Lassi Paavolainen

Andrea Rubbi, Amir Akbarnejad, Mohammad Vali Sanian et al.

Robust generalization under distribution shift remains a key challenge for conditional generative modeling: conditional flow-based methods often fit the training conditions well but fail to extrapolate to unseen ones. We introduce SP-FM, a shortest-path flow-matching framework that improves out-of-distribution (OOD) generalization by conditioning both the base distribution and the flow field on the condition. Specifically, SP-FM learns a condition-dependent base distribution parameterized as a flexible, learnable mixture, together with a condition-dependent vector field trained via shortest-path flow matching. Conditioning the base allows the model to adapt its starting distribution across conditions, enabling smooth interpolation and more reliable extrapolation beyond the observed training range. We provide theoretical insights into the resulting conditional transport and show how mixture-conditioned bases enhance robustness under shift. Empirically, SP-FM is effective across heterogeneous domains, including predicting responses to unseen perturbations in single-cell transcriptomics and modeling treatment effects in high-content microscopy--based drug screening. Overall, SP-FM provides a simple yet effective plug-in strategy for improving conditional generative modeling and OOD generalization across diverse domains.

Vidit Agrawal, John Peters, Tyler N. Thompson et al.

Quantifying cell morphology using images and machine learning has proven to be a powerful tool to study the response of cells to treatments. However, models used to quantify cellular morphology are typically trained with a single microscopy imaging type. This results in specialized models that cannot be reused across biological studies because the technical specifications do not match (e.g., different number of channels), or because the target experimental conditions are out of distribution. Here, we present CHAMMI-75, an open access dataset of heterogeneous, multi-channel microscopy images from 75 diverse biological studies. We curated this resource from publicly available sources to investigate cellular morphology models that are channel-adaptive and can process any microscopy image type. Our experiments show that training with CHAMMI-75 can improve performance in multi-channel bioimaging tasks primarily because of its high diversity in microscopy modalities. This work paves the way to create the next generation of cellular morphology models for biological studies.

Mohammad Vali Sanian, Arshia Hemmat, Amirhossein Vahidi et al.

A scalable and robust 3D tissue transcriptomics profile can enable a holistic understanding of tissue organization and provide deeper insights into human biology and disease. Most predictive algorithms that infer ST directly from histology treat each section independently and ignore 3D structure, while existing 3D-aware approaches are not generative and do not scale well. We present Holographic Tissue Expression Inpainting and Analysis (HoloTea), a 3D-aware flow-matching framework that imputes spot-level gene expression from H&E while explicitly using information from adjacent sections. Our key idea is to retrieve morphologically corresponding spots on neighboring slides in a shared feature space and fuse this cross section context into a lightweight ControlNet, allowing conditioning to follow anatomical continuity. To better capture the count nature of the data, we introduce a 3D-consistent prior for flow matching that combines a learned zero-inflated negative binomial (ZINB) prior with a spatial-empirical prior constructed from neighboring sections. A global attention block introduces 3D H&E scaling linearly with the number of spots in the slide, enabling training and inference on large 3D ST datasets. Across three spatial transcriptomics datasets spanning different tissue types and resolutions, HoloTea consistently improves 3D expression accuracy and generalization compared to 2D and 3D baselines. We envision HoloTea advancing the creation of accurate 3D virtual tissues, ultimately accelerating biomarker discovery and deepening our understanding of disease.