Rao Muhammad Umer

Muhammed Furkan Dasdelen, Fatih Ozlugedik, Ilaria Looser et al.

Multimodal alignment of histopathology encoders with transcriptomic and genomic data has been shown to significantly improve performance in downstream diagnostic tasks. Hematological cytology is unique in that visual single-cell evaluation is often paired with cytogenetics and molecular genetics for blood cancer diagnosis. In this study, we present a framework to align single white blood cell images with chromosomal aberrations (karyotype) and somatic mutations from targeted gene panels. Our training strategy follows a two-stage approach: (i) self-supervised, vision-only pretraining of a transformer aggregator using an iBOT head on a cohort of over 1500 patients, and (ii) genetic alignment via supervised contrastive loss on acute myeloid leukemia patients. Our genetically aligned patient encoder improves hematological diagnostic tasks, outperforming slide-level histopathology foundation models. Additionally, the model provides off-the-shelf retrieval capabilities for diseases and genetic alterations. Incorporating genetic data into patient encoders increases the quality of patient representations, providing a framework that aligns with clinical diagnostic workflows and paves the way for future multimodal hematology-specific AI. The code and model weights are available at https://github.com/marrlab/GenBloom.

Hussain Ahmad Madni, Rao Muhammad Umer, Gian Luca Foresti

Federated Learning (FL) is an evolving machine learning method in which multiple clients participate in collaborative learning without sharing their data with each other and the central server. In real-world applications such as hospitals and industries, FL counters the challenges of data heterogeneity and model heterogeneity as an inevitable part of the collaborative training. More specifically, different organizations, such as hospitals, have their own private data and customized models for local training. To the best of our knowledge, the existing methods do not effectively address both problems of model heterogeneity and data heterogeneity in FL. In this paper, we exploit the data and model heterogeneity simultaneously, and propose a method, MDH-FL (Exploiting Model and Data Heterogeneity in FL) to solve such problems to enhance the efficiency of the global model in FL. We use knowledge distillation and a symmetric loss to minimize the heterogeneity and its impact on the model performance. Knowledge distillation is used to solve the problem of model heterogeneity, and symmetric loss tackles with the data and label heterogeneity. We evaluate our method on the medical datasets to conform the real-world scenario of hospitals, and compare with the existing methods. The experimental results demonstrate the superiority of the proposed approach over the other existing methods.

Rao Muhammad Umer, Armin Gruber, Sayedali Shetab Boushehri et al.

Accurate morphological classification of white blood cells (WBCs) is an important step in the diagnosis of leukemia, a disease in which nonfunctional blast cells accumulate in the bone marrow. Recently, deep convolutional neural networks (CNNs) have been successfully used to classify leukocytes by training them on single-cell images from a specific domain. Most CNN models assume that the distributions of the training and test data are similar, i.e., the data are independently and identically distributed. Therefore, they are not robust to different staining procedures, magnifications, resolutions, scanners, or imaging protocols, as well as variations in clinical centers or patient cohorts. In addition, domain-specific data imbalances affect the generalization performance of classifiers. Here, we train a robust CNN for WBC classification by addressing cross-domain data imbalance and domain shifts. To this end, we use two loss functions and demonstrate their effectiveness in out-of-distribution (OOD) generalization. Our approach achieves the best F1 macro score compared to other existing methods and is able to consider rare cell types. This is the first demonstration of imbalanced domain generalization in hematological cytomorphology and paves the way for robust single cell classification methods for the application in laboratories and clinics.

Rao Muhammad Umer, Christian Micheloni

The current existing deep image super-resolution methods usually assume that a Low Resolution (LR) image is bicubicly downscaled of a High Resolution (HR) image. However, such an ideal bicubic downsampling process is different from the real LR degradations, which usually come from complicated combinations of different degradation processes, such as camera blur, sensor noise, sharpening artifacts, JPEG compression, and further image editing, and several times image transmission over the internet and unpredictable noises. It leads to the highly ill-posed nature of the inverse upscaling problem. To address these issues, we propose a GAN-based SR approach with learnable adaptive sinusoidal nonlinearities incorporated in LR and SR models by directly learn degradation distributions and then synthesize paired LR/HR training data to train the generalized SR model to real image degradations. We demonstrate the effectiveness of our proposed approach in quantitative and qualitative experiments.

