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)
- [A Style-Based Generator Architecture for Generative Adversarial Networks](https://mlsanity.com/paper/1812.04948/) (2018)
- [Classifier-Free Diffusion Guidance](https://mlsanity.com/paper/2207.12598/) (2022)
- [Flow Matching for Generative Modeling](https://mlsanity.com/paper/2210.02747/) (2022)
- [Generative Adversarial Networks](https://mlsanity.com/paper/2203.00667/) (2022)
- [Scaling Rectified Flow Transformers for High-Resolution Image Synthesis](https://mlsanity.com/paper/2403.03206/) (2024)
- [Generative Modeling by Estimating Gradients of the Data Distribution](https://mlsanity.com/paper/1907.05600/) (2019)
- [Auto-Encoding Variational Bayes](https://mlsanity.com/paper/1312.6114/) (2013)
- [Flow Straight and Fast: Learning to Generate and Transfer Data with Rectified Flow](https://mlsanity.com/paper/2209.03003/) (2022)
- [Prompt-to-Prompt Image Editing with Cross Attention Control](https://mlsanity.com/paper/2208.01626/) (2022)
- [FiLM: Visual Reasoning with a General Conditioning Layer](https://mlsanity.com/paper/1709.07871/) (2017)
- [Demystifying MMD GANs](https://mlsanity.com/paper/1801.01401/) (2018)
- [Stochastic Interpolants: A Unifying Framework for Flows and Diffusions](https://mlsanity.com/paper/2303.08797/) (2023)
- [FlowEdit: Inversion-Free Text-Based Editing Using Pre-Trained Flow Models](https://mlsanity.com/paper/2412.08629/) (2024)
- [One Transformer Fits All Distributions in Multi-Modal Diffusion at Scale](https://mlsanity.com/paper/2303.06555/) (2023)
- [Effectively Unbiased FID and Inception Score and where to find them](https://mlsanity.com/paper/1911.07023/) (2019)
- [Semantic Image Inversion and Editing using Rectified Stochastic Differential Equations](https://mlsanity.com/paper/2410.10792/) (2024)
- [OmniFlow: Any-to-Any Generation with Multi-Modal Rectified Flows](https://mlsanity.com/paper/2412.01169/) (2024)
- [FlowSDF: Flow Matching for Medical Image Segmentation Using Distance Transforms](https://mlsanity.com/paper/2405.18087/) (2024)
- [CellFlux: Simulating Cellular Morphology Changes via Flow Matching](https://mlsanity.com/paper/2502.09775/) (2025)
- [PhenDiff: Revealing Subtle Phenotypes with Diffusion Models in Real Images](https://mlsanity.com/paper/2312.08290/) (2023)
- [Progress and new challenges in image-based profiling](https://mlsanity.com/paper/2508.05800/) (2025)

## Abstract (arXiv)

Generative modeling has shown increasing promise for predicting cellular perturbation effects under chemical compound treatments. Existing approaches either model perturbation as a distribution-to-distribution mapping without explicit concentration handling, or treat concentration as a discrete class label, precluding continuous dose control. We introduce a joint flow matching approach that simultaneously models cell latents and drug concentration via a dual-timestep formulation, enabling dose-conditioned single-cell morphing through the invertibility of flow matching. The joint formulation induces a monotonic dose-response geometry in latent space and additionally supports concentration estimation from cell morphology. As proof of concept, we further demonstrate generalization to an unseen dose held out during training. Empirically, our method achieves competitive or improved per-concentration metrics on two compounds compared with representative baselines, while enabling capabilities structurally unavailable to discrete-class methods.