arXiv subjects

Shahira Abousamra

Publications and source records attributed to Shahira Abousamra.

At least 19 recordsLinked to original sources

arXiv2026

RankByGene: Gene-Guided Histopathology Representation Learning Through Cross-Modal Ranking Consistency

Spatial transcriptomics (ST) provides essential spatial context by mapping gene expression within tissue, enabling detailed study of cellular heterogeneity and tissue organization. However, aligning ST data with histology images poses challenges due to inherent spatial distortions and modality-specific variations. Existing methods largely rely on direct alignment, which often fails to capture complex cross-modal relationships. To address these limitations, we propose a novel framework that aligns gene and image features using a ranking-based alignment loss, preserving relative similarity across modalities and enabling robust multi-scale alignment. To further enhance the alignment's stability, we employ self-supervised knowledge distillation with a teacher-student network architecture, which serves as an intra-modal stability regularizer that prevents image-representation drift during cross-modal alignment. Extensive experiments on seven public datasets that encompass gene expression prediction, slide-level classification, and survival analysis demonstrate the efficacy of our method, showing improved alignment and predictive performance over existing methods. Code is available at https://github.com/winston52/RankByGene.

eess.IV↗

arXiv2026

MATCH: Multi-faceted Adaptive Topo-Consistency for Semi-Supervised Histopathology Segmentation

In semi-supervised segmentation, capturing meaningful semantic structures from unlabeled data is essential. This is particularly challenging in histopathology image analysis, where objects are densely distributed. To address this issue, we propose a semi-supervised segmentation framework designed to robustly identify and preserve relevant topological features. Our method leverages multiple perturbed predictions obtained through stochastic dropouts and temporal training snapshots, enforcing topological consistency across these varied outputs. This consistency mechanism helps distinguish biologically meaningful structures from transient and noisy artifacts. A key challenge in this process is to accurately match the corresponding topological features across the predictions in the absence of ground truth. To overcome this, we introduce a novel matching strategy that integrates spatial overlap with global structural alignment, minimizing discrepancies among predictions. Extensive experiments demonstrate that our approach effectively reduces topological errors, resulting in more robust and accurate segmentations essential for reliable downstream analysis. Code is available at https://github.com/Melon-Xu/MATCH.

cs.CV↗

arXiv2026

Act Like a Pathologist: Tissue-Aware Whole Slide Image Reasoning

Computational pathology has advanced rapidly in recent years, driven by domain-specific image encoders and growing interest in using vision-language models to answer natural-language questions about diseases. Yet, the core problem behind pathology question-answering remains unsolved, considering that a gigapixel slide contains far more information than necessary for a given question. Pathologists naturally navigate tissue and morphology complexity by scanning broadly, and zooming in selectively according to the clinical questions. Current models, in contrast, rely on uniform patch sampling or broad attention maps, often attending equally to irrelevant regions while overlooking key visual evidence. In this work, we try to bring models closer to how humans actually examine slides. We propose a question-guided, tissue-aware, and coarse-to-fine retrieval framework, HistoSelect, that consists of two key components: a group sampler that identifies question-relevant tissue regions, followed by a patch selector that retrieves the most informative patches within those regions. By selecting only the most informative patches, our method becomes significantly more efficient: reducing visual token usage by 70% on average, while improving accuracy across three pathology QA tasks. Evaluated on 356,000 question-answer pairs, our approach outperforms existing methods and produces answers grounded in interpretable, pathologist-consistent regions. Our results suggest that bringing human-like search and attention patterns into WSI reasoning is a promising direction for building practical and reliable pathology VLMs. Code is available at https://github.com/winston52/HistoSelect.