Jan Carreras Boada, Rao Muhammad Umer, Carsten Marr

Biomedical datasets are often constrained by stringent privacy requirements and frequently suffer from severe class imbalance. These two aspects hinder the development of accurate machine learning models. While generative AI offers a promising solution, producing synthetic images of sufficient quality for training robust classifiers remains challenging. This work addresses the classification of individual white blood cells, a critical task in diagnosing hematological malignancies such as acute myeloid leukemia (AML). We introduce CytoDiff, a stable diffusion model fine-tuned with LoRA weights and guided by few-shot samples that generates high-fidelity synthetic white blood cell images. Our approach demonstrates substantial improvements in classifier performance when training data is limited. Using a small, highly imbalanced real dataset, the addition of 5,000 synthetic images per class improved ResNet classifier accuracy from 27\% to 78\% (+51\%). Similarly, CLIP-based classification accuracy increased from 62\% to 77\% (+15\%). These results establish synthetic image generation as a valuable tool for biomedical machine learning, enhancing data coverage and facilitating secure data sharing while preserving patient privacy. Paper code is publicly available at https://github.com/JanCarreras24/CytoDiff.

Xudong Sun, Carla Feistner, Alexej Gossmann et al.

Poor generalization performance caused by distribution shifts in unseen domains often hinders the trustworthy deployment of deep neural networks. Many domain generalization techniques address this problem by adding a domain invariant regularization loss terms during training. However, there is a lack of modular software that allows users to combine the advantages of different methods with minimal effort for reproducibility. DomainLab is a modular Python package for training user specified neural networks with composable regularization loss terms. Its decoupled design allows the separation of neural networks from regularization loss construction. Hierarchical combinations of neural networks, different domain generalization methods, and associated hyperparameters, can all be specified together with other experimental setup in a single configuration file. Hierarchical combinations of neural networks, different domain generalization methods, and associated hyperparameters, can all be specified together with other experimental setup in a single configuration file. In addition, DomainLab offers powerful benchmarking functionality to evaluate the generalization performance of neural networks in out-of-distribution data. The package supports running the specified benchmark on an HPC cluster or on a standalone machine. The package is well tested with over 95 percent coverage and well documented. From the user perspective, it is closed to modification but open to extension. The package is under the MIT license, and its source code, tutorial and documentation can be found at https://github.com/marrlab/DomainLab.

Rao Muhammad Umer, Daniel Sens, Jonathan Noll et al.

Timely and accurate lymphoma diagnosis is essential for guiding cancer treatment. Standard diagnostic practice combines hematoxylin and eosin (HE)-stained whole slide images with immunohistochemistry, flow cytometry, and molecular genetic tests to determine lymphoma subtypes, a process requiring costly equipment, skilled personnel, and causing treatment delays. Deep learning methods could assist pathologists by extracting diagnostic information from routinely available HE-stained slides, yet comprehensive benchmarks for lymphoma subtyping on multicenter data are lacking. In this work, we present the first multicenter lymphoma benchmarking dataset covering four common lymphoma subtypes and healthy control tissue. We systematically evaluate five publicly available pathology foundation models (H-optimus-1, H0-mini, Virchow2, UNI2, Titan) combined with attention-based (AB-MIL) and transformer-based (TransMIL) multiple instance learning aggregators across three magnifications (10x, 20x, 40x). On in-distribution test sets, models achieve multiclass balanced accuracies exceeding 80% across all magnifications, with all foundation models performing similarly and both aggregation methods showing comparable results. The magnification study reveals that 40x resolution is sufficient, with no performance gains from higher resolutions or cross-magnification aggregation. However, on out-of-distribution test sets, performance drops substantially to around 60%, highlighting significant generalization challenges. To advance the field, larger multicenter studies covering additional rare lymphoma subtypes are needed. We provide an automated benchmarking pipeline to facilitate such future research.

Christian Grashei, Christian Brechenmacher, Rao Muhammad Umer et al.

Pathology foundation models (FMs) have driven significant progress in computational pathology. However, these high-performing models can easily exceed a billion parameters and produce high-dimensional embeddings, thus limiting their applicability for research or clinical use when computing resources are tight. Here, we introduce Pathryoshka, a multi-teacher distillation framework inspired by RADIO distillation and Matryoshka Representation Learning to reduce pathology FM sizes while allowing for adaptable embedding dimensions. We evaluate our framework with a distilled model on ten public pathology benchmarks with varying downstream tasks. Compared to its much larger teachers, Pathryoshka reduces the model size by 86-92% at on-par performance. It outperforms state-of-the-art single-teacher distillation models of comparable size by a median margin of 7.0 in accuracy. By enabling efficient local deployment without sacrificing accuracy or representational richness, Pathryoshka democratizes access to state-of-the-art pathology FMs for the broader research and clinical community.

