An official website of the United States government
In many real-life image analysis applications, particularly in biomedical research domains, the objects of interest undergo multiple transformations that alter their visual properties while keeping the semantic content unchanged. Disentangling images into semantic content factors and transformations can provide significant benefits into many domain-specific image analysis tasks. To this end, we propose a generic unsupervised framework, Harmony, that simultaneously and explicitly disentangles semantic content from multiple parameterized transformations. Harmony leverages a simple cross-contrastive learning framework with multiple explicitly parameterized latent representations to disentangle content from transformations. To demonstrate the efficacy of Harmony, we apply it to disentangle image semantic content from several parameterized transformations (rotation, translation, scaling, and contrast). Harmony achieves significantly improved disentanglement over the baseline models on several image datasets of diverse domains. With such disentanglement, Harmony is demonstrated to incentivize bioimage analysis research by modeling structural heterogeneity of macromolecules from cryo-ET images and learning transformation-invariant representations of protein particles from single-particle cryo-EM images. Harmony also performs very well in disentangling content from 3D transformations and can perform coarse and fast alignment of 3D cryo-ET subtomograms. Therefore, Harmony is generalizable to many other imaging domains and can potentially be extended to domains beyond imaging as well.
more »
« less
This content will become publicly available on February 10, 2027
Learning Group Actions In Disentangled Latent Image Representations.
Modeling group actions on latent representations enables controllable transformations of high-dimensional image data. Prior works applying group-theoretic priors or modeling transformations typically operate in the high-dimensional data space, where group actions apply uniformly across the entire input, making it difficult to disentangle the subspace that varies under transformations. While latent-space methods offer greater flexibility, they still require manual partitioning of latent variables into equivariant and invariant subspaces, limiting the ability to robustly learn and operate group actions within the representation space. To address this, we introduce a novel end-to-end framework that for the first time learns group actions on latent image manifolds, automatically discovering transformation-relevant structures without manual intervention. Our method uses learnable binary masks with straight-through estimation to dynamically partition latent representations into transformation-sensitive and invariant components. We formulate this within a unified optimization framework that jointly learns latent disentanglement and group transformation mappings. The framework can be seamlessly integrated with any standard encoder-decoder architecture. We validate our approach on five 2D/3D image datasets, demonstrating its ability to automatically learn disentangled latent factors for group actions in diverse data, while downstream classification tasks confirm the effectiveness of the learned representations.
more »
« less
- Award ID(s):
- 2239977
- PAR ID:
- 10687774
- Publisher / Repository:
- IEEE/CVF
- Date Published:
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Hamilton-Jacobi (HJ) reachability is a rigorous mathematical framework that enables robots to simultaneously detect unsafe states and generate actions that prevent future failures. While in theory, HJ reachability can synthesize safe controllers for nonlinear systems and nonconvex constraints, in practice, it has been limited to hand-engineered collision avoidance constraints modeled via low-dimensional state-space representations and first-principles dynamics. In this work, our goal is to generalize safe robot controllers to prevent failures that are hard—if not impossible—to write down by hand, but can be intuitively identified from high-dimensional observations: for example, spilling the contents of a bag. We propose Latent Safety Filters, a latent-space generalization of HJ reachability that tractably operates directly on raw observation data (e.g., RGB images) to automatically computes safety-preserving actions without explicit recovery demonstrations by performing safety analysis in the latent embedding space of a generative world model. Our method leverages diverse robot observation-action data of varying quality (including successes, random exploration, and unsafe demonstrations) to learn a world model. Constraint specification is then transformed into a classification problem in the latent space of the learned world model. In simulation and hardware experiments, we compute an approximation of Latent Safety Filters to safeguard arbitrary policies (from imitation learned policies to direct teleoperation) from complex safety hazards, like preventing a Franka Research 3 manipulator from spilling the contents of a bag or toppling cluttered objects.more » « less
-
null (Ed.)Data transformations (e.g. rotations, reflections,and cropping) play an important role in self supervised learning. Typically, images are transformed into different views, and neural networks trained on tasks involving these views produce useful feature representations for downstream tasks, including anomaly detection. However, for anomaly detection beyond image data, it is often unclear which transformations to use. Here we present a simple end-to-end procedure for anomaly detection with learnable transformations. The key idea is to embed the transformed data into a semantic space such that the transformed data still resemble their untransformed form, while different transformations are easily distinguishable. Extensive experiments on time series show that our proposed method outperforms existing approaches in the one-vs.-rest setting and is competitive in the more challenging n-vs.-rest anomaly detection task. On medical and cyber-security tabular data, our method learns domain-specific transformations and detects anomalies more accurately than previous work.more » « less
-
null (Ed.)Abstract Motivation Single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) provides new opportunities to dissect epigenomic heterogeneity and elucidate transcriptional regulatory mechanisms. However, computational modeling of scATAC-seq data is challenging due to its high dimension, extreme sparsity, complex dependencies and high sensitivity to confounding factors from various sources. Results Here, we propose a new deep generative model framework, named SAILER, for analyzing scATAC-seq data. SAILER aims to learn a low-dimensional nonlinear latent representation of each cell that defines its intrinsic chromatin state, invariant to extrinsic confounding factors like read depth and batch effects. SAILER adopts the conventional encoder-decoder framework to learn the latent representation but imposes additional constraints to ensure the independence of the learned representations from the confounding factors. Experimental results on both simulated and real scATAC-seq datasets demonstrate that SAILER learns better and biologically more meaningful representations of cells than other methods. Its noise-free cell embeddings bring in significant benefits in downstream analyses: clustering and imputation based on SAILER result in 6.9% and 18.5% improvements over existing methods, respectively. Moreover, because no matrix factorization is involved, SAILER can easily scale to process millions of cells. We implemented SAILER into a software package, freely available to all for large-scale scATAC-seq data analysis. Availability and implementation The software is publicly available at https://github.com/uci-cbcl/SAILER. Supplementary information Supplementary data are available at Bioinformatics online.more » « less
-
Generative models have recently gained increasing attention in image generation and editing tasks. However, they often lack a direct connection to object geometry, which is crucial in sensitive domains such as computational anatomy, biology, and robotics. This paper presents a novel framework for Image Generation informed by Geodesic dynamics (IGG) in deformation spaces. Our IGG model comprises two key components: (i) an efficient autoencoder that explicitly learns the geodesic path of image transformations in the latent space; and (ii) a latent geodesic diffusion model that captures the distribution of latent representations of geodesic deformations conditioned on text instructions. By leveraging geodesic paths, our method ensures smooth, topology-preserving, and interpretable deformations, capturing complex variations in image structures while maintaining geometric consistency. We validate the proposed IGG on plant growth data and brain magnetic resonance imaging (MRI). Experimental results show that IGG outperforms the state-of-the-art image generation/editing models with superior performance in generating realistic, high-quality images with preserved object topology and reduced artifacts. Our code is publicly available at https://github.com/nellie689/IGG.more » « less