cs.CV↗

arXiv2026

Topo-R1: Detecting Topological Anomalies via Vision-Language Models

Topology is critical in tubular structures such as blood vessels, nerve fibers, and road networks, where connectivity and loop structure govern downstream functional analysis. Vision-Language Models (VLMs) are promising candidates for understanding such structures, given their reasoning and grounding capabilities. To probe their topological perception, we systematically evaluate leading closed- and open-source VLMs on localizing and classifying four canonical topological anomalies (broken/spurious connections, missing/extra branches) in tubular-network segmentation masks. They perform nearly at random, indicating that topology-aware perception is largely absent from current general-purpose VLMs. As no existing resource pairs segmentation masks with localized anomaly annotations, we build an automated, multi-domain data-curation pipeline that synthesizes diverse topological perturbations with verifiable Betti-number annotations across graduated difficulty levels, yielding the first systematic benchmark with a large-scale training set and held-out in-distribution (ID) and out-of-distribution (OOD) test suites. Building on this benchmark, we introduce Topo-R1, centered on a topology-aware composite reward that jointly scores localization, classification, and skeleton-level structural fidelity. Supervised fine-tuning cold-starts schema-compliant outputs, and Group Relative Policy Optimization (GRPO) then optimizes the policy against this reward, steering predictions toward topologically meaningful structure rather than superficial pixel overlap. Extensive experiments show that Topo-R1 substantially outperforms general-purpose VLMs and matches or exceeds supervised baselines across ID, OOD, and real-segmentation-output protocols, establishing a strong foundation for VLM-based topological understanding of structured visual data.

cs.CV↗

arXiv2025

TopoCellGen: Generating Histopathology Cell Topology with a Diffusion Model

Accurately modeling multi-class cell topology is crucial in digital pathology, as it provides critical insights into tissue structure and pathology. The synthetic generation of cell topology enables realistic simulations of complex tissue environments, enhances downstream tasks by augmenting training data, aligns more closely with pathologists' domain knowledge, and offers new opportunities for controlling and generalizing the tumor microenvironment. In this paper, we propose a novel approach that integrates topological constraints into a diffusion model to improve the generation of realistic, contextually accurate cell topologies. Our method refines the simulation of cell distributions and interactions, increasing the precision and interpretability of results in downstream tasks such as cell detection and classification. To assess the topological fidelity of generated layouts, we introduce a new metric, Topological Frechet Distance (TopoFD), which overcomes the limitations of traditional metrics like FID in evaluating topological structure. Experimental results demonstrate the effectiveness of our approach in generating multi-class cell layouts that capture intricate topological relationships. Code is available at https://github.com/Melon-Xu/TopoCellGen.

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arXiv2024

Hard Negative Sample Mining for Whole Slide Image Classification

Weakly supervised whole slide image (WSI) classification is challenging due to the lack of patch-level labels and high computational costs. State-of-the-art methods use self-supervised patch-wise feature representations for multiple instance learning (MIL). Recently, methods have been proposed to fine-tune the feature representation on the downstream task using pseudo labeling, but mostly focusing on selecting high-quality positive patches. In this paper, we propose to mine hard negative samples during fine-tuning. This allows us to obtain better feature representations and reduce the training cost. Furthermore, we propose a novel patch-wise ranking loss in MIL to better exploit these hard negative samples. Experiments on two public datasets demonstrate the efficacy of these proposed ideas. Our codes are available at https://github.com/winston52/HNM-WSI

cs.CV↗

arXiv2024

Semi-Supervised Contrastive VAE for Disentanglement of Digital Pathology Images

Despite the strong prediction power of deep learning models, their interpretability remains an important concern. Disentanglement models increase interpretability by decomposing the latent space into interpretable subspaces. In this paper, we propose the first disentanglement method for pathology images. We focus on the task of detecting tumor-infiltrating lymphocytes (TIL). We propose different ideas including cascading disentanglement, novel architecture, and reconstruction branches. We achieve superior performance on complex pathology images, thus improving the interpretability and even generalization power of TIL detection deep learning models. Our codes are available at https://github.com/Shauqi/SS-cVAE.

eess.IV↗

arXiv2024

Spatial Diffusion for Cell Layout Generation

Generative models, such as GANs and diffusion models, have been used to augment training sets and boost performances in different tasks. We focus on generative models for cell detection instead, i.e., locating and classifying cells in given pathology images. One important information that has been largely overlooked is the spatial patterns of the cells. In this paper, we propose a spatial-pattern-guided generative model for cell layout generation. Specifically, a novel diffusion model guided by spatial features and generates realistic cell layouts has been proposed. We explore different density models as spatial features for the diffusion model. In downstream tasks, we show that the generated cell layouts can be used to guide the generation of high-quality pathology images. Augmenting with these images can significantly boost the performance of SOTA cell detection methods. The code is available at https://github.com/superlc1995/Diffusion-cell.

cs.CV↗

arXiv2024

Semi-supervised Segmentation of Histopathology Images with Noise-Aware Topological Consistency