Rao Muhammad Umer, Christian Micheloni

Modern digital cameras and smartphones mostly rely on image signal processing (ISP) pipelines to produce realistic colored RGB images. However, compared to DSLR cameras, low-quality images are usually obtained in many portable mobile devices with compact camera sensors due to their physical limitations. The low-quality images have multiple degradations i.e., sub-pixel shift due to camera motion, mosaick patterns due to camera color filter array, low-resolution due to smaller camera sensors, and the rest information are corrupted by the noise. Such degradations limit the performance of current Single Image Super-resolution (SISR) methods in recovering high-resolution (HR) image details from a single low-resolution (LR) image. In this work, we propose a Raw Burst Super-Resolution Iterative Convolutional Neural Network (RBSRICNN) that follows the burst photography pipeline as a whole by a forward (physical) model. The proposed Burst SR scheme solves the problem with classical image regularization, convex optimization, and deep learning techniques, compared to existing black-box data-driven methods. The proposed network produces the final output by an iterative refinement of the intermediate SR estimates. We demonstrate the effectiveness of our proposed approach in quantitative and qualitative experiments that generalize robustly to real LR burst inputs with onl synthetic burst data available for training.

Rao Muhammad Umer, Asad Munir, Christian Micheloni

Recently, most of state-of-the-art single image super-resolution (SISR) methods have attained impressive performance by using deep convolutional neural networks (DCNNs). The existing SR methods have limited performance due to a fixed degradation settings, i.e. usually a bicubic downscaling of low-resolution (LR) image. However, in real-world settings, the LR degradation process is unknown which can be bicubic LR, bilinear LR, nearest-neighbor LR, or real LR. Therefore, most SR methods are ineffective and inefficient in handling more than one degradation settings within a single network. To handle the multiple degradation, i.e. refers to multi-domain image super-resolution, we propose a deep Super-Resolution Residual StarGAN (SR2*GAN), a novel and scalable approach that super-resolves the LR images for the multiple LR domains using only a single model. The proposed scheme is trained in a StarGAN like network topology with a single generator and discriminator networks. We demonstrate the effectiveness of our proposed approach in quantitative and qualitative experiments compared to other state-of-the-art methods.

Goutam Bhat, Martin Danelljan, Radu Timofte et al.

This paper reviews the NTIRE2021 challenge on burst super-resolution. Given a RAW noisy burst as input, the task in the challenge was to generate a clean RGB image with 4 times higher resolution. The challenge contained two tracks; Track 1 evaluating on synthetically generated data, and Track 2 using real-world bursts from mobile camera. In the final testing phase, 6 teams submitted results using a diverse set of solutions. The top-performing methods set a new state-of-the-art for the burst super-resolution task.

Pengxu Wei, Hannan Lu, Radu Timofte et al.

This paper introduces the real image Super-Resolution (SR) challenge that was part of the Advances in Image Manipulation (AIM) workshop, held in conjunction with ECCV 2020. This challenge involves three tracks to super-resolve an input image for $\times$2, $\times$3 and $\times$4 scaling factors, respectively. The goal is to attract more attention to realistic image degradation for the SR task, which is much more complicated and challenging, and contributes to real-world image super-resolution applications. 452 participants were registered for three tracks in total, and 24 teams submitted their results. They gauge the state-of-the-art approaches for real image SR in terms of PSNR and SSIM.

Kai Zhang, Martin Danelljan, Yawei Li et al.

This paper reviews the AIM 2020 challenge on efficient single image super-resolution with focus on the proposed solutions and results. The challenge task was to super-resolve an input image with a magnification factor x4 based on a set of prior examples of low and corresponding high resolution images. The goal is to devise a network that reduces one or several aspects such as runtime, parameter count, FLOPs, activations, and memory consumption while at least maintaining PSNR of MSRResNet. The track had 150 registered participants, and 25 teams submitted the final results. They gauge the state-of-the-art in efficient single image super-resolution.

