arXiv subjects

Amirhossein Kardoost

Publications and source records attributed to Amirhossein Kardoost.

6 recordsLinked to original sources

arXiv2026

3D Masked Autoencoders are Robust Learners of Volumetric and Multimodal Cellular Representations for Microscopy

Self-supervised learning in fluorescence microscopy often relies on 2D projections, despite the inherently three-dimensional nature of cells. We present a systematic comparison of 2D and 3D masked autoencoders (MAE-2D vs. MAE-3D) on volumetric microscopy data. Under matched architectures and training protocols, MAE-3D consistently outperforms 2D max-projection and slice-based variants on downstream single-cell tasks. We further align visual representations with a pretrained protein language model (ESM2) and show that cross-modal supervision yields larger gains for volumetric models. Channel cross-attention and frequency-domain regularization are critical for leveraging 3D spatial context. On protein--protein interaction prediction, our best model achieves a ROC--AUC of 0.86, while on protein localization it reaches an AUC$_{\text{micro}}$ of 0.95 and an F1$_{\text{micro}}$ of 0.74, demonstrating competitive performance on both tasks. Overall, our findings highlight the potential of volumetric modeling and multimodal alignment for representation learning in single-cell microscopy.

cs.LG↗

arXiv2026

HASSL: Hierarchy-Aware Self-Supervised Learning Framework for Single Cell Microscopy

Hierarchical structure is common in image data, where fine-grained clusters often merge into larger, coarser semantic groups. In biological cell images, current self-supervised learning models often suppress this hierarchy, as coarse factors such as imaging modality can obscure finer morphological attributes in the latent space. We propose a hierarchy-aware self-supervised training framework to address this problem. Our method combines two components: a distillation framework with a segmentation teacher to improve morphological awareness in the latent space, and a hierarchy-aware contrastive loss based on HDBSCAN to improve decision boundaries between closely related subtypes at different hierarchical levels. Together, these components reduce the tendency of self-supervised learning to overemphasize coarse factors and instead align embeddings with semantic and morphological cues. This yields biologically meaningful sub-clusters driven by fine morphological detail. We train and evaluate our method on a curated corpus of 2.3 million single cells aggregated from 20 microscopy datasets, both labeled and unlabeled, covering 208 cell classes. Our method improves over baseline and counterpart methods, increasing average top-K accuracy by 2.8%, top-9 retrieval on the dataset with the deepest hierarchy by 6.3%, and downstream F1-score for biologically relevant drug classification from perturbed cell morphology by 7.8%.

cs.CV↗

arXiv2021

Optimizing Edge Detection for Image Segmentation with Multicut Penalties

The Minimum Cost Multicut Problem (MP) is a popular way for obtaining a graph decomposition by optimizing binary edge labels over edge costs. While the formulation of a MP from independently estimated costs per edge is highly flexible and intuitive, solving the MP is NP-hard and time-expensive. As a remedy, recent work proposed to predict edge probabilities with awareness to potential conflicts by incorporating cycle constraints in the prediction process. We argue that such formulation, while providing a first step towards end-to-end learnable edge weights, is suboptimal, since it is built upon a loose relaxation of the MP. We therefore propose an adaptive CRF that allows to progressively consider more violated constraints and, in consequence, to issue solutions with higher validity. Experiments on the BSDS500 benchmark for natural image segmentation as well as on electron microscopic recordings show that our approach yields more precise edge detection and image segmentation.

cs.CV↗

arXiv2021

Uncertainty in Minimum Cost Multicuts for Image and Motion Segmentation

The minimum cost lifted multicut approach has proven practically good performance in a wide range of applications such as image decomposition, mesh segmentation, multiple object tracking, and motion segmentation. It addresses such problems in a graph-based model, where real-valued costs are assigned to the edges between entities such that the minimum cut decomposes the graph into an optimal number of segments. Driven by a probabilistic formulation of minimum cost multicuts, we provide a measure for the uncertainties of the decisions made during the optimization. We argue that access to such uncertainties is crucial for many practical applications and conduct an evaluation by means of sparsifications on three different, widely used datasets in the context of image decomposition (BSDS-500) and motion segmentation (DAVIS2016 and FBMS59) in terms of variation of information (VI) and Rand index (RI).

cs.CV↗

arXiv2020

Self-supervised Sparse to Dense Motion Segmentation

Observable motion in videos can give rise to the definition of objects moving with respect to the scene. The task of segmenting such moving objects is referred to as motion segmentation and is usually tackled either by aggregating motion information in long, sparse point trajectories, or by directly producing per frame dense segmentations relying on large amounts of training data. In this paper, we propose a self supervised method to learn the densification of sparse motion segmentations from single video frames. While previous approaches towards motion segmentation build upon pre-training on large surrogate datasets and use dense motion information as an essential cue for the pixelwise segmentation, our model does not require pre-training and operates at test time on single frames. It can be trained in a sequence specific way to produce high quality dense segmentations from sparse and noisy input. We evaluate our method on the well-known motion segmentation datasets FBMS59 and DAVIS16.

cs.CV↗

arXiv2020

Object Segmentation Tracking from Generic Video Cues

We propose a light-weight variational framework for online tracking of object segmentations in videos based on optical flow and image boundaries. While high-end computer vision methods on this task rely on sequence specific training of dedicated CNN architectures, we show the potential of a variational model, based on generic video information from motion and color. Such cues are usually required for tasks such as robot navigation or grasp estimation. We leverage them directly for video object segmentation and thus provide accurate segmentations at potentially very low extra cost. Our simple method can provide competitive results compared to the costly CNN-based methods with parameter tuning. Furthermore, we show that our approach can be combined with state-of-the-art CNN-based segmentations in order to improve over their respective results. We evaluate our method on the datasets DAVIS 16,17 and SegTrack v2.

cs.CV↗