In digital pathology, segmenting densely distributed objects like glands and nuclei is crucial for downstream analysis. Since detailed pixel-wise annotations are very time-consuming, we need semi-supervised segmentation methods that can learn from unlabeled images. Existing semi-supervised methods are often prone to topological errors, e.g., missing or incorrectly merged/separated glands or nuclei. To address this issue, we propose TopoSemiSeg, the first semi-supervised method that learns the topological representation from unlabeled histopathology images. The major challenge is for unlabeled images; we only have predictions carrying noisy topology. To this end, we introduce a noise-aware topological consistency loss to align the representations of a teacher and a student model. By decomposing the topology of the prediction into signal topology and noisy topology, we ensure that the models learn the true topological signals and become robust to noise. Extensive experiments on public histopathology image datasets show the superiority of our method, especially on topology-aware evaluation metrics. Code is available at https://github.com/Melon-Xu/TopoSemiSeg.

eess.IV↗

arXiv2023

Calibrating Uncertainty for Semi-Supervised Crowd Counting

Semi-supervised crowd counting is an important yet challenging task. A popular approach is to iteratively generate pseudo-labels for unlabeled data and add them to the training set. The key is to use uncertainty to select reliable pseudo-labels. In this paper, we propose a novel method to calibrate model uncertainty for crowd counting. Our method takes a supervised uncertainty estimation strategy to train the model through a surrogate function. This ensures the uncertainty is well controlled throughout the training. We propose a matching-based patch-wise surrogate function to better approximate uncertainty for crowd counting tasks. The proposed method pays a sufficient amount of attention to details, while maintaining a proper granularity. Altogether our method is able to generate reliable uncertainty estimation, high quality pseudolabels, and achieve state-of-the-art performance in semisupervised crowd counting.

cs.CV↗

arXiv2023

GaNDLF: A Generally Nuanced Deep Learning Framework for Scalable End-to-End Clinical Workflows in Medical Imaging

Deep Learning (DL) has the potential to optimize machine learning in both the scientific and clinical communities. However, greater expertise is required to develop DL algorithms, and the variability of implementations hinders their reproducibility, translation, and deployment. Here we present the community-driven Generally Nuanced Deep Learning Framework (GaNDLF), with the goal of lowering these barriers. GaNDLF makes the mechanism of DL development, training, and inference more stable, reproducible, interpretable, and scalable, without requiring an extensive technical background. GaNDLF aims to provide an end-to-end solution for all DL-related tasks in computational precision medicine. We demonstrate the ability of GaNDLF to analyze both radiology and histology images, with built-in support for k-fold cross-validation, data augmentation, multiple modalities and output classes. Our quantitative performance evaluation on numerous use cases, anatomies, and computational tasks supports GaNDLF as a robust application framework for deployment in clinical workflows.

cs.LG↗

arXiv2023

Topology-Guided Multi-Class Cell Context Generation for Digital Pathology

In digital pathology, the spatial context of cells is important for cell classification, cancer diagnosis and prognosis. To model such complex cell context, however, is challenging. Cells form different mixtures, lineages, clusters and holes. To model such structural patterns in a learnable fashion, we introduce several mathematical tools from spatial statistics and topological data analysis. We incorporate such structural descriptors into a deep generative model as both conditional inputs and a differentiable loss. This way, we are able to generate high quality multi-class cell layouts for the first time. We show that the topology-rich cell layouts can be used for data augmentation and improve the performance of downstream tasks such as cell classification.

eess.IV↗

arXiv2022

Evaluating histopathology transfer learning with ChampKit

Histopathology remains the gold standard for diagnosis of various cancers. Recent advances in computer vision, specifically deep learning, have facilitated the analysis of histopathology images for various tasks, including immune cell detection and microsatellite instability classification. The state-of-the-art for each task often employs base architectures that have been pretrained for image classification on ImageNet. The standard approach to develop classifiers in histopathology tends to focus narrowly on optimizing models for a single task, not considering the aspects of modeling innovations that improve generalization across tasks. Here we present ChampKit (Comprehensive Histopathology Assessment of Model Predictions toolKit): an extensible, fully reproducible benchmarking toolkit that consists of a broad collection of patch-level image classification tasks across different cancers. ChampKit enables a way to systematically document the performance impact of proposed improvements in models and methodology. ChampKit source code and data are freely accessible at https://github.com/kaczmarj/champkit .