Rao Muhammad Umer, Gian Luca Foresti, Christian Micheloni

Deep convolutional neural networks (CNNs) have recently achieved great success for single image super-resolution (SISR) task due to their powerful feature representation capabilities. The most recent deep learning based SISR methods focus on designing deeper / wider models to learn the non-linear mapping between low-resolution (LR) inputs and high-resolution (HR) outputs. These existing SR methods do not take into account the image observation (physical) model and thus require a large number of network's trainable parameters with a great volume of training data. To address these issues, we propose a deep Iterative Super-Resolution Residual Convolutional Network (ISRResCNet) that exploits the powerful image regularization and large-scale optimization techniques by training the deep network in an iterative manner with a residual learning approach. Extensive experimental results on various super-resolution benchmarks demonstrate that our method with a few trainable parameters improves the results for different scaling factors in comparison with the state-of-art methods.

Rao Muhammad Umer, Christian Micheloni

Recent deep learning based single image super-resolution (SISR) methods mostly train their models in a clean data domain where the low-resolution (LR) and the high-resolution (HR) images come from noise-free settings (same domain) due to the bicubic down-sampling assumption. However, such degradation process is not available in real-world settings. We consider a deep cyclic network structure to maintain the domain consistency between the LR and HR data distributions, which is inspired by the recent success of CycleGAN in the image-to-image translation applications. We propose the Super-Resolution Residual Cyclic Generative Adversarial Network (SRResCycGAN) by training with a generative adversarial network (GAN) framework for the LR to HR domain translation in an end-to-end manner. We demonstrate our proposed approach in the quantitative and qualitative experiments that generalize well to the real image super-resolution and it is easy to deploy for the mobile/embedded devices. In addition, our SR results on the AIM 2020 Real Image SR Challenge datasets demonstrate that the proposed SR approach achieves comparable results as the other state-of-art methods.

Andreas Lugmayr, Martin Danelljan, Radu Timofte et al.

This paper reviews the NTIRE 2020 challenge on real world super-resolution. It focuses on the participating methods and final results. The challenge addresses the real world setting, where paired true high and low-resolution images are unavailable. For training, only one set of source input images is therefore provided along with a set of unpaired high-quality target images. In Track 1: Image Processing artifacts, the aim is to super-resolve images with synthetically generated image processing artifacts. This allows for quantitative benchmarking of the approaches \wrt a ground-truth image. In Track 2: Smartphone Images, real low-quality smart phone images have to be super-resolved. In both tracks, the ultimate goal is to achieve the best perceptual quality, evaluated using a human study. This is the second challenge on the subject, following AIM 2019, targeting to advance the state-of-the-art in super-resolution. To measure the performance we use the benchmark protocol from AIM 2019. In total 22 teams competed in the final testing phase, demonstrating new and innovative solutions to the problem.

Rao Muhammad Umer, Gian Luca Foresti, Christian Micheloni

Most current deep learning based single image super-resolution (SISR) methods focus on designing deeper / wider models to learn the non-linear mapping between low-resolution (LR) inputs and the high-resolution (HR) outputs from a large number of paired (LR/HR) training data. They usually take as assumption that the LR image is a bicubic down-sampled version of the HR image. However, such degradation process is not available in real-world settings i.e. inherent sensor noise, stochastic noise, compression artifacts, possible mismatch between image degradation process and camera device. It reduces significantly the performance of current SISR methods due to real-world image corruptions. To address these problems, we propose a deep Super-Resolution Residual Convolutional Generative Adversarial Network (SRResCGAN) to follow the real-world degradation settings by adversarial training the model with pixel-wise supervision in the HR domain from its generated LR counterpart. The proposed network exploits the residual learning by minimizing the energy-based objective function with powerful image regularization and convex optimization techniques. We demonstrate our proposed approach in quantitative and qualitative experiments that generalize robustly to real input and it is easy to deploy for other down-scaling operators and mobile/embedded devices.

Rao Muhammad Umer, Gian Luca Foresti, Christian Micheloni

Single Image Super-Resolution (SISR) aims to generate a high-resolution (HR) image of a given low-resolution (LR) image. The most of existing convolutional neural network (CNN) based SISR methods usually take an assumption that a LR image is only bicubicly down-sampled version of an HR image. However, the true degradation (i.e. the LR image is a bicubicly downsampled, blurred and noisy version of an HR image) of a LR image goes beyond the widely used bicubic assumption, which makes the SISR problem highly ill-posed nature of inverse problems. To address this issue, we propose a deep SISR network that works for blur kernels of different sizes, and different noise levels in an unified residual CNN-based denoiser network, which significantly improves a practical CNN-based super-resolver for real applications. Extensive experimental results on synthetic LR datasets and real images demonstrate that our proposed method not only can produce better results on more realistic degradation but also computational efficient to practical SISR applications.