Understanding how cellular morphology, gene expression, and spatial organization jointly shape tissue function is a central challenge in biology. Image-based spatial transcriptomics technologies now provide high-resolution measurements of cell images and gene expression profiles, but machine learning methods typically analyze these modalities in isolation or at limited resolution. We address the problem of learning unified, spatially aware representations that integrate cell morphology, gene expression, and spatial context across biological scales. This requires models that can operate at single-cell resolution, reason across spatial neighborhoods, and generalize to whole-slide tissue organization. Here, we introduce SPATIA, a multi-scale generative and predictive model for spatial transcriptomics. SPATIA learns cell-level embeddings by fusing image-derived morphological tokens and transcriptomic vector tokens using cross-attention and then aggregates them at niche and tissue levels using transformer modules to capture spatial dependencies. SPATIA incorporates token merging in its generative diffusion decoder to synthesize high-resolution cell images conditioned on gene expression. We assembled a multi-scale dataset consisting of 17 million cell-gene pairs, 1 million niche-gene pairs, and 10,000 tissue-gene pairs across 49 donors, 17 tissue types, and 12 disease states. We benchmark SPATIA against 13 existing models across 12 individual tasks, which span several categories including cell annotation, cell clustering, gene imputation, cross-modal prediction, and image generation. SPATIA achieves improved performance over all baselines and generates realistic cell morphologies that reflect transcriptomic perturbations.

ABSTRACT We propose a novel approach to cervical cell image classification for cervical cancer screening using the EV A-02 transformer model. We developed a four-step pipeline: fine-tuning EV A-02, feature extraction, selecting important features through multiple machine learning models, and training a new artificial neural network with optional loss weighting for improved generalization. With this design, our best model achieved an F1-score of 0.85227, outperforming the baseline EV A-02 model (0.84878). We also utilized Kernel SHAP analysis and identified key features correlating with cell morphology and staining characteristics, providing interpretable insights into the decision-making process of the fine-tuned model. Index T erms-- Cell Classification, Cervical Cancer, Explainable AI, Vision Transformers 1. INTRODUCTION Cervical cancer remains a significant global health challenge, ranking as the fourth most common cancer among women with over 600,000 new cases and 300,000 deaths annually [1].

Building a virtual cell capable of accurately simulating cellular behaviors in silico has long been a dream in computational biology. We introduce CellFlow, an image-generative model that simulates cellular morphology changes induced by chemical and genetic perturbations using flow matching. Unlike prior methods, CellFlow models distribution-wise transformations from unperturbed to perturbed cell states, effectively distinguishing actual perturbation effects from experimental artifacts such as batch effects -- a major challenge in biological data. Evaluated on chemical (BBBC021), genetic (RxRx1), and combined perturbation (JUMP) datasets, CellFlow generates biologically meaningful cell images that faithfully capture perturbation-specific morphological changes, achieving a 35% improvement in FID scores and a 12% increase in mode-of-action prediction accuracy over existing methods. Additionally, CellFlow enables continuous interpolation between cellular states, providing a potential tool for studying perturbation dynamics. These capabilities mark a significant step toward realizing virtual cell modeling for biomedical research.

The p16/Ki-67 dual staining method is a new approach for cervical cancer screening with high sensitivity and specificity. However, there are issues of mis-detection and inaccurate recognition when the YOLOv5s algorithm is directly applied to dual-stained cell images. This paper Proposes a novel cervical cancer dual-stained image recognition (DSIR-YOLO) model based on an YOLOv5. By fusing the Swin-Transformer module, GAM attention mechanism, multi-scale feature fusion, and EIoU loss function, the detection performance is significantly improved, with mAP@0.5 and mAP@0.5:0.95 reaching 92.6% and 70.5%, respectively. Compared with YOLOv5s in five-fold cross-validation, the accuracy, recall, mAP@0.5, and mAP@0.5:0.95 of the improved algorithm are increased by 2.3%, 4.1%, 4.3%, and 8.0%, respectively, with smaller variances and higher stability. Compared with other detection algorithms, DSIR-YOLO in this paper sacrifices some performance requirements to improve the network recognition effect. In addition, the influence of dataset quality on the detection results is studied. By controlling the sealing property of pixels, scale difference, unlabelled cells, and diagonal annotation, the model detection accuracy, recall, mAP@0.5, and mAP@0.5:0.95 are improved by 13.3%, 15.3%, 18.3%, and 30.5%, respectively.

Advanced image segmentation and processing tools present an opportunity to study cell processes and their dynamics. However, image analysis is often routine and time-consuming. Nowadays, alternative data-driven approaches using deep learning are potentially offering automatized, accurate, and fast image analysis. In this paper, we extend the applications of Cellpose, a state-of-the-art cell segmentation framework, with feature extraction capabilities to assess morphological characteristics. We also introduce a dataset of DAPI and FITC stained cells to which our new method is applied.