q-bio.QM↗

arXiv2022

Multi-Class Cell Detection Using Spatial Context Representation

In digital pathology, both detection and classification of cells are important for automatic diagnostic and prognostic tasks. Classifying cells into subtypes, such as tumor cells, lymphocytes or stromal cells is particularly challenging. Existing methods focus on morphological appearance of individual cells, whereas in practice pathologists often infer cell classes through their spatial context. In this paper, we propose a novel method for both detection and classification that explicitly incorporates spatial contextual information. We use the spatial statistical function to describe local density in both a multi-class and a multi-scale manner. Through representation learning and deep clustering techniques, we learn advanced cell representation with both appearance and spatial context. On various benchmarks, our method achieves better performance than state-of-the-arts, especially on the classification task. We also create a new dataset for multi-class cell detection and classification in breast cancer and we make both our code and data publicly available.

cs.CV↗

arXiv2022

A Novel Framework for Characterization of Tumor-Immune Spatial Relationships in Tumor Microenvironment

Understanding the impact of tumor biology on the composition of nearby cells often requires characterizing the impact of biologically distinct tumor regions. Biomarkers have been developed to label biologically distinct tumor regions, but challenges arise because of differences in the spatial extent and distribution of differentially labeled regions. In this work, we present a framework for systematically investigating the impact of distinct tumor regions on cells near the tumor borders, accounting their cross spatial distributions. We apply the framework to multiplex immunohistochemistry (mIHC) studies of pancreatic cancer and show its efficacy in demonstrating how biologically different tumor regions impact the immune response in the tumor microenvironment. Furthermore, we show that the proposed framework can be extended to largescale whole slide image analysis.

q-bio.QM↗

arXiv2022

Federated Learning for the Classification of Tumor Infiltrating Lymphocytes

We evaluate the performance of federated learning (FL) in developing deep learning models for analysis of digitized tissue sections. A classification application was considered as the example use case, on quantifiying the distribution of tumor infiltrating lymphocytes within whole slide images (WSIs). A deep learning classification model was trained using 50*50 square micron patches extracted from the WSIs. We simulated a FL environment in which a dataset, generated from WSIs of cancer from numerous anatomical sites available by The Cancer Genome Atlas repository, is partitioned in 8 different nodes. Our results show that the model trained with the federated training approach achieves similar performance, both quantitatively and qualitatively, to that of a model trained with all the training data pooled at a centralized location. Our study shows that FL has tremendous potential for enabling development of more robust and accurate models for histopathology image analysis without having to collect large and diverse training data at a single location.

eess.IV↗

arXiv2020

Localization in the Crowd with Topological Constraints

We address the problem of crowd localization, i.e., the prediction of dots corresponding to people in a crowded scene. Due to various challenges, a localization method is prone to spatial semantic errors, i.e., predicting multiple dots within a same person or collapsing multiple dots in a cluttered region. We propose a topological approach targeting these semantic errors. We introduce a topological constraint that teaches the model to reason about the spatial arrangement of dots. To enforce this constraint, we define a persistence loss based on the theory of persistent homology. The loss compares the topographic landscape of the likelihood map and the topology of the ground truth. Topological reasoning improves the quality of the localization algorithm especially near cluttered regions. On multiple public benchmarks, our method outperforms previous localization methods. Additionally, we demonstrate the potential of our method in improving the performance in the crowd counting task.

cs.CV↗

arXiv2020

Utilizing Automated Breast Cancer Detection to Identify Spatial Distributions of Tumor Infiltrating Lymphocytes in Invasive Breast Cancer

Quantitative assessment of Tumor-TIL spatial relationships is increasingly important in both basic science and clinical aspects of breast cancer research. We have developed and evaluated convolutional neural network (CNN) analysis pipelines to generate combined maps of cancer regions and tumor infiltrating lymphocytes (TILs) in routine diagnostic breast cancer whole slide tissue images (WSIs). We produce interactive whole slide maps that provide 1) insight about the structural patterns and spatial distribution of lymphocytic infiltrates and 2) facilitate improved quantification of TILs. We evaluated both tumor and TIL analyses using three CNN networks - Resnet-34, VGG16 and Inception v4, and demonstrated that the results compared favorably to those obtained by what believe are the best published methods. We have produced open-source tools and generated a public dataset consisting of tumor/TIL maps for 1,015 TCGA breast cancer images. We also present a customized web-based interface that enables easy visualization and interactive exploration of high-resolution combined Tumor-TIL maps for 1,015TCGA invasive breast cancer cases that can be downloaded for further downstream analyses.

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