In hematology, computational models offer significant potential to improve diagnostic accuracy, streamline workflows, and reduce the tedious work of analyzing single cells in peripheral blood or bone marrow smears. However, clinical adoption of computational models has been hampered by the lack of generalization due to large batch effects, small dataset sizes, and poor performance in transfer learning from natural images. To address these challenges, we introduce DinoBloom, the first foundation model for single cell images in hematology, utilizing a tailored DINOv2 pipeline. Our model is built upon an extensive collection of 13 diverse, publicly available datasets of peripheral blood and bone marrow smears, the most substantial open-source cohort in hematology so far, comprising over 380,000 white blood cell images. To assess its generalization capability, we evaluate it on an external dataset with a challenging domain shift. We show that our model outperforms existing medical and non-medical vision models in (i) linear probing and k-nearest neighbor evaluations for cell-type classification on blood and bone marrow smears and (ii) weakly supervised multiple instance learning for acute myeloid leukemia subtyping by a large margin. A family of four DinoBloom models (small, base, large, and giant) can be adapted for a wide range of downstream applications, be a strong baseline for classification problems, and facilitate the assessment of batch effects in new datasets. All models are available at github.com/marrlab/DinoBloom.

Cell line authentication plays a crucial role in the biomedical field, ensuring researchers work with accurately identified cells. Supervised deep learning has made remarkable strides in cell line identification by studying cell morphological features through cell imaging. However, batch effects, a significant issue stemming from the different times at which data is generated, lead to substantial shifts in the underlying data distribution, thus complicating reliable differentiation between cell lines from distinct batch cultures. To address this challenge, we introduce CLANet, a pioneering framework for cross-batch cell line identification using brightfield images, specifically designed to tackle three distinct batch effects. We propose a cell cluster-level selection method to efficiently capture cell density variations, and a self-supervised learning strategy to manage image quality variations, thus producing reliable patch representations. Additionally, we adopt multiple instance learning(MIL) for effective aggregation of instance-level features for cell line identification. Our innovative time-series segment sampling module further enhances MIL's feature-learning capabilities, mitigating biases from varying incubation times across batches. We validate CLANet using data from 32 cell lines across 93 experimental batches from the AstraZeneca Global Cell Bank. Our results show that CLANet outperforms related approaches (e.g. domain adaptation, MIL), demonstrating its effectiveness in addressing batch effects in cell line identification.

An algorithm based on a deep probabilistic architecture referred to as a tree-structured sum-product network (t-SPN) is considered for cell classification. The t-SPN is constructed such that the unnormalized probability is represented as conditional probabilities of a subset of most similar cell classes. The constructed t-SPN architecture is learned by maximizing the margin, which is the difference in the conditional probability between the true and the most competitive false label. To enhance the generalization ability of the architecture, L2-regularization (REG) is considered along with the maximum margin (MM) criterion in the learning process. To highlight cell features, this paper investigates the effectiveness of two generic high-pass filters: ideal high-pass filtering and the Laplacian of Gaussian (LOG) filtering. On both HEp-2 and Feulgen benchmark datasets, the t-SPN architecture learned based on the max-margin criterion with regularization produced the highest accuracy rate compared to other state-of-the-art algorithms that include convolutional neural network (CNN) based algorithms. The ideal high-pass filter was more effective on the HEp-2 dataset, which is based on immunofluorescence staining, while the LOG was more effective on the Feulgen dataset, which is based on Feulgen staining.

One of the main obstacles standing in front of many machine learning tasks is the lack of labeled data. Labeling data might be exhausting and expensive. Thus, many times it is not reasonable to even try to solve a problem using machine learning methods due to lack of labels. To alleviate this problem, a field in machine learning has emerged, called Active Learning. Active Learning is a method in machine learning that provides a framework for prioritizing the unlabeled data samples based on the labeled data that a model already saw.

Due to the ever-growing demands for electronic chips in different sectors the semiconductor companies have been mandated to offshore their manufacturing processes. This unwanted matter has made security and trustworthiness of their fabricated chips concerning and caused creation of hardware attacks. In this condition, different entities in the semiconductor supply chain can act maliciously and execute an attack on the design computing layers, from devices to systems. Our attack is a hardware Trojan that is inserted during mask generation/fabrication in an untrusted foundry. The Trojan leaves a footprint in the fabricated through addition, deletion, or change of design cells. In order to tackle this problem, we propose Explainable Vision System for Hardware Testing and Assurance (EVHA) in this work that can detect the smallest possible change to a design in a low-cost, accurate, and fast manner. The inputs to this system are Scanning Electron Microscopy (SEM) images acquired from the Integrated Circuits (ICs) under examination. The system output is determination of IC status in terms of having any defect and/or hardware Trojan through addition, deletion, or change in the design cells at the cell-level. This article provides an overview on the design, development, implementation, and analysis of our defense system.